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Chen YY, Wang YH, Chen CC, Huang CE, Hsu CC, Hsiao SH, Leu YW. Exogenous Janus Kinase 617 Codon Influences Small Noncoding RNAs and Gene Expression in Ba/F3 Cells. JOURNAL OF PHYSIOLOGICAL INVESTIGATION 2024:02275668-990000000-00013. [PMID: 39324984 DOI: 10.4103/ejpi.ejpi-d-24-00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/09/2024] [Indexed: 09/27/2024]
Abstract
ABSTRACT Myeloproliferative neoplasms (MPNs) are blood cancers caused by mutations that originate from hematopoietic stem cells. More than 50%-90% of MPN patients had a dominant negative valine (V) to phenylalanine (F) mutation at the Janus kinase 617 codon (JAK2V617F) within the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway; however, this mutation was also found in a high percentage of the general population, its penetrance varied, and its onset was shown to be polygenic. Consequently, it is still unknown what molecular mechanism underlies the MPN transformation produced by JAK2V617F. Patients with MPN have been shown to have dysregulation of noncoding RNAs, such as microRNA (miRNA) and PIWI-interacting RNA (piRNA), although there is not any concrete proof that JAK2V617F alone is responsible for the aberrant regulation of miRNA and piRNA. Human wild type versus V617F-mutated JAK2 are expressed in mouse Ba/F3 cells, and the expressed small and total RNAs were subjected to next generation sequencing analysis to determine the direct induction. Differentially expressed miRNAs, gene expression, and transcript and gene variations were found between exogenously expressed JAK2 and JAK2V617F in Ba/F3 cells. The differently expressed variations contained enriched transposable elements and piRNAs, indicating a rearranged epigenome. The results of the pathway analysis show that the transformation that self-validated the chosen sequencing target genes is impacted by the JAK-STAT pathway. The induction route is functionally conserved, according to exogenously produced miRNA and gene expression. These results may clarify how the JAK2V617F induces transformation.
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Affiliation(s)
- Yi-Yang Chen
- Division of Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ying-Hsuan Wang
- Division of Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Cheng Chen
- Division of Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cih-En Huang
- Division of Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Chen Hsu
- Division of Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Shu-Huei Hsiao
- Department of Biomedical Sciences, Institute of Molecular Biology and Institute of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Yu-Wei Leu
- Department of Biomedical Sciences, Institute of Molecular Biology and Institute of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
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Amor M, Diaz M, Bianco V, Svecla M, Schwarz B, Rainer S, Pirchheim A, Schooltink L, Mukherjee S, Grabner GF, Beretta G, Lamina C, Norata GD, Hackl H, Kratky D. Identification of regulatory networks and crosstalk factors in brown adipose tissue and liver of a cold-exposed cardiometabolic mouse model. Cardiovasc Diabetol 2024; 23:298. [PMID: 39143620 PMCID: PMC11325583 DOI: 10.1186/s12933-024-02397-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Activation of brown adipose tissue (BAT) has gained attention due to its ability to dissipate energy and counteract cardiometabolic diseases (CMDs). METHODS This study investigated the consequences of cold exposure on the BAT and liver proteomes of an established CMD mouse model based on LDL receptor-deficient (LdlrKO) mice fed a high-fat, high-sucrose, high-cholesterol diet for 16 weeks. We analyzed energy metabolism in vivo and performed untargeted proteomics on BAT and liver of LdlrKO mice maintained at 22 °C or 5 °C for 7 days. RESULTS We identified several dysregulated pathways, miRNAs, and transcription factors in BAT and liver of cold-exposed Ldlrko mice that have not been previously described in this context. Networks of regulatory interactions based on shared downstream targets and analysis of ligand-receptor pairs identified fibrinogen alpha chain (FGA) and fibronectin 1 (FN1) as potential crosstalk factors between BAT and liver in response to cold exposure. Importantly, genetic variations in the genes encoding FGA and FN1 have been associated with cardiometabolic-related phenotypes and traits in humans. DISCUSSION This study describes the key factors, pathways, and regulatory networks involved in the crosstalk between BAT and the liver in a cold-exposed CMD mouse model. These findings may provide a basis for future studies aimed at testing whether molecular mediators, as well as regulatory and signaling mechanisms involved in tissue adaption upon cold exposure, could represent a target in cardiometabolic disorders.
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Affiliation(s)
- Melina Amor
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
| | - Malena Diaz
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
| | - Valentina Bianco
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Monika Svecla
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
- Department of Neurosurgery, Charité- Universitätsmedizin Berlin, Berlin, Germany
| | - Birgit Schwarz
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
| | - Silvia Rainer
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
| | - Anita Pirchheim
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
| | - Laszlo Schooltink
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
| | - Suravi Mukherjee
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
| | - Gernot F Grabner
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria
| | - Giangiacomo Beretta
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Claudia Lamina
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Giuseppe Danilo Norata
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Hubert Hackl
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6/4, Graz, 8010, Austria.
- BioTechMed-Graz, Graz, Austria.
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Ye Q, Ren M, Fan D, Mao Y, Zhu YZ. Identification and Validation of the miR/RAS/RUNX2 Autophagy Regulatory Network in AngII-Induced Hypertensive Nephropathy in MPC5 Cells Treated with Hydrogen Sulfide Donors. Antioxidants (Basel) 2024; 13:958. [PMID: 39199205 PMCID: PMC11351630 DOI: 10.3390/antiox13080958] [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: 06/01/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 09/01/2024] Open
Abstract
The balanced crosstalk between miRNAs and autophagy is essential in hypertensive nephropathy. Hydrogen sulfide donors have been reported to attenuate renal injury, but the mechanism is unclear. We aimed to identify and verify the miRNAs and autophagy regulatory networks in hypertensive nephropathy treated with hydrogen sulfide donors through bioinformatics analysis and experimental verification. From the miRNA dataset, autophagy was considerably enriched in mice kidney after angiotensin II (AngII) and combined hydrogen sulfide treatment (H2S_AngII), among which there were 109 differentially expressed miRNAs (DEMs) and 21 hub ADEGs (autophagy-related differentially expressed genes) in the AngII group and 70 DEMs and 13 ADEGs in the H2S_AngII group. A miRNA-mRNA-transcription factors (TFs) autophagy regulatory network was then constructed and verified in human hypertensive nephropathy samples and podocyte models. In the network, two DEMs (miR-98-5p, miR-669b-5p), some hub ADEGs (KRAS, NRAS), and one TF (RUNX2) were altered, accompanied by a reduction in autophagy flux. However, significant recovery occurred after treatment with endogenous or exogenous H2S donors, as well as an overexpression of miR-98-5p and miR-669b-5p. The miR/RAS/RUNX2 autophagy network driven by H2S donors was related to hypertensive nephropathy. H2S donors or miRNAs increased autophagic flux and reduced renal cell injury, which could be a potentially effective medical therapy.
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Affiliation(s)
- Qing Ye
- Shanghai Key Laboratory of Bioactive Small Molecules, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Mi Ren
- The Department of Hepatobiliary Surgery and Liver Transplantation, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China
| | - Di Fan
- Shanghai Key Laboratory of Bioactive Small Molecules, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yicheng Mao
- Shanghai Key Laboratory of Bioactive Small Molecules, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yi-Zhun Zhu
- Shanghai Key Laboratory of Bioactive Small Molecules, School of Pharmacy, Fudan University, Shanghai 201203, China
- State Key Laboratory of Quality Research in Chinese Medicines, (R & D Center) Lab. for Drug Discovery from Natural Resource, School of Pharmacy, Macau University of Science and Technology, Macau 999078, China
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Khemka N, Morris G, Kazemzadeh L, Costard LS, Neubert V, Bauer S, Rosenow F, Venø MT, Kjems J, Henshall DC, Prehn JHM, Connolly NMC. Integrative network analysis of miRNA-mRNA expression profiles during epileptogenesis in rats reveals therapeutic targets after emergence of first spontaneous seizure. Sci Rep 2024; 14:15313. [PMID: 38961125 PMCID: PMC11222454 DOI: 10.1038/s41598-024-66117-7] [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: 05/25/2023] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Epileptogenesis is the process by which a normal brain becomes hyperexcitable and capable of generating spontaneous recurrent seizures. The extensive dysregulation of gene expression associated with epileptogenesis is shaped, in part, by microRNAs (miRNAs) - short, non-coding RNAs that negatively regulate protein levels. Functional miRNA-mediated regulation can, however, be difficult to elucidate due to the complexity of miRNA-mRNA interactions. Here, we integrated miRNA and mRNA expression profiles sampled over multiple time-points during and after epileptogenesis in rats, and applied bi-clustering and Bayesian modelling to construct temporal miRNA-mRNA-mRNA interaction networks. Network analysis and enrichment of network inference with sequence- and human disease-specific information identified key regulatory miRNAs with the strongest influence on the mRNA landscape, and miRNA-mRNA interactions closely associated with epileptogenesis and subsequent epilepsy. Our findings underscore the complexity of miRNA-mRNA regulation, can be used to prioritise miRNA targets in specific systems, and offer insights into key regulatory processes in epileptogenesis with therapeutic potential for further investigation.
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Affiliation(s)
- Niraj Khemka
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Gareth Morris
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Neuroscience, Physiology and Pharmacology, University College London, London, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
| | - Laleh Kazemzadeh
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Lara S Costard
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University, Frankfurt, Germany
| | - Valentin Neubert
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University, Frankfurt, Germany
| | - Sebastian Bauer
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University, Frankfurt, Germany
| | - Felix Rosenow
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University, Frankfurt, Germany
| | - Morten T Venø
- Interdisciplinary Nanoscience Center, Dept. of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Omiics ApS, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Dept. of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - David C Henshall
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Jochen H M Prehn
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
| | - Niamh M C Connolly
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
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Liu M, Li H, Huo Z, Chen H, Kang X, Xu B. Bioinformatics Research and qRT-PCR Verify Hub Genes and a Transcription Factor-MicroRNA Feedback Network in Intervertebral Disc Degeneration. Appl Biochem Biotechnol 2024; 196:3184-3198. [PMID: 37632659 DOI: 10.1007/s12010-023-04699-0] [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] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
The present study explores the potentials of bioinformatics analysis to identify hub genes linked to intervertebral disc degeneration (IDD) and explored the potential molecular mechanism of transcription factor-microRNA regulatory network. Furthermore, the hub genes were identified through quantitative reverse transcriptase PCR (qRT-PCR). GEO database expression profile datasets for candidate genes (GSE124272) were downloaded. Genes that were differentially expressed (DEGs) were detected utilizing limma technique in the R programming language. Search Tool for the Retrieval of Interacting Genes/Proteins and NetworkAnalyst software identified hub genes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis as well as Gene Ontology annotation of the DEGs were performed using Metascape. Using Bioinformatics data from the TRRUST, StarBase, and TransmiR databases, a TF-miRNA-hub genes network was constructed. qRT-PCR was utilized to confirm the result. As compared to healthy persons, 521 DEGs, comprising 203 down-regulated and 318 up-regulated genes, as well as 7 core genes, were found in people with IDD. Analysis revealed that all seven essential genes were under-expressed. qRT-PCR further confirmed the low expression of these seven important genes. Based on the TRRUST database, 16 TFs that could target five junction genes were then predicted. According to the StarBase database, four miRNAs were linked to crucial genes, while the TransmiR database predicted regulatory connections between four miRNAs and five TFs. The expression of the TP53-(hsa-miR-183-5p)-CCNB1 TF-miRNA-mRNA interaction network was discovered to be correlated with IDD. Throughout this investigation, a network of TF-miRNA-mRNA connections was built for investigation of the probable molecular mechanisms responsible for IDD. The identification of hub genes associated with IDD may reveal promising IDD treatment strategies.
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Affiliation(s)
- Mingli Liu
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Hao Li
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Zhenxin Huo
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Houcong Chen
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Xinjian Kang
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Baoshan Xu
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, No. 406 Jiefangnan Road, Hexi District, Tianjin, 300211, China.
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Azam HMH, Rößling RI, Geithe C, Khan MM, Dinter F, Hanack K, Prüß H, Husse B, Roggenbuck D, Schierack P, Rödiger S. MicroRNA biomarkers as next-generation diagnostic tools for neurodegenerative diseases: a comprehensive review. Front Mol Neurosci 2024; 17:1386735. [PMID: 38883980 PMCID: PMC11177777 DOI: 10.3389/fnmol.2024.1386735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/12/2024] [Indexed: 06/18/2024] Open
Abstract
Neurodegenerative diseases (NDs) are characterized by abnormalities within neurons of the brain or spinal cord that gradually lose function, eventually leading to cell death. Upon examination of affected tissue, pathological changes reveal a loss of synapses, misfolded proteins, and activation of immune cells-all indicative of disease progression-before severe clinical symptoms become apparent. Early detection of NDs is crucial for potentially administering targeted medications that may delay disease advancement. Given their complex pathophysiological features and diverse clinical symptoms, there is a pressing need for sensitive and effective diagnostic methods for NDs. Biomarkers such as microRNAs (miRNAs) have been identified as potential tools for detecting these diseases. We explore the pivotal role of miRNAs in the context of NDs, focusing on Alzheimer's disease, Parkinson's disease, Multiple sclerosis, Huntington's disease, and Amyotrophic Lateral Sclerosis. The review delves into the intricate relationship between aging and NDs, highlighting structural and functional alterations in the aging brain and their implications for disease development. It elucidates how miRNAs and RNA-binding proteins are implicated in the pathogenesis of NDs and underscores the importance of investigating their expression and function in aging. Significantly, miRNAs exert substantial influence on post-translational modifications (PTMs), impacting not just the nervous system but a wide array of tissues and cell types as well. Specific miRNAs have been found to target proteins involved in ubiquitination or de-ubiquitination processes, which play a significant role in regulating protein function and stability. We discuss the link between miRNA, PTM, and NDs. Additionally, the review discusses the significance of miRNAs as biomarkers for early disease detection, offering insights into diagnostic strategies.
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Affiliation(s)
- Hafiz Muhammad Husnain Azam
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Rosa Ilse Rößling
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christiane Geithe
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
| | - Muhammad Moman Khan
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Franziska Dinter
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- PolyAn GmbH, Berlin, Germany
| | - Katja Hanack
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Harald Prüß
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Britta Husse
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Dirk Roggenbuck
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Peter Schierack
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
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Chettiar V, Patel A, Chettiar SS, Jhala DD. Meta-analysis of endometrial transcriptome data reveals novel molecular targets for recurrent implantation failure. J Assist Reprod Genet 2024; 41:1417-1431. [PMID: 38456991 PMCID: PMC11143096 DOI: 10.1007/s10815-024-03077-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: 09/19/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
PURPOSE Gene expression analysis of the endometrium has been shown to be a useful approach for identifying the molecular signatures and pathways involved in recurrent implantation failure (RIF). Nevertheless, individual studies have limitations in terms of study design, methodology and analysis to detect minor changes in expression levels or identify novel gene signatures associated with RIF. METHOD To overcome this, we conducted an in silico meta-analysis of nine studies, the systematic collection and integration of gene expression data, utilizing rigorous selection criteria and statistical techniques to ensure the robustness of our findings. RESULTS Our meta-analysis successfully unveiled a meta-signature of 49 genes closely associated with RIF. Of these genes, 38 were upregulated and 11 downregulated in RIF patients' endometrium and believed to participate in key processes like cell differentiation, communication, and adhesion. GADD45A, IGF2, and LIF, known for their roles in implantation, were identified, along with lesser-studied genes like OPRK1, PSIP1, SMCHD1, and SOD2 related to female infertility. Many of these genes are involved in MAPK and PI3K-Akt pathways, indicating their role in inflammation. We also investigated to look for key miRNAs regulating these 49 dysregulated mRNAs as potential diagnostic biomarkers. Along with this, we went to associate protein-protein interactions of 49 genes, and we could recognize one cluster consisting of 11 genes (consisted of 22 nodes and 11 edges) with the highest score (p = 0.001). Finally, we validated some of the genes by qRT-PCR in our samples. CONCLUSION In summary, the meta-signature genes hold promise for improving RIF patient identification and facilitating the development of personalized treatment strategies, illuminating the multifaceted nature of this complex condition.
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Affiliation(s)
- Venkatlaxmi Chettiar
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Alpesh Patel
- GeneXplore Diagnostics and Research Centre PVT. LTD., Ahmedabad, Gujarat, India
| | | | - Devendrasinh D Jhala
- Department of Zoology, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India.
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Zhao X, Wang S, Du T, Jiang Y, Zhao Y, Ma Y, Shen D, Shen Y, Ma J. Demystifying the landscape of endometrial immune microenvironment in luteal-phase from cuprotosis: Implications for the mechanism and treatment of RPL. Gene 2024; 903:148191. [PMID: 38253297 DOI: 10.1016/j.gene.2024.148191] [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: 10/11/2023] [Revised: 12/22/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024]
Abstract
BACKGROUND Adaptive changes in the endometrial immune microenvironment during the luteal phase are essential for pregnancy, and their abnormalities are associated with recurrent pregnancy loss (RPL). Nevertheless, the specific mechanism is still unknown. Cuprotosis, an innovatively discovered type of programmed cell death, provides us with a pioneering perspective to decipher the landscape of luteal-phase endometrial immune microenvironment in RPL. This study aimed to analyze the immune landscape of luteal-phase endometrial microenvironment in RPL and explore the association of cuprotosis with it through integrative bioinformatics analysis. METHODS The microarrays involving the luteal phase endometrial tissue of RPL were obtained from the GEO database. Differentially expressed genes (DEGs) of RPL were screened and key modules were detected by WGCNA. GO, KEGG, and GSEA immune enrichment analyses were performed on the DEGs in the most relevant modules to RPL. Then, the endometrial immune microenvironment landscape of RPL was analyzed, including immune infiltration analysis and correlation analysis between immune cells or immune functions. The interaction of cuprotosis-related genes (CRGs), the expression level between groups, the immune localization and their correlation with immune cells and immune function were analyzed. LASSO regression and Nomogram evaluated the diagnostic value of immune-related CRGS in RPL. Functional enrichment analysis was performed on the RPL signature CRGs. And RPL samples were grouped according to the expression of 7 RPL signature CRGs through unsupervised clustering analysis. After that, we analyzed the expression level of CRGs and immune infiltration, as well as performed immune function enrichment analysis in subtypes. In addition, we also screened potential drugs that might act on CRGs to improve the pathological mechanism of RPL. RESULTS In this study, we uncovered that DEGs and genes in key modules derived from weighted gene co-expression network analysis (WGCNA) were involved in immune regulation. And the immune infiltration landscape of RPL was significantly different from healthy controls. Furthermore, six hub genes were screened from CRGs based on Cytohubba, and their expression profilings were verified in RPL and normal mouse samples. Besides, seven CRGs closely associated with the immune regulation of RPL were identified by Spearman correlation analysis, including SLC31A1, LIAS, DLD, DLAT, DBT, ATP7B, and ATP7A, named as immune-related CRGs. Furthermore, three subgroups clustered according to these seven genes showed significant differences in immune landscape, suggesting a remarkable effect of CRGs on immune regulation. Last but not least, we analyzed the regulation network of transcription factors, miRNAs, and CRGs, and screened potential compounds for the treatment of RPL by targeting CRGs. CONCLUSIONS The abnormal endometrial immune microenvironment in the luteal phase was associated with the pathomechanism of RPL, and cuprotosis was closely involved in the immune microenvironment in the luteal phase endometrium of RPL. Collectively, this study revealed the potential contribution of CRGs to the pathogenesis of RPL, providing a novel breakthroughs in insights into the pathogenesis, diagnosis, and treatment of RPL.
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Affiliation(s)
- Xiaoxuan Zhao
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Sihui Wang
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Tingting Du
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuepeng Jiang
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Yang Zhao
- The First Clinical Medical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yiming Ma
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Dan Shen
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Yi Shen
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Jing Ma
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, China.
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Wang Y, Tang X, Lu J. Convergent and divergent evolution of microRNA-mediated regulation in metazoans. Biol Rev Camb Philos Soc 2024; 99:525-545. [PMID: 37987240 DOI: 10.1111/brv.13033] [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: 08/22/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The evolution of microRNAs (miRNAs) has been studied extensively to understand their roles in gene regulation and evolutionary processes. This review focuses on how miRNA-mediated regulation has evolved in bilaterian animals, highlighting both convergent and divergent evolution. Since animals and plants display significant differences in miRNA biogenesis and target recognition, the 'independent origin' hypothesis proposes that miRNA pathways in these groups independently evolved from the RNA interference (RNAi) pathway, leading to modern miRNA repertoires through convergent evolution. However, recent evidence raises the alternative possibility that the miRNA pathway might have already existed in the last common ancestor of eukaryotes, and that the differences in miRNA pathway and miRNA repertoires among animal and plant lineages arise from lineage-specific innovations and losses of miRNA pathways, miRNA acquisition, and loss of miRNAs after eukaryotic divergence. The repertoire of miRNAs has considerably expanded during bilaterian evolution, primarily through de novo creation and duplication processes, generating new miRNAs. Although ancient functionally established miRNAs are rarely lost, many newly emerged miRNAs are transient and lineage specific, following a birth-death evolutionary pattern aligning with the 'out-of-the-testis' and 'transcriptional control' hypotheses. Our focus then shifts to the convergent molecular evolution of miRNAs. We summarize how miRNA clustering and seed mimicry contribute to this phenomenon, and we review how miRNAs from different sources converge to degrade maternal messenger RNAs (mRNAs) during animal development. Additionally, we describe how miRNAs evolve across species due to changes in sequence, seed shifting, arm switching, and spatiotemporal expression patterns, which can result in variations in target sites among orthologous miRNAs across distant strains or species. We also provide a summary of the current understanding regarding how the target sites of orthologous miRNAs can vary across strains or distantly related species. Although many paralogous miRNAs retain their seed or mature sequences after duplication, alterations can occur in the seed or mature sequences or expression patterns of paralogous miRNAs, leading to functional diversification. We discuss our current understanding of the functional divergence between duplicated miRNAs, and illustrate how the functional diversification of duplicated miRNAs impacts target site evolution. By investigating these topics, we aim to enhance our current understanding of the functions and evolutionary dynamics of miRNAs. Additionally, we shed light on the existing challenges in miRNA evolutionary studies, particularly the complexity of deciphering the role of miRNA-mediated regulatory network evolution in shaping gene expression divergence and phenotypic differences among species.
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Affiliation(s)
- Yirong Wang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
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10
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Ilker E, Hinczewski M. Bioenergetic costs and the evolution of noise regulation by microRNAs. Proc Natl Acad Sci U S A 2024; 121:e2308796121. [PMID: 38386708 PMCID: PMC10907262 DOI: 10.1073/pnas.2308796121] [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: 05/27/2023] [Accepted: 01/14/2024] [Indexed: 02/24/2024] Open
Abstract
Noise control, together with other regulatory functions facilitated by microRNAs (miRNAs), is believed to have played important roles in the evolution of multicellular eukaryotic organisms. miRNAs can dampen protein fluctuations via enhanced degradation of messenger RNA (mRNA), but this requires compensation by increased mRNA transcription to maintain the same expression levels. The overall mechanism is metabolically expensive, leading to questions about how it might have evolved in the first place. We develop a stochastic model of miRNA noise regulation, coupled with a detailed analysis of the associated metabolic costs. Additionally, we calculate binding free energies for a range of miRNA seeds, the short sequences which govern target recognition. We argue that natural selection may have fine-tuned the Michaelis-Menten constant [Formula: see text] describing miRNA-mRNA affinity and show supporting evidence from analysis of experimental data. [Formula: see text] is constrained by seed length, and optimal noise control (minimum protein variance at a given energy cost) is achievable for seeds of 6 to 7 nucleotides in length, the most commonly observed types. Moreover, at optimality, the degree of noise reduction approaches the theoretical bound set by the Wiener-Kolmogorov linear filter. The results illustrate how selective pressure toward energy efficiency has potentially shaped a crucial regulatory pathway in eukaryotes.
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Affiliation(s)
- Efe Ilker
- Max Planck Institute for the Physics of Complex Systems, Dresden01187, Germany
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, OH44106
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11
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Morselli Gysi D, Barabási AL. Noncoding RNAs improve the predictive power of network medicine. Proc Natl Acad Sci U S A 2023; 120:e2301342120. [PMID: 37906646 PMCID: PMC10636370 DOI: 10.1073/pnas.2301342120] [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: 01/24/2023] [Accepted: 09/09/2023] [Indexed: 11/02/2023] Open
Abstract
Network medicine has improved the mechanistic understanding of disease, offering quantitative insights into disease mechanisms, comorbidities, and novel diagnostic tools and therapeutic treatments. Yet, most network-based approaches rely on a comprehensive map of protein-protein interactions (PPI), ignoring interactions mediated by noncoding RNAs (ncRNAs). Here, we systematically combine experimentally confirmed binding interactions mediated by ncRNA with PPI, constructing a comprehensive network of all physical interactions in the human cell. We find that the inclusion of ncRNA expands the number of genes in the interactome by 46% and the number of interactions by 107%, significantly enhancing our ability to identify disease modules. Indeed, we find that 132 diseases lacked a statistically significant disease module in the protein-based interactome but have a statistically significant disease module after inclusion of ncRNA-mediated interactions, making these diseases accessible to the tools of network medicine. We show that the inclusion of ncRNAs helps unveil disease-disease relationships that were not detectable before and expands our ability to predict comorbidity patterns between diseases. Taken together, we find that including noncoding interactions improves both the breath and the predictive accuracy of network medicine.
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Affiliation(s)
- Deisy Morselli Gysi
- Network Science Institute, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
- US Department of Veteran Affairs, Boston, MA02130
| | - Albert-László Barabási
- Network Science Institute, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
- US Department of Veteran Affairs, Boston, MA02130
- Department of Network and Data Science, Central European University, Budapest1051, Hungary
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12
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Hameed Y. Decoding the significant diagnostic and prognostic importance of maternal embryonic leucine zipper kinase in human cancers through deep integrative analyses. J Cancer Res Ther 2023; 19:1852-1864. [PMID: 38376289 DOI: 10.4103/jcrt.jcrt_1902_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/11/2022] [Indexed: 02/21/2024]
Abstract
BACKGROUND Cancer is a multifactorial disease and the second leading cause of human deaths worldwide. So far, the underlying mechanisms of cancer have not been yet fully elucidated. METHODS By using TCGA expression data, we determine the pathogenic roles of the maternal embryonic leucine zipper kinase (MELK) gene in various human cancers in this study. For this purpose, different online databases and tools (UALCAN, Kaplan-Meier (KM) plotter, TNMplot, GENT2, GEPIA, HPA, cBioPortal, STRING, Enrichr, TIMER, Cytoscape, DAVID, MuTarget, and CTD) were used. RESULTS MELK gene expression was analyzed in a total of 24 human cancers and was found notably up-regulated in all the 24 analyzed tumor tissues relative to controls. Moreover, across a few specific cancers, including kidney renal clear cell carcinoma (KIRC), stomach adenocarcinoma (STAD), lung adenocarcinoma (LUAD), and liver hepatocellular carcinoma (LIHC) patients, MELK up-regulation was observed to be correlated with the shorter survival duration and metastasis. This valuable information highlighted that MELK plays a significant role in the development and progression of these four cancers. Based on clinical variables, MELK higher expression was also found in KIRC, STAD, LUAD, and LIHC patients with different clinical variables. Gene ontology and pathway analysis outcomes showed that MELK-associated genes notably co-expressed with MELK and belongs to a variety of diverse biological processes, molecular functions, and pathways. MELK expression was also correlated with promoter methylation levels, genetic alterations, other mutant genes, tumor purity, CD8+ T, and CD+4 T immune cells infiltrations in KIRC, STAD, LUAD, and LIHC. CONCLUSION This pan-cancer study revealed the diagnostic and prognostic roles of MELK across four different cancers.
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Affiliation(s)
- Yasir Hameed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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13
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Zhang J, Liu L, Wei X, Zhao C, Li S, Li J, Le TD. Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers. PLoS Comput Biol 2023; 19:e1011308. [PMID: 37812646 PMCID: PMC10586676 DOI: 10.1371/journal.pcbi.1011308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/19/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023] Open
Abstract
Non-coding RNAs (ncRNAs) act as important modulators of gene expression and they have been confirmed to play critical roles in the physiology and development of malignant tumors. Understanding the synergism of multiple ncRNAs in competing endogenous RNA (ceRNA) regulation can provide important insights into the mechanisms of malignant tumors caused by ncRNA regulation. In this work, we present a framework, SCOM, for identifying ncRNA synergistic competition. We systematically construct the landscape of ncRNA synergistic competition across 31 malignant tumors, and reveal that malignant tumors tend to share hub ncRNAs rather than the ncRNA interactions involved in the synergistic competition. In addition, the synergistic competition ncRNAs (i.e. ncRNAs involved in the synergistic competition) are likely to be involved in drug resistance, contribute to distinguishing molecular subtypes of malignant tumors, and participate in immune regulation. Furthermore, SCOM can help to infer ncRNA synergistic competition across malignant tumors and uncover potential diagnostic and prognostic biomarkers of malignant tumors. Altogether, the SCOM framework (https://github.com/zhangjunpeng411/SCOM/) and the resulting web-based database SCOMdb (https://comblab.cn/SCOMdb/) serve as a useful resource for exploring ncRNA regulation and to accelerate the identification of carcinogenic biomarkers.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Lin Liu
- UniSA STEM, University of South Australia, Mawson Lakes, South Australia, Australia
| | - Xuemei Wei
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Chunwen Zhao
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Sijing Li
- School of Engineering, Dali University, Dali, Yunnan, People’s Republic of China
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Mawson Lakes, South Australia, Australia
| | - Thuc Duy Le
- UniSA STEM, University of South Australia, Mawson Lakes, South Australia, Australia
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14
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Hojjati F, Roointan A, Gholaminejad A, Eshraghi Y, Gheisari Y. Identification of key genes and biological regulatory mechanisms in diabetic nephropathy: Meta-analysis of gene expression datasets. Nefrologia 2023; 43:575-586. [PMID: 36681521 DOI: 10.1016/j.nefroe.2022.06.006] [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: 01/30/2022] [Accepted: 06/27/2022] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) which refers to the cases with biopsy proven kidney lesions, is one of the main complications of diabetes all around the world; however, the underlying biological changes causing DN remain to be understood. Studying the alterations in gene expression profiles could give a holistic view of the molecular pathogenicity of DN and aid to discover key molecules as potential therapeutic targets. Here, we performed a meta-analysis study that included microarray gene expression profiles coming from glomerular samples of DN patients in order to acquire a list of consensus Differentially Expressed Genes (meta-DEGs) correlated with DN. METHODS After quality control and normalization steps, five gene expression datasets (GES1009, GSE30528, GSE47183, GSE104948, and GSE93804) were entered into the meta-analysis. The meta-analysis was performed by random effect size method and the meta-DEGs were put through network analysis and different pathway enrichment analyses steps. MiRTarBase and TRRUST databases were utilized to predict the meta-DEGs related miRNAs and transcription factors. A co-regulatory network including DEGs, transcription factors and miRNAs was constructed by Cytoscape, and top molecules were identified based on centrality scores in the network. RESULTS The identified meta-DEGs were 1364 DEGs including 665 downregulated and 669 upregulated DEGs. The results of pathway enrichment analysis showed, "immune system", "extracellular matrix organization", "hemostasis", "signal transduction", and "platelet activation" to be the top enriched terms with involvement of the meta-DEGs. After construction of the multilayer regulatory network, several top DEGs (TP53, MYC, BTG2, VEGFA, PTEN, etc.), as well as top miRNAs (miR-335, miR-16, miR-17, miR-20a, and miR-93), and transcription factors (SP1, STAT3, NF-KB1, RELA, E2F1), were introduced as potential therapeutic targets in DN. Among the regulatory molecules, miR-335-5p and SP1 were the most interactive miRNA and transcription factor molecules with the highest degree scores in the constructed network. CONCLUSION By performing a meta-analysis of available DN-related transcriptomics datasets, we reached a consensus list of DEGs for this complicated disorder. Further enrichment and network analyses steps revealed the involved pathways in the DN pathogenesis and marked the most potential therapeutic targets in this disease.
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Affiliation(s)
- Fatemeh Hojjati
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Amir Roointan
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Alieh Gholaminejad
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Yasin Eshraghi
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Yousof Gheisari
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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15
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Khazaei-Poul Y, Mirmotalebisohi SA, Zali H, Molavi Z, Mohammadi-Yeganeh S. Identification of miR-3182 and miR-3143 target genes involved in the cell cycle as a novel approach in TNBC treatment: A systems biology approach. Chem Biol Drug Des 2023; 101:662-677. [PMID: 36310371 DOI: 10.1111/cbdd.14167] [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: 05/08/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 02/04/2023]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a poor prognosis, lacking therapeutic targets. miRNAs play crucial roles in TNBC through regulating various mechanisms, including cellular growth and proliferation. This study aims to identify critical target genes of two novel miRNAs (miR-3143 and miR-3182) involved in the cell cycle of TNBC as possible therapeutic targets and investigates their regulatory and therapeutic roles through a systems biology approach and in vitro experiment. Datasets related to the TNBC cell line (MDA-MB-231) were screened and retrieved, and Gene regulatory networks were constructed. Significant regulatory motifs were detected and analyzed using the FANMOD and Cytoscape analyzer, and the clusters and seeds were identified using the MCODE. Functional enrichment analysis was also performed using DAVID and STRING. The most critical genes were determined using the analysis of GRN motifs and PPI clusters. The essential genes involved in the cell cycle were selected and verified using the bc-GenExMiner v4.7. We overexpressed miR-3143 and miR-3182 in the MDA-MB-231 cell line using human umbilical cord mesenchymal stem cell (HUCMSC)-miRNA loaded exosomes, and the expression of the critical target genes was investigated using RT-qPCR. We identified eight critical genes as potential therapeutic targets. Their expression decreased by overexpression of miR-3143 and miR-3182 in RT-qPCR. The identified critical genes have probably significant roles in the pathogenesis of TNBC through the cell cycle. We suggest that the overexpression of miR-3143 and miR-3182 could be a new therapeutic candidate in TNBC and is worth more investigation.
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Affiliation(s)
- Yalda Khazaei-Poul
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Amir Mirmotalebisohi
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Molavi
- Proteomics Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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16
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Roy B, Dwivedi Y. An insight into the sprawling microverse of microRNAs in depression pathophysiology and treatment response. Neurosci Biobehav Rev 2023; 146:105040. [PMID: 36639069 PMCID: PMC9974865 DOI: 10.1016/j.neubiorev.2023.105040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 01/12/2023]
Abstract
Stress-related neuropathologies are pivotal in developing major depressive disorder (MDD) and are often governed by gene-regulatory changes. Being a stress-responsive gene-regulatory factor, microRNAs (miRNAs) have tremendous biomolecular potential to define an altered gene-regulatory landscape in the MDD brain. MiRNAs' regulatory roles in the MDD brain are closely aligned with changes in plasticity, neurogenesis, and stress-axis functions. MiRNAs act at the epigenetic interface between stress-induced environmental stimuli and cellular pathologies by triggering large-scale gene expression changes in a highly coordinated fashion. The parallel changes in peripheral circulation may provide an excellent opportunity for miRNA to devise more effective treatment strategies and help explore their potential as biomarkers in treatment response. This review discusses the role of miRNAs as epigenetic modifiers in the etiopathogenesis of MDD. Concurrently, key research is highlighted to show the progress in using miRNAs as predictive biomarkers for treatment response.
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Affiliation(s)
- Bhaskar Roy
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yogesh Dwivedi
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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17
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Thakur A, Kumar M. Integration of Human and Viral miRNAs in Epstein-Barr Virus-Associated Tumors and Implications for Drug Repurposing. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:93-108. [PMID: 36927073 DOI: 10.1089/omi.2023.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Epstein-Barr virus (EBV) is associated with several tumors, and has substantial relevance for public health. Therapeutics innovation for EBV-related disorders is much needed. In this context, miRNAs are noncoding RNA molecules that play vital roles in EBV infection. miRNA-Seq and RNA-Seq data for EBV-associated clinical samples and cell lines have been generated, but their detailed integrative analyses, and exploitation for drug repurposing against EBV are lacking. Hence, we identified and analyzed the differentially expressed miRNAs (DEmiRs) in EBV-infected cell lines (28) and infected (28) and uninfected human tissue (20) samples using an in-house pipeline. We found significantly enriched host miRNAs like hsa-mir-3651, hsa-mir-1248, and hsa-mir-29c-3p in EBV-infected samples from EBV-associated nasopharyngeal carcinoma and Hodgkin's lymphoma, among others. Furthermore, we also identified significantly enriched novel miRNAs such as hsa-mir-29c-3p, hsa-mir-3651, and hsa-mir-98-3p, which were not previously reported in EBV-related tumors. Differentially expressed mRNAs (DEMs) were identified in EBV-infected cell lines (21) and uninfected human tissue (14) samples. We predicted and selected 1572 DEMs (upregulated) that are targeted by 547 DEmiRs (downregulated). These were further classified into essential (870) and nonessential (702) genes. Moreover, a miRNA-mRNA network was developed for the hub miRNAs. Importantly, we used the DEMs during EBV latent infection types I, II, and III to identify the candidate drugs for repurposing: Glyburide, Levodopa, Nateglinide, and Stiripentol, among others. To the best of our knowledge, this is the first integrative analyses that identified DEmiRs and DEMs as potential therapeutic targets and predicted drugs as potential candidates for repurposing against EBV-related tumors.
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Affiliation(s)
- Anamika Thakur
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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18
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Deng L, Li X, Ren X, Lai S, Zhu Y, Li J, Huang H, Mu Y. A grooved porous hydroxyapatite scaffold induces osteogenic differentiation via regulation of PKA activity by upregulating miR-129-5p expression. J Periodontal Res 2022; 57:1238-1255. [PMID: 36222334 DOI: 10.1111/jre.13060] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND AND OBJECTIVE Hydroxyapatite scaffolds with different morphologies have been widely used in bone tissue engineering. Moreover, microRNAs (miRNAs) have been proven to be extensively involved in regulating bone regeneration. We developed grooved porous hydroxyapatite (HAG) scaffolds with good osteogenic efficiency. However, little is known about the role of miRNAs in HAG scaffold-mediated promotion of bone regeneration. The objective of this study was to reveal the mechanism from the perspective of differential miRNA expression. METHODS Scanning electron microscopy (SEM) was used to perform the coculture of cells and scaffolds. The miRNA profiles were generated by a microarray assay. A synthetic miR-129-5p mimic and inhibitor were used for overexpression or inhibition. The expression of osteogenic marker mRNAs and proteins was detected by quantitative real-time PCR (qRT-PCR), Western blotting, and immunofluorescence. An ALP activity kit and alizarin red staining (ARS) were used to measure ALP activity and mineral deposition formation. Cell migration ability was examined by wound healing and transwell assays. Protein kinase A (PKA) activity was measured by enzyme-linked immunosorbent assay (ELISA) after miR-129-5p transfection. Target genes were identified by a dual-luciferase reporter assay. H89 preculture evaluated the cross talk between miR-129-5p and PKA activity. Heterotopic implantation models, hematoxylin-eosin (HE), immunohistochemistry staining, and micro-CT were used to evaluate miR-129-5p osteogenesis in vivo. RESULTS miRNAs were differentially expressed during osteogenic differentiation induced by HAG in vitro and in vivo. miR-129-5p was the only highly expressed miRNA both in vitro and in vivo. miR-129-5p overexpression promoted osteoblast differentiation and cell migration, while its inhibition weakened the effect of HAG. Moreover, miR-129-5p activated PKA to regulate the phosphorylation of β-catenin and cAMP-response element binding protein (CREB) by inhibiting cAMP-dependent protein kinase inhibitor alpha (Pkia). H89 prevented the effects of miR-129-5p on osteogenic differentiation and cell migration. HE, immunohistochemistry staining and micro-CT results showed that miR-129-5p promoted in vivo osteogenesis of the HAG scaffold. CONCLUSION The HAG scaffold activates Pka by upregulating miR-129-5p and inhibiting Pkia, resulting in CREB-dependent transcriptional activation and accumulation of β-catenin and promoting osteogenic marker expression.
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Affiliation(s)
- Li Deng
- Stomatology Department, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical College of North Sichuan Medical College, Nanchong, China
| | - Xinlun Li
- Stomatology Department, Sichuan Provincial People's Hospital, Chengdu, China
| | - Xiaohua Ren
- Stomatology Department, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shuang Lai
- Stomatology Department, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yushu Zhu
- Stomatology Department, Sichuan Provincial People's Hospital, Chengdu, China
| | - Jing Li
- Stomatology Department, Sichuan Provincial People's Hospital, Chengdu, China
| | - Hao Huang
- Key Laboratory of Advanced Technologies of Materials (Ministry of Education), School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Yandong Mu
- Stomatology Department, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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19
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Abdolahi S, Zare-Chahoki A, Noorbakhsh F, Gorji A. A Review of Molecular Interplay between Neurotrophins and miRNAs in Neuropsychological Disorders. Mol Neurobiol 2022; 59:6260-6280. [PMID: 35916975 PMCID: PMC9463196 DOI: 10.1007/s12035-022-02966-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/17/2022] [Indexed: 01/10/2023]
Abstract
Various neurotrophins (NTs), including nerve growth factor, brain-derived neurotrophic factor, neurotrophin-3, and neurotrophin-4, promote cellular differentiation, survival, and maintenance, as well as synaptic plasticity, in the peripheral and central nervous system. The function of microRNAs (miRNAs) and other small non-coding RNAs, as regulators of gene expression, is pivotal for the appropriate control of cell growth and differentiation. There are positive and negative loops between NTs and miRNAs, which exert modulatory effects on different signaling pathways. The interplay between NTs and miRNAs plays a crucial role in the regulation of several physiological and pathological brain procedures. Emerging evidence suggests the diagnostic and therapeutic roles of the interactions between NTs and miRNAs in several neuropsychological disorders, including epilepsy, multiple sclerosis, Alzheimer's disease, Huntington's disease, amyotrophic lateral sclerosis, schizophrenia, anxiety disorders, depression, post-traumatic stress disorder, bipolar disorder, and drug abuse. Here, we review current data regarding the regulatory interactions between NTs and miRNAs in neuropsychological disorders, for which novel diagnostic and/or therapeutic strategies are emerging. Targeting NTs-miRNAs interactions for diagnostic or therapeutic approaches needs to be validated by future clinical studies.
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Affiliation(s)
- Sara Abdolahi
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran
| | - Ameneh Zare-Chahoki
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Gorji
- Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Neurosurgery, Westfälische Wilhelms-Universität, Münster, Germany.
- Department of Neurology and Institute for Translational Neurology, Westfälische Wilhelms-Universität, Münster, Germany.
- Epilepsy Research Center, Westfälische Wilhelms-Universität, 48149, Münster, Germany.
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20
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Yang J, Chen S, Xu X, Lin G, Lin S, Bai J, Song Q, You M, Xie M. Novel-miR-310 mediated response mechanism to Cry1Ac protoxin in Plutella xylostella (L.). Int J Biol Macromol 2022; 219:587-596. [PMID: 35952810 DOI: 10.1016/j.ijbiomac.2022.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/16/2022] [Accepted: 08/02/2022] [Indexed: 12/12/2022]
Abstract
The diamondback moth (DBM), Plutella xylostella (L.), has evolved resistance to multiple insecticides including Bacillus thuringiensis (Bt). ATP-binding cassette (ABC) transporters are a class of transmembrane protein families, involved in multiple physiological processes and pesticide resistances in insects. However, the role and regulatory mechanism of ABC transporter in mediating the response to Bt Cry1Ac toxin remain unclear. Here, we characterized a MAPK signaling pathway-enriched ABCG subfamily gene PxABCG20 from DBM, and found it was differentially expressed in the Cry1Ac-resistant and Cry1Ac-susceptible strains. RNAi knockdown of PxABCG20 increased the tolerance of DBM to Cry1Ac protoxin. To explore the regulatory mechanism of PxABCG20 expression, we predicted the potential miRNAs targeting PxABCG20 using two target prediction algorithms. Luciferase reporter assay confirmed that novel-miR-310 was able to down-regulate PxABCG20 expression in HEK293T cells. Furthermore, injection of novel-miR-310 agomir markedly inhibited PxABCG20 expression, resulting in increased tolerance to Cry1Ac protoxin in susceptible strain, while injection of novel-miR-310 antagomir markedly induced the expression of PxABCG20, leading to decreased tolerance to Cry1Ac protoxin. Our work provides theoretical basis for exploring novel targets for the DBM response to Cry1Ac toxin and expands the understanding of miRNA role in mediating the susceptibility of insect pest to Cry1Ac toxin.
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Affiliation(s)
- Jie Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shiyao Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuejiao Xu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Guifang Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sujie Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianlin Bai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qisheng Song
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Miao Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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21
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He Y, Liu Y, Yang Y, Liu Y, Jia X, Shen Y, Xu X, Li J. elk1/miR-462-731 Feedback Loop Regulates Macrophages Polarization and Phagocytosis in Grass Carp (Ctenopharyngodon idella). Front Immunol 2022; 13:946857. [PMID: 35911773 PMCID: PMC9330907 DOI: 10.3389/fimmu.2022.946857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNA clusters are microRNAs (miRNAs) that are distributed in close proximity on chromosomes. In this study, we report a miRNA cluster identified from grass carp (Ctenopharyngodon idella), miR-462-731, which plays a positive role in host antibacterial immunity. The expression of miR-462-731 was disrupted after infection by Aeromonas hydrophila. Transcription factor ETS transcription factor ELK1 was identified to bind to the promoter of the miR-462-731 cluster and suppress its expression. In addition, miR-731 negatively regulates the expression of elk1, forms an elk1/miR-462-731 double negative feedback loop. In addition, we found that miR-731 directly targets ezrin a (ezra), participates in inducing PI3K/AKT signaling in macrophage, to induce macrophage polarization to the M1 phenotype with stronger phagocytosis. Our results demonstrate a novel elk1/miR-462-731 feedback loop. The data deepen our understanding of the relationship between macrophage polarization and phagocytosis in teleost fish.
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Affiliation(s)
- Yan He
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yuting Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yuyue Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Yang Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xuewen Jia
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, 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
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, 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
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- *Correspondence: Xiaoyan Xu, ; Jiale Li,
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- *Correspondence: Xiaoyan Xu, ; Jiale Li,
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22
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Coradduzza D, Solinas T, Balzano F, Culeddu N, Rossi N, Cruciani S, Azara E, Maioli M, Zinellu A, De Miglio MR, Madonia M, Falchi M, Carru C. miRNAs as molecular biomarkers for prostate cancer. J Mol Diagn 2022; 24:1171-1180. [PMID: 35835374 DOI: 10.1016/j.jmoldx.2022.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNA able to regulate specific mRNA stability, thus influencing target gene expression. Disrupted levels of several miRNA have been associated with prostate cancer, the leading cause of cancer death among men and the fifth leading cause of death worldwide. Here, we investigated whether miR-145, miR-148, and miR-185 circulating levels in plasma could be used as molecular biomarkers, to allow distinguishing between individuals with benign prostatic hyperplasia, precancerous lesion, and prostate cancer. In this study, we recruited 170 urological clinic patients with suspected prostate cancer who underwent prostate biopsy. Total RNA was isolated from plasma, and TaqMan MicroRNA assays were used to analyze miR-145, miR-185, and miR-148 expression. First, differential miRNA expression among patient groups was evaluated. Then, miRNA levels were combined with clinical assessment outcomes, including results from invasive tests, using multivariate analysis to examine their ability in discriminating among the three patient groups. Our results suggest that miRNA is a promising molecular tool for clinical management of at-risk patients.
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Affiliation(s)
| | - Tatiana Solinas
- Urologic Clinic, Dep. of Clinical and Experimental Medicine, University of Sassari
| | - Francesca Balzano
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Nicola Culeddu
- Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy
| | - Niccolò Rossi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sara Cruciani
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Emanuela Azara
- Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy
| | - Margherita Maioli
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | - Massimo Madonia
- Urologic Clinic, Dep. of Clinical and Experimental Medicine, University of Sassari
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy; University Hospital of Sassari (AOU), Sassari, Italy.
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23
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Identification of key genes and biological regulatory mechanisms in diabetic nephropathy: Meta-analysis of gene expression datasets. Nefrologia 2022. [PMID: 36681521 DOI: 10.1016/j.nefro.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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24
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Du L, Liu Y, Li C, Deng J, Sang Y. The interaction between ETS transcription factor family members and microRNAs: A novel approach to cancer therapy. Biomed Pharmacother 2022; 150:113069. [PMID: 35658214 DOI: 10.1016/j.biopha.2022.113069] [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: 03/08/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
In cancer biology, ETS transcription factors promote tumorigenesis by mediating transcriptional regulation of numerous genes via the conserved ETS DNA-binding domain. MicroRNAs (miRNAs) act as posttranscriptional regulators to regulate various tumor-promoting or tumor-suppressing factors. Interactions between ETS factors and miRNAs regulate complex tumor-promoting and tumor-suppressing networks. This review discusses the progress of ETS factors and miRNAs in cancer research in detail. We focused on characterizing the interaction of the miRNA/ETS axis with competing endogenous RNAs (ceRNAs) and its regulation in posttranslational modifications (PTMs) and the tumor microenvironment (TME). Finally, we explore the prospect of ETS factors and miRNAs in therapeutic intervention. Generally, interactions between ETS factors and miRNAs provide fresh perspectives into tumorigenesis and development and novel therapeutic approaches for malignant tumors.
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Affiliation(s)
- Liwei Du
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China
| | - Yuchen Liu
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China; Stomatology College of Nanchang University, Nanchang, China
| | - Chenxi Li
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China
| | - Jinkuang Deng
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China
| | - Yi Sang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, Department of Center Laboratory, The Third Affiliated Hospital of Nanchang University & The First Hospital of Nanchang, Nanchang 330008, China.
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25
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Mazloom AR, Xu H, Reig-Palou J, Vasileva A, Román AC, Mulero-Navarro S, Lemischka IR, Sevilla A. Esrrb Regulates Specific Feed-Forward Loops to Transit From Pluripotency Into Early Stages of Differentiation. Front Cell Dev Biol 2022; 10:820255. [PMID: 35652095 PMCID: PMC9149258 DOI: 10.3389/fcell.2022.820255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/24/2022] [Indexed: 01/15/2023] Open
Abstract
Characterization of pluripotent states, in which cells can both self-renew or differentiate, with the irreversible loss of pluripotency, are important research areas in developmental biology. Although microRNAs (miRNAs) have been shown to play a relevant role in cellular differentiation, the role of miRNAs integrated into gene regulatory networks and its dynamic changes during these early stages of embryonic stem cell (ESC) differentiation remain elusive. Here we describe the dynamic transcriptional regulatory circuitry of stem cells that incorporate protein-coding and miRNA genes based on miRNA array expression and quantitative sequencing of short transcripts upon the downregulation of the Estrogen Related Receptor Beta (Esrrb). The data reveals how Esrrb, a key stem cell transcription factor, regulates a specific stem cell miRNA expression program and integrates dynamic changes of feed-forward loops contributing to the early stages of cell differentiation upon its downregulation. Together these findings provide new insights on the architecture of the combined transcriptional post-transcriptional regulatory network in embryonic stem cells.
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Affiliation(s)
- Amin R. Mazloom
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Huilei Xu
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jaume Reig-Palou
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Ana Vasileva
- Center for Radiological Research, Columbia University, New York, NY, United States
| | - Angel-Carlos Román
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Sonia Mulero-Navarro
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Ihor R. Lemischka
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ana Sevilla
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- *Correspondence: Ana Sevilla,
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26
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Correlation between innate and adaptive immunity response in TB children post BCG vaccination. Is it effective or not?: Cross-sectional study. Ann Med Surg (Lond) 2022; 77:103586. [PMID: 35638072 PMCID: PMC9142374 DOI: 10.1016/j.amsu.2022.103586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/04/2022] [Accepted: 04/02/2022] [Indexed: 11/26/2022] Open
Abstract
Background How far the role of innate immunity and adaptive immunity do in children who have been BCG vaccinated in controlling the course and the severity of the TB disease has not been completely known. Mycobacterium tuberculosis entry to the body will be recognized by Toll-like receptors found on macrophages, neutrophils, and dendritic cells as part of the innate immune response, after which the dendritic cells will then present the antigen to lymphocyte T0 cells and initiate the adaptive immune response (of which CD4 T cells have an important role in). Was one or were both of these immune responses function well or not in a BCG Vaccinated Children with TB? Objective This study aim to find a better understanding of the role of innate immune response assessed by TLR2/TLR4 mRNA gene expression and serum TLR2/TLR4 levels, while the role of adaptive immune response is assessed by analyzing serum CD4 level in children with TB who have had BCG vaccination. Methods This cross-sectional study was conducted among children with TB at the outpatient and inpatient wards at Bhakti Medicare and Jakarta Islamic Hospital. Expression of mRNA gene was measured using the Boom method and protein serum levels were measured using the ELISA method. The results were analyzed by using the SPSS v.23 program. Results Sixty-nine children were recruited as subjects. In this study, 68.1% of whom had BCG scars. TLR4 mRNA gene expression was found to be higher than TLR2 mRNA gene expression. Serum CD4 level was found to be highest out of TLR2 and TLR4 level, but serum TLR2 level was higher than TLR4 level. TLR2/TLR4 mRNA gene expression, serum TLR2/TLR4 levels, and CD4 levels in subjects with BCG scar were also found to be significantly higher than in subjects without BCG scar (p < 0.001). There was a significant positive correlation between TLR2/TLR4 mRNA gene expression and serum TLR2/TLR4 levels (r = 0.860; r = 0.864; p < 0.001) and between serum levels TLR2/TLR4 with serum CD4 levels (r = 0.822; r = 0.832 p < 0.001). Conclusion As early as possible, BCG vaccine administration is needed in endemic countries, but it must be ensured that scars can be formed. It is also important to control Latent TB Infection (LTBI) to prevent transmission and relapse of disease. For the prevention of TB disease, it is important to understand the innate and adaptive immune responses according BCG scar. Mycobacterium tuberculosis recognition by TLR as the innate immune response followed by the adaptive immune response by CD4 cells. There is a strong positive correlation between the expression of mRNA gene and the concentration of TLR and CD4 in BCG-vaccinated subjects. BCG vaccination should be done as early as possible in endemic countries, as it provides better protection against TB infection.
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27
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Biswas K, Jolly MK, Ghosh A. Mean residence times of TF-TF and TF-miRNA toggle switches. J Biosci 2022. [DOI: 10.1007/s12038-022-00261-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Gao X, Zhao D, Han J, Zhang Z, Wang Z. Identification of microRNA-mRNA-TF regulatory networks in periodontitis by bioinformatics analysis. BMC Oral Health 2022; 22:118. [PMID: 35397550 PMCID: PMC8994180 DOI: 10.1186/s12903-022-02150-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/24/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Periodontitis is a complex infectious disease with various causes and contributing factors. The aim of this study was to identify key genes, microRNAs (miRNAs) and transcription factors (TFs) and construct a miRNA-mRNA-TF regulatory networks to investigate the underlying molecular mechanism in periodontitis. METHODS The GSE54710 miRNA microarray dataset and the gene expression microarray dataset GSE16134 were downloaded from the Gene Expression Omnibus database. The differentially expressed miRNAs (DEMis) and mRNAs (DEMs) were screened using the "limma" package in R. The intersection of the target genes of candidate DEMis and DEMs were considered significant DEMs in the regulatory network. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. Subsequently, DEMs were uploaded to the STRING database, a protein-protein interaction (PPI) network was established, and the cytoHubba and MCODE plugins were used to screen out key hub mRNAs and significant modules. Ultimately, to investigate the regulatory network underlying periodontitis, a global triple network including miRNAs, mRNAs, and TFs was constructed using Cytoscape software. RESULTS 8 DEMis and 121 DEMs were found between the periodontal and control groups. GO analysis showed that mRNAs were most significantly enriched in positive regulation of the cell cycle, and KEGG pathway analysis showed that mRNAs in the regulatory network were mainly involved in the IL-17 signalling pathway. A PPI network was constructed including 81 nodes and 414 edges. Furthermore, 12 hub genes ranked by the top 10% genes with high degree connectivity and five TFs, including SRF, CNOT4, SIX6, SRRM3, NELFA, and ONECUT3, were identified and might play crucial roles in the molecular pathogenesis of periodontitis. Additionally, a miRNA-mRNA-TF coregulatory network was established. CONCLUSION In this study, we performed an integrated analysis based on public databases to identify specific TFs, miRNAs, and mRNAs that may play a pivotal role in periodontitis. On this basis, a TF-miRNA-mRNA network was established to provide a comprehensive perspective of the regulatory mechanism networks of periodontitis.
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Affiliation(s)
- Xiaoli Gao
- Department of Stomatology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gongti Nan Lu, Chaoyang District, Beijing, 100020 China
| | - Dong Zhao
- Department of Stomatology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gongti Nan Lu, Chaoyang District, Beijing, 100020 China
| | - Jing Han
- Department of Stomatology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gongti Nan Lu, Chaoyang District, Beijing, 100020 China
| | - Zheng Zhang
- Department of Periodontology, Tianjin Stomatological Hospital, School of Medicine, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Oral and Maxillofacial Function Reconstruction, 75 Dagu Bei Lu, Heping District, Tianjin, 300041 China
| | - Zuomin Wang
- Department of Stomatology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gongti Nan Lu, Chaoyang District, Beijing, 100020 China
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29
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Lovino M, Montemurro M, Barrese VS, Ficarra E. Identifying the oncogenic potential of gene fusions exploiting miRNAs. J Biomed Inform 2022; 129:104057. [PMID: 35339665 DOI: 10.1016/j.jbi.2022.104057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/11/2022]
Abstract
It is estimated that oncogenic gene fusions cause about 20% of human cancer morbidity. Identifying potentially oncogenic gene fusions may improve affected patients' diagnosis and treatment. Previous approaches to this issue included exploiting specific gene-related information, such as gene function and regulation. Here we propose a model that profits from the previous findings and includes the microRNAs in the oncogenic assessment. We present ChimerDriver, a tool to classify gene fusions as oncogenic or not oncogenic. ChimerDriver is based on a specifically designed neural network and trained on genetic and post-transcriptional information to obtain a reliable classification. The designed neural network integrates information related to transcription factors, gene ontologies, microRNAs and other detailed information related to the functions of the genes involved in the fusion and the gene fusion structure. As a result, the performances on the test set reached 0.83 f1-score and 96% recall. The comparison with state-of-the-art tools returned comparable or higher results. Moreover, ChimerDriver performed well in a real-world case where 21 out of 24 validated gene fusion samples were detected by the gene fusion detection tool Starfusion. ChimerDriver integrates transcriptional and post-transcriptional information in an ad-hoc designed neural network to effectively discriminate oncogenic gene fusions from passenger ones. ChimerDriver source code is freely available at https://github.com/martalovino/ChimerDriver.
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Affiliation(s)
- Marta Lovino
- University of Modena and Reggio Emilia, Via Vivarelli 10/1, 41125 Modena, Italy.
| | | | - Venere S Barrese
- Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino, Italy
| | - Elisa Ficarra
- University of Modena and Reggio Emilia, Via Vivarelli 10/1, 41125 Modena, Italy
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30
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Marques TM, Gama-Carvalho M. Network Approaches to Study Endogenous RNA Competition and Its Impact on Tissue-Specific microRNA Functions. Biomolecules 2022; 12:332. [PMID: 35204832 PMCID: PMC8868585 DOI: 10.3390/biom12020332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
microRNAs are small non-coding RNAs that play a key role in regulating gene expression. These molecules exert their function through sequence complementarity with microRNA responsive elements and are typically located in the 3' untranslated region of mRNAs, negatively regulating expression. Even though the relevant role of miRNA-dependent regulation is broadly recognized, the principles governing their ability to lead to specific functional outcomes in distinct cell types are still not well understood. In recent years, an intriguing hypothesis proposed that miRNA-responsive elements act as communication links between different RNA species, making the investigation of microRNA function even more complex than previously thought. The competing endogenous RNA hypothesis suggests the presence of a new level of regulation, whereby a specific RNA transcript can indirectly influence the abundance of other transcripts by limiting the availability of a common miRNA, acting as a "molecular sponge". Since this idea has been proposed, several studies have tried to pinpoint the interaction networks that have been established between different RNA species and whether they contribute to normal cell function and disease. The focus of this review is to highlight recent developments and achievements made towards the process of characterizing competing endogenous RNA networks and their role in cellular function.
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Affiliation(s)
| | - Margarida Gama-Carvalho
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal;
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31
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Ahmad M, Khan M, Asif R, Sial N, Abid U, Shamim T, Hameed Z, Iqbal MJ, Sarfraz U, Saeed H, Asghar Z, Akram M, Ullah Q, Younas QUA, Rauf L, Hadi A, Maryam S, Hameed Y, Khan MR, Tariq E, Saeed S. Expression Characteristics and Significant Diagnostic and Prognostic Values of ANLN in Human Cancers. Int J Gen Med 2022. [DOI: 10.2147/ijgm.s343975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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32
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Yehia R, Schaalan M, Abdallah DM, Saad AS, Sarhan N, Saleh S. Impact of TNF-α Gene Polymorphisms on Pancreatic and Non-Small Cell Lung Cancer-Induced Cachexia in Adult Egyptian Patients: A Focus on Pathogenic Trajectories. Front Oncol 2021; 11:783231. [PMID: 34900737 PMCID: PMC8651494 DOI: 10.3389/fonc.2021.783231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 10/25/2021] [Indexed: 01/06/2023] Open
Abstract
Background Cachexia is a frequent syndrome in pancreatic and non-small cell lung (NSCL) cancer patients. The storm of cancer-induced inflammatory cytokines, in particular TNF-α, is a crucial pathogenic mechanism. Among the molecular alterations accused of cancer-induced cachexia, TNF-α 308 G/A (rs1800629) and −1031T/C (rs1799964) are single-nucleotide polymorphisms (SNPs) within the gene encoding this pro-inflammatory cytokine. Recent studies have demonstrated the crucial role of non-coding microRNAs (miRNAs) in pathogenesis of different diseases including cachexia. Moreover, the mechanistic cytokine signaling pathway of miR-155, as a TNF-α regulator, supports the involvement of SOCS1, TAB2, and Foxp3, which are direct targets of TNF-α gene. Aim A case–control study (NCT04131478) was conducted primarily to determine the incidence of TNF-α 308 G/A (rs1800629) and −1031T/C (rs1799964) gene polymorphisms in adult Egyptian patients with local/advanced or metastatic pancreatic or NSCL cancer and investigate both as cachexia risk factors. The association of gene polymorphism with cachexia severity and the expression of miR-155 in cachectic patients were analyzed. A mechanistic investigation of the cytokine signaling pathway, involving SOCS1, TAB2, and Foxp3, was also performed. Results In both pancreatic and NSCL cancer cohorts, the mutant TNF-α variant of 308 G/A was positively associated with cachexia; on the contrary, that of 1031T/C was negatively associated with cachexia in the NSCL cancer patients. MiR-155 was higher in cachexia and in alignment with its severity in the cachectic group as compared with the non-cachectic group in both the pancreatic and NSCL cancer patients. Though TAB2 did not change to any significant extent in cachectic patients, the levels of SOCS1 and Foxp3 were significantly lower in the cachectic group as compared with the non-cachectic group. Conclusion Carriers of the A allele 308 G/A gene and high miR-155 are at greater risk of cachexia in both the pancreatic and NSCL cancer patients; however, the mutant variant of 1031T/C gene is protective against cachexia in the NSCL cancer patients. Finally, high levels of miR-155 in the cachectic group lead to negative feedback inhibition of both SOCS1 and Foxp3 in both the pancreatic and NSCL cancer patients.
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Affiliation(s)
- Rana Yehia
- Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Mona Schaalan
- Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Dalaal M Abdallah
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Amr S Saad
- Oncology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Neven Sarhan
- Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Samira Saleh
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Gao L, Zhou L, Huang X. Identification of Novel Kinase-Transcription Factor-mRNA-miRNA Regulatory Network in Nasopharyngeal Carcinoma by Bioinformatics Analysis. Int J Gen Med 2021; 14:7453-7469. [PMID: 34744455 PMCID: PMC8566004 DOI: 10.2147/ijgm.s327657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022] Open
Abstract
Purpose Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors of the head and neck. This study aimed to investigate the crucial genes and regulatory networks involved in the carcinogenesis of NPC using a bioinformatics approach. Methods Five mRNA and two miRNA expression datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and miRNAs (DEMs) between NPC and normal samples were analyzed using R software. The WebGestalt tool was used for functional enrichment analysis, and protein-protein interaction (PPI) network analysis of DEGs was performed using STRING database. Transcription factors (TFs) were predicted using TRRUST and Transcriptional Regulatory Element Database (TRED). Kinases were identified using X2Kgui. The miRNAs of DEGs were predicted using miRWalk database. A kinase-TF-mRNA-miRNA integrated network was constructed, and hub nodes were selected. The hub genes were validated using NPC datasets from the GEO and Oncomine databases. Finally, candidate small-molecule agents were predicted using CMap. Results A total of 122 DEGs and 44 DEMs were identified. DEGs were associated with the immune response, leukocyte activation, endoplasmic reticulum stress in GO analysis, and the NF-κB signaling pathway in KEGG analysis. Four significant modules were identified using PPI network analysis. Subsequently, 26 TFs, 73 kinases, and 2499 miRNAs were predicted. The predicted miRNAs were cross-referenced with DEMs, and seven overlapping miRNAs were selected. In the kinase-TF-mRNA-miRNA integrated network, eight genes (PTGS2, FN1, MMP1, PLAU, MMP3, CD19, BMP2, and PIGR) were identified as hub genes. Hub genes were validated with consistent results, indicating the reliability of our findings. Finally, six candidate small-molecule agents (phenoxybenzamine, luteolin, thioguanosine, reserpine, blebbistatin, and camptothecin) were predicted. Conclusion We identified DEGs and an NPC regulatory network involving kinases, TFs, mRNAs, and miRNAs, which might provide promising insight into the pathogenesis, treatment, and prognosis of NPC.
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Affiliation(s)
- Li Gao
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Lei Zhou
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Zhongshan Hospital Affiliated to Fudan University, Shanghai, People's Republic of China
| | - Xinsheng Huang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Zhongshan Hospital Affiliated to Fudan University, Shanghai, People's Republic of China
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Burgos M, Hurtado A, Jiménez R, Barrionuevo FJ. Non-Coding RNAs: lncRNAs, miRNAs, and piRNAs in Sexual Development. Sex Dev 2021; 15:335-350. [PMID: 34614501 DOI: 10.1159/000519237] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are a group of RNAs that do not encode functional proteins, including long non-coding RNAs (lncRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), and short interfering RNAs (siRNAs). In the last 2 decades an effort has been made to uncover the role of ncRNAs during development and disease, and nowadays it is clear that these molecules have a regulatory function in many of the developmental and physiological processes where they have been studied. In this review, we provide an overview of the role of ncRNAs during gonad determination and development, focusing mainly on mammals, although we also provide information from other species, in particular when there is not much information on the function of particular types of ncRNAs during mammalian sexual development.
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Affiliation(s)
- Miguel Burgos
- Departamento de Genética e Instituto de Biotecnología, Lab. 127, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Alicia Hurtado
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Rafael Jiménez
- Departamento de Genética e Instituto de Biotecnología, Lab. 127, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Francisco J Barrionuevo
- Departamento de Genética e Instituto de Biotecnología, Lab. 127, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
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Ding P, Ouyang W, Luo J, Kwoh CK. Heterogeneous information network and its application to human health and disease. Brief Bioinform 2021; 21:1327-1346. [PMID: 31566212 DOI: 10.1093/bib/bbz091] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/29/2019] [Accepted: 06/30/2019] [Indexed: 12/11/2022] Open
Abstract
The molecular components with the functional interdependencies in human cell form complicated biological network. Diseases are mostly caused by the perturbations of the composite of the interaction multi-biomolecules, rather than an abnormality of a single biomolecule. Furthermore, new biological functions and processes could be revealed by discovering novel biological entity relationships. Hence, more and more biologists focus on studying the complex biological system instead of the individual biological components. The emergence of heterogeneous information network (HIN) offers a promising way to systematically explore complicated and heterogeneous relationships between various molecules for apparently distinct phenotypes. In this review, we first present the basic definition of HIN and the biological system considered as a complex HIN. Then, we discuss the topological properties of HIN and how these can be applied to detect network motif and functional module. Afterwards, methodologies of discovering relationships between disease and biomolecule are presented. Useful insights on how HIN aids in drug development and explores human interactome are provided. Finally, we analyze the challenges and opportunities for uncovering combinatorial patterns among pharmacogenomics and cell-type detection based on single-cell genomic data.
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Affiliation(s)
- Pingjian Ding
- School of Computer Science, University of South China, Hengyang, China
| | - Wenjue Ouyang
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Chee-Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
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Jia H, Aadland K, Kolaczkowski O, Kolaczkowski B. Direct molecular evidence for an ancient, conserved developmental toolkit controlling post-transcriptional gene regulation in land plants. Mol Biol Evol 2021; 38:4765-4777. [PMID: 34196710 PMCID: PMC8557471 DOI: 10.1093/molbev/msab201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In plants, miRNA production is orchestrated by a suite of proteins that control transcription of the pri-miRNA gene, post-transcriptional processing and nuclear export of the mature miRNA. Post-transcriptional processing of miRNAs is controlled by a pair of physically interacting proteins, hyponastic leaves 1 (HYL1) and Dicer-like 1 (DCL1). However, the evolutionary history and structural basis of the HYL1–DCL1 interaction is unknown. Here we use ancestral sequence reconstruction and functional characterization of ancestral HYL1 in vitro and in Arabidopsis thaliana to better understand the origin and evolution of the HYL1–DCL1 interaction and its impact on miRNA production and plant development. We found the ancestral plant HYL1 evolved high affinity for both double-stranded RNA (dsRNA) and its DCL1 partner before the divergence of mosses from seed plants (∼500 Ma), and these high-affinity interactions remained largely conserved throughout plant evolutionary history. Structural modeling and molecular binding experiments suggest that the second of two dsRNA-binding motifs (DSRMs) in HYL1 may interact tightly with the first of two C-terminal DCL1 DSRMs to mediate the HYL1–DCL1 physical interaction necessary for efficient miRNA production. Transgenic expression of the nearly 200 Ma-old ancestral flowering-plant HYL1 in A. thaliana was sufficient to rescue many key aspects of plant development disrupted by HYL1− knockout and restored near-native miRNA production, suggesting that the functional partnership of HYL1–DCL1 originated very early in and was strongly conserved throughout the evolutionary history of terrestrial plants. Overall, our results are consistent with a model in which miRNA-based gene regulation evolved as part of a conserved plant “developmental toolkit.”
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Affiliation(s)
- Haiyan Jia
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Kelsey Aadland
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA
| | - Oralia Kolaczkowski
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Bryan Kolaczkowski
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL
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Qi P, Niu Y, Wang B. MicroRNA-181a/b-1-encapsulated PEG/PLGA nanofibrous scaffold promotes osteogenesis of human mesenchymal stem cells. J Cell Mol Med 2021; 25:5744-5752. [PMID: 33991050 PMCID: PMC8184675 DOI: 10.1111/jcmm.16595] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
Bioactive nanofibres play a useful role in increasing the efficiency of tissue engineering scaffolds. MicroRNAs (miRs) alone, and in combination with tissue engineering scaffolds, can be effective in treating bone fractures and osteoporosis by regulating many post‐transcriptional cellular pathways. Herein, miR‐181a/b‐1 was incorporated in the electrospun poly (lactic‐co‐glycolic acid) (PLGA) nanofibres (PLGA‐miR). After characterization scaffolds, the osteoinductive capacity of the nanofibres was investigated when adipose‐derived mesenchymal stem cells (AT‐MSCs) were cultured on the PLGA and PLGA‐miR nanofibres. miR incorporating in the nanofibres has not any significant effect on the size and morphology of the nanofibres, but its biocompatibility was increased significantly compared to the empty nanofibres. Alkaline phosphatase (ALP) activity and calcium measures were evaluated as two important osteogenic markers, and the results revealed that the highest measures were observed in the AT‐MSCs cultured on PLGA‐miR nanofibres. Detected ALP activity and calcium measures in miR‐transduced AT‐MSCs cultured on TCPS were also significantly higher than AT‐MSCs cultured on PLGA and TCPS groups. The highest expression levels of bone‐related genes were observed in the AT‐MSCs cultured on PLGA‐miR nanofibres. This improvement in the osteogenic differentiation potential of the AT‐MSCs was also confirmed by evaluating osteopontin protein in the cells cultured on PLGA‐miR. It can be concluded that miR‐181a/b‐1 has a significant impact on the AT‐MSC osteogenic differentiation, and this impact synergistically increased when incorporated in the PLGA nanofibres.
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Affiliation(s)
- Peiyi Qi
- Department of Emergency Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yali Niu
- Department of Lung Transplantation Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bin Wang
- Department of Thoracic Heart Surgery, Changyi People's Hospital, Weifang, China
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Extracellular vesicle-enriched miRNA profiles across pregnancy in the MADRES cohort. PLoS One 2021; 16:e0251259. [PMID: 33979365 PMCID: PMC8115775 DOI: 10.1371/journal.pone.0251259] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/22/2021] [Indexed: 12/31/2022] Open
Abstract
MicroRNA (miRNA) circulating in plasma have been proposed as biomarkers for a variety of conditions and diseases, including complications during pregnancy. During pregnancy, about 15-25% of maternal plasma exosomes, a small size-class of EVs, are hypothesized to originate in the placenta, and may play a role in communication between the fetus and mother. However, few studies have addressed changes in miRNA over the course of pregnancy with repeated measures, nor focused on diverse populations. We describe changes in miRNA in early and late pregnancy from the MADRES cohort of primarily low-income Hispanic women based in Los Angeles, CA. miRNA derived from extracellular-vesicles (EVs) were isolated from maternal blood plasma samples collected in early and late pregnancy. In this study, we identified 64 of 130 detectable miRNA which significantly increased with gestational age at the time of collection (GA), and 26 which decreased with GA. Possible fetal sex-specific associations were observed for 30 of these 90 significant miRNA. Predicted gene targets for miRNA significantly associated with GA were identified using MirDIP and were found to be enriched for Gene Ontology categories that included energetic and metabolic processes but were underrepresented in immune-related categories. Circulating EV-associated miRNA during pregnancy are likely important for maternal-fetal communication, and may play roles in supporting and maintaining a healthy pregnancy, given the changing needs of the fetus.
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Kim Y, Lee DH, Park SH, Jeon TI, Jung CH. The interplay of microRNAs and transcription factors in autophagy regulation in nonalcoholic fatty liver disease. Exp Mol Med 2021; 53:548-559. [PMID: 33879861 PMCID: PMC8102505 DOI: 10.1038/s12276-021-00611-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
The autophagy-lysosomal degradation system has an important role in maintaining liver homeostasis by removing unnecessary intracellular components. Impaired autophagy has been linked to nonalcoholic fatty liver disease (NAFLD), which includes hepatitis, steatosis, fibrosis, and cirrhosis. Thus, gaining an understanding of the mechanisms that regulate autophagy and how autophagy contributes to the development and progression of NAFLD has become the focus of recent studies. Autophagy regulation has been thought to be primarily regulated by cytoplasmic processes; however, recent studies have shown that microRNAs (miRNAs) and transcription factors (TFs) also act as key regulators of autophagy by targeting autophagy-related genes. In this review, we summarize the miRNAs and TFs that regulate the autophagy pathway in NAFLD. We further focus on the transcriptional and posttranscriptional regulation of autophagy and discuss the complex regulatory networks involving these regulators in autophagy. Finally, we highlight the potential of targeting miRNAs and TFs involved in the regulation of autophagy for the treatment of NAFLD.
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Affiliation(s)
- Yumi Kim
- grid.418974.70000 0001 0573 0246Research Division of Food Functionality, Korea Food Research Institute, Wanju-gun, Jeollabuk-do 55365 Republic of Korea
| | - Da-Hye Lee
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - So-Hyun Park
- grid.418974.70000 0001 0573 0246Research Division of Food Functionality, Korea Food Research Institute, Wanju-gun, Jeollabuk-do 55365 Republic of Korea ,grid.412786.e0000 0004 1791 8264Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Tae-Il Jeon
- grid.14005.300000 0001 0356 9399Department of Animal Science, Chonnam National University, Gwangju, Republic of Korea
| | - Chang Hwa Jung
- grid.418974.70000 0001 0573 0246Research Division of Food Functionality, Korea Food Research Institute, Wanju-gun, Jeollabuk-do 55365 Republic of Korea ,grid.412786.e0000 0004 1791 8264Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, Republic of Korea
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Ghafouri-Fard S, Abak A, Fattahi F, Hussen BM, Bahroudi Z, Shoorei H, Taheri M. The interaction between miRNAs/lncRNAs and nuclear factor-κB (NF-κB) in human disorders. Biomed Pharmacother 2021; 138:111519. [PMID: 33756159 DOI: 10.1016/j.biopha.2021.111519] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/27/2021] [Accepted: 03/14/2021] [Indexed: 12/13/2022] Open
Abstract
Nuclear factor-κB (NF-κB) represents a group of inducible transcription factors (TFs) regulating the expression of a great variety of genes implicated in diverse processes, particularly modulation of immune system responses. This TF has functional interactions with non-coding RNAs, constructing a complicated network through which NF-κB, miRNAs, and lncRNAs coordinately regulate gene expression at different facets. This type of interaction is involved in the pathophysiology of several human disorders including both neoplastic disorders and non-neoplastic conditions. MALAT1 and NKILA are among lncRNAs whose interactions with NF-κB have been vastly assessed in different conditions including cancer and inflammatory conditions. In addition, miR-146a/b has functional interactions with this TF in different contexts. Although miRNAs have mutual interactions with NF-κB, the regulatory role of miRNAs on this TF has been more clarified. The aim of the current review is to explore the function of NF-κB-related miRNAs and lncRNAs in these two types of human disorders.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afete Abak
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faranak Fattahi
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Bashdar M Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Zahra Bahroudi
- Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Shoorei
- Department of Anatomical Sciences, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Dwivedi SKD, Rao G, Dey A, Mukherjee P, Wren JD, Bhattacharya R. Small Non-Coding-RNA in Gynecological Malignancies. Cancers (Basel) 2021; 13:1085. [PMID: 33802524 PMCID: PMC7961667 DOI: 10.3390/cancers13051085] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Gynecologic malignancies, which include cancers of the cervix, ovary, uterus, vulva, vagina, and fallopian tube, are among the leading causes of female mortality worldwide, with the most prevalent being endometrial, ovarian, and cervical cancer. Gynecologic malignancies are complex, heterogeneous diseases, and despite extensive research efforts, the molecular mechanisms underlying their development and pathology remain largely unclear. Currently, mechanistic and therapeutic research in cancer is largely focused on protein targets that are encoded by about 1% of the human genome. Our current understanding of 99% of the genome, which includes noncoding RNA, is limited. The discovery of tens of thousands of noncoding RNAs (ncRNAs), possessing either structural or regulatory functions, has fundamentally altered our understanding of genetics, physiology, pathophysiology, and disease treatment as they relate to gynecologic malignancies. In recent years, it has become clear that ncRNAs are relatively stable, and can serve as biomarkers for cancer diagnosis and prognosis, as well as guide therapy choices. Here we discuss the role of small non-coding RNAs, i.e., microRNAs (miRs), P-Element induced wimpy testis interacting (PIWI) RNAs (piRNAs), and tRNA-derived small RNAs in gynecological malignancies, specifically focusing on ovarian, endometrial, and cervical cancer.
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Affiliation(s)
- Shailendra Kumar Dhar Dwivedi
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Geeta Rao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
| | - Anindya Dey
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Priyabrata Mukherjee
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jonathan D. Wren
- Biochemistry and Molecular Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
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Jin H, Liang G, Yang L, Liu L, Wang B, Yan F. SP1-induced AFAP1-AS1 contributes to proliferation and invasion by regulating miR-497-5p/CELF1 pathway in nasopharyngeal carcinoma. Hum Cell 2021; 34:491-501. [PMID: 33400247 DOI: 10.1007/s13577-020-00475-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022]
Abstract
Nasopharyngeal carcinoma is a type of otolaryngological malignancy with high incidence. Long non-coding RNAs (lncRNAs) are closely related to nasopharyngeal carcinoma. LncRNA AFAP1-AS1 (AFAP1-AS1) has been found to play important roles in nasopharyngeal carcinoma progression and poor prognosis. However, the mechanism underlying AFAP1-AS1 in regulating nasopharyngeal carcinoma is still unclear. In current study, AFAP1-AS1 was found to be up-regulated in nasopharyngeal carcinoma tissues and cells. AFAP1-AS1 overexpression and knockdown were conducted in nasopharyngeal carcinoma cells. The results proved that AFAP1-AS1 promoted the survival and migration of nasopharyngeal carcinoma cells. Additionally, specificity protein 1 (SP1) was enhanced in nasopharyngeal carcinoma tissues and cells, and induced AFAP1-AS1 expression. The interaction between AFAP1-AS1 and miR-497-5p was confirmed. AFAP1-AS1 was demonstrated to regulate CELF1, a target gene of miR-497-5p. Further functional analysis revealed that AFAP1-AS1 knockdown attenuated SP1-induced nasopharyngeal carcinoma progression. These results indicate that SP1-induced AFAP1-AS1 facilitates nasopharyngeal carcinoma progression by regulating miR-497-5p/CELF1 pathway, which provides a new target for nasopharyngeal carcinoma treatment.
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Affiliation(s)
- Hui Jin
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Gengtian Liang
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Liping Yang
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Li Liu
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Binru Wang
- Department of Otolaryngology, Wuhan Third Hospital, Wuhan, 430000, Hubei, China
| | - Fengqin Yan
- Department of Head and Neck Radiation Therapy, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No. 1 Banshan Road, Gongshu District, Hangzhou, 310021, Zhejiang, China.
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, 310021, Zhejiang, China.
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piRNAs as Modulators of Disease Pathogenesis. Int J Mol Sci 2021; 22:ijms22052373. [PMID: 33673453 PMCID: PMC7956838 DOI: 10.3390/ijms22052373] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
Advances in understanding disease pathogenesis correlates to modifications in gene expression within different tissues and organ systems. In depth knowledge about the dysregulation of gene expression profiles is fundamental to fully uncover mechanisms in disease development and changes in host homeostasis. The body of knowledge surrounding mammalian regulatory elements, specifically regulators of chromatin structure, transcriptional and translational activation, has considerably surged within the past decade. A set of key regulators whose function still needs to be fully elucidated are small non-coding RNAs (sncRNAs). Due to their broad range of unfolding functions in the regulation of gene expression during transcription and translation, sncRNAs are becoming vital to many cellular processes. Within the past decade, a novel class of sncRNAs called PIWI-interacting RNAs (piRNAs) have been implicated in various diseases, and understanding their complete function is of vital importance. Historically, piRNAs have been shown to be indispensable in germline integrity and stem cell development. Accumulating research evidence continue to reveal the many arms of piRNA function. Although piRNA function and biogenesis has been extensively studied in Drosophila, it is thought that they play similar roles in vertebrate species, including humans. Compounding evidence suggests that piRNAs encompass a wider functional range than small interfering RNAs (siRNAs) and microRNAs (miRNAs), which have been studied more in terms of cellular homeostasis and disease. This review aims to summarize contemporary knowledge regarding biogenesis, and homeostatic function of piRNAs and their emerging roles in the development of pathologies related to cardiomyopathies, cancer, and infectious diseases.
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Bantounas I, Lopes FM, Rooney KM, Woolf AS, Kimber SJ. The miR-199a/214 Cluster Controls Nephrogenesis and Vascularization in a Human Embryonic Stem Cell Model. Stem Cell Reports 2021; 16:134-148. [PMID: 33306987 PMCID: PMC7897558 DOI: 10.1016/j.stemcr.2020.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are gene expression regulators and they have been implicated in acquired kidney diseases and in renal development, mostly through animal studies. We hypothesized that the miR-199a/214 cluster regulates human kidney development. We detected its expression in human embryonic kidneys by in situ hybridization. To mechanistically study the cluster, we used 2D and 3D human embryonic stem cell (hESC) models of kidney development. After confirming expression in each model, we inhibited the miRNAs using lentivirally transduced miRNA sponges. This reduced the WT1+ metanephric mesenchyme domain in 2D cultures. Sponges did not prevent the formation of 3D kidney-like organoids. These organoids, however, contained dysmorphic glomeruli, downregulated WT1, aberrant proximal tubules, and increased interstitial capillaries. Thus, the miR-199a/214 cluster fine-tunes differentiation of both metanephric mesenchymal-derived nephrons and kidney endothelia. While clinical implications require further study, it is noted that patients with heterozygous deletions encompassing this miRNA locus can have malformed kidneys.
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Affiliation(s)
- Ioannis Bantounas
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK.
| | - Filipa M Lopes
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Kirsty M Rooney
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK; Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, and the Manchester Academic Health Science Centre, Manchester, UK.
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Hong Z, Wang Q, Hong C, Liu M, Qiu P, Lin R, Lin X, Chen F, Li Q, Liu L, Wang C, Chen D. Identification of Seven Cell Cycle-Related Genes with Unfavorable Prognosis and Construction of their TF-miRNA-mRNA regulatory network in Breast Cancer. J Cancer 2021; 12:740-753. [PMID: 33403032 PMCID: PMC7778540 DOI: 10.7150/jca.48245] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC), with complex tumorigenesis and progression, remains the most common malignancy in women. We aimed to explore some novel and significant genes with unfavorable prognoses and potential pathways involved in BC initiation and progression via bioinformatics methods. BC tissue-specific microarray datasets of GSE42568, GSE45827 and GSE54002, which included a total of 651 BC tissues and 44 normal breast tissues, were obtained from the Gene Expression Omnibus (GEO) database, and 124 differentially expressed genes (DEGs) were identified between BC tissues and normal breast tissues via R software and an online Venn diagram tool. Database for Annotation, Visualization and Integration Discovery (DAVID) software showed that 65 upregulated DEGs were mainly enriched in the regulation of the cell cycle, and Search Tool for the Retrieval of Interacting Genes (STRING) software identified the 39 closest associated upregulated DEGs in protein-protein interactions (PPIs), which validated the high expression of genes in BC tissues by the Gene Expression Profiling Interactive Analysis (GEPIA) tool. In addition, 36 out of 39 BC patients showed significantly worse outcomes by Kaplan-Meier plotter (KM plotter), and an additional Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that seven genes (cyclin E2 (CCNE2), cyclin B1 (CCNB1), cyclin B2 (CCNB2), mitotic checkpoint serine/threonine kinase B (BUB1B), dual-specificity protein kinase (TTK), cell division cycle 20 (CDC20), and pituitary tumor transforming gene 1 (PTTG1)) were markedly enriched in the cell cycle pathway. Analysis of the clinicopathological characteristics of hub genes revealed that seven cell cycle-related genes (CCRGs) were significantly highly expressed in four BC subtypes (luminal A, luminal B, HER2-positive and triple-negative (TNBC)), and except for the CCNE2 gene, high expression levels were significantly associated with tumor pathological grade and stage and metastatic events of BC. Furthermore, genetic mutation analysis indicated that genetic alterations of CCRGs could also significantly affect BC patients' prognosis. A quantitative real-time polymerase chain reaction (qRT-PCR) assay found that the seven CCRGs were significantly differentially expressed in BC cell lines. Integration of published multilevel expression data and a bioinformatics computational approach were used to predict and construct a regulation mechanism: a transcription factor (TF)-microRNA (miRNA)-messenger RNA (mRNA) regulation network. The present work is the first to construct a regulatory network of TF-miRNA-mRNA in BC for CCRGs and provides new insights into the molecular mechanism of BC.
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Affiliation(s)
- Zhipeng Hong
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China.,Department of Breast Surgery and General Surgery, The Affiliated Union Hospital of Fujian Medical University, Fuzhou, Fujian Province, 350001, P. R. China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province, 350001, P.R. China
| | - Qinglan Wang
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
| | - Chengye Hong
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
| | - Meimei Liu
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
| | - Pengqin Qiu
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
| | - Rongrong Lin
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
| | - Xiaolan Lin
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
| | - Fangfang Chen
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
| | - Qiuhuang Li
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
| | - Lingling Liu
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
| | - Chuan Wang
- Department of Breast Surgery and General Surgery, The Affiliated Union Hospital of Fujian Medical University, Fuzhou, Fujian Province, 350001, P. R. China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province, 350001, P.R. China
| | - Debo Chen
- Department of Breast Surgery, Affiliated Quanzhou First Hospital of Fujian Medical University, Quanzhou, Fujian Province, 362000, P. R. China
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Khurana P, Gupta A, Sugadev R, Sharma YK, Varshney R, Ganju L, Kumar B. nSARS-Cov-2, pulmonary edema and thrombosis: possible molecular insights using miRNA-gene circuits in regulatory networks. ACTA ACUST UNITED AC 2020; 2:16. [PMID: 33209992 PMCID: PMC7596315 DOI: 10.1186/s41544-020-00057-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/18/2020] [Indexed: 12/11/2022]
Abstract
Background Given the worldwide spread of the novel Severe Acute Respiratory Syndrome Coronavirus 2 (nSARS-CoV-2) infection pandemic situation, research to repurpose drugs, identify novel drug targets, vaccine candidates have created a new race to curb the disease. While the molecular signature of nSARS-CoV-2 is still under investigation, growing literature shows similarity among nSARS-CoV-2, pulmonary edema, and thromboembolic disorders due to common symptomatic features. A network medicine approach is used to to explore the molecular complexity of the disease and to uncover common molecular trajectories of edema and thrombosis with nSARS-CoV-2. Results and conclusion A comprehensive nSARS-CoV-2 responsive miRNA: Transcription Factor (TF): gene co-regulatory network was built using host-responsive miRNAs and it’s associated tripartite, Feed-Forward Loops (FFLs) regulatory circuits were identified. These regulatory circuits regulate signaling pathways like virus endocytosis, viral replication, inflammatory response, pulmonary vascularization, cell cycle control, virus spike protein stabilization, antigen presentation, etc. A unique miRNA-gene regulatory circuit containing a consortium of four hub FFL motifs is proposed to regulate the virus-endocytosis and antigen-presentation signaling pathways. These regulatory circuits also suggest potential correlations/similarity in the molecular mechanisms during nSARS-CoV-2 infection, pulmonary diseases and thromboembolic disorders and thus could pave way for repurposing of drugs. Some important miRNAs and genes have also been proposed as potential candidate markers. A detailed molecular snapshot of TGF signaling as the common pathway, that could play an important role in controlling common pathophysiologies among diseases, is also put forth. Supplementary information Supplementary information accompanies this paper at 10.1186/s41544-020-00057-y.
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Affiliation(s)
- P Khurana
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - A Gupta
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - R Sugadev
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - Y K Sharma
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - R Varshney
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - L Ganju
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - B Kumar
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
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Patel RK, West JD, Jiang Y, Fogarty EA, Grimson A. Robust partitioning of microRNA targets from downstream regulatory changes. Nucleic Acids Res 2020; 48:9724-9746. [PMID: 32821933 PMCID: PMC7515711 DOI: 10.1093/nar/gkaa687] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/19/2020] [Accepted: 08/08/2020] [Indexed: 11/14/2022] Open
Abstract
The biological impact of microRNAs (miRNAs) is determined by their targets, and robustly identifying direct miRNA targets remains challenging. Existing methods suffer from high false-positive rates and are unable to effectively differentiate direct miRNA targets from downstream regulatory changes. Here, we present an experimental and computational framework to deconvolute post-transcriptional and transcriptional changes using a combination of RNA-seq and PRO-seq. This novel approach allows us to systematically profile the regulatory impact of a miRNA. We refer to this approach as CARP: Combined Analysis of RNA-seq and PRO-seq. We apply CARP to multiple miRNAs and show that it robustly distinguishes direct targets from downstream changes, while greatly reducing false positives. We validate our approach using Argonaute eCLIP-seq and ribosome profiling, demonstrating that CARP defines a comprehensive repertoire of targets. Using this approach, we identify miRNA-specific activity of target sites within the open reading frame. Additionally, we show that CARP facilitates the dissection of complex changes in gene regulatory networks triggered by miRNAs and identification of transcription factors that mediate downstream regulatory changes. Given the robustness of the approach, CARP would be particularly suitable for dissecting miRNA regulatory networks in vivo.
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Affiliation(s)
- Ravi K Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, New York 14853, USA
| | - Jessica D West
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ya Jiang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, New York 14853, USA
| | - Elizabeth A Fogarty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Andrew Grimson
- To whom correspondence should be addressed. Tel: +1 607 254 1307; Fax: +1 607 254 1307;
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Hernandez Y, Goswami K, Sanan‐Mishra N. Stress induced dynamic adjustment of conserved miR164:NAC module. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2020; 1:134-151. [PMID: 37283725 PMCID: PMC10168063 DOI: 10.1002/pei3.10027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 07/02/2020] [Accepted: 07/14/2020] [Indexed: 06/08/2023]
Abstract
Aims including the rationale Salinity and drought are the two major stresses limiting the productivity of economically important crops such as Glycine max (soybean). The incidence of these stresses during the pod development stages affects the quality and quantity of seeds, which compromise the yield of soybean. The miR164:NAC module has been shown to play a critical role in regulating the response to salt and drought stress in several plant species. However, biological role of miR164:NAC module in salt stress in soybean is not fully understood. Methods In this study, we identified 215 salt responsive miRNAs, using miScript miRNA array with a sensitive and a tolerant soybean genotype, William82 and INCASoy36, respectively. The targets of these salt regulated miRNAs were searched in the degradome datasets. Key results It was found that four salt stress deregulated miRNAs targeted the NAC transcription factor and among these miR164k and miR408d showed antagonistic expression in the two soybean genotypes. The expression of miR164k was higher in salt tolerant INCASoy36 as compared to salt sensitive William82, under unstressed conditions. However under salt stress, miR164k was downregulated in INCASoy36 (-2.65 fold), whereas it was upregulated in William82 (4.68 fold). A transient co-expression assay validated that gma-miR164k directs the cleavage of GmNAC1 transcript. Bioinformatics analysis revealed that the regulation of NAC transcription factor family by members of miR164 family is conserved across many species. The dynamic expression profiles of miR164 and NAC-TFs were captured in different tissues of rice, tobacco, and two soybean genotypes under drought and salt stress conditions. Main conclusion Collectively, our results suggest that genetically determined dynamic modulation of the conserved miR164:NAC-TF module may play an important role in determining the adaptive response of plants to stress.
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Affiliation(s)
- Yuniet Hernandez
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Kavita Goswami
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Neeti Sanan‐Mishra
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
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Kandettu A, Radhakrishnan R, Chakrabarty S, Sriharikrishnaa S, Kabekkodu SP. The emerging role of miRNA clusters in breast cancer progression. Biochim Biophys Acta Rev Cancer 2020; 1874:188413. [PMID: 32827583 DOI: 10.1016/j.bbcan.2020.188413] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/01/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
Abstract
Micro RNAs (miRNAs) are small non-coding RNAs that are essential for regulation of gene expression of the target genes. Large number of miRNAs are organized into defined units known as miRNA clusters (MCs). The MCs consist of two or more than two miRNA encoding genes driven by a single promoter, transcribed together in the same orientation, that are not separated from each other by a transcription unit. Aberrant miRNA clusters expression is reported in breast cancer (BC), exhibiting both pro-tumorogenic and anti-tumorigenic role. Altered MCs expression facilitates to breast carcinogenesis by promoting the breast cells to acquire the various hallmarks of the cancer. Since miRNA clusters contain multiple miRNA encoding genes, targeting cluster may be more attractive than targeting individual miRNAs. Besides targeting dysregulated miRNA clusters in BC, studies have focused on the mechanism of action, and its contribution to the progression of the BC. The present review provides a comprehensive overview of dysregulated miRNA clusters and its role in the acquisition of cancer hallmarks in BC. More specifically, we have presented the regulation, differential expression, classification, targets, mechanism of action, and signaling pathways of miRNA clusters in BC. Additionally, we have also discussed the potential utility of the miRNA cluster as a diagnostic and prognostic indicator in BC.
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Affiliation(s)
- Amoolya Kandettu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India; Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - S Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India; Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
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Hurtado A, Palomino R, Georg I, Lao M, Real FM, Carmona FD, Burgos M, Jiménez R, Barrionuevo FJ. Deficiency of the onco-miRNA cluster, miR-106b∼25, causes oligozoospermia and the cooperative action of miR-106b∼25 and miR-17∼92 is required to maintain male fertility. Mol Hum Reprod 2020; 26:389-401. [PMID: 32330263 DOI: 10.1093/molehr/gaaa027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/27/2020] [Accepted: 04/15/2020] [Indexed: 12/28/2022] Open
Abstract
The identification of new genes involved in sexual development and gonadal function as potential candidates causing male infertility is important for both diagnostic and therapeutic purposes. Deficiency of the onco-miRNA cluster miR-17∼92 has been shown to disrupt spermatogenesis, whereas mutations in its paralog cluster, miR-106b∼25, that is expressed in the same cells, were reported to have no effect on testis development and function. The aim of this work is to determine the role of these two miRNA clusters in spermatogenesis and male fertility. For this, we analyzed miR-106b∼25 and miR-17∼92 single and double mouse mutants and compared them to control mice. We found that miR-106b∼25 knock out testes show reduced size, oligozoospermia and altered spermatogenesis. Transcriptomic analysis showed that multiple molecular pathways are deregulated in these mutant testes. Nevertheless, mutant males conserved normal fertility even when early spermatogenesis and other functions were disrupted. In contrast, miR-17∼92+/-; miR-106b∼25-/- double mutants showed severely disrupted testicular histology and significantly reduced fertility. Our results indicate that miR-106b∼25 and miR-17∼92 ensure accurate gene expression levels in the adult testis, keeping them within the required thresholds. They play a crucial role in testis homeostasis and are required to maintain male fertility. Hence, we have identified new candidate genetic factors to be screened in the molecular diagnosis of human males with reproductive disorders. Finally, considering the well-known oncogenic nature of these two clusters and the fact that patients with reduced fertility are more prone to testicular cancer, our results might also help to elucidate the molecular mechanisms linking both pathologies.
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Affiliation(s)
- Alicia Hurtado
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Labs 127 and 105a, Centro de Investigación Biomédica, Avenida del Conocimiento, 18016 Armilla, Granada, Spain
| | - Rogelio Palomino
- Departamento de Bioquímica y Biología Molecular I e Instituto de Investigación Biosanitaria de Granada, Universidad de Granada, Laboratorio 127 Centro de Investigación Biomédica, Avenida del Conocimiento, 18016 Armilla, Granada, Spain
| | - Ina Georg
- Genetics of Complex Diseases Unit, Pfizer-University of Granada-Junta de Andalucía "Centre for Genomics and Oncological Research" (GENYO), Avenida de la Ilustración 114, 18016 Granada, Spain
| | - Miguel Lao
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Labs 127 and 105a, Centro de Investigación Biomédica, Avenida del Conocimiento, 18016 Armilla, Granada, Spain
| | | | - F David Carmona
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Labs 127 and 105a, Centro de Investigación Biomédica, Avenida del Conocimiento, 18016 Armilla, Granada, Spain
| | - Miguel Burgos
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Labs 127 and 105a, Centro de Investigación Biomédica, Avenida del Conocimiento, 18016 Armilla, Granada, Spain
| | - Rafael Jiménez
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Labs 127 and 105a, Centro de Investigación Biomédica, Avenida del Conocimiento, 18016 Armilla, Granada, Spain
| | - Francisco J Barrionuevo
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Labs 127 and 105a, Centro de Investigación Biomédica, Avenida del Conocimiento, 18016 Armilla, Granada, Spain
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