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Jin MH, Feng L, Xiang HY, Sun HN, Han YH, Kwon T. Exploring the role of Prx II in mitigating endoplasmic reticulum stress and mitochondrial dysfunction in neurodegeneration. Cell Commun Signal 2024; 22:231. [PMID: 38637880 PMCID: PMC11025193 DOI: 10.1186/s12964-024-01613-x] [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: 02/01/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Neurodegenerative diseases are increasingly recognized for their association with oxidative stress, which leads to progressive dysfunction and loss of neurons, manifesting in cognitive and motor impairments. This study aimed to elucidate the neuroprotective role of peroxiredoxin II (Prx II) in counteracting oxidative stress-induced mitochondrial damage, a key pathological feature of neurodegeneration. METHODS We investigated the impact of Prx II deficiency on endoplasmic reticulum stress and mitochondrial dysfunction using HT22 cell models with knocked down and overexpressed Prx II. We observed alcohol-treated HT22 cells using transmission electron microscopy and monitored changes in the length of mitochondria-associated endoplasmic reticulum membranes and their contact with endoplasmic reticulum mitochondria contact sites (EMCSs). Additionally, RNA sequencing and bioinformatic analysis were conducted to identify the role of Prx II in regulating mitochondrial transport and the formation of EMCSs. RESULTS Our results indicated that Prx II preserves mitochondrial integrity by facilitating the formation of EMCSs, which are essential for maintaining mitochondrial Ca2+ homeostasis and preventing mitochondria-dependent apoptosis. Further, we identified a novel regulatory axis involving Prx II, the transcription factor ATF3, and miR-181b-5p, which collectively modulate the expression of Armcx3, a protein implicated in mitochondrial transport. Our findings underscore the significance of Prx II in protecting neuronal cells from alcohol-induced oxidative damage and suggest that modulating the Prx II-ATF3-miR-181b-5p pathway may offer a promising therapeutic strategy against neurodegenerative diseases. CONCLUSIONS This study not only expands our understanding of the cytoprotective mechanisms of Prx II but also offers necessary data for developing targeted interventions to bolster mitochondrial resilience in neurodegenerative conditions.
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Affiliation(s)
- Mei-Hua Jin
- College of Life Science & Biotechnology Technology, Heilongjiang Bayi Agricultural University, 163319, Daqing, China
| | - Lin Feng
- College of Life Science & Biotechnology Technology, Heilongjiang Bayi Agricultural University, 163319, Daqing, China
| | - Hong-Yi Xiang
- College of Life Science & Biotechnology Technology, Heilongjiang Bayi Agricultural University, 163319, Daqing, China
| | - Hu-Nan Sun
- College of Life Science & Biotechnology Technology, Heilongjiang Bayi Agricultural University, 163319, Daqing, China
| | - Ying-Hao Han
- College of Life Science & Biotechnology Technology, Heilongjiang Bayi Agricultural University, 163319, Daqing, China.
| | - Taeho Kwon
- Primate Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 351-33 Neongme-gil, Ibam-myeon, 56216, Jeongeup-si, Jeonbuk, Republic of Korea.
- Department of Applied Biological Engineering, KRIBB School of Biotechnology, National University of Science and Technology (UST), 34113, Daejeon, Republic of Korea.
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Gao Z, Li J, Li L, Yang Y, Li J, Fu C, Zhu D, He H, Cai H, Li L. Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:747-764. [PMID: 33662619 PMCID: PMC9880815 DOI: 10.1016/j.gpb.2020.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 12/04/2019] [Accepted: 06/14/2020] [Indexed: 01/31/2023]
Abstract
MicroRNAs (miRNAs) are trans-acting small regulatory RNAs that work coordinately with transcription factors (TFs) to shape the repertoire of cellular mRNAs available for translation. Despite our growing knowledge of individual plant miRNAs, their global roles in gene regulatory networks remain mostly unassessed. Based on interactions obtained from public databases and curated from the literature, we reconstructed an integrated miRNA network in Arabidopsis that includes 66 core TFs, 318 miRNAs, and 1712 downstream genes. We found that miRNAs occupy distinct niches and enrich miRNA-containing feed-forward loops (FFLs), particularly those with miRNAs as intermediate nodes. Further analyses revealed that miRNA-containing FFLs coordinate TFs located in different hierarchical layers and that intertwined miRNA-containing FFLs are associated with party and date miRNA hubs. Using the date hub MIR858A as an example, we performed detailed molecular and genetic analyses of three interconnected miRNA-containing FFLs. These analyses revealed individual functions of the selected miRNA-containing FFLs and elucidated how the date hub miRNA fulfills multiple regulatory roles. Collectively, our findings highlight the prevalence and importance of miRNA-containing FFLs, and provide new insights into the design principles and control logics of miRNA regulatory networks governing gene expression programs in plants.
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Affiliation(s)
- Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jun Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Li Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yanzhi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jian Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Chunxiang Fu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China,Corresponding author.
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Tong Z, Cui Q, Wang J, Zhou Y. TransmiR v2.0: an updated transcription factor-microRNA regulation database. Nucleic Acids Res 2020; 47:D253-D258. [PMID: 30371815 PMCID: PMC6323981 DOI: 10.1093/nar/gky1023] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression and play vital roles in various biological processes. It has been reported that aberrant regulation of miRNAs was associated with the development and progression of various diseases, but the underlying mechanisms are not fully deciphered. Here, we described our updated TransmiR v2.0 database for more comprehensive information about transcription factor (TF)-miRNA regulations. 3730 TF–miRNA regulations among 19 species from 1349 reports were manually curated by surveying >8000 publications, and more than 1.7 million tissue-specific TF–miRNA regulations were further incorporated based on ChIP-seq data. Besides, we constructed a ‘Predict’ module to query the predicted TF–miRNA regulations in human based on binding motifs of TFs. To facilitate the community, we provided a ‘Network’ module to visualize TF–miRNA regulations for each TF and miRNA, or for a specific disease. An ‘Enrichment analysis’ module was also included to predict TFs that are likely to regulate a miRNA list of interest. In conclusion, with improved data coverage and webserver functionalities, TransmiR v2.0 would be a useful resource for investigating the regulation of miRNAs. TransmiR v2.0 is freely accessible at http://www.cuilab.cn/transmir.
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Affiliation(s)
- Zhan Tong
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Juan Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
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Brennan S, Keon M, Liu B, Su Z, Saksena NK. Panoramic Visualization of Circulating MicroRNAs Across Neurodegenerative Diseases in Humans. Mol Neurobiol 2019; 56:7380-7407. [PMID: 31037649 PMCID: PMC6815273 DOI: 10.1007/s12035-019-1615-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases (NDs) such as Alzheimer’s disease (AD), Parkinson’s disease (PD), multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), and dementia pose one of the greatest health challenges this century. Although these NDs have been looked at as single entities, the underlying molecular mechanisms have never been collectively visualized to date. With the advent of high-throughput genomic and proteomic technologies, we now have the opportunity to visualize these diseases in a whole new perspective, which will provide a clear understanding of the primary and secondary events vital in achieving the final resolution of these diseases guiding us to new treatment strategies to possibly treat these diseases together. We created a knowledge base of all microRNAs known to be differentially expressed in various body fluids of ND patients. We then used several bioinformatic methods to understand the functional intersections and differences between AD, PD, ALS, and MS. These results provide a unique panoramic view of possible functional intersections between AD, PD, MS, and ALS at the level of microRNA and their cognate genes and pathways, along with the entities that unify and separate them. While the microRNA signatures were apparent for each ND, the unique observation in our study was that hsa-miR-30b-5p overlapped between all four NDS, and has significant functional roles described across NDs. Furthermore, our results also show the evidence of functional convergence of miRNAs which was associated with the regulation of their cognate genes represented in pathways that included fatty acid synthesis and metabolism, ECM receptor interactions, prion diseases, and several signaling pathways critical to neuron differentiation and survival, underpinning their relevance in NDs. Envisioning this group of NDs together has allowed us to propose new ways of utilizing circulating miRNAs as biomarkers and in visualizing diverse NDs more holistically . The critical molecular insights gained through the discovery of ND-associated miRNAs, overlapping miRNAs, and the functional convergence of microRNAs on vital pathways strongly implicated in neurodegenerative processes can prove immensely valuable in the identifying new generation of biomarkers, along with the development of miRNAs into therapeutics.
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Affiliation(s)
- Samuel Brennan
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
| | - Matthew Keon
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
| | - Bing Liu
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
| | - Zheng Su
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
| | - Nitin K. Saksena
- Neurodegenerative Disease section, Iggy Get Out, 19a Boundary Street, Darlinghurst NSW 2010, Sydney, Australia
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Saxena S, Gupta A, Shukla V, Rani V. Functional annotation of differentially expressed fetal cardiac microRNA targets: implication for microRNA-based cardiovascular therapeutics. 3 Biotech 2018; 8:494. [PMID: 30498667 DOI: 10.1007/s13205-018-1520-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/17/2018] [Indexed: 01/23/2023] Open
Abstract
Gene expression pattern of a failing heart depicts remarkable similarity with developing fetal heart. Elucidating genetic as well as epigenetic mechanisms regulating the gene expression during cardiac development will improve our understanding of cardiovascular diseases. In the present study, we aimed to validate and characterize differentially expressed known microRNAs (miRNA) obtained from next generation sequencing data of two fetal cardiac developmental stages (days 4th and 14th) from chicken (G. gallus domesticus) using bioinformatic approaches. Potential mRNA targets of individual miRNA were identified and classified according to their biological, cellular, and molecular functions. Functional annotation of putative target genes was performed to predict their association with cardiovascular diseases. We identified a total of 19 differentially expressed miRNAs between 4th and 14th day sample from the data sets obtained by next generation sequencing. A total of nearly 1522 potential targets ranging from 15 to 270 for each miRNA were predicted out of which 1221 were unique, while 301 were overlapping. Gene ontology and KEGG analysis revealed that majority of these target genes regulate critical cellular and molecular processes including transcriptional regulation, protein transport, signal transduction, matrix remodeling, Ras signaling, MAPK signaling, and TGF-beta signaling pathways indicating the complex nature of microRNA-mediated gene regulation during cardiogenesis. We found a significant association between potential target genes and cardiovascular diseases validating a link between fetal cardiac miRNAs and regulation of cardiovascular disease-related genes. These important findings may lay a foundation for further understanding the regulatory mechanisms operative in gene re-programming in the failing heart.
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Zhao JF, Zhao Q, Hu H, Liao JZ, Lin JS, Xia C, Chang Y, Liu J, Guo AY, He XX. The ASH1-miR-375-YWHAZ Signaling Axis Regulates Tumor Properties in Hepatocellular Carcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 11:538-553. [PMID: 29858089 PMCID: PMC5944419 DOI: 10.1016/j.omtn.2018.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is a worldwide malignance, and the underlying mechanisms of this disease are not fully elucidated. In this study, the existence and function of achaete-scute homolog-1 (ASH1)-miR-375-YWHAZ signaling axis in HCC were determined. Our experiments and the Cancer Genome Atlas (TCGA) sequencing data analyses showed that ASH1 and miR-375 were significantly downregulated, whereas YWHAZ was significantly upregulated in HCC. Furthermore, we found that ASH1 positively regulates miR-375, and miR-375 directly downregulates its target YWHAZ. Gain- and loss-of-function study demonstrated ASH1 and miR-375 function as tumor suppressors, whereas YWHAZ acts as an oncogene in HCC. Animal experiment indicated that YWHAZ small interfering RNAs (siRNAs) (si-YWHAZ) delivered by nanoliposomes could suppress the growth of hepatoma xenografts and was well tolerant by nude mice. Further studies revealed that YWHAZ was involved in several protein networks, such as cell autophagy, epithelial-mesenchymal transition (EMT), apoptosis, cell cycle, invasion, and migration. In addition, the patient group with ASH1-high-expression-miR-375-high-expression-YWHAZ-low-expression was correlated with a better clinical prognosis compared with the opposite expression group. In conclusion, we proved the existence of ASH1-miR-375-YWHAZ signaling axis and interpreted its important role in driving HCC tumor progression.
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Affiliation(s)
- Juan-Feng Zhao
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hui Ya Hospital of The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Hu
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jia-Zhi Liao
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ju-Sheng Lin
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chao Xia
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Chang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jing Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - An-Yuan Guo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Xing-Xing He
- Institute of Liver Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Reviewing the Utility of EUS FNA to Advance Precision Medicine in Pancreatic Cancer. Cancers (Basel) 2018; 10:cancers10020035. [PMID: 29382047 PMCID: PMC5836067 DOI: 10.3390/cancers10020035] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/24/2018] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Advanced pancreatic cancer (PC) is an aggressive malignancy with few effective therapeutic options. While the evolution of precision medicine in recent decades has changed the treatment landscape in many cancers, at present no targeted therapies are used in the routine management of PC. Only a minority of patients with PC present with surgically resectable disease, and in the remainder obtaining high quality biopsy material for both diagnosis and molecular testing can prove challenging. Endoscopic ultrasound-guided fine needle aspiration (EUS FNA) is a widely used diagnostic procedure in PC, and allows tumour sampling in patients with both early and late stage disease. This review will provide an update on the role of EUS FNA as a diagnostic tool, as well as a source of genetic material which can be used both for molecular analysis and for the creation of valuable preclinical disease models. We will also consider relevant clinical applications of EUS FNA in the management of PC, and the path towards bringing precision medicine closer to the clinic in this challenging disease.
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Osorio JS, Vailati-Riboni M, Palladino A, Luo J, Loor JJ. Application of nutrigenomics in small ruminants: Lactation, growth, and beyond. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.06.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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