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Vaghf A, Sadegh M, Khansarinejad B, Mondanizadeh M. MicroRNA-124-3p targets Sp1 transcription factor to regulate glioma progression in rats. Gene 2024; 930:148858. [PMID: 39153708 DOI: 10.1016/j.gene.2024.148858] [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: 05/14/2024] [Revised: 07/13/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Gliomas are the most prevalent malignancies of the central nervous system (CNS). Downregulation of microRNA‑124 (miR‑124) has been identified in glioma; however, its biological functions in glioma are not yet fully understood. Specificity protein 1 (SP1) is a type of transcription factor that is involved in cancer progression. In this study, we examined the targeting of Sp1 mRNA by miR-124-3p in a rat glioma model. After confirming and selecting the binding of Sp1 to miR-124 with the help of bioinformatics methods, adult male Wistar rats were used to induce glioma by microinjection of 1 × 106 C6 cells into the striatum area of brain. The rats were divided into 3 groups; intact, sham and glioma groups. The presence of glioma was confirmed 21 days after implantation through histological analysis. The expression levels of miR-124 and SP1 genes in the experimental groups were examined using quantitative real-time polymerase chain reaction (qRT-PCR). Our data showed that the expression of miR-124 was significantly downregulated in glioma group compared to the sham and intact group, while the expression of SP1 was significantly upregulated. We found that the expression levels of miR-124 and Sp1 were decreased and increased in C6 cell line compared to the normal brain tissue cell line, respectively. The results indicated that Sp1 was identified as a direct target of miR‑124 through luciferase reporter assays. In summary, this study demonstrated for the first time that miR-124 expression is downregulated and Sp1 expression is upregulated in an animal model of glioma, which, in turn, may be involved in the development of glioma brain cancer.
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Affiliation(s)
- Atena Vaghf
- Department of Biotechnology and Molecular Medicine, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Mehdi Sadegh
- Departments of Physiology, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | | | - Mahdieh Mondanizadeh
- Department of Biotechnology and Molecular Medicine, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran; Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran.
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2
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He B, Xu HM, Li SW, Zhang YF, Tian JW. Emerging regulatory roles of noncoding RNAs induced by bisphenol a (BPA) and its alternatives in human diseases. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124447. [PMID: 38942269 DOI: 10.1016/j.envpol.2024.124447] [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: 04/07/2024] [Revised: 06/07/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Bisphenols (BPs), including BPA, BPF, BPS, and BPAF, are synthetic phenolic organic compounds and endocrine-disrupting chemicals. These organics have been broadly utilized to produce epoxy resins, polycarbonate plastics, and other products. Mounting evidence has shown that BPs, especially BPA, may enter into the human body and participate in the development of human diseases mediated by nuclear hormone receptors. Moreover, BPA may negatively affect human health at the epigenetic level through processes such as DNA methylation and histone acetylation. Recent studies have demonstrated that, as part of epigenetics, noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and small nucleolar RNAs (snoRNAs), have vital impacts on BP-related diseases, such as reproductive system diseases, nervous system diseases, digestive system diseases, endocrine system diseases, and other diseases. Moreover, based on the bioinformatic analysis, changes in ncRNAs may be relevant to normal activities and functions and BP-induced diseases. Thus, we conducted a meta-analysis to identify more promising ncRNAs as biomarkers and therapeutic targets for BP exposure and relevant human diseases. In this review, we summarize the regulatory functions of ncRNAs induced by BPs in human diseases and latent molecular mechanisms, as well as identify prospective biomarkers and therapeutic targets for BP exposure and upper diseases.
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Affiliation(s)
- Bo He
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China
| | - Hai-Ming Xu
- Department of Occupational and Environmental Medicine, School of Public Health and Management, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China
| | - Shu-Wei Li
- Department of Neurology, Qingdao Huangdao District Central Hospital, Qingdao 266555, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Deng Zhou Road 38, Qingdao 266021, China.
| | - Jia-Wei Tian
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China.
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3
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Ni JB, Ding CJ, Zhang JS, Fang XM, Xiao HW. Insight into the surface discharge cold plasma efficient inactivation of Pseudomonas fluorescens in water based on exogenous reactive oxygen and nitrogen species: Synergistic mechanism and energy benefits. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134984. [PMID: 38943891 DOI: 10.1016/j.jhazmat.2024.134984] [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: 02/28/2024] [Revised: 06/08/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024]
Abstract
As well known, surface discharge cold plasma has efficient inactivation ability and a variety of RONS are main active particles for inactivation, but their synergistic mechanism is still not clear. Therefore, surface discharge cold plasma system was applied to treat Pseudomonas fluorescens to study bacterial inactivation mechanism and energy benefit. Results showed that energy efficiency was directly proportional to applied voltage and inversely proportional to initial concentration. Cold plasma treatment for 20 min was inactivated by approximately > 4-log10Pseudomonas fluorescens and application of •OH and 1O2 scavengers significantly improved survival rate. In addition, •OH and 1O2 destroyed cell membrane structure and membrane permeability, which promoted diffusion of RONS into cells and affecting energy metabolism and antioxidant capacity, leading to bacterial inactivation. Furthermore, accumulation of intracellular NO and ONOOH was related to infiltration of exogenous RNS, while accumulation of •OH, H2O2, 1O2, O2- was the result of joint action of endogenous and exogenous ROS. Transcriptome analysis revealed that different RONS of cold plasma were responsible for Pseudomonas fluorescens inactivation and related to activation of intracellular antioxidant defense system and regulation of genes expression related to amino acid metabolism and energy metabolism, which promoting cellular process, catalytic activity and other biochemical pathways.
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Affiliation(s)
- Jia-Bao Ni
- College of Engineering, China Agricultural University, P.O. Box 194, 17 Qinghua Donglu, Beijing 100083, China; State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 1 Xiangshan Beigou, Beijing 100093, China
| | - Chang-Jiang Ding
- College of Science, Inner Mongolia University of Technology, Hohhot, China
| | - Jing-Shou Zhang
- College of Engineering, China Agricultural University, P.O. Box 194, 17 Qinghua Donglu, Beijing 100083, China
| | - Xiao-Ming Fang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 1 Xiangshan Beigou, Beijing 100093, China.
| | - Hong-Wei Xiao
- College of Engineering, China Agricultural University, P.O. Box 194, 17 Qinghua Donglu, Beijing 100083, China.
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4
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Wang J, Wei T, Zhang W, Chu Y, Zhang D, Zhang M, Hu J, Ji Z, Hao Q. Inhibition of miR-194-5p avoids DUSP9 downregulation thus limiting sepsis-induced cardiomyopathy. Sci Rep 2024; 14:20313. [PMID: 39218968 DOI: 10.1038/s41598-024-71166-z] [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: 02/21/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
Sepsis-induced cardiomyopathy (SIC) is described as a reversible myocardial depression that occurs in patients with septic shock. Increasing evidence shows that microRNA-194-5p (miR-194-5p) participates in the regulation of oxidative stress, mitochondrial dysfunction, and apoptosis and its expression is associated with the occurrence and progression of cardiovascular disease; however, the effects of miR-194-5p in SIC are still unclear. This study explores whether miR-194-5p could modulate SIC by affecting oxidative stress, mitochondrial function, and apoptosis. Experimental septic mice were induced by intraperitoneal injection of lipopolysaccharide (LPS) in C57BL/6J mice. The biological role of miR-194-5p in SIC in vivo was investigated using cardiac echocardiography, ELISA, western blot, qRT-PCR, transmission electron microscopy, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, bioinformatics analysis, and dual-luciferase reporter gene assay. Our major finding is that miR-194-5p antagomir mitigates sepsis-induced cardiac dysfunction, inflammation, oxidative stress, apoptosis and mitochondrial dysfunction in the hearts of septic mice, while miR-194-5p agomir triggers the opposite effects. Furthermore, dual-specificity phosphatase 9 (DUSP9) is a direct target of miR-194-5p and the cardioprotective effects of miR-194-5p antagomir on cardiac dysfunction, inflammation, apoptosis, mitochondrial dysfunction and oxidative stress are abolished through inhibiting DUSP9. Therefore, miR-194-5p inhibition could mitigate SIC via DUSP9 in vivo and the novel miR-194-5p/DUSP9 axis might be the potential treatment targets for SIC patients.
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Affiliation(s)
- Jie Wang
- Department of Cardiology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Ting Wei
- Department of Cardiology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Wei Zhang
- Department of Cardiology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Yi Chu
- Department of Cardiology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Dongwei Zhang
- Department of Cardiology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Mingming Zhang
- Department of Cardiology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Jianqiang Hu
- Department of Cardiology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China
| | - Zhaole Ji
- Department of Cardiology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China.
| | - Qimeng Hao
- Department of Cardiology, Tangdu Hospital, Air Force Medical University, Xi'an, 710032, Shaanxi, China.
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Ji J, Xu J, Wang S, Wang Q, Li H. Hairpin self-assembly powered by exonuclease III for highly sensitive and cross-validated miRNA-155 detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39211941 DOI: 10.1039/d4ay01135j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Cancer is one of the most important causes of human death and poses a serious threat to human health. As a cancer biomarker, microRNA-155 (miRNA-155) is highly expressed in various types of cancer tissues and is involved in the proliferation of tumor cells. Therefore, developing a miRNA-155 detection technology with high specificity and sensitivity is of great significance for the early detection, accurate treatment and prognostic evaluation of tumors. Here, we developed a fluorescence detection method using exonuclease III-assisted target cycling and catalytic hairpin assembly (CHA) as a signal amplification technique. This study developed a biosensor for the detection of miRNA-155, utilizing a DNA hairpin (Hp) for target recognition and generating double-stranded DNA (dual-Hp-T). The 3' flat end of the double-stranded DNA can be cleaved by exonuclease III to achieve the target cycle, and a large amount of single-stranded DNA (fuel) can trigger CHA to achieve signal amplification. Simultaneously, the fluorescence resonance energy transfer (FRET) of signal probes with different fluorescence labels on H1 and H2 ends occurs with the CHA reaction. The two fluorescence signals obtained can be used to cross-validate the experimental results. The biosensor exhibits excellent performance of high recovery, high sensitivity and high operability, which can achieve the specific detection of miRNA-155 with a detection limit as low as 8.3 pM. Additionally, the detection efficacy in a human serum environment is also highly satisfactory. This technology provides strong technical support for the development of nucleic acid probes and the diagnosis and treatment of cancer, demonstrating significant practical application value.
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Affiliation(s)
- Jiayi Ji
- College of Chemistry and Materials, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Jun Xu
- College of Chemistry and Materials, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Suqin Wang
- College of Chemistry and Materials, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Qian Wang
- College of Chemistry and Materials, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Hongbo Li
- College of Chemistry and Materials, Jiangxi Normal University, Nanchang 330022, P. R. China.
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6
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He Z, Sun H, Zhao F, Ma L, Wang J, Liu X, Li M, Hao Z, Li S. MicroRNA expression profiles reveal wool development and fineness regulation in Gansu alpine fine-wool sheep. Genomics 2024; 116:110922. [PMID: 39178999 DOI: 10.1016/j.ygeno.2024.110922] [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: 05/28/2024] [Revised: 07/04/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
The development of wool has a complex regulatory mechanism both influenced by genetic and environmental factors. MicroRNAs (miRNA) were involved in various biological processes of animals, and may play an important role in the regulation of wool development. In this study, we comprehensively analyzed and identified the histological parameters of hair follicles, as well as the miRNAs, target genes, pathways, and Gene Ontology terms related to wool fineness regulation and wool growth and development using HE staining and RNA-Seqs methods. Both coarse (group C, mean fiber diameter (MFD) = 22.26 ± 0.69 μm, n = 6) and fine (group F, MFD = 16.91 ± 0.29 μm, n = 6) of Gansu alpine fine-wool sheep with different wool fineness were used in this study. The results showed that the primary follicle diameter and secondary wool fiber diameter in group C were significantly higher than those in group F (P < 0.05). And the number of primary and secondary hair follicles in group C was significantly lower than that in group F (P < 0.05). Furthermore, a total of 67 DE miRNAs and 290 potential DE miRNAs target genes were screened in the skin tissues of sheep from groups F and C, and some potential target genes related to wool fineness regulation were screened, such as CDH2, KRT82, FOXN1, LOC101106296, KRT20, MCOLN3, KRT71, and TERT. These genes were closely related to Glutathione metabolism, epidermal cell differentiation, keratinization, and regulation of hair cycle. Moreover, the regulatory network of miRNAs-mRNAs suggested that miRNAs (miR-129-x, novel m0079-3p, miR-2484-z, novel m0025-5P, etc.) may play a key role in the wool development and wool fineness regulation of Gansu alpine fine-wool sheep. In summary, this study expands the existing miRNAs database and provides new information for studying the regulation of wool development in Gansu alpine fine wool sheep.
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Affiliation(s)
- Zhaohua He
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Hongxian Sun
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Longxia Ma
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Mingna Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China.
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Chen S, Zhao Q, Zhang R, Liu J, Peng W, Xu H, Li X, Wang X, Wu S, Li G, Nan A. A transcribed ultraconserved noncoding RNA, uc.285+, promotes colorectal cancer proliferation through dual targeting of CDC42 by directly binding mRNA and protein. Transl Res 2024; 270:52-65. [PMID: 38552953 DOI: 10.1016/j.trsl.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 03/15/2024] [Accepted: 03/24/2024] [Indexed: 04/12/2024]
Abstract
The transcribed ultraconserved region (T-UCR) belongs to a new type of lncRNAs that are conserved in homologous regions of the rat, mouse and human genomes. A lot of research has reported that differential expression of T-UCRs can influence the development of various cancers, revealing the ability of T-UCRs as new therapeutic targets or potential cancer biomarkers. Most studies on the molecular mechanisms of T-UCRs in cancer have focused on ceRNA regulatory networks and interactions with target proteins, but the present study reveals an innovative dual-targeted regulatory approach in which T-UCRs bind directly to mRNAs and directly to proteins. We screened T-UCRs that may be related to colorectal cancer (CRC) by performing a whole-genome T-UCR gene microarray and further studied the functional mechanism of T-UCR uc.285+ in the development of CRC. Modulation of uc.285+ affected the proliferation of CRC cell lines and influenced the expression of the CDC42 gene. We also found that uc.285+ promoted the proliferation of CRC cells by directly binding to CDC42 mRNA and enhancing its stability while directly binding to CDC42 protein and affecting its stability. In short, our research on the characteristics of cell proliferation found that uc.285+ has a biological function in promoting CRC proliferation. uc.285+ may have considerable potential as a new diagnostic biomarker for CRC.
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Affiliation(s)
- Sixian Chen
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Qingyun Zhao
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Ruirui Zhang
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Jungang Liu
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, PR China
| | - Wenyi Peng
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Haotian Xu
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Xiaofei Li
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Xin Wang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Shuilian Wu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Gang Li
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China.
| | - Aruo Nan
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China.
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8
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Chen L, Gu J, Zhou B. PMiSLocMF: predicting miRNA subcellular localizations by incorporating multi-source features of miRNAs. Brief Bioinform 2024; 25:bbae386. [PMID: 39154195 PMCID: PMC11330342 DOI: 10.1093/bib/bbae386] [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: 04/24/2024] [Revised: 07/04/2024] [Accepted: 07/23/2024] [Indexed: 08/19/2024] Open
Abstract
The microRNAs (miRNAs) play crucial roles in several biological processes. It is essential for a deeper insight into their functions and mechanisms by detecting their subcellular localizations. The traditional methods for determining miRNAs subcellular localizations are expensive. The computational methods are alternative ways to quickly predict miRNAs subcellular localizations. Although several computational methods have been proposed in this regard, the incomplete representations of miRNAs in these methods left the room for improvement. In this study, a novel computational method for predicting miRNA subcellular localizations, named PMiSLocMF, was developed. As lots of miRNAs have multiple subcellular localizations, this method was a multi-label classifier. Several properties of miRNA, such as miRNA sequences, miRNA functional similarity, miRNA-disease, miRNA-drug, and miRNA-mRNA associations were adopted for generating informative miRNA features. To this end, powerful algorithms [node2vec and graph attention auto-encoder (GATE)] and one newly designed scheme were adopted to process above properties, producing five feature types. All features were poured into self-attention and fully connected layers to make predictions. The cross-validation results indicated the high performance of PMiSLocMF with accuracy higher than 0.83, average area under the receiver operating characteristic curve (AUC) and area under the precision-recall curve (AUPR) exceeding 0.90 and 0.77, respectively. Such performance was better than all previous methods based on the same dataset. Further tests proved that using all feature types can improve the performance of PMiSLocMF, and GATE and self-attention layer can help enhance the performance. Finally, we deeply analyzed the influence of miRNA associations with diseases, drugs, and mRNAs on PMiSLocMF. The dataset and codes are available at https://github.com/Gu20201017/PMiSLocMF.
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Affiliation(s)
- Lei Chen
- College of Information Engineering, Shanghai Maritime University, 1550 Haigang Avenue, Pudong New District, Shanghai 201306, China
| | - Jiahui Gu
- College of Information Engineering, Shanghai Maritime University, 1550 Haigang Avenue, Pudong New District, Shanghai 201306, China
| | - Bo Zhou
- School of Basic Medical Sciences, Shanghai University of Medicine and Health Sciences, 279 Zhouzhu Road, Pudong New District, Shanghai 201318, China
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Lebenzon JE, Toxopeus J. Knock down to level up: Reframing RNAi for invertebrate ecophysiology. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111703. [PMID: 39029617 DOI: 10.1016/j.cbpa.2024.111703] [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: 02/21/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
Comparative ecophysiologists strive to understand physiological problems in non-model organisms, but molecular tools such as RNA interference (RNAi) are under-used in our field. Here, we provide a framework for invertebrate ecophysiologists to use RNAi to answer questions focused on physiological processes, rather than as a tool to investigate gene function. We specifically focus on non-model invertebrates, in which the use of other genetic tools (e.g., genetic knockout lines) is less likely. We argue that because RNAi elicits a temporary manipulation of gene expression, and resources to carry out RNAi are technically and financially accessible, it is an effective tool for invertebrate ecophysiologists. We cover the terminology and basic mechanisms of RNA interference as an accessible introduction for "non-molecular" physiologists, include a suggested workflow for identifying RNAi gene targets and validating biologically relevant gene knockdowns, and present a hypothesis-testing framework for using RNAi to answer common questions in the realm of invertebrate ecophysiology. This review encourages invertebrate ecophysiologists to use these tools and workflows to explore physiological processes and bridge genotypes to phenotypes in their animal(s) of interest.
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Affiliation(s)
- Jacqueline E Lebenzon
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4.
| | - Jantina Toxopeus
- Department of Biology, St. Francis Xavier University, 2321 Notre Dame Ave, Antigonish, NS, Canada B2G 2W5
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10
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Zhang H, Zhou Y, Jiang C, Jian N, Wang J. Crosstalk of ubiquitin system and non-coding RNA in fibrosis. Int J Biol Sci 2024; 20:3802-3822. [PMID: 39113708 PMCID: PMC11302871 DOI: 10.7150/ijbs.93644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 06/14/2024] [Indexed: 08/10/2024] Open
Abstract
Chronic tissue injury triggers changes in the cell type and microenvironment at the site of injury and eventually fibrosis develops. Current research suggests that fibrosis is a highly dynamic and reversible process, which means that human intervention after fibrosis has occurred has the potential to slow down or cure fibrosis. The ubiquitin system regulates the biological functions of specific proteins involved in the development of fibrosis, and researchers have designed small molecule drugs to treat fibrotic diseases on this basis, but their therapeutic effects are still limited. With the development of molecular biology technology, researchers have found that non-coding RNA (ncRNA) can interact with the ubiquitin system to jointly regulate the development of fibrosis. More in-depth explorations of the interaction between ncRNA and ubiquitin system will provide new ideas for the clinical treatment of fibrotic diseases.
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Affiliation(s)
- Huamin Zhang
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Yutong Zhou
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Canhua Jiang
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, 410078, China
| | - Ni Jian
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Jie Wang
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha, 410078, China
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11
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Szala D, Kopańska M, Trojniak J, Jabłoński J, Hanf-Osetek D, Snela S, Zawlik I. The Role of MicroRNAs in the Pathophysiology of Osteoarthritis. Int J Mol Sci 2024; 25:6352. [PMID: 38928059 PMCID: PMC11204066 DOI: 10.3390/ijms25126352] [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: 05/05/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Worldwide, osteoarthritis (OA) is the most common cause of joint pain in older people. Many factors contribute to osteoarthritis' development and progression, including secondary osteoarthritis' underlying causes. It is important to note that osteoarthritis affects all four tissues: cartilage, bone, joint capsule, and articular apparatus. An increasingly prominent area of research in osteoarthritis regulation is microRNAs (miRNAs), a small, single-stranded RNA molecule that controls gene expression in eukaryotes. We aimed to assess and summarize current knowledge about the mechanisms of the action of miRNAs and their clinical significance. Osteoarthritis (OA) is affected by the interaction between miRNAs and inflammatory processes, as well as cartilage metabolism. MiRNAs also influence cartilage cell apoptosis, contributing to the degradation of the cartilage in OA. Studies have shown that miRNAs may have both an inhibitory and promoting effect on osteoporosis progression through their influence on molecular mechanisms. By identifying these regulators, targeted treatments for osteoarthritis may be developed. In addition, microRNA may also serve as a biomarker for osteoarthritis. By using these biomarkers, the disease could be detected faster, and early intervention can be instituted to prevent mobility loss and slow deterioration.
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Affiliation(s)
| | - Marta Kopańska
- Department of Pathophysiology, Institute of Medical Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Julia Trojniak
- Student Research Club “Reh-Tech”, Medical College of Rzeszow University, 35-959 Rzeszow, Poland;
| | - Jarosław Jabłoński
- Faculty of Orthopaedic and Reumatology, Institute of Medical Sciences, Collegium Medicum, University of Rzeszow, 35-959 Rzeszow, Poland; (J.J.); (D.H.-O.); (S.S.)
- Orthopaedics and Traumatology Clinic, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
| | - Dorota Hanf-Osetek
- Faculty of Orthopaedic and Reumatology, Institute of Medical Sciences, Collegium Medicum, University of Rzeszow, 35-959 Rzeszow, Poland; (J.J.); (D.H.-O.); (S.S.)
- Orthopaedics and Traumatology Clinic, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
| | - Sławomir Snela
- Faculty of Orthopaedic and Reumatology, Institute of Medical Sciences, Collegium Medicum, University of Rzeszow, 35-959 Rzeszow, Poland; (J.J.); (D.H.-O.); (S.S.)
- Orthopaedics and Traumatology Clinic, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
| | - Izabela Zawlik
- Department of General Genetics, Institute of Medical Sciences, Medical College of Rzeszow University, Kopisto 2a, 35-959 Rzeszow, Poland;
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12
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Trojniak J, Sendera A, Banaś-Ząbczyk A, Kopańska M. The MicroRNAs in the Pathophysiology of Osteoporosis. Int J Mol Sci 2024; 25:6240. [PMID: 38892426 PMCID: PMC11172499 DOI: 10.3390/ijms25116240] [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: 04/26/2024] [Revised: 05/26/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Globally, osteoporosis is the most common systemic skeletal disease. There are many factors that influence osteoporosis' development and progression. During the pathogenesis of this disease, bone turnover is imbalanced between resorption and the formation of bone tissue. A growing interest has been devoted to the role that microRNA (miRNA) plays in osteoporosis regulation. A microRNA (miRNA) is a group of small single-stranded RNA molecules involved in regulating gene expression in eukaryotic organisms. As microRNAs (miRNAs) are key regulators of gene expression and can modulate processes related to bone metabolism, they have become increasingly important for studying osteoporosis pathogenesis. The available research suggests that miRNAs play an important role in regulating processes associated with bone metabolism, especially by influencing bone resorption and synthesis. Furthermore, microRNAs can also serve as potential therapeutic targets for osteoporosis, besides being a rapid and specific biomarker.
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Affiliation(s)
- Julia Trojniak
- Student Research Club “Reh-Tech”, Medical College of Rzeszow University, 35-959 Rzeszow, Poland;
| | - Anna Sendera
- Department of Biology, Institute of Medical Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland; (A.S.); (A.B.-Z.)
| | - Agnieszka Banaś-Ząbczyk
- Department of Biology, Institute of Medical Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland; (A.S.); (A.B.-Z.)
| | - Marta Kopańska
- Department of Pathophysiology, Institute of Medical Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
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Wang J, Huang Y, Wu X, Li D. MicroRNA-939 amplifies Staphylococcus aureus-induced matrix metalloproteinase expression in atopic dermatitis. Front Immunol 2024; 15:1354154. [PMID: 38903509 PMCID: PMC11188349 DOI: 10.3389/fimmu.2024.1354154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Background Atopic dermatitis (AD) is a common chronic inflammatory skin diseases that seriously affects life quality of the patients. Staphylococcus aureus (S. aureus) colonization on the skin plays an important role in the pathogenesis of AD; however, the mechanism of how it modulates skin immunity to exacerbate AD remains unclear. MicroRNAs are short non-coding RNAs that act as post-transcriptional regulators of genes. They are involved in the pathogenesis of various inflammatory skin diseases. Methods In this study, we established miRNA expression profiles for keratinocytes stimulated with heat-killed S. aureus (HKSA). The expression of miR-939 in atopic dermatitis patients was analyzed by fluorescence in situ hybridization (FISH). miR-939 mimic was transfected to human primary keratinocyte to investigate its impact on the expression of matrix metalloproteinase genes (MMPs) in vitro. Subsequently, miR-939, along with Polyplus transfection reagent, was administered to MC903-induced atopic dermatitis skin to assess its function in vivo. Results MiR-939 was highly upregulated in HKSA-stimulated keratinocytes and AD lesions. In vitro studies revealed that miR-939 increased the expression of matrix metalloproteinase genes, including MMP1, MMP3, and MMP9, as well as the cell adhesion molecule ICAM1 in human primary keratinocytes. In vivo studies indicated that miR-939 increased the expression of matrix metalloproteinases to promote the colonization of S. aureus and exacerbated S. aureus-induced AD-like skin inflammation. Conclusions Our work reveals miR-939 is an important regulator of skin inflammation in AD that could be used as a potential therapeutic target for AD.
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Affiliation(s)
- Jiating Wang
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Yejing Huang
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Xinfeng Wu
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Dongqing Li
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
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Xie L, Du B, Yu H, Gui L, Qiu J, Yuan L, Shen Y, Xu X, Li J. MicroRNA-30e-3p regulates the inflammatory response by targeting the gimap8 gene in Ctenopharyngodon idella kidney (CIK) cells. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109524. [PMID: 38527657 DOI: 10.1016/j.fsi.2024.109524] [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: 12/12/2023] [Revised: 02/19/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024]
Abstract
Recent studies have increasingly linked miRNAs with the modulation of inflammatory responses and immunosuppressive activities. This investigation reveals that mir-30e-3p selectively binds to and modulates gimap8, as demonstrated by luciferase reporter assays and qPCR analyses. Upon LPS stimulation of CIK cells, mir-30e-3p expression was notably elevated, inversely correlating with a decrease in gimap8 mRNA levels. Overexpression of mir-30e-3p attenuated the mRNA levels of pro-inflammatory cytokines beyond the effect of LPS alone, suggesting a regulatory role of mir-30e-3p in inflammation mediated by the gimap8 gene. These insights contribute to our understanding of the complex mechanisms governing inflammatory and immune responses.
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Affiliation(s)
- Lingli Xie
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Biao Du
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Hongyan Yu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Lang Gui
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Junqiang Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Li Yuan
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
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15
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Billi M, De Marinis E, Gentile M, Nervi C, Grignani F. Nuclear miRNAs: Gene Regulation Activities. Int J Mol Sci 2024; 25:6066. [PMID: 38892257 PMCID: PMC11172810 DOI: 10.3390/ijms25116066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs which contribute to the regulation of many physiological and pathological processes. Conventionally, miRNAs perform their activity in the cytoplasm where they regulate gene expression by interacting in a sequence-specific manner with mature messenger RNAs. Recent studies point to the presence of mature miRNAs in the nucleus. This review summarizes current findings regarding the molecular activities of nuclear miRNAs. These molecules can regulate gene expression at the transcriptional level by directly binding DNA on the promoter or the enhancer of regulated genes. miRNAs recruit different protein complexes to these regions, resulting in activation or repression of transcription, through a number of molecular mechanisms. Hematopoiesis is presented as a paradigmatic biological process whereby nuclear miRNAs possess a relevant regulatory role. Nuclear miRNAs can influence gene expression by affecting nuclear mRNA processing and by regulating pri-miRNA maturation, thus impacting the biogenesis of miRNAs themselves. Overall, nuclear miRNAs are biologically active molecules that can be critical for the fine tuning of gene expression and deserve further studies in a number of physiological and pathological conditions.
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Affiliation(s)
- Monia Billi
- General Pathology and Department of Medicine, University of Perugia, 06132 Perugia, Italy;
| | - Elisabetta De Marinis
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Martina Gentile
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Clara Nervi
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Francesco Grignani
- General Pathology and Department of Medicine, University of Perugia, 06132 Perugia, Italy;
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Gao J, Mang Q, Liu Y, Sun Y, Xu G. Integrated mRNA and miRNA analysis reveals the regulatory network of oxidative stress and inflammation in Coilia nasus brains during air exposure and salinity mitigation. BMC Genomics 2024; 25:446. [PMID: 38714962 PMCID: PMC11075292 DOI: 10.1186/s12864-024-10327-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Air exposure is an inevitable source of stress that leads to significant mortality in Coilia nasus. Our previous research demonstrated that adding 10‰ NaCl to aquatic water could enhance survival rates, albeit the molecular mechanisms involved in air exposure and salinity mitigation remained unclear. Conversely, salinity mitigation resulted in decreased plasma glucose levels and improved antioxidative activity. To shed light on this phenomenon, we characterized the transcriptomic changes in the C. nasus brain upon air exposure and salinity mitigation by integrated miRNA-mRNA analysis. RESULTS The plasma glucose level was elevated during air exposure, whereas it decreased during salinity mitigation. Antioxidant activity was suppressed during air exposure, but was enhanced during salinity mitigation. A total of 629 differentially expressed miRNAs (DEMs) and 791 differentially expressed genes (DEGs) were detected during air exposure, while 429 DEMs and 1016 DEGs were identified during salinity mitigation. GO analysis revealed that the target genes of DEMs and DEGs were enriched in biological process and cellular component during air exposure and salinity mitigation. KEGG analysis revealed that the target genes of DEMs and DEGs were enriched in metabolism. Integrated analysis showed that 24 and 36 predicted miRNA-mRNA regulatory pairs participating in regulating glucose metabolism, Ca2+ transport, inflammation, and oxidative stress. Interestingly, most of these miRNAs were novel miRNAs. CONCLUSION In this study, substantial miRNA-mRNA regulation pairs were predicted via integrated analysis of small RNA sequencing and RNA-Seq. Based on predicted miRNA-mRNA regulation and potential function of DEGs, miRNA-mRNA regulatory network involved in glucose metabolism and Ca2+ transport, inflammation, and oxidative stress in C. nasus brain during air exposure and salinity mitigation. They regulated the increased/decreased plasma glucose and inhibited/promoted antioxidant activity during air exposure and salinity mitigation. Our findings would propose novel insights to the mechanisms underlying fish responses to air exposure and salinity mitigation.
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Affiliation(s)
- Jun Gao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, 214081, China
| | - Qi Mang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, 214081, China
| | - Yuqian Liu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yi Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, 214081, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, 214081, China.
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, 214081, China.
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Abdul Manap AS, Wisham AA, Wong FW, Ahmad Najmi HR, Ng ZF, Diba RS. Mapping the function of MicroRNAs as a critical regulator of tumor-immune cell communication in breast cancer and potential treatment strategies. Front Cell Dev Biol 2024; 12:1390704. [PMID: 38726321 PMCID: PMC11079208 DOI: 10.3389/fcell.2024.1390704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 05/12/2024] Open
Abstract
Among women, breast cancer ranks as the most prevalent form of cancer, and the presence of metastases significantly reduces prognosis and diminishes overall survival rates. Gaining insights into the biological mechanisms governing the conversion of cancer cells, their subsequent spread to other areas of the body, and the immune system's monitoring of tumor growth will contribute to the advancement of more efficient and targeted therapies. MicroRNAs (miRNAs) play a critical role in the interaction between tumor cells and immune cells, facilitating tumor cells' evasion of the immune system and promoting cancer progression. Additionally, miRNAs also influence metastasis formation, including the establishment of metastatic sites and the transformation of tumor cells into migratory phenotypes. Specifically, dysregulated expression of these genes has been associated with abnormal expression of oncogenes and tumor suppressor genes, thereby facilitating tumor development. This study aims to provide a concise overview of the significance and function of miRNAs in breast cancer, focusing on their involvement as tumor suppressors in the antitumor immune response and as oncogenes in metastasis formation. Furthermore, miRNAs hold tremendous potential as targets for gene therapy due to their ability to modulate specific pathways that can either promote or suppress carcinogenesis. This perspective highlights the latest strategies developed for miRNA-based therapies.
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Affiliation(s)
- Aimi Syamima Abdul Manap
- Department of Biomedical Science, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | | | - Fei Wen Wong
- Faculty of Biosciences, MAHSA University, Kuala Langat, Selangor, Malaysia
| | | | - Zhi Fei Ng
- Faculty of Biosciences, MAHSA University, Kuala Langat, Selangor, Malaysia
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18
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Wang C, Yang X. CircRAPGEF5 sponges miR-582-3p and targets KIF3A to regulate bladder cancer cell proliferation, migration and invasion. Int Immunopharmacol 2024; 131:111613. [PMID: 38489970 DOI: 10.1016/j.intimp.2024.111613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Bladder cancer (BCa) is a common malignant disease with high recurrence and poor prognosis. Several circular RNAs (circRNAs) have been found to be associated with the malignant progression of bladder cancer (BCa). Here, the aim of this study was to investigate the expression, role and mechanism of circRAPGEF5 in BCa progression. METHODS Quantitative real-time PCR (qRT-PCR) and immunoblotting were used to detect gene and protein expression levels. In vitro functional studies were performed using CCK-8, colony formation, wound healing and Transwell assays, respectively, and a mouse xenograft tumor model was established to perform in vivo experiments. Bioinformatic predictions as well as luciferase reporter assays and RNA pull-down assays were used to probe circRAPGEF5-mediated competitive endogenous RNA (ceRNA) network. RESULTS CircRAPGEF5 was significantly overexpressed in BCa patients (p < 0.05), indicating a potential unsatisfactory prognosis. Functionally, knockdown of circRAPGEF5 inhibited the growth, migration and invasion of BCa cells in vitro (p < 0.05), as well as BCa growth in vivo (p < 0.05). Mechanistically, circRAPGEF5 acted as a sponge for miR-582-3p and targeted kinesin family member 3A (KIF3A). In addition, rescue experiments showed that inhibition of miR-582-3p or overexpression of KIF3A reversed the anticancer effects of circRAPGEF5 knockdown on BCa cells (p < 0.05). CONCLUSION Silencing circRAPGEF5 inhibits BCa proliferation, migration and invasion via the miR-582-3p/KIF3A axis, demonstrating a promising target for BCa-targeted therapy.
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Affiliation(s)
- Chao Wang
- Department of Urology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121000, Liaoning Province, China
| | - Xianxu Yang
- Department of Urology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121000, Liaoning Province, China.
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Kaur S, Seem K, Duhan N, Kumar S, Kaundal R, Mohapatra T. Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress. PLANTA 2024; 259:128. [PMID: 38639776 DOI: 10.1007/s00425-024-04399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
MAIN CONCLUSION Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
- ICAR-Research Complex for North Eastern Hill Region (NEH), Umiam, Meghalaya, 793103, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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Wang X, Yue Y, Tan J, Kou F, Su B, Xie J, Yan S. LncRNA EBLN3P Accelerates Cell Proliferation and Invasion of Colon Cancer through Modulating the miR-519d-3p/ZFP91 Axis. Cancer Biother Radiopharm 2024. [PMID: 38597324 DOI: 10.1089/cbr.2022.0089] [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: 04/11/2024] Open
Abstract
Purpose: The study aims to explore the roles and underlying mechanisms of long noncoding RNAs endogenous bornavirus-like nucleoprotein (lncRNA EBLN3P) in colon cancer, emphasizing the potential impact of these insights on advancing colon cancer treatment strategies. By shedding light on lncRNA EBLN3P's involvement, this research could contribute to the development of novel therapeutic approaches, enhancing the efficacy of interventions for colon cancer patients. Methods: We employed quantitative reverse transcription polymerase chain reaction to assess the levels of lncRNA EBLN3P, zinc finger protein (ZFP91), and miR-519d-3p, alongside CCK-8 and EdU assays for cell proliferation, flow cytometry for apoptosis, and Transwell and wound healing assays for migration and invasion. The in vivo function of lncRNA EBLN3P was investigated through a xenograft model, and protein levels were evaluated via Western blot analysis. Results: LncRNA EBLN3P was found to be upregulated in colon cancer tissues and cells, promoting cell proliferation and metastasis while inhibiting apoptosis. Downregulation of lncRNA EBLN3P reduced tumor size, volume, and weight in a mouse model. MiR-519d-3p, which negatively interacts with lncRNA EBLN3P, was found to be downregulated in colon cancer tissues and cell lines. Its upregulation hindered cancer cell proliferation and metastasis while enhancing apoptosis. ZFP91, a binding partner of miR-519d-3p, was upregulated in colon cancer and inversely related to miR-519d-3p levels. Rescue experiments indicated that the effects of lncRNA EBLN3P silencing could be reversed by miR-519d-3p suppression, but were mitigated by ZFP91 downregulation. Conclusion: LncRNA EBLN3P facilitates colon cancer progression via the miR-519d-3p/ZFP91 axis, presenting a novel understanding of lncRNA EBLN3P's role and offering potential therapeutic insights for colon cancer treatment. This study fills a critical gap by linking lncRNA EBLN3P with the miR-519d-3p/ZFP91 axis in the context of colon cancer, thereby broadening our understanding of the molecular mechanisms underlying colon cancer progression.
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Affiliation(s)
- Xiaohui Wang
- Department of General Surgery, Bayinguoleng Mongolian Autonomous Prefecture People's Hospital, Korla, People's Republic of China
| | - Yinzi Yue
- Department of General Surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, People's Republic of China
| | - Jinhua Tan
- Department of General Surgery, Bayinguoleng Mongolian Autonomous Prefecture People's Hospital, Korla, People's Republic of China
| | - Fei Kou
- Department of General Surgery, Bayinguoleng Mongolian Autonomous Prefecture People's Hospital, Korla, People's Republic of China
| | - Bude Su
- Department of General Surgery, Bayinguoleng Mongolian Autonomous Prefecture People's Hospital, Korla, People's Republic of China
| | - Jin Xie
- Department of General Surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, People's Republic of China
| | - Shuai Yan
- Department of Anorectal Surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, People's Republic of China
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Wu Y, Chen D, Li L. Morinda officinalis polysaccharide promotes the osteogenic differentiation of human bone marrow-derived mesenchymal stem cells via microRNA-210-3p/scavenger receptor class A member 3. J Investig Med 2024; 72:370-382. [PMID: 38264863 DOI: 10.1177/10815589241229693] [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] [Indexed: 01/25/2024]
Abstract
Morinda officinalis polysaccharide (MOP) is the bioactive ingredient extracted from the root of Morinda officinalis, and Morinda officinalis is applied to treat osteoporosis (OP). The purpose of this study was to determine the role of MOP on human bone marrow mesenchymal stem cells (hBMSCs) and the underlying mechanism. HBMSCs were isolated from bone marrow samples of patients with OP and treated with MOP. Quantitative real-time polymerase chain reaction was adopted to quantify the expression of microRNA-210-3p (miR-210-3p) and scavenger receptor class A member 3 (SCARA3) mRNA. Cell Counting Kit-8 assay was employed to detect cell viability; Terminal-deoxynucleotidyl Transferase Mediated Nick End Labeling assay and flow cytometry were adopted to detect apoptosis; Alkaline Phosphatase (ALP) activity assay kit was applied to detect ALP activity; Western blot was executed to quantify the expression levels of SCARA3, osteogenic and adipogenic differentiation markers. Ovariectomized rats were treated with MOP. Bone mineral density (BMD), serum tartrate-resistant acid phosphatase 5b (TRACP 5b), and N-telopeptide of type I collagen (NTx) levels were assessed by BMD detector and Enzyme-linked immunosorbent assay kits. It was revealed that MOP could promote hBMSCs' viability and osteogenic differentiation and inhibit apoptosis and adipogenic differentiation. MOP could also upregulate SCARA3 expression through repressing miR-210-3p expression. Treatment with MOP increased the BMD and decreased the TRACP 5b and NTx levels in ovariectomized rats. MOP may boost the osteogenic differentiation and inhibit adipogenic differentiation of hBMSCs by miR-210-3p/SCARA3 axis.
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Affiliation(s)
- Yue Wu
- Department of Thoracic Surgery, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Dan Chen
- Department of Rehabilitation, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Longguang Li
- Department of Rehabilitation, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
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Khorasani ABS, Hafezi N, Sanaei MJ, Jafari-Raddani F, Pourbagheri-Sigaroodi A, Bashash D. The PI3K/AKT/mTOR signaling pathway in breast cancer: Review of clinical trials and latest advances. Cell Biochem Funct 2024; 42:e3998. [PMID: 38561964 DOI: 10.1002/cbf.3998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/11/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer mortality in women. As the phosphatidylinositol 3-kinase (PI3K) signaling pathway is involved in a wide range of physiological functions of cells including growth, proliferation, motility, and angiogenesis, any alteration in this axis could induce oncogenic features; therefore, numerous preclinical and clinical studies assessed agents able to inhibit the components of this pathway in BC patients. To the best of our knowledge, this is the first study that analyzed all the registered clinical trials investigating safety and efficacy of the PI3K/AKT/mTOR axis inhibitors in BC. Of note, we found that the trends of PI3K inhibitors in recent years were superior as compared with the inhibitors of either AKT or mTOR. However, most of the trials entering phase III and IV used mTOR inhibitors (majorly Everolimus) followed by PI3K inhibitors (majorly Alpelisib) leading to the FDA approval of these drugs in the BC context. Despite favorable efficacies, our analysis shows that the majority of trials are utilizing PI3K pathway inhibitors in combination with hormone therapy and chemotherapy; implying monotherapy cannot yield huge clinical benefits, at least partly, due to the activation of compensatory mechanisms. To emphasize the beneficial effects of these inhibitors in combined-modal strategies, we also reviewed recent studies which investigated the conjugation of nanocarriers with PI3K inhibitors to reduce harmful toxicities, increase the local concentration, and improve their efficacies in the context of BC therapy.
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Affiliation(s)
| | - Nasim Hafezi
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farideh Jafari-Raddani
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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da Silva Rosa PM, Bridi A, de Ávila Ferronato G, Prado CM, Bastos NM, Sangalli JR, Meirelles FV, Perecin F, da Silveira JC. Corpus luteum presence in the bovine ovary increase intrafollicular progesterone concentration: consequences in follicular cells gene expression and follicular fluid small extracellular vesicles miRNA contents. J Ovarian Res 2024; 17:65. [PMID: 38500173 PMCID: PMC10946200 DOI: 10.1186/s13048-024-01387-3] [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: 11/14/2023] [Accepted: 03/07/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND It is well described that circulating progesterone (P4) plays a key role in several reproductive events such as oocyte maturation. However, during diestrus, when circulating P4 is at the highest concentrations, little is known about its local impact on the follicular cells such as intrafollicular P4 concentration due to corpus luteum (CL) presence within the same ovary. Based on that, our hypothesis is that the CL presence in the ovary during diestrus alters intrafollicular P4 concentrations, oocyte competence acquisition, follicular cells gene expression, and small extracellular vesicles (sEVs) miRNAs contents. RESULTS P4 hormonal analysis revealed that ipsilateral to the CL follicular fluid (iFF) presented higher P4 concentration compared to contralateral follicular fluid (cFF). Furthermore, oocyte maturation and miRNA biogenesis pathways transcripts (ADAMTS-1 and AGO2, respectively) were increased in cumulus and granulosa cells of iFF, respectively. Nevertheless, a RT-PCR screening of 382 miRNAs showed that three miRNAs were upregulated and two exclusively expressed in sEVs from iFF and are predicted to regulate cell communication pathways. Similarly, seven miRNAs were higher and two exclusively expressed from cFF sEVs and are predicted to modulate proliferation signaling pathways. CONCLUSION In conclusion, intrafollicular P4 concentration is influenced by the presence of the CL and modulates biological processes related to follicular cell development and oocyte competence, which may influence the oocyte quality. Altogether, these results are crucial to improve our knowledge about the follicular microenvironment involved in oocyte competence acquisition.
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Affiliation(s)
- Paola Maria da Silva Rosa
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Alessandra Bridi
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Giuliana de Ávila Ferronato
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Cibele Maria Prado
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Natália Marins Bastos
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Juliano Rodrigues Sangalli
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Flávio Vieira Meirelles
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Felipe Perecin
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13635-900, Brazil
| | - Juliano Coelho da Silveira
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, São Paulo, 13635-900, Brazil.
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Qi JL, Zhang ZD, Dong Z, Shan T, Yin ZS. mir-150-5p inhibits the osteogenic differentiation of bone marrow-derived mesenchymal stem cells by targeting irisin to regulate the p38/MAPK signaling pathway. J Orthop Surg Res 2024; 19:190. [PMID: 38500202 PMCID: PMC10949585 DOI: 10.1186/s13018-024-04671-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
PURPOSE To study the effect of miR-150-5p on the osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs), and further explore the relationship between its regulatory mechanism and irisin. METHODS We isolated mouse BMSCs, and induced osteogenic differentiation by osteogenic induction medium. Using qPCR to detect the expression of osteogenic differentiation-related genes, western blot to detect the expression of osteogenic differentiation-related proteins, and luciferase reporter system to verify that FNDC5 is the target of miR-150-5p. Irisin intraperitoneal injection to treat osteoporosis in mice constructed by subcutaneous injection of dexamethasone. RESULTS Up-regulation of miR-150-5p inhibited the proliferation of BMSCs, and decreased the content of osteocalcin, ALP activity, calcium deposition, the expression of osteogenic differentiation genes (Runx2, OSX, OCN, OPN, ALP and BMP2) and protein (BMP2, OCN, and Runx2). And down-regulation of miR-150-5p plays the opposite role of up-regulation of miR-150-5p on osteogenic differentiation of BMSCs. Results of luciferase reporter gene assay showed that FNDC5 gene was the target gene of miR-150-5p, and miR-150-5p inhibited the expression of FNDC5 in mouse BMSCs. The expression of osteogenic differentiation genes and protein, the content of osteocalcin, ALP activity and calcium deposition in BMSCs co-overexpressed by miR-150-5p and FNDC5 was significantly higher than that of miR-150-5p overexpressed alone. In addition, the overexpression of FNDC5 reversed the blocked of p38/MAPK pathway by the overexpression of miR-150-5p in BMSCs. Irisin, a protein encoded by FNDC5 gene, improved symptoms in osteoporosis mice through intraperitoneal injection, while the inhibitor of p38/MAPK pathway weakened this function of irisin. CONCLUSION miR-150-5p inhibits the osteogenic differentiation of BMSCs by targeting irisin to regulate the/p38/MAPK signaling pathway, and miR-150-5p/irisin/p38 pathway is a potential target for treating osteoporosis.
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Affiliation(s)
- Jia-Long Qi
- Department of Orthopedics, First Affiliated Hospital of Anhui Medical University, Hefei City, 230022, Anhui Province, China
- Department of Spine Surgery, Hefei First People's Hospital, Hefei City, 230061, Anhui Province, China
| | - Zhi-Dong Zhang
- Department of Spine Surgery, Hefei First People's Hospital, Hefei City, 230061, Anhui Province, China
| | - Zhou Dong
- Department of Spine Surgery, Hefei First People's Hospital, Hefei City, 230061, Anhui Province, China
| | - Tao Shan
- Department of Spine Surgery, Hefei First People's Hospital, Hefei City, 230061, Anhui Province, China
| | - Zong-Sheng Yin
- Department of Orthopedics, First Affiliated Hospital of Anhui Medical University, Hefei City, 230022, Anhui Province, China.
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Gu N, Wang Y, Li L, Sui X, Liu Z. The mechanism of lncRNA MALAT1 targeting the miR-124-3p/IGF2BP1 axis to regulate osteogenic differentiation of periodontal ligament stem cells. Clin Oral Investig 2024; 28:219. [PMID: 38492123 DOI: 10.1007/s00784-024-05616-3] [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: 11/14/2023] [Accepted: 03/10/2024] [Indexed: 03/18/2024]
Abstract
OBJECTIVES This study aimed to investigate the regulatory roles of lncRNA MALAT1, miR-124-3p, and IGF2BP1 in osteogenic differentiation of periodontal ligament stem cells (PDLSCs). MATERIALS AND METHODS We characterized PDLSCs by employing quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot analyses to evaluate the expression of key osteogenic markers including ALPL, SPP1, and RUNX2. Manipulation of lncRNA MALAT1 and miR-124-3p expression levels was achieved through transfection techniques. In addition, early osteogenic differentiation was assessed via Alkaline phosphatase (ALP) staining, and mineral deposition was quantified using Alizarin Red S (ARS) staining. Cellular localization of lncRNA MALAT1 was determined through Fluorescence In Situ Hybridization (FISH). To elucidate the intricate regulatory network, we conducted dual-luciferase reporter assays to decipher the binding interactions between lncRNA MALAT1 and miR-124-3P as well as between miR-124-3P and IGF2BP1. RESULTS Overexpression of lncRNA MALAT1 robustly promoted osteogenesis in PDLSCs, while its knockdown significantly inhibited the process. We confirmed the direct interaction between miR-124-3p and lncRNA MALAT1, underscoring its role in impeding osteogenic differentiation. Notably, IGF2BP1 was identified as a direct binding partner of lncRNA MALAT1, highlighting its pivotal role within this intricate network. Moreover, we determined the optimal IGF2BP1 concentration (50 ng/ml) as a potent enhancer of osteogenesis, effectively countering the inhibition induced by si-MALAT1. Furthermore, in vivo experiments utilizing rat calvarial defects provided compelling evidence, solidifying lncRNA MALAT1's crucial role in bone formation. CONCLUSIONS Our study reveals the regulatory network involving lncRNA MALAT1, miR-124-3p, and IGF2BP1 in PDLSCs' osteogenic differentiation. CLINICAL RELEVANCE These findings enhance our understanding of lncRNA-mediated osteogenesis, offering potential therapeutic implications for periodontal tissue regeneration and the treatment of bone defects.
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Affiliation(s)
- Nan Gu
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Hospital of Stomatology, Jilin University, Changchun, 130021, China
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Qinghua Road No.1500, Changchun, 130021, People's Republic of China
| | - Yao Wang
- Department of Stomatology, The First Hospital of Jilin University, Changchun, 130021, China
| | - Lingfeng Li
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Hospital of Stomatology, Jilin University, Changchun, 130021, China
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Qinghua Road No.1500, Changchun, 130021, People's Republic of China
| | - Xin Sui
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Hospital of Stomatology, Jilin University, Changchun, 130021, China
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Qinghua Road No.1500, Changchun, 130021, People's Republic of China
| | - Zhihui Liu
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Hospital of Stomatology, Jilin University, Changchun, 130021, China.
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Qinghua Road No.1500, Changchun, 130021, People's Republic of China.
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Ma S, Chen F, Lin C, Sun W, Wang D, Zhou S, Chang S, Lu Z, Zhang D. MiR-186-5p prevents hepatocellular carcinoma progression by targeting methyltransferase-like 3 that regulates m6A-mediated stabilization of follistatin-like 5. Heliyon 2024; 10:e26767. [PMID: 38463829 PMCID: PMC10920164 DOI: 10.1016/j.heliyon.2024.e26767] [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: 06/28/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a multistep process involving sophisticated genetic, epigenetic, and transcriptional changes. However, studies on microRNA (miRNA)'s regulatory effects of N6-methyladenosine (m6A) modifications on HCC progression are limited. Methods Cell Counting Kit-8 (CCK-8), clone formation, and Transwell assays were used to investigate changes in cancer cell proliferation, invasion, and migration. RNA m6A levels were verified using methylated RNA immunoprecipitation. Luciferase reporter assay was used to study the potential binding between miRNAs and mRNA. A mouse tumor transplant model was established to study the changes in tumor progression. Results Follistatin-like 5 (FSTL5) was significantly downregulated in HCC and inhibited its further progression. Additionally, methyltransferase-like 3 (METTL3) reduced FSTL5 mRNA stability in an m6A-YTH domain family 2(YTHDF2)-dependent manner. Functional experiments revealed that METTL3 downregulation inhibited HCC progression by upregulating FSTL5 in vitro and in vivo. Luciferase reporter assay verified that miR-186-5p directly targets METTL3. Additionally, miR-186-5p inhibits the proliferation, migration, and invasion of HCC cells by downregulating METTL3 expression. Conclusions The miR-186-5p/METTL3/YTHDF2/FSTL5 axis may offer new directions for targeted HCC therapy.
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Affiliation(s)
- Shuoshuo Ma
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
- Liver Transplantation Center and Hepatobiliary and Pancreatic Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Fangfang Chen
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Chuanle Lin
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Wanliang Sun
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Dongdong Wang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Shuo Zhou
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - ShiRu Chang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Zheng Lu
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
| | - Dengyong Zhang
- Department of General Surgery, The First Affiliated Hospital of BengBu Medical College, BengBu, 233000, China
- The University of Texas MD Anderson Cancer Center, Department of Translational Molecular Pathology, Houston, USA
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27
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Ji T, Yan D, Huang Y, Luo M, Zhang Y, Xu T, Gao S, Zhang L, Ruan L, Zhang C. Fibulin 1, targeted by microRNA-24-3p, promotes cell proliferation and migration in vascular smooth muscle cells, contributing to the development of atherosclerosis in APOE -/- mice. Gene 2024; 898:148129. [PMID: 38184021 DOI: 10.1016/j.gene.2024.148129] [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: 09/27/2023] [Revised: 12/05/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024]
Abstract
Extracellular matrix (ECM) and vascular smooth muscle cells (VSMCs) are the main components of atherosclerosis (AS) plaque. VSMCs participate in plaque formation through phenotypic transformation. The complex interplay between ECM and VSMCs plays vital roles in the progression of AS throughout the disease. An in-depth investigation into the functions of ECM-related molecules in VSMC development might contribute to deciphering the complexity of AS pathogenesis. In this study, the roles and molecular mechanisms of the ECM-related molecule Fibulin-1 (FBLN1) in the development of AS and VSMCs were explored using RNA sequencing, bioinformatics analysis, and cell experiments. Furthermore, the expression of FBLN1, as determined by western blot analysis, immunohistochemistry, and real-time quantitative PCR, was significantly increased in AS vascular samples compared to normal vascular samples. Silencing the FBLN1 through AAV viral injection in mice revealed an improvement in AS. Functional analyses revealed that FBLN1 promoted VSMC proliferation, migration, and wound healing. Combined with RNA sequencing and TargetScan7.2 prediction data, 22 microRNAs (miRNAs) were found to have the potential for direct interaction with the FBLN1 3'UTR in VSMCs. Among these 22 miRNAs, it was demonstrated that microRNA-24-3p (miR-24-3p) could negatively regulate FBLN1 expression by directly binding to the FBLN1 3'UTR. Moreover, miR-24-3p inhibited cell proliferation, migration, and wound healing, and suppressed the expression of Ki67, matrix metalloproteinase-2 and -9 (MMP2/9) by targeting FBLN1 in VSMCs. Meanwhile, inhibition of FBLN1 expression could restrain VSMC phenotypic transformation. In conclusion, miR-24-3p inhibited VSMC proliferation and migration by targeting FBLN1. Additionally, multiple miRNAs with the potential to interact with the FBLN1 3'UTR were identified. These findings might deepen our understanding of ECM gene regulatory networks and the complex etiology of AS.
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Affiliation(s)
- Tianyi Ji
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Dan Yan
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yi Huang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Mandi Luo
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yucong Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Ting Xu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Shangbang Gao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Le Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Lei Ruan
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
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Nan L, Kaisi F, Mengzhen Z, Yang Y, Jiaming Y, Huirong Y, Xinwei H, Chen W, Liucheng Y, Kai W. miR-375-3p targets YWHAB to attenuate intestine injury in neonatal necrotizing enterocolitis. Pediatr Surg Int 2024; 40:63. [PMID: 38431920 DOI: 10.1007/s00383-024-05653-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Necrotizing enterocolitis (NEC) is a significant contributor to neonatal mortality. This study aimed to investigate the role of high levels of miR-375-3p in breast milk in the development of NEC and elucidate its mechanism. METHODS Differential expression of miR-375-3p in the intestines of breast-fed and formula-fed mice was confirmed using real-time polymerase chain reaction (RT-PCR). NEC mice models were established, and intestinal injury was assessed using HE staining. RT-PCR and Western blot were conducted to examine the expression of miR-375-3p, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein β (YWHAB), as well as the inflammatory in IEC-6 cells, and intestinal tissues obtained from NEC mice and patients. Flow cytometry and cell counting kit-8 (CCK-8) were employed to elucidate the impact of miR-375-3p and YWHAB on cell apoptosis and proliferation. RESULTS Breastfeeding increases miR-375-3p expression in the intestines. The expression of miR-375-3p in NEC intestinal tissues exhibited a significant decrease compared to the healthy group. Additionally, the expression of interleukin-6 (IL-6), interleukin-10 (IL-10), and tumor necrosis factor-α (TNF-α) was higher in the NEC group compared to the control group. Down-regulation of miR-375-3p inhibited IEC-6 cell proliferation, increased apoptosis, and elevated secretion of inflammatory factors. Bioinformatics revealed that YWHAB may be a target of miR-375-3p. RT-PCR and Western blot indicated a down-regulation of YWHAB expression in intestines of NEC patients and mice. Furthermore, YWHAB was found to be positively connected with miR-375-3p. Knockdown miR-375-3p down-regulated YWHAB expression in cells. Inhibition of YWHAB exhibited similar effects to miR-375-3p in IEC-6 cells. YWHAB plasmid partially reverse cellular functional impairment induced by miR-375-3p knockdown. CONCLUSIONS Breastfeeding elevated miR-375-3p expression in intestines in neonatal mice. MiR-375-3p leads to a decrease in apoptosis of intestinal epithelial cells, an increase in cell proliferation, and a concomitant reduction in the expression of inflammatory factors partly through targeting YWHAB.
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Affiliation(s)
- Li Nan
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Fan Kaisi
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Zhang Mengzhen
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Yang Yang
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Yang Jiaming
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Yang Huirong
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Hou Xinwei
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Wang Chen
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Yang Liucheng
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Wu Kai
- Department of Pediatric Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China.
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Wu XX, Zhao YX, Xu SL, Wang LX, Mao JH, Wang B, Yang H. A comprehensive evaluation of circ_0065214/ miR-188-3p/GPNMB axis in breast cancer. Cell Signal 2024; 115:111019. [PMID: 38141793 DOI: 10.1016/j.cellsig.2023.111019] [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: 10/12/2023] [Revised: 12/10/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
CircRNAs are involved in multiple aspects during carcinogenesis, including tumorigenesis, vascularization, apoptosis and others. Exploring the role of circRNAs in breast cancer (BC) enables us to understand the development mechanism of BC more comprehensively. Here, we screened out and verified an up-regulated circRNA in BC from GEO data. Quantitative Real-time PCR (qRT-PCR) showed that circ_0065214 had a high expression level in BC patients. Besides, circ_0065214 had good diagnostic value in BC serum, and the area under the diagnostic curve, sensitivity and specificity were 0.78, 0.63 and 0.85, respectively. The combined application of circ_0065214 with CEA and CA-153 can further improve the diagnostic efficiency. The knockdown of circ_0065214 in vivo and in vitro inhibited the proliferation, migration and invasion of BC, but promoted autophagy. At last, dual-luciferase reporter assay and rescue assays revealed that circ_0065214 acted as a decoy to adsorb miR-188-3p, and then relieved the repressive effect of miR-188-3p on its target GPNMB. Our results demonstrated that circ_0065214 regulated the expression of GPNMB by competitively binding to miR-188-3p, thus promoting the proliferation, migration and invasion of breast cancer cells and inhibiting autophagy. These findings provided an original therapeutic strategy for BC.
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Affiliation(s)
- Xi-Xi Wu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China; The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Yue-Xin Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Shi-Liang Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Ling-Xia Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jia-Hui Mao
- Department of Central Laboratory, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Bo Wang
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.
| | - Huan Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China.
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Eritja À, Caus M, Belmonte T, de Gonzalo-Calvo D, García-Carrasco A, Martinez A, Martínez M, Bozic M. microRNA Expression Profile in Obesity-Induced Kidney Disease Driven by High-Fat Diet in Mice. Nutrients 2024; 16:691. [PMID: 38474819 DOI: 10.3390/nu16050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Obesity is one of the main causes of chronic kidney disease; however, the precise molecular mechanisms leading to the onset of kidney injury and dysfunction in obesity-associated nephropathy remain unclear. The present study aimed to unveil the kidney microRNA (miRNA) expression profile in a model of obesity-induced kidney disease in C57BL/6J mice using next-generation sequencing (NGS) analysis. High-fat diet (HFD)-induced obesity led to notable structural alterations in tubular and glomerular regions of the kidney, increased renal expression of proinflammatory and profibrotic genes, as well as an elevated renal expression of genes involved in cellular lipid metabolism. The miRNA sequencing analysis identified a set of nine miRNAs differentially expressed in the kidney upon HFD feeding, with miR-5099, miR-551b-3p, miR-223-3p, miR-146a-3p and miR-21a-3p showing the most significant differential expression between standard diet (STD) and HFD mice. A validation analysis showed that the expression levels of miR-5099, miR-551b-3p and miR-146a-3p were consistent with NGS results, while Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses revealed that these three validated miRNAs modulated target genes involved in metabolic and adipocytokine pathways, fatty acid and lipid metabolism, and inflammatory, senescence and profibrotic pathways. Our results suggest that differentially expressed miRNAs play pivotal roles in the intricate pathophysiology of obesity-associated kidney disease and could potentially create novel treatment strategies to counteract the deleterious effects of obesity on kidney function.
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Affiliation(s)
- Àuria Eritja
- Vascular and Renal Translational Research Group, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLleida), 25196 Lleida, Spain
| | - Maite Caus
- Vascular and Renal Translational Research Group, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLleida), 25196 Lleida, Spain
| | - Thalia Belmonte
- Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova-Santa Maria, Biomedical Research Institute of Lleida (IRBLleida), 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova-Santa Maria, Biomedical Research Institute of Lleida (IRBLleida), 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Alicia García-Carrasco
- Vascular and Renal Translational Research Group, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLleida), 25196 Lleida, Spain
| | - Ana Martinez
- Vascular and Renal Translational Research Group, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLleida), 25196 Lleida, Spain
| | - Montserrat Martínez
- Biostatistics Unit (Biostat), Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLleida), 25196 Lleida, Spain
| | - Milica Bozic
- Vascular and Renal Translational Research Group, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLleida), 25196 Lleida, Spain
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Lee DH, Bae WH, Ha H, Kim WR, Park EG, Lee YJ, Kim JM, Shin HJ, Kim HS. The human PTGR1 gene expression is controlled by TE-derived Z-DNA forming sequence cooperating with miR-6867-5p. Sci Rep 2024; 14:4723. [PMID: 38413664 PMCID: PMC10899170 DOI: 10.1038/s41598-024-55332-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Z-DNA, a well-known non-canonical form of DNA involved in gene regulation, is often found in gene promoters. Transposable elements (TEs), which make up 45% of the human genome, can move from one location to another within the genome. TEs play various biological roles in host organisms, and like Z-DNA, can influence transcriptional regulation near promoter regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a critical role in the regulation of gene expression. Although TEs can generate Z-DNA and miRNAs can bind to Z-DNA, how these factors affect gene transcription has yet to be elucidated. Here, we identified potential Z-DNA forming sequence (ZFS), including TE-derived ZFS, in the promoter of prostaglandin reductase 1 (PTGR1) by data analysis. The transcriptional activity of these ZFS in PTGR1 was confirmed using dual-luciferase reporter assays. In addition, we discovered a novel ZFS-binding miRNA (miR-6867-5p) that suppressed PTGR1 expression by targeting to ZFS. In conclusion, these findings suggest that ZFS, including TE-derived ZFS, can regulate PTGR1 gene expression and that miR-6867-5p can suppress PTGR1 by interacting with ZFS.
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Affiliation(s)
- Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hongseok Ha
- Institute of Endemic Diseases, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Jung-Min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea.
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.
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Dong S, Jiang S, Hou B, Li Y, Sun B, Guo Y, Deng M, Liu D, Liu G. miR-128-3p Regulates Follicular Granulosa Cell Proliferation and Apoptosis by Targeting the Growth Hormone Secretagogue Receptor. Int J Mol Sci 2024; 25:2720. [PMID: 38473968 DOI: 10.3390/ijms25052720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
The proliferation and apoptosis of granulosa cells (GCs) affect follicle development and reproductive disorders, with microRNAs playing a crucial regulatory role. Previous studies have shown the differential expression of miR-128-3p at different stages of goat follicle development, which suggests its potential regulatory role in follicle development. In this study, through the Cell Counting Kit-8 assay, the EDU assay, flow cytometry, quantitative real-time polymerase chain reaction, Western blot, and the dual-luciferase reporter assay, we used immortal human ovarian granulosa tumor cell line (KGN) cells as materials to investigate the effects of miR-128-3p and its predicted target gene growth hormone secretagogue receptor (GHSR) on GC proliferation and apoptosis. The results show that overexpression of miR-128-3p inhibited the proliferation of KGN cells, promoted cell apoptosis, and suppressed the expression of proliferating cell nuclear antigen (PCNA) and B-cell lymphoma-2 (BCL2) while promoting that of Bcl-2 associated X protein (BAX). The dual-luciferase reporter assay revealed that miR-128-3p bound to the 3' untranslated region sequence of GHSR, which resulted in the inhibited expression of GHSR protein. Investigation of the effects of GHSR on GC proliferation and apoptosis revealed that GHSR overexpression promoted the expression of PCNA and BCL2, enhanced GC proliferation, and inhibited cell apoptosis, whereas the opposite effects were observed when GHSR expression was inhibited. In addition, miR-128-3p and GHSR can influence the expression of extracellular signal-regulated kinase 1/2 protein. In conclusion, miR-128-3p inhibits KGN cell proliferation and promotes cell apoptosis by downregulating the expression of the GHSR gene.
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Affiliation(s)
- Shucan Dong
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Shengwei Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Biwei Hou
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yaokun Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Baoli Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yongqing Guo
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Ming Deng
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Dewu Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Guangbin Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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Wang Z, She D, Liu L, Hua X, Zhu H, Yu L, Wang H, Zhu Y, Fan G, Wang Y, Xu M, Zhou G. Circular RNA CircSATB2 facilitates osteosarcoma progression through regulating the miR-661/FUS-mediated mRNA of ZNFX1. Cell Signal 2024; 114:110977. [PMID: 37984605 DOI: 10.1016/j.cellsig.2023.110977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs which take part in the regulation of the initiation and development of different types of cancer. Numerous studies have demonstrated that circRNAs are involved in the progression of osteosarcoma (OS) as well. Thus, we put our emphasis on the exploration of crucial circRNAs in the process of OS initiation and progression. Using RNA sequencing, we found that circSATB2 was highly expressed in OS tissues compared with adjacent normal tissues. Then, we confirmed the high expression of circSATB2 in OS cell lines and OS tissues and its high expression was related to poor prognosis of OS patients. Functional experiments exhibited that circSATB2 promoted OS proliferation and migration in vitro, primary OS model and OS lung metastasis model showed that circSATB2 aggravated OS progression in vivo. Mechanistically, circSATB2 was found to promote OS progression through sponging miR-661 and FUS regulating the mRNA of ZNFX1. Therefore, circSATB2 could act as a prognostic marker and a therapeutic target for osteosarcoma in the future.
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Affiliation(s)
- Zhen Wang
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China; Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China; Department of Orthopaedics, The General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Diankun She
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Lei Liu
- Department of Orthopedics,The Affiliated Yixing Hospital of Jiangsu University, Yixing, Jiangsu, China
| | - Xianming Hua
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Hao Zhu
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Lingfeng Yu
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Han Wang
- Department of Pharmacy, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yan Zhu
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Gentao Fan
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Yicun Wang
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Meng Xu
- Department of Orthopaedics, The General Hospital of Chinese People's Liberation Army, Beijing, China.
| | - Guangxin Zhou
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China; Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China.
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Seyhan AA. Trials and Tribulations of MicroRNA Therapeutics. Int J Mol Sci 2024; 25:1469. [PMID: 38338746 PMCID: PMC10855871 DOI: 10.3390/ijms25031469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
The discovery of the link between microRNAs (miRNAs) and a myriad of human diseases, particularly various cancer types, has generated significant interest in exploring their potential as a novel class of drugs. This has led to substantial investments in interdisciplinary research fields such as biology, chemistry, and medical science for the development of miRNA-based therapies. Furthermore, the recent global success of SARS-CoV-2 mRNA vaccines against the COVID-19 pandemic has further revitalized interest in RNA-based immunotherapies, including miRNA-based approaches to cancer treatment. Consequently, RNA therapeutics have emerged as highly adaptable and modular options for cancer therapy. Moreover, advancements in RNA chemistry and delivery methods have been pivotal in shaping the landscape of RNA-based immunotherapy, including miRNA-based approaches. Consequently, the biotechnology and pharmaceutical industry has witnessed a resurgence of interest in incorporating RNA-based immunotherapies and miRNA therapeutics into their development programs. Despite substantial progress in preclinical research, the field of miRNA-based therapeutics remains in its early stages, with only a few progressing to clinical development, none reaching phase III clinical trials or being approved by the US Food and Drug Administration (FDA), and several facing termination due to toxicity issues. These setbacks highlight existing challenges that must be addressed for the broad clinical application of miRNA-based therapeutics. Key challenges include establishing miRNA sensitivity, specificity, and selectivity towards their intended targets, mitigating immunogenic reactions and off-target effects, developing enhanced methods for targeted delivery, and determining optimal dosing for therapeutic efficacy while minimizing side effects. Additionally, the limited understanding of the precise functions of miRNAs limits their clinical utilization. Moreover, for miRNAs to be viable for cancer treatment, they must be technically and economically feasible for the widespread adoption of RNA therapies. As a result, a thorough risk evaluation of miRNA therapeutics is crucial to minimize off-target effects, prevent overdosing, and address various other issues. Nevertheless, the therapeutic potential of miRNAs for various diseases is evident, and future investigations are essential to determine their applicability in clinical settings.
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Affiliation(s)
- Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA;
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
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Jiang L, Fang T, Hu T, Feng J, Yan P. Mir-338-3p targeting THBS1 attenuates glioma progression by inhibiting the PI3K/Akt pathway. Biol Direct 2024; 19:9. [PMID: 38267974 PMCID: PMC10807173 DOI: 10.1186/s13062-023-00443-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Glioma is a brain tumor with high morbidity and mortality rates. Understanding its molecular pathogenesis can provide targets and therapeutic strategies for glioma treatment. miR-338-3p represses tumor growth in several cancers, including glioma. Thus, this study aimed to identify the regulatory effects of miR-338-3p/phosphoinositide 3-kinase (PI3K)/Akt/thrombospondins 1 (THBS1) on glioma progression. MATERIALS AND METHODS Quantitative reverse transcription polymerase chain reaction and western blotting were performed to evaluate the levels of miR-338-3p, THBS1, and PI3K/Akt phosphorylation-related proteins. TargetScan software predicted that miR-338-3p targeted THBS1. This was confirmed by performing the dual-luciferase assay. Wound-healing and cell-counting-kit-8 experiments were performed to analyze how THBS1 and miR-338-3p affect the ability of glioma cells to migrate and proliferate. The effect of miR-338-3p on tumorigenicity in mice was also analyzed. RESULTS miR-338-3p downregulation was observed in gliomas, whereas THBS1 showed the opposite trend. By suppressing the PI3K/Akt signaling pathway activation, miR-338-3p overregulated the ability of glioma cells to migrate and proliferate in vitro. Additionally, miR-338-3p inhibited the development of glioma tumors in vivo. Moreover, miR-338-3p directly targeted THBS1. THBS1 overexpression promoted glioma cell migration and proliferation by increasing PI3K/Akt phosphorylation. Nonetheless, miR-338-3p overregulation alleviated the effects of THBS1 overexpression. CONCLUSION The miR-338-3p/PI3K/Akt/THBS1 regulatory axis can modulate the progression of glioma cell proliferation and migration; thus, it can be considered a therapeutic biomarker.
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Affiliation(s)
- Lianglei Jiang
- Department of Neurosurgery, , Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , 430022, Wuhan, China
| | - Ting Fang
- Department of Neurosurgery, , Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , 430022, Wuhan, China
| | - Tingting Hu
- Department of Neurosurgery, , Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , 430022, Wuhan, China
| | - Jun Feng
- Department of Neurosurgery, , Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , 430022, Wuhan, China.
| | - Pengfei Yan
- Department of Neurosurgery, , Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , 430022, Wuhan, China.
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Amber S, Zahid S. An in silico approach to identify potential downstream targets of miR-153 involved in Alzheimer's disease. Front Genet 2024; 15:1271404. [PMID: 38299037 PMCID: PMC10824926 DOI: 10.3389/fgene.2024.1271404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024] Open
Abstract
Background: In recent years, microRNAs (miRNAs) have emerged as key players in the pathophysiology of multiple diseases including Alzheimer's disease (AD). Messenger RNA (mRNA) targeting for regulation of gene expression by miRNAs has been implicated in the annotation of disease pathophysiology as well as in the explication of their starring role in contemporary therapeutic interventions. One such miRNA is miR-153 which mediates the survival of cortical neurons and inhibits plaque formation. However, the core mRNA targets of miR-153 have not been fully illustrated. Objective: The present study aimed to elucidate the potential involvement of miR-153 in AD pathogenesis and to reveal its downstream targets. Methods: miRanda was used to identify AD-associated targets of miR-153. TargetScan, PicTar, miRmap, and miRDB were further used to validate these targets. STRING 12 was employed to assess the protein-protein interaction network while Gene ontology (GO) analysis was carried out to identify the molecular functions exhibited by these gene targets. Results: In silico analysis using miRanda predicted five important AD-related targets of miR-153, including APP, SORL1, PICALM, USF1, and PSEN1. All five target genes are negatively regulated by miR-153 and are substantially involved in AD pathogenesis. A protein interaction network using STRING 12 uncovered 30 potential interacting partners for SORL1, PICALM, and USF1. GO analysis revealed that miR-153 target genes play a critical role in neuronal survival, differentiation, exon guidance, amyloid precursor protein processing, and synapse formation. Conclusion: These findings unravel the potential role of miR-153 in the pathogenesis of AD and provide the basis for forthcoming experimental studies.
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Affiliation(s)
| | - Saadia Zahid
- Department of Healthcare Biotechnology, Neurobiology Research Laboratory, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Li W, Wei J, Huang P, Wei Y, Chang L, Liu G. Differential expression of miRNAs revealed by small RNA sequencing in traumatic tracheal stenosis. Front Genet 2024; 14:1291488. [PMID: 38259609 PMCID: PMC10800880 DOI: 10.3389/fgene.2023.1291488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Traumatic tracheal stenosis (TTS) is a major cause of complex difficult airways, without clinically definitive efficacious drugs available. The aim of this study was to provide a general view of interactions between micro and messenger ribonucleic acids (miRNAs and mRNAs) and many potential mechanisms in TTS via small RNA sequencing. Methods: In this study, the identification of miRNAs was completed using small RNA sequencing and samples from four TTS patients and four normal control cases. By using bioinformatics tools, such as miRanda and RNAhybrid, for identifying the candidate target genes of miRNAs with differential expression in each sample, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were employed for enriching the predicted target genes of miRNAs with differential expression based on the correspondence between miRNAs and their target genes. We detected the expression of the candidate miRNAs using quantitative real-time polymerase chain reaction (qRT-PCR). Results: Twenty-four miRNAs with significant differential expression were identified, including 13 upregulated and 11 downregulated ones. Bioinformation technology was adopted to predict 2,496 target genes. These miRNA-target genes were shown to be primarily enriched in cells and organelles with catalytic activity and binding function, such as binding proteins, small molecules, and nucleotides. Finally, they were observed to process into TTS through the intercellular and signal regulation of related inflammatory signaling and fibrosis signaling pathways. QRT-PCR confirmed the upregulation of miR21-5p and miR214-3p and the downregulation of miR141-3p and miR29b-3p, which was expected to become a high-specific miRNA for TTS. Conclusion: Among all the miRNAs detected, 24 miRNAs demonstrated differential expression between the TTS and normal control groups. A total of 2,496 target genes were predicted by bioinformation technology and enriched in inflammatory and fibrotic signaling pathways. These results provide new ideas for further studies and the selection of targets for TTS in the future.
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Affiliation(s)
- Wentao Li
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Medical University, Nanning, China
| | - Jinmei Wei
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Pingping Huang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuhui Wei
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li Chang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Department of Dermatology of Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan Uninversity, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Guangnan Liu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Medical University, Nanning, China
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Müller T, Mautner S, Videm P, Eggenhofer F, Raden M, Backofen R. CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites. Gigascience 2024; 13:giae022. [PMID: 38837942 PMCID: PMC11152173 DOI: 10.1093/gigascience/giae022] [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: 09/27/2023] [Revised: 03/04/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND RNA-RNA interactions are key to a wide range of cellular functions. The detection of potential interactions helps to understand the underlying processes. However, potential interactions identified via in silico or experimental high-throughput methods can lack precision because of a high false-positive rate. RESULTS We present CheRRI, the first tool to evaluate the biological relevance of putative RNA-RNA interaction sites. CheRRI filters candidates via a machine learning-based model trained on experimental RNA-RNA interactome data. Its unique setup combines interactome data and an established thermodynamic prediction tool to integrate experimental data with state-of-the-art computational models. Applying these data to an automated machine learning approach provides the opportunity to not only filter data for potential false positives but also tailor the underlying interaction site model to specific needs. CONCLUSIONS CheRRI is a stand-alone postprocessing tool to filter either predicted or experimentally identified potential RNA-RNA interactions on a genomic level to enhance the quality of interaction candidates. It is easy to install (via conda, pip packages), use (via Galaxy), and integrate into existing RNA-RNA interaction pipelines.
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Affiliation(s)
- Teresa Müller
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Stefan Mautner
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Pavankumar Videm
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Martin Raden
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Signalling Research Centre CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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Chen J, Liu T, Cui H, Na Q, Liu S. MiRNA-26a-5p inhibits preterm labor initiation by targeting and regulating TRPC3 ion channel protein expression. ENVIRONMENTAL TOXICOLOGY 2024; 39:357-366. [PMID: 37755144 DOI: 10.1002/tox.23972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/03/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
The incidence of preterm birth (PTB) is increasing annually worldwide, leading to various health problems or even fetal deaths. Our previous work demonstrated the activation of transient receptor potential cation channel subfamily C 3 (TRPC3) in mice with PTB, and its activation could promote inward flow of calcium ions and uterine smooth muscle (USM) contraction via regulation of Cav3.2, Cav3.1, and Cav1.2. However, the upstream regulators of TRPC3 and its mechanisms remain unknown. In the present study, the binding of miR-26a-5p to the 3' untranslated region of TRPC3 was predicted by bioinformatics databases (TargetScanHuman and starBase v3.0) and confirmed by a dual-luciferase assay. MiR-26a-5p was downregulated, while TRPC3 was upregulated in the USM tissues of patients with PTB compared to people without PTB. The results showed that miR-26a-5p mimic transfection markedly reduced TRPC3 expression in LPS-stimulated USM cells. Additionally, miR-26a-5p regulated intracellular Ca2+ levels in USM cells by targeting TRPC3. Furthermore, miR-26a-5p inhibited the CPI17/PKC/PLCγ signaling pathway and reduced the expression of Cav3.2, Cav3.1, and Cav1.2. In conclusion, miR-26a-5p regulated the initiation of PTB by targeting TRPC3 and regulating intracellular Ca2+ levels. This study provides a promising diagnostic biomarker and therapeutic target for PTB.
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Affiliation(s)
- Jing Chen
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Tong Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Hong Cui
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Quan Na
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
| | - Sishi Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, P.R. China
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Si X, Liu H, Cheng X, Xu C, Han Z, Dai Z, Wang R, Pan C, Lu G. Integrative transcriptomic analysis unveils lncRNA-miRNA-mRNA interplay in tomato plants responding to Ralstonia solanacearum. Int J Biol Macromol 2023; 253:126891. [PMID: 37709224 DOI: 10.1016/j.ijbiomac.2023.126891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/26/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Ralstonia solanacearum, a bacterial plant pathogen, poses a significant threat to tomato (Solanum lycopersicum) production through destructive wilt disease. While noncoding RNA has emerged as a crucial regulator in plant disease, its specific involvement in tomato bacterial wilt remains limited. Here, we conducted a comprehensive analysis of the transcriptional landscape, encompassing both mRNAs and noncoding RNAs, in a tomato resistant line ('ZRS_7') and a susceptible line ('HTY_9') upon R. solanacearum inoculation using high-throughput RNA sequencing. Differential expression (DE) analysis revealed significant alterations in 7506 mRNAs, 997 lncRNAs, and 69 miRNAs between 'ZRS_7' and 'HTY_9' after pathogen exposure. Notably, 4548 mRNAs, 367 lncRNAs, and 26 miRNAs exhibited genotype-specific responses to R. solanacearum inoculation. GO and KEGG pathway analyses unveiled the potential involvement of noncoding RNAs in the response to bacterial wilt disease, targeting receptor-like kinases, cell wall-related genes, glutamate decarboxylases, and other key pathways. Furthermore, we constructed a comprehensive competing endogenous RNA (ceRNA) network incorporating 13 DE-miRNAs, 30 DE-lncRNAs, and 127 DEGs, providing insights into their potential contributions to the response against bacterial inoculation. Importantly, the characterization of possible endogenous target mimics (eTMs) of Sly-miR482e-3p via VIGS technology demonstrated the significant impact of eTM482e-3p-1 silencing on tomato's sensitivity to R. solanacearum. These findings support the existence of an eTM482e-3p-1-Sly-miR482e-3p-NBS-LRRs network in regulating tomato's response to the pathogen. Collectively, our findings shed light on the intricate interactions among lncRNAs, miRNAs, and mRNAs as underlying factors in conferring resistance to R. solanacearum in tomato.
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Affiliation(s)
- Xiuyang Si
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongyan Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xi Cheng
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chengcui Xu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanghui Han
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhongren Dai
- Branch Academy of Horticultural Research, Harbin Academy of Agricultural Sciences, Harbin 150029, China
| | - Rongqing Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China
| | - Changtian Pan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China
| | - Gang Lu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China.
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Wen JL, Ruan ZB, Wang F, Hu Y. Progress of circRNA/lncRNA-miRNA-mRNA axis in atrial fibrillation. PeerJ 2023; 11:e16604. [PMID: 38144204 PMCID: PMC10740593 DOI: 10.7717/peerj.16604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/15/2023] [Indexed: 12/26/2023] Open
Abstract
Atrial fibrillation (AF) is a prevalent arrhythmia that requires effective biomarkers and therapeutic targets for clinical management. In recent years, non-coding RNAs (ncRNAs) have emerged as key players in the pathogenesis of AF, particularly through the ceRNA (competitive endogenous RNA) mechanism. By acting as ceRNAs, ncRNAs can competitively bind to miRNAs and modulate the expression of target mRNAs, thereby influencing the biological behavior of AF. The ceRNA axis has shown promise as a diagnostic and prognostic biomarker for AF. This review provides a comprehensive overview of the roles of ncRNAs in the development and progression of AF, highlighting the intricate crosstalk between different ncRNAs in AF pathophysiology. Furthermore, we discuss the potential implications of targeting the circRNA/lncRNA-miRNA-mRNA axis for the diagnosis, prognosis, and therapeutic intervention of AF.
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Affiliation(s)
- Jia-le Wen
- Department of Cardiology, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China
- Dalian Medical University, Dalian, China
| | - Zhong-bao Ruan
- Department of Cardiology, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China
| | - Fei Wang
- Department of Cardiology, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China
| | - Yuhua Hu
- Dalian Medical University, Dalian, China
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Liu F, Zhao H, Li Q, Wu L, Cao D, Zhang Y, Huang ZY. MicroRNA ame-let-7 targets Amdop2 to increase sucrose sensitivity in honey bees (Apis mellifera). Front Zool 2023; 20:41. [PMID: 38110949 PMCID: PMC10726540 DOI: 10.1186/s12983-023-00519-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND As an important catecholamine neurotransmitter in invertebrates and vertebrates, dopamine plays multiple roles in the life of the honey bee. Dopamine receptors (DA), which specifically bind to dopamine to activate downstream cascades, have been reported to be involved in honey bee reproduction, division of labour, as well as learning and motor behaviour. However, how dopamine receptors regulate honey bee behavior remains uninvestigated. RESULTS The expression level of Amdop2 in the brain increased with the age of worker bees, which was just the opposite trend of ame-let-7. Inhibition of ame-let-7 through feeding an inhibitor upregulated Amdop2 expression; conversely, overexpression of ame-let-7 through a mimic downregulated Amdop2. Moreover, knockdown of Amdop2 in forager brain led to significantly higher sucrose responsiveness, which is similar to the phenotype of overexpression of ame-let-7. Finally, we confirmed that ame-let-7 directly targets Amdop2 in vitro by a luciferase reporter assay. CONCLUSIONS ame-let-7 is involved in the dopamine receptor signaling pathway to modulate the sucrose sensitivity in honey bees. Specifically, it down-regulates Amdop2, which then induces higher responses to sucrose. These results further unraveled the diverse mechanisms of the dopamine pathway in the regulation of insect behavior.
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Affiliation(s)
- Fang Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, People's Republic of China.
| | - Hongxia Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, People's Republic of China
| | - Qiang Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, People's Republic of China
| | - Lixian Wu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, People's Republic of China
| | - Dainan Cao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, People's Republic of China
| | - Yuan Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, 650224, Kunming, Yunnan, People's Republic of China
| | - Zachary Y Huang
- Department of Entomology, Michigan State University, East Lansing, MI, 48824, USA.
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Zhao Z, Wang W, Wang G, Huang Z, Zhou L, Lin L, Ou Y, Huang W, Zhang X, Wu C, Tao L, Wang Q. Dual peptides-modified cationic liposomes for enhanced Lung cancer gene therapy by a gap junction regulating strategy. J Nanobiotechnology 2023; 21:473. [PMID: 38066528 PMCID: PMC10709977 DOI: 10.1186/s12951-023-02242-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/03/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Gene therapy for lung cancer has emerged as a novel tumor-combating strategy for its superior tumor specificity, low systematical toxicity and huge clinical translation potential. Especially, the applications of microRNA shed led on effective tumor ablation by directly interfering with the crucial gene expression, making it one of the most promising gene therapy agents. However, for lung cancer therapy, the microRNA treatment confronted three bottlenecks, the poor tumor tissue penetration effect, the insufficient lung drug accumulation and unsatisfied gene transfection efficiency. To address these issues, an inhalable RGD-TAT dual peptides-modified cationic liposomes loaded with microRNA miR-34a and gap junction (GJ) regulation agent all-trans retinoic acid (ATRA) was proposed, which was further engineered into dry powder inhalers (DPIs). RESULTS Equipped with a rough particle surface and appropriate aerodynamic size, the proposed RGD-TAT-CLPs/ARTA@miR-34a DPIs were expected to deposit into the deep lung and reach lung tumor lesions guided by targeting peptide RGD. Assisted by cellular transmembrane peptides TAT, the RGD-TAT-CLPs/ARTA@miR-34a was proven to be effectively internalized by cancer cells, enhancing gene transfection efficiency. Then, the GJ between tumor cells was upregulated by ARTA, facilitating the intercellular transport of miR-34a and boosting the gene expression in the deep tumor. CONCLUSION Overall, the proposed RGD-TAT-CLPs/ARTA@miR-34a DPIs could enhance tumor tissue penetration, elevate lung drug accumulation and boost gene transfection efficiency, breaking the three bottlenecks to enhancing tumor elimination in vitro and in vivo. We believe that the proposed RGD-TAT-CLPs/ARTA@miR-34a DPIs could serve as a promising pulmonary gene delivery platform for multiple lung local disease treatments.
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Affiliation(s)
- Ziyu Zhao
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, PR China
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, Guangdong, 510632, PR China
- College of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, PR China
| | - Wenhao Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, PR China
| | - Guanlin Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, PR China
| | - Zhengwei Huang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, Guangdong, 510632, PR China
- College of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, PR China
| | - Liping Zhou
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, PR China
| | - Li Lin
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, PR China
| | - Yueling Ou
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, PR China
| | - Wanzhen Huang
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, PR China
| | - Xuejuan Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, Guangdong, 510632, PR China.
- College of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, PR China.
| | - Chuanbin Wu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou, Guangdong, 510632, PR China
- College of Pharmacy, Jinan University, Guangzhou, Guangdong, 510632, PR China
| | - Liang Tao
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, PR China.
- Nanchang Research Institute, Sun Yat-Sen University, Nanchang, Jiangxi, 330096, PR China.
| | - Qin Wang
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, PR China.
- Nanchang Research Institute, Sun Yat-Sen University, Nanchang, Jiangxi, 330096, PR China.
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Ji X, Liu X, Li X, Du X, Fan L. MircoRNA-322-5p promotes lipopolysaccharide-induced acute kidney injury mouse models and mouse primary proximal renal tubular epithelial cell injury by regulating T-box transcription factor 21/mitogen-activated protein kinase/extracellular signal-related kinase axis. Nefrologia 2023; 43 Suppl 2:8-20. [PMID: 37179213 DOI: 10.1016/j.nefroe.2023.05.004] [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: 11/15/2022] [Accepted: 01/25/2023] [Indexed: 05/15/2023] Open
Abstract
INTRODUCTION AND OBJECTIVES Acute kidney injury (AKI) is a common devastating complication characterized by an abrupt loss of renal function. It is of great significance to explore promising biomarkers for AKI treatment. MATERIALS AND METHODS Here, we established LPS (lipopolysaccharide)-induced AKI mice models and LPS-induced AKI mouse renal tubular epithelial cell model. The severity of AKI was determined by the levels of BUN (blood urea nitrogen) and SCr (serum creatinine), the observation of pathological section as well as the renal tubular injury score. The apoptosis was determined by the measurement of Caspase-3 and Caspase-9 activities, and cell apoptosis assays. qRT-PCR (quantitative real-time PCR) and western blot revealed that miR-322-5p (microRNA-322-5p) was up-regulated in LPS -induced AKI models while Tbx21 (T-box transcription factor 21) was down-regulated in LPS-induced AKI models. Dual-luciferase reporter and RNA pulldown assays detected the interaction of Tbx21 with miR-322-5p. RESULTS We found that miR-322-5p was overtly over-expressed in the in vitro LPS-induced AKI model and promoted the apoptosis of AKI mouse renal tubular epithelial cells via inhibiting Tbx21, which suppressed the mitochondrial fission and cell apoptosis through MAPK/ERK (mitogen-activated protein kinase/extracellular signal-related kinase) pathway. CONCLUSIONS We demonstrated that miR-322-5p promotes LPS-induced mouse AKI by regulating Tbx21/MAPK/ERK axis, which might provide new sights for AKI research.
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Affiliation(s)
- Xiaobing Ji
- Department of Nephrology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Xiaodong Liu
- Department of Nephrology, The Second People's Hospital of Lianyungang,Affiliated to Kangda College of Nanjing Medical University, Lianyungang 222023, Jiangsu, China
| | - Xiangxiang Li
- Department of Nephrology, Nanjing Yuhua Hospital, Yuhua Branch of Nanjing First Hospital, Nanjing 210039, Jiangsu, China
| | - Xin Du
- Department of Nephrology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Li Fan
- Department of Nephrology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China.
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Begum MIA, Chuan L, Hong ST, Chae HS. The Pathological Role of miRNAs in Endometriosis. Biomedicines 2023; 11:3087. [PMID: 38002087 PMCID: PMC10669455 DOI: 10.3390/biomedicines11113087] [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: 09/30/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Association studies investigating miRNA in relation to diseases have consistently shown significant alterations in miRNA expression, particularly within inflammatory pathways, where they regulate inflammatory cytokines, transcription factors (such as NF-κB, STAT3, HIF1α), and inflammatory proteins (including COX-2 and iNOS). Given that endometriosis (EMS) is characterized as an inflammatory disease, albeit one influenced by estrogen levels, it is natural to speculate about the connection between EMS and miRNA. Recent research has indeed confirmed alterations in the expression levels of numerous microRNAs (miRNAs) in both endometriotic lesions and the eutopic endometrium of women with EMS, when compared to healthy controls. The undeniable association of miRNAs with EMS hints at the emergence of a new era in the study of miRNA in the context of EMS. This article reviews the advancements made in understanding the pathological role of miRNA in EMS and its association with EMS-associated infertility. These findings contribute to the ongoing pursuit of developing miRNA-based therapeutics and diagnostic markers for EMS.
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Affiliation(s)
- Mst Ismat Ara Begum
- Department of Biomedical Sciences, Institute for Medical Science, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea; (M.I.A.B.); (L.C.)
| | - Lin Chuan
- Department of Biomedical Sciences, Institute for Medical Science, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea; (M.I.A.B.); (L.C.)
| | - Seong-Tshool Hong
- Department of Biomedical Sciences, Institute for Medical Science, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea; (M.I.A.B.); (L.C.)
| | - Hee-Suk Chae
- Department of Obstetrics and Gynecology, Research Institute of Clinical Medicine, Jeonbuk National University, Jeonju 54907, Republic of Korea
- Biomedical Research Institute, Jeonbuk National University Hospital, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea
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Liu BW, Sun N, Lin H, Zhou XJ, Ma HY, Wang X, Cao XC, Yu Y. The p53/ZEB1-PLD3 feedback loop regulates cell proliferation in breast cancer. Cell Death Dis 2023; 14:751. [PMID: 37978168 PMCID: PMC10656518 DOI: 10.1038/s41419-023-06271-4] [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: 01/31/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
Breast cancer is the most prevalent cancer globally, endangering women's physical and mental health. Phospholipase D3 (PLD3) belongs to the phosphodiesterase family (PLD). PLD3 is related to insulin-mediated phosphorylation of the AKT pathway, suggesting that it may play a role in the occurrence and development of malignant tumors. This study may further explore the molecular mechanism of PLD3 inhibiting breast cancer cell proliferation. In this study, we demonstrated that PLD3 and miR-6796 are co-expressed in breast cancer. PLD3 can bind with CDK1 and inhibit its expression, leading to mitotic arrest and inhibiting breast cancer proliferation. Wild-type p53 regulates PLD3 and miR-6796 expression by competitively binding to the PLD3 promoter with ZEB1. DNMT3B, as the target gene of miR-6796, is recruited into the PLD3 promoter by combining with ZEB1 to regulate the DNA methylation of the PLD3 promoter and ultimately affect PLD3 and miR-6796 expression. In conclusion, we revealed the role and molecular mechanism of PLD3 and its embedded miR-6796 in breast cancer proliferation, providing clues and a theoretical foundation for future research and development of therapeutic targets and prognostic markers for breast cancer.
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Affiliation(s)
- Bo-Wen Liu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Ning Sun
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Department of Thyroid and Breast Surgery, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Hui Lin
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Wenzhou, Zhejiang, 317099, China
| | - Xue-Jie Zhou
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Hai-Yan Ma
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xin Wang
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xu-Chen Cao
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| | - Yue Yu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
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Dandare A, Khan MJ, Naeem A, Liaquat A. Clinical relevance of circulating non-coding RNAs in metabolic diseases: Emphasis on obesity, diabetes, cardiovascular diseases and metabolic syndrome. Genes Dis 2023; 10:2393-2413. [PMID: 37554181 PMCID: PMC10404886 DOI: 10.1016/j.gendis.2022.05.022] [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: 01/26/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022] Open
Abstract
Non-coding RNAs (ncRNAs) participate in the regulation of several cellular processes including transcription, RNA processing and genome rearrangement. The aberrant expression of ncRNAs is associated with several pathological conditions. In this review, we focused on recent information to elucidate the role of various regulatory ncRNAs i.e., micro RNAs (miRNAs), circular RNAs (circRNAs) and long-chain non-coding RNAs (lncRNAs), in metabolic diseases, e.g., obesity, diabetes mellitus (DM), cardiovascular diseases (CVD) and metabolic syndrome (MetS). The mechanisms by which ncRNAs participated in disease pathophysiology were also highlighted. miRNAs regulate the expression of genes at transcriptional and translational levels. circRNAs modulate the regulation of gene expression via miRNA sponging activity, interacting with RNA binding protein and polymerase II transcription regulation. lncRNAs regulate the expression of genes by acting as a protein decoy, miRNA sponging, miRNA host gene, binding to miRNA response elements (MRE) and the recruitment of transcriptional element or chromatin modifiers. We examined the role of ncRNAs in the disease pathogenesis and their potential role as molecular markers for diagnosis, prognosis and therapeutic targets. We showed the involvement of ncRNAs in the onset of obesity and its progression to MetS and CVD. miRNA-192, miRNA-122, and miRNA-221 were dysregulated in all these metabolic diseases. Other ncRNAs, implicated in at least three diseases include miRNA-15a, miRNA-26, miRNA-27a, miRNA-320, and miRNA-375. Dysregulation of ncRNAs increased the risk of development of DM and MetS and its progression to CVD in obese individuals. Hence, these molecules are potential targets to arrest or delay the progression of metabolic diseases.
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Affiliation(s)
- Abdullahi Dandare
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Department of Biochemistry, Usmanu Danfodiyo University, Sokoto 840104, Nigeria
| | - Muhammad Jawad Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | - Aisha Naeem
- Ministry of Public Health, POB42, Doha, Qatar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Afrose Liaquat
- Shifa College of Medicine, Shifa Tameer-E-Millat University, Islamabad 45550, Pakistan
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Temaj G, Chichiarelli S, Saha S, Telkoparan-Akillilar P, Nuhii N, Hadziselimovic R, Saso L. An intricate rewiring of cancer metabolism via alternative splicing. Biochem Pharmacol 2023; 217:115848. [PMID: 37813165 DOI: 10.1016/j.bcp.2023.115848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
All human genes undergo alternative splicing leading to the diversity of the proteins. However, in some cases, abnormal regulation of alternative splicing can result in diseases that trigger defects in metabolism, reduced apoptosis, increased proliferation, and progression in almost all tumor types. Metabolic dysregulations and immune dysfunctions are crucial factors in cancer. In this respect, alternative splicing in tumors could be a potential target for therapeutic cancer strategies. Dysregulation of alternative splicing during mRNA maturation promotes carcinogenesis and drug resistance in many cancer types. Alternative splicing (changing the target mRNA 3'UTR binding site) can result in a protein with altered drug affinity, ultimately leading to drug resistance.. Here, we will highlight the function of various alternative splicing factors, how it regulates the reprogramming of cancer cell metabolism, and their contribution to tumor initiation and proliferation. Also, we will discuss emerging therapeutics for treating tumors via abnormal alternative splicing. Finally, we will discuss the challenges associated with these therapeutic strategies for clinical applications.
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Affiliation(s)
- Gazmend Temaj
- Faculty of Pharmacy, College UBT, 10000 Prishtina, Kosovo
| | - Silvia Chichiarelli
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, 00185 Rome, Italy.
| | - Sarmistha Saha
- Department of Biotechnology, GLA University, Mathura 00185, Uttar Pradesh, India
| | | | - Nexhibe Nuhii
- Department of Pharmacy, Faculty of Medical Sciences, State University of Tetovo, 1200 Tetovo, Macedonia
| | - Rifat Hadziselimovic
- Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University, 00185 Rome, Italy.
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Chen Y, Zhang Y, Luo S, Yang X, Liu C, Zhang Q, Liu Y, Zhang X. Foldback-crRNA-Enhanced CRISPR/Cas13a System (FCECas13a) Enables Direct Detection of Ultrashort sncRNA. Anal Chem 2023; 95:15606-15613. [PMID: 37824705 DOI: 10.1021/acs.analchem.3c02687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
The CRISPR/Cas13a system has promising applications in clinical small noncoding RNA (sncRNA) detection because it is free from the interference of genomic DNA. However, detecting ultrashort sncRNAs (less than 20 nucleotides) has been challenging because the Cas13a nuclease requires longer crRNA-target RNA hybrids to be activated. Here, we report the development of a foldback-crRNA-enhanced CRISPR/Cas13a (FCECas13a) system that overcomes the limitations of the current CRISPR/Cas13a system in detecting ultrashort sncRNAs. The FCECas13a system employs a 3'-terminal foldback crRNA that hybridizes with the target ultrashort sncRNA, forming a double strand that "tricks" the Cas13a nuclease into activating the HEPN structural domain and generating trans-cleavage activity. The FCECas13a system can accurately detect miRNA720 (a sncRNA currently known as tRNA-derived small RNA), which is only 17 nucleotides long and has a concentration as low as 15 fM within 20 min. This FCECas13a system opens new avenues for ultrashort sncRNA detection with significant implications for basic biological research, disease prognosis, and molecular diagnosis.
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Affiliation(s)
- Yong Chen
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, P. R. China
- Graphene Composite Research Center, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, P. R. China
| | - Yibin Zhang
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, P. R. China
| | - Siyuan Luo
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, P. R. China
| | - Xinyao Yang
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, P. R. China
| | - Conghui Liu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, P. R. China
| | - Qianling Zhang
- Graphene Composite Research Center, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, P. R. China
| | - Yizhen Liu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, P. R. China
- Shenzhen Key Laboratory of Nano-Biosensing Technology, Shenzhen 518060, Guangdong, P. R. China
| | - Xueji Zhang
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, P. R. China
- Shenzhen Key Laboratory of Nano-Biosensing Technology, Shenzhen 518060, Guangdong, P. R. China
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50
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Tomczyk I, Rokicki M, Sieńko W, Rożek K, Nalepa A, Wiench J, Grzmil P. Mouse Pxt1 expression is regulated by Mir6996 miRNA. Theriogenology 2023; 210:9-16. [PMID: 37467697 DOI: 10.1016/j.theriogenology.2023.07.010] [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: 10/16/2022] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023]
Abstract
Mouse Pxt1 gene is expressed exclusively in male germ cells and encodes for a small, cell death inducing protein. However, upon PXT1 interaction with BAG6, cell death is prevented. In transiently transfected cell lines the PXT1 expression triggered massive cell death, thus we ask the question whether the interaction of PXT1 and BAG6 is the only mechanism preventing normal, developing male germ cells from being killed by PXT1. The Pxt1 gene contains a long 3'UTR thus we have hypothesized that Pxt1 can be regulated by miRNA. We have applied Pxt1 knockout and used Pxt1 transgenic mice that overexpressed this gene to shed more light on Pxt1 regulation. Using the ELISA assay we have demonstrated that PXT1 protein is expressed in adult mouse testis, though at low abundance. The application of dual-Glo luciferase assay and the 3'UTR cloned into p-MIR-Glo plasmid showed that Pxt1 is regulated by miRNA. Combining the use of mirDB and the site-directed mutagenesis further demonstrated that Pxt1 translation is suppressed by Mir6996-3p. Considering previous reports and our current results we propose a model for Pxt1 regulation in the mouse male germ cells.
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Affiliation(s)
- Igor Tomczyk
- Department of Genetics and Evolution, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland
| | - Mikołaj Rokicki
- Department of Genetics and Evolution, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland
| | - Wioleta Sieńko
- Department of Genetics and Evolution, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland
| | - Katarzyna Rożek
- Department of Plant Ecology, Institute of Botany, Jagiellonian University, Gronostajowa 3, 30-387, Krakow, Poland
| | - Anna Nalepa
- Department of Chemical Technology and Environmental Analytics, Cracow University of Technology, Warszawska 24, 31-155, Krakow, Poland
| | - Jasmin Wiench
- Department of Genetics and Evolution, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland
| | - Paweł Grzmil
- Department of Genetics and Evolution, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland.
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