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Lin H, Chen X, Wang L, Zhu T, Feng X, Liu X, Chen H, Pan S. Unraveling the role of microRNAs: potential biomarkers for gestational diabetes mellitus revealed through RNA sequencing analysis. Arch Gynecol Obstet 2024; 310:1255-1264. [PMID: 38814453 PMCID: PMC11258170 DOI: 10.1007/s00404-024-07518-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) poses significant health risks for both mothers and children, contributing to long-term complications such as type 2 diabetes and cardiovascular disease. This study explores the potential of microRNAs (miRNAs) as biomarkers for GDM by analyzing peripheral blood samples from GDM patients. METHOD Ten samples, including peripheral blood from 5 GDM patients and 5 controls, were collected to perform the RNA sequencing analysis. Differentially expressed miRNAs were further validated by quantitative real-time polymerase chain reaction. RESULTS A total of 2287 miRNAs were identified, 229 of which showed differential expression. Validation by qRT-PCR confirmed significant up-regulation of miR-5193, miR-5003-3p, miR-3127-5p, novel-miR-96, miR-6734-5p, and miR-122-5p, while miR-10395-3p was down-regulated. Bioinformatics analyses revealed the involvement of these miRNAs in pathways associated with herpes simplex virus 1 infection. CONCLUSION This study provides insights into the differential expression of miRNAs in GDM patients and their potential roles in disease pathogenesis. It suggests that the differentially expressed miRNAs could serve as potential biomarkers for GDM, shedding light on the complex molecular mechanisms involved.
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Affiliation(s)
- Huizhen Lin
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Xiao Chen
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Lisui Wang
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Tang Zhu
- Key Laboratory of Translational Tumor Medicine in Fujian Province, Putian University, School of Basic Medicine Science, Putian, 351100, Fujian, China
| | - Xiaohui Feng
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Xiaomei Liu
- Department of Clinical Laboratory, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, 351100, China
| | - Haiying Chen
- Key Laboratory of Translational Tumor Medicine in Fujian Province, Putian University, School of Basic Medicine Science, Putian, 351100, Fujian, China
| | - Si Pan
- Key Laboratory of Translational Tumor Medicine in Fujian Province, Putian University, School of Basic Medicine Science, Putian, 351100, Fujian, China.
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2
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Aravind VA, Kouznetsova VL, Kesari S, Tsigelny IF. Using Machine Learning and miRNA for the Diagnosis of Esophageal Cancer. J Appl Lab Med 2024; 9:684-695. [PMID: 38721901 DOI: 10.1093/jalm/jfae037] [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: 12/13/2023] [Accepted: 02/20/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND Esophageal cancer (EC) remains a global health challenge, often diagnosed at advanced stages, leading to high mortality rates. Current diagnostic tools for EC are limited in their efficacy. This study aims to harness the potential of microRNAs (miRNAs) as novel, noninvasive diagnostic biomarkers for EC. Our objective was to determine the diagnostic accuracy of miRNAs, particularly in distinguishing miRNAs associated with EC from control miRNAs. METHODS We applied machine learning (ML) techniques in WEKA (Waikato Environment for Knowledge Analysis) and TensorFlow Keras to a dataset of miRNA sequences and gene targets, assessing the predictive power of several classifiers: naïve Bayes, multilayer perceptron, Hoeffding tree, random forest, and random tree. The data were further subjected to InfoGain feature selection to identify the most informative miRNA sequence and gene target descriptors. The ML models' abilities to distinguish between miRNA implicated in EC and control group miRNA was then tested. RESULTS Of the tested WEKA classifiers, the top 3 performing ones were random forest, Hoeffding tree, and naïve Bayes. The TensorFlow Keras neural network model was subsequently trained and tested, the model's predictive power was further validated using an independent dataset. The TensorFlow Keras gave an accuracy 0.91. The WEKA best algorithm (naïve Bayes) model yielded an accuracy of 0.94. CONCLUSIONS The results demonstrate the potential of ML-based miRNA classifiers in diagnosing EC. However, further studies are necessary to validate these findings and explore the full clinical potential of this approach.
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Affiliation(s)
- Vishnu A Aravind
- REHS program, San Diego Supercomputer Center, UC San Diego, San Diego, CA, United States
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, UC San Diego, San Diego, CA, United States
- BiAna, La Jolla, CA, United States
- CureScience Institute, San Diego, CA, United States
| | - Santosh Kesari
- Pacific Neuroscience Institute, Department of Translational Neurosciences, Santa Monica, United States
| | - Igor F Tsigelny
- San Diego Supercomputer Center, UC San Diego, San Diego, CA, United States
- BiAna, La Jolla, CA, United States
- CureScience Institute, San Diego, CA, United States
- Department of Neurosciences, UC San Diego, San Diego, CA, United States
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3
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Nazou E, Potiris A, Mavrogianni D, Drakaki E, Vogiatzis AA, Sarli V, Vrantza T, Zikopoulos A, Louis K, Skentou C, Panagopoulos P, Drakakis P, Stavros S. Oocyte Maturation and miRNAs: Studying a Complicate Interaction to Reveal Possible Biomarkers for Female Infertility. Diseases 2024; 12:121. [PMID: 38920553 PMCID: PMC11202488 DOI: 10.3390/diseases12060121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024] Open
Abstract
Cellular metabolism, apoptosis, fertilization, and proliferation of granulosa cells belong to a battery of processes where microRNAs can be detected and associated with infertility. The aim of the present review is to focus on mammalian oocyte maturation events and the association between oocyte growth and miRNA expression. PubMed/Medline, Google Scholar and Scopus databases were searched, and 33 studies were included. Regarding the correlation among miRNA expression and the regulation of granulosa cells and cumulus cells, the most important miRNAs were let-7b, let-7c and miR-21. Additionally, the loss of Dicer, an enzyme involved in miRNA biogenesis, is probably a crucial factor in oogenesis, oocyte maturation and embryogenesis. Furthermore, miRNAs interfere with different cellular mechanisms like apoptosis, steroidogenesis, genome integrity, angiogenesis, antioxidative response and, consequently, oocyte maturation. Hence, it is of major importance to clarify the role and mechanism of each miRNA as understanding its action may develop new tools and establish new diagnostic and treatment approaches for infertility and ovarian disorders.
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Affiliation(s)
- Eleni Nazou
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Anastasios Potiris
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Despoina Mavrogianni
- First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, 115 28 Athens, Greece; (D.M.); (E.D.)
| | - Eirini Drakaki
- First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, 115 28 Athens, Greece; (D.M.); (E.D.)
| | - Aris-Anargyros Vogiatzis
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Vaia Sarli
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Tereza Vrantza
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Athanasios Zikopoulos
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Konstantinos Louis
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Chara Skentou
- Department of Obstetrics and Gynecology, Medical School, University of Ioannina, 45110 Ioannina, Greece;
| | - Periklis Panagopoulos
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Peter Drakakis
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Sofoklis Stavros
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
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Ahmed T. Lipid nanoparticle mediated small interfering RNA delivery as a potential therapy for Alzheimer's disease. Eur J Neurosci 2024; 59:2915-2954. [PMID: 38622050 DOI: 10.1111/ejn.16336] [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: 09/18/2023] [Revised: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 04/17/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative condition that exhibits a gradual decline in cognitive function and is prevalent among a significant number of individuals globally. The use of small interfering RNA (siRNA) molecules in RNA interference (RNAi) presents a promising therapeutic strategy for AD. Lipid nanoparticles (LNPs) have been developed as a delivery vehicle for siRNA, which can selectively suppress target genes, by enhancing cellular uptake and safeguarding siRNA from degradation. Numerous research studies have exhibited the effectiveness of LNP-mediated siRNA delivery in reducing amyloid beta (Aβ) levels and enhancing cognitive function in animal models of AD. The feasibility of employing LNP-mediated siRNA delivery as a therapeutic approach for AD is emphasized by the encouraging outcomes reported in clinical studies for other medical conditions. The use of LNP-mediated siRNA delivery has emerged as a promising strategy to slow down or even reverse the progression of AD by targeting the synthesis of tau phosphorylation and other genes linked to the condition. Improvement of the delivery mechanism and determination of the most suitable siRNA targets are crucial for the efficacious management of AD. This review focuses on the delivery of siRNA through LNPs as a promising therapeutic strategy for AD, based on the available literature.
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Affiliation(s)
- Tanvir Ahmed
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
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5
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Piccinno E, Scalavino V, Labarile N, De Marinis L, Armentano R, Giannelli G, Serino G. Identification of a Novel miR-195-5p/PNN Axis in Colorectal Cancer. Int J Mol Sci 2024; 25:5980. [PMID: 38892168 PMCID: PMC11172886 DOI: 10.3390/ijms25115980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Pinin (PNN) is a desmosome-associated protein that reinforces the organization of keratin intermediate filaments and stabilizes the anchoring of the cytoskeleton network to the lateral surface of the plasma membrane. The aberrant expression of PNN affects the strength of cell adhesion as well as modifies the intracellular signal transduction pathways leading to the onset of CRC. In our previous studies, we characterized the role of miR-195-5p in the regulation of desmosome junctions and in CRC progression. Here, with the aim of investigating additional mechanisms related to the desmosome complex, we identified PNN as a miR-195-5p putative target. Using a public data repository, we found that PNN was a negative prognostic factor and was overexpressed in colon cancer tissues from stage 1 of the disease. Then, we assessed PNN expression in CRC tissue specimens, confirming the overexpression of PNN in tumor sections. The increase in intracellular levels of miR-195-5p revealed a significant decrease in PNN at the mRNA and protein levels. As a consequence of PNN regulation by miR-195-5p, the expression of KRT8 and KRT19, closely connected to PNN, was affected. Finally, we investigated the in vivo effect of miR-195-5p on PNN expression in the colon of AOM/DSS-treated mice. In conclusion, we have revealed a new mechanism driven by miR-195-5p in the regulation of desmosome components, suggesting a potential pharmacological target for CRC therapy.
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Affiliation(s)
| | | | | | | | | | | | - Grazia Serino
- National Institute of Gastroenterology S. De Bellis, IRCCS Research Hospital, Via Turi 27, 70013 Castellana Grotte, BA, Italy; (E.P.); (V.S.); (N.L.); (L.D.M.); (R.A.); (G.G.)
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6
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Feddersen S, Philippsen TJ, Hansen MS, Christensen LS, Nybo M, Brandes A. No Detectable Differences in microRNA Plasma Levels between Diabetic Hypertensive Patients with and without Incident Subclinical Atrial Fibrillation. J Clin Med 2024; 13:2554. [PMID: 38731083 PMCID: PMC11084405 DOI: 10.3390/jcm13092554] [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: 03/19/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Background: Long-term rhythm monitoring (LTRM) can detect undiagnosed atrial fibrillation (AF) in patients at risk of AF and stroke. Circulating microRNAs (miRNAs), which have been shown to play a role in atrial electrical and structural remodelling, could help to select patients who would benefit most from LTRM. The aim of this study was to investigate whether patients with diabetes mellitus (DM) and hypertension and screen-detected subclinical AF (SCAF) using an insertable cardiac monitor (ICM) have significantly different plasma baseline levels of five selected miRNAs playing a role in the modulation of atrial electrical and structural remodelling (miR-21-5p, miR-29b-3p, miR-150-5p, miR-328-3p, and miR-432-5p) compared to those without SCAF. Methods: This study was performed at the outpatient clinic of a secondary academic teaching hospital between December 2013 and November 2015. Eligible patients were ≥65 years of age with DM and hypertension but without known heart diseases. All patients received an ICM. On the day of ICM implantation, blood samples for the measurement of plasma levels of the five miRNAs were drawn. In this post hoc analysis, we investigated their expression by reverse transcription-quantitative polymerase chain reaction. MiRNA plasma levels in patients with and without newly detected SCAF were compared. Results: We included 82 consecutive patients (median age of 71.3 years (IQR 67.4-75.1)), who were followed for a median of 588 days (IQR: 453-712 days). Seventeen patients (20.7%) had ICM-detected SCAF. Plasma levels of miR-328-3p, miR-29b-3p, miR-21-5p, miR-432-5p, and miR-150-5p were slightly but not significantly different in patients with incident SCAF compared with patients without. Conclusions: In patients with hypertension and DM, newly detected SCAF was not significantly associated with changes in expression levels of miR-21-5p, miR-29b-3p, miR-150-5p, miR-328-3p, and miR-432-5p.
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Affiliation(s)
- Søren Feddersen
- Department of Clinical Biochemistry, Odense University Hospital, J.B. Winsløws Vej 4, 5000 Odense, Denmark; (S.F.); (M.N.)
- Department of Clinical Research, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Tine J. Philippsen
- Department of Cardiology, Hospital of Southern Jutland, Kresten Philipsens Vej 15, 6200 Aabenraa, Denmark; (T.J.P.); (M.S.H.); (L.S.C.)
| | - Michael S. Hansen
- Department of Cardiology, Hospital of Southern Jutland, Kresten Philipsens Vej 15, 6200 Aabenraa, Denmark; (T.J.P.); (M.S.H.); (L.S.C.)
| | - Lene S. Christensen
- Department of Cardiology, Hospital of Southern Jutland, Kresten Philipsens Vej 15, 6200 Aabenraa, Denmark; (T.J.P.); (M.S.H.); (L.S.C.)
| | - Mads Nybo
- Department of Clinical Biochemistry, Odense University Hospital, J.B. Winsløws Vej 4, 5000 Odense, Denmark; (S.F.); (M.N.)
- Department of Clinical Research, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Axel Brandes
- Department of Cardiology, Esbjerg Hospital—University Hospital of Southern Denmark, Finsensgade 35, 6700 Esbjerg, Denmark
- Department of Regional Health Research, University of Southern Denmark—Esbjerg, Finsensgade 35, 6700 Esbjerg, Denmark
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7
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Alam MJ, Rahman MH, Hossain MA, Hoque MR, Aktaruzzaman M. Bioinformatics and Systems Biology Approaches to Identify the Synergistic Effects of Alcohol Use Disorder on the Progression of Neurological Diseases. Neuroscience 2024; 543:65-82. [PMID: 38401711 DOI: 10.1016/j.neuroscience.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024]
Abstract
Clinical investigations showed that individuals with Alcohol Use Disorder (AUD) have worse Neurological Disease (ND) development, pointing to possible pathogenic relationships between AUD and NDs. It remains difficult to identify risk factors that are predisposing between AUD and NDs. In order to fix these issues, we created the bioinformatics pipeline and network-based approaches for employing unbiased methods to discover genes abnormally stated in both AUD and NDs and to pinpoint some of the common molecular pathways that might underlie AUD and ND interaction. We found 100 differentially expressed genes (DEGs) in both the AUD and ND patient's tissue samples. The most important Gene Ontology (GO) terms and metabolic pathways, including positive control of cytotoxicity caused by T cells, proinflammatory responses, antigen processing and presentation, and platelet-triggered interactions with vascular and circulating cell pathways were then extracted using the overlapped DEGs. Protein-protein interaction analysis was used to identify hub proteins, including CCL2, IL1B, TH, MYCN, HLA-DRB1, SLC17A7, and HNF4A, in the pathways that have been reported as playing a function in these disorders. We determined several TFs (HNF4A, C4A, HLA-B, SNCA, HLA-DMB, SLC17A7, HLA-DRB1, HLA-C, HLA-A, and HLA-DPB1) and potential miRNAs (hsa-mir-34a-5p, hsa-mir-34c-5p, hsa-mir-449a, hsa-mir-155-5p, and hsa-mir-1-3p) were crucial for regulating the expression of AUD and ND which could serve as prospective targets for treatment. Our methodologies discovered unique putative biomarkers that point to the interaction between AUD and various neurological disorders, as well as pathways that could one day be the focus of therapeutic intervention.
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Affiliation(s)
- Md Jahangir Alam
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh; Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia 7003, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh; Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia 7003, Bangladesh.
| | - Md Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh; Department of Microbiology, Primeasia University, Banani, Dhaka 1213, Bangladesh
| | - Md Robiul Hoque
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Md Aktaruzzaman
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
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8
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Arora A, Tsigelny IF, Kouznetsova VL. Laryngeal cancer diagnosis via miRNA-based decision tree model. Eur Arch Otorhinolaryngol 2024; 281:1391-1399. [PMID: 38147113 DOI: 10.1007/s00405-023-08383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023]
Abstract
PURPOSE Laryngeal cancer (LC) is the most common head and neck cancer, which often goes undiagnosed due to the inaccessible nature of current diagnosis methods in some parts of the world. Many recent studies have shown that microRNAs (miRNAs) are crucial biomarkers for a variety of cancers. METHODS In this study, we create a decision tree model for the diagnosis of laryngeal cancer using a created series of miRNA attributes, such as sequence-based characteristics, predicted miRNA target genes, and gene pathways. This series of attributes is extracted from both differentially expressed blood-based miRNAs in laryngeal cancer and random, non-associated with cancer miRNAs. RESULTS Several machine-learning (ML) algorithms were tested in the ML model, and the Hoeffding Tree classifier yields the highest accuracy (86.8%) in miRNAs-based recognition of laryngeal cancer. Furthermore, our model is validated with the independent laryngeal cancer datasets and can accurately diagnose laryngeal cancer with 86% accuracy. We also explored the biological relationships of the attributes used in our model to understand their relationship with cancer proliferation or suppression pathways. CONCLUSION Our study demonstrates that the proposed model and an inexpensive miRNA testing strategy have the potential to serve as an additional method for diagnosing laryngeal cancer.
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Affiliation(s)
- Aarav Arora
- REHS Program, San Diego Supercomputer Center, UC San Diego, La Jolla, CA, USA
| | - Igor F Tsigelny
- San Diego Supercomputer Center, UC San Diego, La Jolla, CA, USA.
- BiAna, La Jolla, CA, USA.
- Department of Neurosciences, UC San Diego, La Jolla, CA, USA.
- CureScience, San Diego, CA, USA.
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, UC San Diego, La Jolla, CA, USA
- BiAna, La Jolla, CA, USA
- CureScience, San Diego, CA, USA
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9
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Do VQ, Hoang-Thi C, Pham TT, Bui NL, Kim DT, Chu DT. Computational tools supporting known miRNA identification. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:225-242. [PMID: 38360000 DOI: 10.1016/bs.pmbts.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The study of small RNAs is a field that is expanding quickly. Other functional short RNA molecules other than microRNAs, and gene expression regulators, have been found in animals and plants. MicroRNAs play a significant role in host-microbe interactions, and parasite microRNAs may affect the host's innate immunity. Furthermore, short RNAs are intriguing non-invasive biomarker possibilities because they can be found in physiological fluids. These trends suggest that for many researchers, quick and simple techniques for expression profiling and subsequent downstream analysis of miRNA-seq data are crucial. We selected sRNAtoolbox to make integrated sRNA research easier. Each tool can be used separately or to explore and analyze sRNAbench results in further depth. A special focus was placed on the tools' usability. We review available miRNA research tools to have an overview of the evaluation of the tools. Mainly we evaluate the tool sRNAtoolbox.
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Affiliation(s)
- Van-Quy Do
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Chuc Hoang-Thi
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Thanh-Truong Pham
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Nhat-Le Bui
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Thai Kim
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
| | - Dinh-Toi Chu
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.
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10
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Meng L, Shang H, Liu Q, Li Z, Wang X, Li Q, Li F, Zhao Z, Liu C. Lnc-PSMA8-1 activated by GEFT promotes rhabdomyosarcoma progression via upregulation of mTOR expression by sponging miR-144-3p. BMC Cancer 2024; 24:79. [PMID: 38225540 PMCID: PMC10789031 DOI: 10.1186/s12885-023-11798-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/26/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND GEFT is a key regulator of tumorigenesis in rhabdomyosarcoma (RMS), and overexpression of GEFT is significantly correlated with distant metastasis, lymph node metastasis, and a poor prognosis, yet the underlying molecular mechanism is still poorly understood. This study aimed to investigate and validate the molecular mechanism of GEFT-activated lncRNAs in regulating mTOR expression to promote the progression of RMS. METHODS GEFT-regulated lncRNAs were identified through microarray analysis. The effects of GEFT-regulated lncRNAs on the proliferation, apoptosis, invasion, and migration of RMS cells were confirmed through cell functional experiments. The target miRNAs of GEFT-activated lncRNAs in the regulation of mTOR expression were predicted by bioinformatics analysis combined with quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The expression of lnc-PSMA8-1, miR-144-3p, and mTOR was measured by qRT-PCR in RMS tissue samples and cell lines. The regulatory mechanisms of the lnc-PSMA8-1-miR-144-3p-mTOR signaling axis were verified by RNA-binding protein immunoprecipitation (RIP), a luciferase reporter assay, qRT-PCR analysis, Western blot analysis, and cell functional experiments. RESULTS The microarray-based analysis identified 31 differentially expressed lncRNAs (fold change > 2.0, P < 0.05). Silencing the 4 upregulated lncRNAs (lnc-CEACAM19-1, lnc-VWCE-2, lnc-GPX7-1, and lnc-PSMA8-1) and overexpressing the downregulated lnc-FAM59A-1 inhibited the proliferation, invasion, and migration and induced the apoptosis of RMS cells. Among the factors analyzed, the expression of lnc-PSMA8-1, miR-144-3p, and mTOR in RMS tissue samples and cells was consistent with the correlations among their expression indicated by the lncRNA-miRNA-mRNA regulatory network based on the ceRNA hypothesis. lnc-PSMA8-1 promoted RMS progression by competitively binding to miR-144-3p to regulate mTOR expression. CONCLUSION Our research demonstrated that lnc-PSMA8-1 was activated by GEFT and that the former positively regulated mTOR expression by sponging miR-144-3p to promote the progression of RMS. Therefore, targeting this network may constitute a potential therapeutic approach for the management of RMS.
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Affiliation(s)
- Lian Meng
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine/The First Affiliated Hospital, Shihezi University, Shihezi, China
| | - Hao Shang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine/The First Affiliated Hospital, Shihezi University, Shihezi, China
- Judicial Appraisal Institute, Tongde Hospital of Zhejiang Province (Zhejiang Mental Health Center), Hangzhou, China
| | - Qianqian Liu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine/The First Affiliated Hospital, Shihezi University, Shihezi, China
| | - Zhenzhen Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine/The First Affiliated Hospital, Shihezi University, Shihezi, China
| | - Xiaomeng Wang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine/The First Affiliated Hospital, Shihezi University, Shihezi, China
| | - Qianru Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine/The First Affiliated Hospital, Shihezi University, Shihezi, China
| | - Feng Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine/The First Affiliated Hospital, Shihezi University, Shihezi, China
- Department of Pathology and Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Zhenguo Zhao
- Department of Orthopedics, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Chunxia Liu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine/The First Affiliated Hospital, Shihezi University, Shihezi, China.
- Department of Pathology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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11
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Legaz I, Jimenez-Coll V, González-López R, Fernández-González M, Alegría-Marcos MJ, Galián JA, Botella C, Moya-Quiles R, Muro-Pérez M, Minguela A, Llorente S, Muro M. MicroRNAs as Potential Graft Rejection or Tolerance Biomarkers and Their Dilemma in Clinical Routines Behaving like Devilish, Angelic, or Frightening Elements. Biomedicines 2024; 12:116. [PMID: 38255221 PMCID: PMC10813128 DOI: 10.3390/biomedicines12010116] [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: 12/06/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Allograft rejection is a widespread complication in allograft recipients with chronic kidney disease. Undertreatment of subclinical and clinical rejection and later post-transplant problems are caused by an imperfect understanding of the mechanisms at play and a lack of adequate diagnostic tools. Many different biomarkers have been analyzed and proposed to detect and monitor these crucial events in transplant outcomes. In this sense, microRNAs may help diagnose rejection or tolerance and indicate appropriate treatment, especially in patients with chronic allograft rejection. As key epigenetic regulators of physiological homeostasis, microRNAs have therapeutic potential and may indicate allograft tolerance or rejection. However, more evidence and clinical validation are indispensable before microRNAs are ready for clinical prime time.
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Affiliation(s)
- Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute of Murcia (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum,” Faculty of Medicine, University of Murcia (UMU), 30100 Murcia, Spain
| | - Víctor Jimenez-Coll
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Rosana González-López
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | | | | | - José Antonio Galián
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Carmen Botella
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Rosa Moya-Quiles
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Manuel Muro-Pérez
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Alfredo Minguela
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
| | - Santiago Llorente
- Service of Nephrology, Unit Hospital Clinic Universitario Virgen de la Arrixaca, IMIB-Arrixaca, 30120 Murcia, Spain
| | - Manuel Muro
- Immunology Service, University Clinical Hospital “Virgen de la Arrixaca”—IMIB, 30120 Murcia, Spain
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12
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Ahirwar SS, Rizwan R, Sethi S, Shahid Z, Malviya S, Khandia R, Agarwal A, Kotnis A. Comparative Analysis of Published Database Predicting MicroRNA Binding in 3'UTR of mRNA in Diverse Species. Microrna 2024; 13:2-13. [PMID: 37929739 DOI: 10.2174/0122115366261005231018070640] [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: 05/06/2023] [Revised: 09/03/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Micro-RNAs are endogenous non-coding RNA moieties of 22-27 nucleotides that play a crucial role in the regulation of various biological processes and make them useful prognostic and diagnostic biomarkers. Discovery and experimental validation of miRNA is a laborious and time-consuming process. For early prediction, multiple bioinformatics databases are available for miRNA target prediction; however, their utility can confuse amateur researchers in selecting the most appropriate tools for their study. OBJECTIVE This descriptive review aimed to analyse the usability of the existing database based on the following criteria: accessibility, efficiency, interpretability, updatability, and flexibility for miRNA target prediction of 3'UTR of mRNA in diverse species so that the researchers can utilize the database most appropriate to their research. METHODS A systematic literature search was performed in PubMed, Google Scholar and Scopus databases up to November 2022. ≥10,000 articles found online, including ⁓130 miRNA tools, which contain various information on miRNA. Out of them, 31 databases that provide information on validated 3'UTR miRNAs target databases were included and analysed in this review. RESULTS These miRNA database tools are being used in varied areas of biological research to select the most suitable miRNA for their experimental validation. These databases, updated until the year 2021, consist of miRNA-related data from humans, animals, mice, plants, viruses etc. They contain 525-29806351 data entries, and information from most databases is freely available on the online platform. CONCLUSION Reviewed databases provide significant information, but not all information is accurate or up-to-date. Therefore, Diana-TarBase and miRWalk are the most comprehensive and up-to-date databases.
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Affiliation(s)
- Sonu Singh Ahirwar
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Rehma Rizwan
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Samdish Sethi
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Zainab Shahid
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Shivani Malviya
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Amit Agarwal
- Department of Neurosurgery, All India Institute of Medical Sciences Bhopal, Bhopal MP, 462020, India
| | - Ashwin Kotnis
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
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13
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Wang W, Wang Y. Integrative bioinformatics analysis of biomarkers and pathways for exploring the mechanisms and molecular targets associated with pyroptosis in type 2 diabetes mellitus. Front Endocrinol (Lausanne) 2023; 14:1207142. [PMID: 38034011 PMCID: PMC10684677 DOI: 10.3389/fendo.2023.1207142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Research has shown that pyroptosis contributes greatly to the progression of diabetes and its complications. However, the exact relationship between this particular cell death process and the pathology of type 2 diabetes mellitus (T2DM) remains unclear. In this study, we used bioinformatic tools to identify the pyroptosis-related genes (PRGs) associated with T2DM and to analyze their roles in the disease pathology. Methods Two microarray datasets, GSE7014 and GSE25724, were obtained from the GEO database and assessed for differentially expressed genes (DEGs). The T2DM-associated DEGs that overlapped with differentially expressed PRGs were noted as T2DM-PRGs. Subsequently, 25 T2DM-PRGs were validated and subjected to functional enrichment analysis through Gene Ontology annotation analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, and gene set enrichment analysis (GSEA). The diagnostic and predictive value of the T2DM-PRGs was evaluated using receiver operating characteristic curves (ROC). Additionally, a single-sample GSEA algorithm was applied to study immune infiltration in T2DM and assess immune infiltration levels. Results We identified 25 T2DM-PRGs that were significantly enriched in the nuclear factor-kappa B signaling and prostate cancer pathways. The top five differentially expressed prognostic T2DM-PRGs targeted by miRNAs were PTEN, BRD4, HSP90AB1, VIM, and PKN2. The top five differentially expressed T2DM-PRGs associated with transcription factors were HSP90AB1, VIM, PLCG1, SCAF11, and PTEN. The genes PLCG1, PTEN, TP63, CHI3L1, SDHB, DPP8, BCL2, SERPINB1, ACE2, DRD2, DDX58, and BTK showed excellent diagnostic performance. The immune infiltration analysis revealed notable differences in immune cells between T2DM and normal tissues in both datasets. These findings suggest that T2DM-PRGs play a crucial role in the development and progression of T2DM and could be used as potential diagnostic biomarkers and therapeutic targets. Discussion Investigating the mechanisms and biomarkers associated with pyroptosis may offer valuable insights into the pathophysiology of T2DM and lead to novel therapeutic approaches to treat the disease.
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Affiliation(s)
- Wei Wang
- Department of Endocrinology, School of Medicine, Zhongda Hospital, Institute of Diabetes, Southeast University, Nanjing, Jiangsu, China
- Department of Endocrinology, First Affiliated Hospital of Baotou Medical Collage, Baotou, China
| | - Yao Wang
- Department of Endocrinology, School of Medicine, Zhongda Hospital, Institute of Diabetes, Southeast University, Nanjing, Jiangsu, China
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14
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Zhang Y, Zhao T, Hu L, Xue J. Integrative Analysis of Core Genes and Biological Process Involved in Polycystic Ovary Syndrome. Reprod Sci 2023; 30:3055-3070. [PMID: 37171773 DOI: 10.1007/s43032-023-01259-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 04/29/2023] [Indexed: 05/13/2023]
Abstract
Polycystic ovary syndrome (PCOS) is a common gynecological endocrine disordered disease, affecting the function of the ovaries in women of reproductive age. However, there are limited curative therapies for PCOS due to lack of reliable candidates. Hence, this study aimed to identify hub pathogenic genes and potential therapeutic targets for PCOS using bioinformatics tools. We obtained the expression profiles of 29 PCOS samples and 24 normal samples from three Gene Expression Omnibus (GEO) datasets. Then, the differentially expressed genes (DEGs) were screened, which were subjected to functional enrichment analyses. Moreover, we found 30 ferroptosis-related genes out of the 89 DEGs. Among the top 10 significant ferroptosis-related DEGs, 8 genes showed good predictive performance. We constructed interaction network of top three ferroptosis-related DEGs (SLC38A1, ACO1, DDIT3). Finally, real-time PCR was performed to test the relative expression of these genes. In conclusions, we have identified ferroptosis-related DEGs as core genes and potential therapeutic targets of PCOS based on comprehensive bioinformatics analysis. The findings are conducive to understanding of the pathogenesis of PCOS and paving the way towards curative therapies.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Obstetrics and Gynecology, Yan'an University Affiliated Hospital, No. 43 North Street, Baota District, Yan'an, 716000, Shaanxi, People's Republic of China
| | - Tianyi Zhao
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Lishuang Hu
- Department of Obstetrics and Gynecology, Yan'an University Affiliated Hospital, No. 43 North Street, Baota District, Yan'an, 716000, Shaanxi, People's Republic of China
| | - Juan Xue
- Department of Obstetrics and Gynecology, Yan'an University Affiliated Hospital, No. 43 North Street, Baota District, Yan'an, 716000, Shaanxi, People's Republic of China.
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15
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Chen J, Lin Y, Sun Z. Inhibition of miR-101-3p prevents human aortic valve interstitial cell calcification through regulation of CDH11/SOX9 expression. Mol Med 2023; 29:24. [PMID: 36809926 PMCID: PMC9945614 DOI: 10.1186/s10020-023-00619-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Calcific aortic valve disease (CAVD) is the second leading cause of adult heart diseases. The purpose of this study is to investigate whether miR-101-3p plays a role in the human aortic valve interstitial cells (HAVICs) calcification and the underlying mechanisms. METHODS Small RNA deep sequencing and qPCR analysis were used to determine changes in microRNA expression in calcified human aortic valves. RESULTS The data showed that miR-101-3p levels were increased in the calcified human aortic valves. Using cultured primary HAVICs, we demonstrated that the miR-101-3p mimic promoted calcification and upregulated the osteogenesis pathway, while anti-miR-101-3p inhibited osteogenic differentiation and prevented calcification in HAVICs treated with the osteogenic conditioned medium. Mechanistically, miR-101-3p directly targeted cadherin-11 (CDH11) and Sry-related high-mobility-group box 9 (SOX9), key factors in the regulation of chondrogenesis and osteogenesis. Both CDH11 and SOX9 expressions were downregulated in the calcified human HAVICs. Inhibition of miR-101-3p restored expression of CDH11, SOX9 and ASPN and prevented osteogenesis in HAVICs under the calcific condition. CONCLUSION miR-101-3p plays an important role in HAVIC calcification through regulation of CDH11/SOX9 expression. The finding is important as it reveals that miR-1013p may be a potential therapeutic target for calcific aortic valve disease.
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Affiliation(s)
- Jianglei Chen
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Yi Lin
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Zhongjie Sun
- Department of Physiology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA. .,Department of Physiology, College of Medicine, UT Cardiovascular Institute, University of Tennessee Health Science Center, 956 Court Avenue, Memphis, TN, 38163, USA.
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16
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Lu Y, Liu M, Guo X, Wang P, Zeng F, Wang H, Tang J, Qin Z, Tao T. miR-26a-5p alleviates CFA-induced chronic inflammatory hyperalgesia through Wnt5a/CaMKII/NFAT signaling in mice. CNS Neurosci Ther 2023; 29:1254-1271. [PMID: 36756710 PMCID: PMC10068476 DOI: 10.1111/cns.14099] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Inflammation often leads to the occurrence of chronic pain, and many miRNAs have been shown to play a key role in the development of inflammatory pain. However, whether miR-26a-5p relieves pain induced by inflammation and its possible mechanism are still unclear. METHODS The complete Freund's adjuvant (CFA)-induced inflammatory pain mouse model was employed. Intrathecal or subcutaneous injection of miR-26a-5p agomir was performed after modeling to study its antinociceptive effect and the comparison of different administration methods. Bioinformatics analysis of miRNAs was performed to study the downstream mechanisms of miR-26a-5p. HE staining, RT-qPCR, Western blotting, and immunofluorescence were used for further validation. RESULTS A single intrathecal and subcutaneous injection of miR-26a-5p both reversed mechanical hypersensitivity and thermal latency in the left hind paw of mice with CFA-induced inflammatory pain. HE staining and immunofluorescence studies found that both administrations of miR-26a-5p alleviated inflammation in the periphery and spinal cord. Bioinformatics analysis and dual-luciferase reporter gene analysis identified Wnt5a as a direct downstream target gene of miR-26a-5p. Wnt5a was mainly expressed in neurons and microglia in the spinal cord of mice with inflammatory pain. Intrathecal injection of miR-26a-5p could significantly reduce the expression level of Wnt5a and inhibit the downstream molecules of noncanonical Wnt signaling Camk2/NFAT, inhibiting the release of spinal cord inflammatory factors and alleviating the activation of microglia. In addition, miR-26a-5p could also inhibit lipopolysaccharide (LPS)-stimulated BV2 cell inflammation in vitro through a noncanonical Wnt signaling pathway. CONCLUSIONS miR-26a-5p is a promising therapy for CFA-induced inflammatory pain. Both intrathecal and subcutaneous injections provide relief for inflammatory pain. miR-26a-5p regulated noncanonical Wnt signaling to be involved in analgesia partly through antineuroinflammation, suggesting a pain-alleviating effect via noncanonical Wnt signaling pathway in the CFA-induced inflammatory pain model in vivo.
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Affiliation(s)
- Yitian Lu
- Department of Anesthesiology, Nanfang hospital, Southern Medical University, Guangzhou, China.,Department of Anesthesiology, Central People's Hospital of Zhanjiang, Zhanjiang, China
| | - Maozhu Liu
- Department of pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiangna Guo
- Department of Anesthesiology, Nanfang hospital, Southern Medical University, Guangzhou, China
| | - Peng Wang
- Department of Anesthesiology, Nanfang hospital, Southern Medical University, Guangzhou, China
| | - Fanning Zeng
- Department of Anesthesiology, Nanfang hospital, Southern Medical University, Guangzhou, China
| | - Haitao Wang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jing Tang
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zaisheng Qin
- Department of Anesthesiology, Nanfang hospital, Southern Medical University, Guangzhou, China
| | - Tao Tao
- Department of Anesthesiology, Central People's Hospital of Zhanjiang, Zhanjiang, China
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Chen X, Xie L, Jiang Y, Zhang R, Wu W. LCK, FOXC1 and hsa-miR-146a-5p as potential immune effector molecules associated with rheumatoid arthritis. Biomarkers 2023; 28:130-138. [PMID: 36420648 DOI: 10.1080/1354750x.2022.2150315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rheumatoid arthritis (RA) is a type of systemic immune disease characterized by chronic inflammatory disease of the joints. However, the aetiology and underlying molecular events of RA are unclear. Here, we applied bioinformatics analysis to identify potential immune effector molecules involved in RA. The three microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database. We used the R software screen 115 overlapping differentially expressed genes (DEGs). Subsequently, we constructed a protein-protein interaction (PPI) network encoded by these DEGs and identified 10 genes closely associated with RA - LCK, GZMA, GZMB, CD2, LAG3, IL-15, TNFRSF4, CD247, CCR5 and CCR7. Furthermore, in the miRNA-hub gene networks, we screened out hsa-miR-146a-5p, which is the miRNA controlling the largest number of hub genes. Finally, we found some transcription factors that closely interact with hub genes, such as FOXC1, GATA2, YY1, RUNX2, SREBF1, CEBPB and NFIC. This study successfully predicted that LCK, FOXC1 and hsa-miR-146a-5p can be used as potential immune effector molecules of RA. Our study may have potential implications for future prediction of disease progression in patients with symptomatic RA, and has important significance for the pathogenesis and targeted therapy of RA.
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Affiliation(s)
- Xuemeng Chen
- Department of Traditional Chinese Medicine and rheumatism immunology, the First Affiliated Hospital of Army Medical University, Chongqing City, China
| | - Li Xie
- Department of Traditional Chinese Medicine, Chongqing Dadukou District People's Hospital, Chongqing City, China
| | - Yi Jiang
- Department of Traditional Chinese Medicine and rheumatism immunology, the First Affiliated Hospital of Army Medical University, Chongqing City, China
| | - Ronghua Zhang
- Department of Traditional Chinese Medicine and rheumatism immunology, the First Affiliated Hospital of Army Medical University, Chongqing City, China
| | - Wei Wu
- Department of Traditional Chinese Medicine and rheumatism immunology, the First Affiliated Hospital of Army Medical University, Chongqing City, China
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18
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Exploration of Hub Genes in Retinopathy of Prematurity Based on Bioinformatics Analysis of the Oxygen-Induced Retinopathy Model. J Ophthalmol 2022; 2022:9835524. [PMID: 36124139 PMCID: PMC9482502 DOI: 10.1155/2022/9835524] [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: 07/06/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Retinopathy of prematurity (ROP) is a major blindness-causing disease that is characterized by an arrest of normal vascular development and neovascularization of the retina. Previous studies have shown that genetic factors may be associated with the development and severity of ROP. However, the genes and mechanisms underlying ROP remain unclear. We aimed to identify hub genes in ROP and drugs related to these genes by integrative analysis. The expression profiles of GSE158799 and GSE135844 were acquired from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were identified. Then, an integrative analysis was performed including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), gene set enrichment analysis (GSEA), protein-protein interaction (PPI) network, transcription factor (TF)-gene, and miRNA-gene networks analysis. Moreover, we verified hub genes and identified potential drugs. 225 common DEGs were identified. Biological function analysis indicated that angiogenesis, cell surface, cell adhesion, extracellular matrix, and focal adhesion genes were enriched among DEGs. The PI3K/Akt signalingpathway, focal adhesion, and extracellular matrix (ECM)-receptor interaction were markedly enriched in the KEGG pathway analysis. Finally, 5 hub genes related to the nosogenesis of ROP were identified and found to be targeted by VEGFA inhibitors, TLR4 antagonists, and sunitinib. The present study showed that VEGFA, ACTA2, MKI67, CD68, and TLR4 are potential hub genes involved in the pathogenesis of ROP. Moreover, TLR4 antagonists and sunitinib may be new candidate drugs for ROP therapy, in addition to VEGFA inhibitors.
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Zhao Z, He S, Tang S, Lai X, Ren J, Yu X, Lin J, Wang M, El Akkawi MM, Zeng S, Zha D. CLP1 is a Prognosis-Related Biomarker and Correlates With Immune Infiltrates in Rheumatoid Arthritis. Front Pharmacol 2022; 13:827215. [PMID: 35721104 PMCID: PMC9201986 DOI: 10.3389/fphar.2022.827215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, heterogeneous autoimmune disease with a high disability rate that seriously affects society and individuals. However, there is a lack of effective and reliable diagnostic markers and therapeutic targets. In this study, we identified diagnostic markers of RA based on RNA modification and explored its role as well as degree of immune cell infiltration. We used the gene expression profile data of three synovial tissues (GSE55235, GSE55457, GSE77298) from the Gene Expression Omnibus (GEO) database and the gene of 5 RNA modification genes (including m6A, m1A, m5C, APA, A-1), combined with cluster analysis, identified four RNA modifiers closely related to RA (YTHDC1, LRPPRC, NOP2, and CLP1) and five immune cells namely T cell CD8, CD4 memory resting, T cells regulatory (Tregs) Macrophages M0, and Neutrophils. Based on the LASSO regression algorithm, hub genes and immune cell prediction models were established respectively in RA and a nomogram based on the immune cell model was built. Around 4 key RNA modification regulator genes, miRNA-mRNA, mRNA-TF networks have been established, and GSEA-GO, KEGG-GSEA enrichment analysis has been carried out. Finally, CLP1 was established as an effective RA diagnostic marker, and was highly positively correlated with T cells follicular helper (Tfh) infiltration. On the other hand, highly negatively correlated with the expression of mast cells. In short, CLP1 may play a non-negligible role in the onset and development of RA by altering immune cell infiltration, and it is predicted to represent a novel target for RA clinical diagnosis and therapy.
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Affiliation(s)
- Zhenyu Zhao
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Shaojie He
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Sheng Tang
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Xiaofeng Lai
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jie Ren
- Department of Rheumatology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - XinCheng Yu
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jinhua Lin
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Mohan Wang
- School of Basic Medicine and Public Health, Jinan University, Guangzhou, China
| | - Mariya M El Akkawi
- Department of Plastic and Reconstructive Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Shan Zeng
- Department of Rheumatology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Dingsheng Zha
- Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China
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20
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Xiong Y, Song J, Huang X, Pan Z, Goldbrunner R, Stavrinou L, Lin S, Hu W, Zheng F, Stavrinou P. Exosomes Derived From Mesenchymal Stem Cells: Novel Effects in the Treatment of Ischemic Stroke. Front Neurosci 2022; 16:899887. [PMID: 35585925 PMCID: PMC9108502 DOI: 10.3389/fnins.2022.899887] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022] Open
Abstract
Ischemic stroke is defined as an infarction in the brain, caused by impaired cerebral blood supply, leading to local brain tissue ischemia, hypoxic necrosis, and corresponding neurological deficits. At present, revascularization strategies in patients with acute ischemic stroke include intravenous thrombolysis and mechanical endovascular treatment. However, due to the short treatment time window (<4.5 h) and method restrictions, clinical research is focused on new methods to treat ischemic stroke. Exosomes are nano-sized biovesicles produced in the endosomal compartment of most eukaryotic cells, containing DNA, complex RNA, and protein (30-150 nm). They are released into surrounding extracellular fluid upon fusion between multivesicular bodies and the plasma membrane. Exosomes have the characteristics of low immunogenicity, good innate stability, high transmission efficiency, and the ability to cross the blood-brain barrier, making them potential therapeutic modalities for the treatment of ischemic stroke. The seed sequence of miRNA secreted by exosomes is base-paired with complementary mRNA to improve the microenvironment of ischemic tissue, thereby regulating downstream signal transduction activities. With exosome research still in the theoretical and experimental stages, this review aims to shed light on the potential of exosomes derived from mesenchymal stem cells in the treatment of ischemic stroke.
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Affiliation(s)
- Yu Xiong
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Jianping Song
- Department of Neurosurgery, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
- National Center for Neurological Disorders, Shanghai, China
- Neurosurgical Institute of Fudan University, Shanghai, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
- Department of Neurosurgery, National Regional Medical Center, Fudan University Huashan Hospital Fujian Campus, The First Affiliated Hospital Binhai Campus, Fujian Medical University, Fuzhou, China
| | - Xinyue Huang
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Zhigang Pan
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Roland Goldbrunner
- Department of Neurosurgery, Faculty of Medicine and University Hospital, Center for Neurosurgery, University of Cologne, Cologne, Germany
| | - Lampis Stavrinou
- 2nd Department of Neurosurgery, Athens Medical School, “Attikon” University Hospital, National and Kapodistrian University, Athens, Greece
| | - Shu Lin
- Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Weipeng Hu
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Feng Zheng
- Department of Neurosurgery, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Pantelis Stavrinou
- Department of Neurosurgery, Faculty of Medicine and University Hospital, Center for Neurosurgery, University of Cologne, Cologne, Germany
- Department of Neurosurgery, Metropolitan Hospital, Athens, Greece
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21
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Navarrete S, Solar C, Tapia R, Pereira J, Fuentes E, Palomo I. Pathophysiology of deep vein thrombosis. Clin Exp Med 2022:10.1007/s10238-022-00829-w. [PMID: 35471714 DOI: 10.1007/s10238-022-00829-w] [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: 09/03/2021] [Accepted: 03/31/2022] [Indexed: 12/29/2022]
Abstract
Deep venous thrombosis is a frequent, multifactorial disease and a leading cause of morbidity and mortality. Most of the time deep venous thrombosis is triggered by the interaction between acquired risk factors, such as hip fracture, pregnancy, and immobility, and hereditary risk factors such as thrombophilias. The mechanisms underlying deep venous thrombosis are not fully elucidated; however, in recent years, important advances have shed light on the role of venous flow, endothelium, platelets, leukocytes, and the interaction between inflammation and hemostasis. It has been described that the alteration of venous blood flow produces endothelial activation, favoring the adhesion of platelets and leukocytes, which, through tissue factor expression and neutrophil extracellular traps formation, contribute to the activation of coagulation, trapping more cells, such as red blood cells. Thus, the concerted interaction of these phenomena allows the formation and growth of the thrombus. In this work, the main mechanisms involved in the pathophysiology of deep vein thrombosis will be described.
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Affiliation(s)
- Simón Navarrete
- Thrombosis Research Center, Medical Technology School, Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Av. Lircay s/n, 3460000, Talca, Chile
| | - Carla Solar
- Thrombosis Research Center, Medical Technology School, Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Av. Lircay s/n, 3460000, Talca, Chile
| | | | - Jaime Pereira
- Department of Hematology-Oncology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo Fuentes
- Thrombosis Research Center, Medical Technology School, Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Av. Lircay s/n, 3460000, Talca, Chile
| | - Iván Palomo
- Thrombosis Research Center, Medical Technology School, Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Av. Lircay s/n, 3460000, Talca, Chile.
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22
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Li Q, Liang Z, Wang X, Zhou F, Ma X, Wei W, Tian D, Yu H. The emerging role of epigenetics and gut microbiota in Vogt-Koyanagi-Harada syndrome. Gene 2022; 818:146222. [PMID: 35092860 DOI: 10.1016/j.gene.2022.146222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/01/2022]
Abstract
Vogt-Koyanagi-Harada (VKH) syndrome is an autoimmune disorder characterized often by acute diffuse uveitis, also known as idiopathic uveoencephalitis. The associated complications can potentially affect multiple systems throughout the body, including eyes, ears, skin and nervous system. Although the pathogenesis of VKH syndrome remains unclear, it has been established that the various genetic factors, epigenetic factors and the imbalance in immune regulation can significantly contribute to the development of this disease. In addition, the experimental autoimmune uveitis (EAU) has been commonly used to further explore the pathogenesis of the disease. Herein, in this review article, we discuss about the major research advances made in understanding of the different epigenetic factors and gut microbes involved in the pathogenesis of VKH syndrome as well as EAU. The information discussed can help to better understand the pathogenesis of VKH syndrome, and thereby might provide a basis for finding novel molecular targets and innovative treatment strategies in the future.
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Affiliation(s)
- Qinxingzi Li
- School of Basic Medical Sciences, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Guizhou 563000, China
| | - Zhongzhi Liang
- Affiliated Hospital of Zunyi Medical University, Guizhou 563000, China
| | - Xin Wang
- School of Basic Medical Sciences, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Guizhou 563000, China
| | - Fangyu Zhou
- School of Basic Medical Sciences, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Guizhou 563000, China
| | - Xiaomin Ma
- School of Basic Medical Sciences, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Guizhou 563000, China
| | - Wenwen Wei
- School of Basic Medical Sciences, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Guizhou 563000, China
| | - Dan Tian
- School of Basic Medical Sciences, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Guizhou 563000, China
| | - Hongsong Yu
- School of Basic Medical Sciences, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Guizhou 563000, China.
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23
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MicroRNAs in Leukemias: A Clinically Annotated Compendium. Int J Mol Sci 2022; 23:ijms23073469. [PMID: 35408829 PMCID: PMC8998245 DOI: 10.3390/ijms23073469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Leukemias are a group of malignancies of the blood and bone marrow. Multiple types of leukemia are known, however reliable treatments have not been developed for most leukemia types. Furthermore, even relatively reliable treatments can result in relapses. MicroRNAs (miRNAs) are a class of short, noncoding RNAs responsible for epigenetic regulation of gene expression and have been proposed as a source of potential novel therapeutic targets for leukemias. In order to identify central miRNAs for leukemia, we conducted data synthesis using two databases: miRTarBase and DISNOR. A total of 137 unique miRNAs associated with 16 types of leukemia were retrieved from miRTarBase and 86 protein-coding genes associated with leukemia were retrieved from the DISNOR database. Based on these data, we formed a visual network of 248 miRNA-target interactions (MTI) between leukemia-associated genes and miRNAs associated with ≥4 leukemia types. We then manually reviewed the literature describing these 248 MTIs for interactions identified in leukemia studies. This manually curated data was then used to visualize a network of 64 MTIs identified in leukemia patients, cell lines and animal models. We also formed a visual network of miRNA-leukemia associations. Finally, we compiled leukemia clinical trials from the ClinicalTrials database. miRNAs with the highest number of MTIs were miR-125b-5p, miR-155-5p, miR-181a-5p and miR-19a-3p, while target genes with the highest number of MTIs were TP53, BCL2, KIT, ATM, RUNX1 and ABL1. The analysis of 248 MTIs revealed a large, highly interconnected network. Additionally, a large MTI subnetwork was present in the network visualized from manually reviewed data. The interconnectedness of the MTI subnetwork suggests that certain miRNAs represent central disease molecules for multiple leukemia types. Additional studies on miRNAs, their target genes and associated biological pathways are required to elucidate the therapeutic potential of miRNAs in leukemia.
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24
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Asadirad A, Baghaei K, Hashemi SM, Dehnavi S, Ghanbarian H, Mortaz E, Anissian A, Asadzadeh Aghdaei H, Amani D. Dendritic cell immunotherapy with miR-155 enriched tumor-derived exosome suppressed cancer growth and induced antitumor immune responses in murine model of colorectal cancer induced by CT26 cell line. Int Immunopharmacol 2022; 104:108493. [PMID: 35032826 DOI: 10.1016/j.intimp.2021.108493] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/12/2021] [Accepted: 12/18/2021] [Indexed: 01/03/2023]
Abstract
Nowadays, various strategies are considered to prime Dendritic cells (DCs) with tumor antigens. The tumor cell-derived exosomes are recognized as one of the most efficient strategies for achieving this purpose. In this regard, MicroRNA 155 (miR-155) is employed as one of the most prominent miRNAs, which play substantial roles in DCs maturation and IL-12 production. This study investigates the tumor growth suppression and antitumor effects of DCs primed with miR-155-enriched exosome on the BALB/c murine model of colorectal cancer induced by CT-26 cell lines. Therefore, a holistic framework is proposed for the analysis procedure. In the first stage, miRNA-155 was electroporated into texosomes. In the second stage, bonemarrow-derived DCs were treated with miRNA-155 enriched texosomes. Then, antitumor properties of manipulated DC have been evaluated in the BALB/c mice model of colorectal cancer. After DC immunotherapy, several features have been assessed for each animal, including survival, body weight, tumor volume/size, histopathology, and serum cytokine levels. Also, flow cytometric evaluation has been performed for the spleen and the tumor tissue T-cell subsets. The findings demonstrated that the primed DCs could significantly increase IL-12p70 and IFN-γ in serum and accelerate the differentiation, proliferation, and cytotoxicity effects on the Th and CTL cells. Also, the treatment also increased the infiltration of Th and CTL cells into the tumor microenvironment while decreasing Tregs. This situation causes tumor growth control, and survival improvement. Therefore, DC immunotherapywith miR-155-enriched texosomes can be employed as a the desired approach for inducing antitumor immune responses, controlling tumor growth, and improving survival in mice with colorectal cancer. However, it is essential to perform more investigations to confirm the clinical application of this approach in humans and other types of tumors.
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Affiliation(s)
- Ali Asadirad
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Cancer, Petroleum and Environmental Pollutants Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Kaveh Baghaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorder Research Center, Research Institute for Gastroenterology and Liver Disease, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Seyed Mahmoud Hashemi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sajad Dehnavi
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hossein Ghanbarian
- Cellular and Molecular Biology Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Esmaeil Mortaz
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Anissian
- Veterinary Pathology Department, Islamic Azad University, Abhar Branch, Abhar, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorder Research Center, Research Institute for Gastroenterology and Liver Disease, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Davar Amani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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25
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Roy B, Lee E, Li T, Rampersaud M. Role of miRNAs in Neurodegeneration: From Disease Cause to Tools of Biomarker Discovery and Therapeutics. Genes (Basel) 2022; 13:genes13030425. [PMID: 35327979 PMCID: PMC8951370 DOI: 10.3390/genes13030425] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
Neurodegenerative diseases originate from neuronal loss in the central nervous system (CNS). These debilitating diseases progress with age and have become common due to an increase in longevity. The National Institute of Environmental Health Science’s 2021 annual report suggests around 6.2 million Americans are living with Alzheimer’s disease, and there is a possibility that there will be 1.2 million Parkinson’s disease patients in the USA by 2030. There is no clear-cut universal mechanism for identifying neurodegenerative diseases, and therefore, they pose a challenge for neurobiology scientists. Genetic and environmental factors modulate these diseases leading to familial or sporadic forms. Prior studies have shown that miRNA levels are altered during the course of the disease, thereby suggesting that these noncoding RNAs may be the contributing factor in neurodegeneration. In this review, we highlight the role of miRNAs in the pathogenesis of neurodegenerative diseases. Through this review, we aim to achieve four main objectives: First, we highlight how dysregulation of miRNA biogenesis led to these diseases. Second, we highlight the computational or bioinformatics tools required to identify the putative molecular targets of miRNAs, leading to biological molecular pathways or mechanisms involved in these diseases. Third, we focus on the dysregulation of miRNAs and their target genes leading to several neurodegenerative diseases. In the final section, we highlight the use of miRNAs as potential diagnostic biomarkers in the early asymptomatic preclinical diagnosis of these age-dependent debilitating diseases. Additionally, we discuss the challenges and advances in the development of miRNA therapeutics for brain targeting. We list some of the innovative strategies employed to deliver miRNA into target cells and the relevance of these viral and non-viral carrier systems in RNA therapy for neurodegenerative diseases. In summary, this review highlights the relevance of studying brain-enriched miRNAs, the mechanisms underlying their regulation of target gene expression, their dysregulation leading to progressive neurodegeneration, and their potential for biomarker marker and therapeutic intervention. This review thereby highlights ways for the effective diagnosis and prevention of these neurodegenerative disorders in the near future.
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Affiliation(s)
- Bidisha Roy
- Life Science Centre, Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07012, USA
- Correspondence:
| | - Erica Lee
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
| | - Teresa Li
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
| | - Maria Rampersaud
- Department of Pathology, Icahn School of Medicine, New York, NY 10029, USA; (E.L.); (T.L.); (M.R.)
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26
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Xu A, Kouznetsova VL, Tsigelny IF. Alzheimer's Disease Diagnostics Using miRNA Biomarkers and Machine Learning. J Alzheimers Dis 2022; 86:841-859. [PMID: 35147545 DOI: 10.3233/jad-215502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The current standard for Alzheimer's disease (AD) diagnosis is often imprecise, as with memory tests, and invasive or expensive, as with brain scans. However, the dysregulation patterns of miRNA in blood hold potential as useful biomarkers for the non-invasive diagnosis and even treatment of AD. OBJECTIVE The goal of this research is to elucidate new miRNA biomarkers and create a machine-learning (ML) model for the diagnosis of AD. METHODS We utilized pathways and target gene networks related to confirmed miRNA biomarkers in AD diagnosis and created multiple models to use for diagnostics based on the significant differences among miRNA expression between blood profiles (serum and plasma). RESULTS The best performing serum-based ML model, trained on filtered disease-specific miRNA datasets, was able to identify miRNA biomarkers with 92.0% accuracy and the best performing plasma-based ML model, trained on filtered disease-specific miRNA datasets, was able to identify miRNA biomarkers with 90.9% accuracy. Through analysis of AD implicated miRNA, thousands of descriptors reliant on target gene and pathways were created which can then be used to identify novel biomarkers and strengthen disease diagnosis. CONCLUSION Development of a ML model including miRNA and their genomic and pathway descriptors made it possible to achieve considerable accuracy for the prediction of AD.
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Affiliation(s)
- Amy Xu
- IUL Science Internship Program, San Diego, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.,BiAna, San Diego, CA, USA
| | - Igor F Tsigelny
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.,BiAna, San Diego, CA, USA.,Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
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27
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Takegawa-Araki T, Kumagai S, Yasukawa K, Kuroda M, Sasaki T, Obika S. Structure-Activity Relationships of Anti-microRNA Oligonucleotides Containing Cationic Guanidine-Modified Nucleic Acids. J Med Chem 2022; 65:2139-2148. [PMID: 35084859 DOI: 10.1021/acs.jmedchem.1c01680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anti-microRNA oligonucleotides (AMOs) are valuable tools for the treatment of diseases caused by the dysregulation of microRNA expression. However, the correlation between chemical modifications in AMO sequences and the microRNA-inhibitory activity has not been fully elucidated. In this study, we synthesized a series of AMOs containing cationic guanidine-bridged nucleic acids (GuNA) and evaluated their activities using a dual luciferase assay. We also optimized the site of GuNA substitution and found an effective design for the inhibition of microRNA-21, which was partially different from that of conventional nucleic acid derivatives. This study showed that GuNA-substituted AMOs are effective in inhibiting the function of microRNA.
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Affiliation(s)
- Tomo Takegawa-Araki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Shinji Kumagai
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Kai Yasukawa
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Masataka Kuroda
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Takashi Sasaki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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28
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Li Q, Xi M, Shen F, Fu F, Wang J, Chen Y, Zhou J. Identification of Candidate Gene Signatures and Regulatory Networks in Endometriosis and its Related Infertility by Integrated Analysis. Reprod Sci 2022; 29:411-426. [PMID: 34993929 DOI: 10.1007/s43032-021-00766-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 10/04/2021] [Indexed: 11/28/2022]
Abstract
Endometriosis is a common gynecological disease associated with infertility, and it represents an economic burden worldwide. However, the molecular mechanisms underlying endometriosis development have not yet been fully elucidated. Here, we aimed to identify reliable key genes and the related regulatory network that may be involved in endometriosis. Differentially expressed genes (DEGs) were identified through integrated analysis of four expression datasets of endometriosis from Gene Expression Omnibus. Gene functional analysis and protein-protein interaction network construction were performed to reveal the potential function of DEGs. Subsequently, candidate hub genes were defined and validated in GSE105764 dataset, and the associated regulatory networks were constructed. Additionally, GSE120103 dataset was applied to identify the differential expression between the infertile and fertile groups of patients with stage IV endometriosis. Finally, real-time quantitative polymerase chain reaction analysis was performed to identify the differential expression of hub genes in the collected clinical specimens. Robust rank aggregation integrated analysis determined 158 DEGs. Epithelial cell differentiation was the most significantly enriched biological process, and leukocyte transendothelial migration was the most significantly enriched pathway. Eight hub genes including CLDN3, CLDN5, CLDN7, CLDN11, HOXC8, HOXC6, HOXB6, and HOXB7 were identified, and most of these were validated as abnormally expressed genes in both the infertile group and patients with endometriosis. Transcriptional factors and microRNAs related to these genes were identified. Altogether, our integrated analysis identified critical gene signatures, involved pathways, and regulatory networks, which could provide clinically significant insights into the molecular mechanisms underlying endometriosis and its related infertility.
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Affiliation(s)
- Qiutong Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.,Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China
| | - Min Xi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.,Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China
| | - Fangrong Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.,Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China
| | - Fengqing Fu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China.,Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China
| | - Juan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China. .,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China. .,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China. .,Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China.
| | - Youguo Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China. .,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China. .,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China. .,Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China.
| | - Jinhua Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China. .,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China. .,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China. .,Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, People's Republic of China.
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29
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Lewis KA, Chang L, Cheung J, Aouizerat BE, Jelliffe-Pawlowski LL, McLemore MR, Piening B, Rand L, Ryckman KK, Flowers E. Systematic review of transcriptome and microRNAome associations with gestational diabetes mellitus. Front Endocrinol (Lausanne) 2022; 13:971354. [PMID: 36704034 PMCID: PMC9871895 DOI: 10.3389/fendo.2022.971354] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
PURPOSE Gestational diabetes (GDM) is associated with increased risk for preterm birth and related complications for both the pregnant person and newborn. Changes in gene expression have the potential to characterize complex interactions between genetic and behavioral/environmental risk factors for GDM. Our goal was to summarize the state of the science about changes in gene expression and GDM. DESIGN The systematic review was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. METHODS PubMed articles about humans, in English, from any date were included if they described mRNA transcriptome or microRNA findings from blood samples in adults with GDM compared with adults without GDM. RESULTS Sixteen articles were found representing 1355 adults (n=674 with GDM, n=681 controls) from 12 countries. Three studies reported transcriptome results and thirteen reported microRNA findings. Identified pathways described various aspects of diabetes pathogenesis, including glucose and insulin signaling, regulation, and transport; natural killer cell mediated cytotoxicity; and fatty acid biosynthesis and metabolism. Studies described 135 unique miRNAs that were associated with GDM, of which eight (miR-16-5p, miR-17-5p, miR-20a-5p, miR-29a-3p, miR-195-5p, miR-222-3p, miR-210-3p, and miR-342-3p) were described in 2 or more studies. Findings suggest that miRNA levels vary based on the time in pregnancy when GDM develops, the time point at which they were measured, sex assigned at birth of the offspring, and both the pre-pregnancy and gestational body mass index of the pregnant person. CONCLUSIONS The mRNA, miRNA, gene targets, and pathways identified in this review contribute to our understanding of GDM pathogenesis; however, further research is warranted to validate previous findings. In particular, longitudinal repeated-measures designs are needed that control for participant characteristics (e.g., weight), use standardized data collection methods and analysis tools, and are sufficiently powered to detect differences between subgroups. Findings may be used to improve early diagnosis, prevention, medication choice and/or clinical treatment of patients with GDM.
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Affiliation(s)
- Kimberly A. Lewis
- School of Nursing, Department of Physiological Nursing, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Kimberly A. Lewis,
| | - Lisa Chang
- School of Nursing, Department of Physiological Nursing, University of California, San Francisco, San Francisco, CA, United States
| | - Julinna Cheung
- College of Biological Sciences, University of California at Davis, Davis, CA, United States
| | | | - Laura L. Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, School of Medicine, University of California at San Francisco, San Francisco, CA, United States
| | - Monica R. McLemore
- School of Nursing, Department of Family Health Care Nursing, University of California, San Francisco, San Francisco, CA, United States
| | - Brian Piening
- Earle A. Chiles Research Institute, Providence St Joseph Health, Portland, OR, United States
| | - Larry Rand
- Obstetrics and Gynecology, Reproductive Sciences, School of Medicine, University of California at San Francisco, San Francisco, CA, United States
| | - Kelli K. Ryckman
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Elena Flowers
- School of Nursing, Department of Physiological Nursing, University of California, San Francisco, San Francisco, CA, United States
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30
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Zhang J, Xie S, Chen Y, Zhou X, Zheng Z, Yang L, Li Y. Comprehensive analysis of endoplasmic reticulum stress and immune infiltration in major depressive disorder. Front Psychiatry 2022; 13:1008124. [PMID: 36353576 PMCID: PMC9638134 DOI: 10.3389/fpsyt.2022.1008124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is a life-threatening, debilitating mental health condition. An important factor in the development of depression is endoplasmic reticulum stress (ERS). However, their roles in MDD have not yet been established. The goal of this study was to examine ERS and its underlying molecular mechanisms in MDD. METHODS We used data from two microarray datasets (GSE98793 and GSE39653) and the GeneCards database to examine the reticulum stress-related differentially expressed genes (ERSR-DEGs) associated with MDD. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and Gene Set Variation Analysis (GSVA) were used to further investigate the function and mechanism of ERS in MDD. Moreover, we constructed protein-protein interaction (PPI) networks to identify hub genes as well as the regulatory network of microRNAs (miRNAs), transcription factors (TFs), and potential drugs related to ERSR-DEGs. CIBERSORT was then used to evaluate the immune activity of MDD samples and conduct a correlation analysis between the hub genes and immune cells. RESULTS In total, 37 ERSR-DEGs and five hub genes were identified (NCF1, MAPK14, CASP1, CYBA, and TNF). Functional enrichment analysis revealed that ERSR-DEGs were predominantly enriched in inflammation-and immunity-related pathways, such as tumor necrosis factor signaling, NF-κB signaling, and Toll-like receptor signaling pathways. Additionally, 179 miRNAs, 25 TFs, and 15 potential drugs were tested for their interactions with the ERSR-DEGs. CIBERSORT found high proportions of Tregs, monocytes, and macrophages M0 in the MDD samples. Among these, hub genes showed a significant correlation with immune cell infiltration in patients with MDD. CONCLUSIONS NCF1, MAPK14, CASP1, CYBA, and TNF are potential ERS-related biomarkers for the diagnosis of MDD. Our research has revealed a significant correlation between immune cells and ERS-related genes with MDD. Not only did our study contribute to a better understanding of the regulatory mechanisms of ERS in underlying MDD pathology, but it also established a paradigm for future studies on ERS.
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Affiliation(s)
- Jing Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shujun Xie
- Department of Internal Medicine Teaching and Research, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yujia Chen
- Department of Internal Medicine Teaching and Research, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xin Zhou
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhuanfang Zheng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lingling Yang
- Department of Psychological Sleep, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yan Li
- Department of Psychological Sleep, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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Mao Y, Ni N, Huang L, Fan J, Wang H, He F, Liu Q, Shi D, Fu K, Pakvasa M, Wagstaff W, Tucker AB, Chen C, Reid RR, Haydon RC, Ho SH, Lee MJ, He TC, Yang J, Shen L, Cai L, Luu HH. Argonaute (AGO) proteins play an essential role in mediating BMP9-induced osteogenic signaling in mesenchymal stem cells (MSCs). Genes Dis 2021; 8:918-930. [PMID: 34522718 PMCID: PMC8427325 DOI: 10.1016/j.gendis.2021.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/04/2021] [Accepted: 04/16/2021] [Indexed: 01/03/2023] Open
Abstract
As multipotent progenitor cells, mesenchymal stem cells (MSCs) can renew themselves and give rise to multiple lineages including osteoblastic, chondrogenic and adipogenic lineages. It's previously shown that BMP9 is the most potent BMP and induces osteogenic and adipogenic differentiation of MSCs. However, the molecular mechanism through which BMP9 regulates MSC differentiation remains poorly understood. Emerging evidence indicates that noncoding RNAs, especially microRNAs, may play important roles in regulating MSC differentiation and bone formation. As highly conserved RNA binding proteins, Argonaute (AGO) proteins are essential components of the multi-protein RNA-induced silencing complexes (RISCs), which are critical for small RNA biogenesis. Here, we investigate possible roles of AGO proteins in BMP9-induced lineage-specific differentiation of MSCs. We first found that BMP9 up-regulated the expression of Ago1, Ago2 and Ago3 in MSCs. By engineering multiplex siRNA vectors that express multiple siRNAs targeting individual Ago genes or all four Ago genes, we found that silencing individual Ago expression led to a decrease in BMP9-induced early osteogenic marker alkaline phosphatase (ALP) activity in MSCs. Furthermore, we demonstrated that simultaneously silencing all four Ago genes significantly diminished BMP9-induced osteogenic and adipogenic differentiation of MSCs and matrix mineralization, and ectopic bone formation. Collectively, our findings strongly indicate that AGO proteins and associated small RNA biogenesis pathway play an essential role in mediating BMP9-induced osteogenic differentiation of MSCs.
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Affiliation(s)
- Yukun Mao
- Departments of Spine Surgery and Musculoskeletal Tumor, and Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Na Ni
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Linjuan Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Departments of Nephrology, and Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Jiaming Fan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Qing Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Spine Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan Province, 410011, PR China
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430022, PR China
| | - Kai Fu
- Departments of Spine Surgery and Musculoskeletal Tumor, and Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Mikhail Pakvasa
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Andrew Blake Tucker
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R. Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Sherwin H. Ho
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Michael J. Lee
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jian Yang
- Department of Biomedical Engineering, Materials Research Institute, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Lin Cai
- Departments of Spine Surgery and Musculoskeletal Tumor, and Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
- Corresponding author. Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital, Wuhan University, Wuhan, Hubei Province, 430071, China.
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Corresponding author. Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, 5841 South Maryland Avenue, MC3079, Chicago, IL 60637, USA. Fax: +(773) 834 4598.
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Luo C, Zhou X, Wang L, Zeng Q, Fan J, He S, Zhang H, Wei A. Screening and identification of NOTCH1, CDKN2A, and NOS3 as differentially expressed autophagy-related genes in erectile dysfunction. PeerJ 2021; 9:e11986. [PMID: 34447638 PMCID: PMC8366525 DOI: 10.7717/peerj.11986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
Background Loss of function of key autophagy genes are associated with a variety of diseases. However specific role of autophagy-related genes in erectile dysfunction ED remains unclear. This study explores the autophagy-related differentially expressed genes (ARGs) profiles and related molecular mechanisms in Corpus Cavernosum endothelial dysfunction, which is a leading cause of ED. Methods The Gene Expression Omnibus (GEO) database was used to identify the key genes and pathways. Differentially expressed genes (DEGs) were mined using the limma package in R language. Next, ARGs were obtained by matching DEGs and autophagy-related genes from GeneCard using Venn diagrams. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of ARGs were described using clusterProfiler and org.Hs.eg.db in R. Moreover, hub ARGs were screened out through protein-protein interaction (PPI), gene-microRNAs, and gene-transcription factors (TFs) networks then visualized using Cytoscape. Of note, the rat model of diabetic ED was established to validate some hub ARGs with qRT-PCR and Western blots. Results Twenty ARGs were identified from four ED samples and eight non-ED samples. GO analysis revealed that molecular functions (MF) of upregulated ARGs were mainly enriched in nuclear receptor activity. Also, MF of downregulated ARGs were mainly enriched in oxidoreductase activity, acting on NAD(P)H and heme proteins as acceptors. Moreover, six hub ARGs were identified by setting high degrees in the network. Additionally, hsa-mir-24-3p and hsa-mir-335-5p might play a central role in several ARGs regulation, and the transcription factors-hub genes network was centered with 13 ARGs. The experimental results further showed that the expression of Notch1, NOS3, and CDKN2A in the diabetic ED group was downregulated compared to the control. Conclusions Our study deepens the autophagy-related mechanistic understanding of endothelial dysfunction of ED. NOTCH1, CDKN2A, and NOS3 are involved in the regulation of endothelial dysfunction and may be potential therapeutic targets for ED by modulating autophagy.
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Affiliation(s)
- Chao Luo
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiongcai Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Department of Urology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Wang
- School of Basic Medical Science, Southern Medical University, Guangzhou, Guangdong, China
| | - Qinyu Zeng
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Junhong Fan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shuhua He
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Haibo Zhang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Anyang Wei
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Boštjančič E, Večerić-Haler Ž, Kojc N. The Role of Immune-Related miRNAs in the Pathology of Kidney Transplantation. Biomolecules 2021; 11:biom11081198. [PMID: 34439863 PMCID: PMC8393721 DOI: 10.3390/biom11081198] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are members of the non-coding regulatory RNA family that play pivotal roles in physiological and pathological conditions, including immune response. They are particularly interesting as promising therapeutic targets, prognostic and diagnostic markers due to their easy detection in body fluids and stability. There is accumulating evidence that different miRNAs provide disease-specific signatures in liquid samples of distinct kidney injuries. Using experimental models and human samples, there have been numerous suggestions that immune-related miRNAs are also important contributors to the development of different kidney diseases as well as important markers for monitoring response after kidney transplantation. However, there are limited data for understanding their function in the molecular pathways of allograft pathologies. In our review, we focused on microRNAs that are related to different aspects of immune response after kidney transplantation.
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Affiliation(s)
- Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Željka Večerić-Haler
- Department of Nephrology, University Medical Centre, 1000 Ljubljana, Slovenia;
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nika Kojc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia;
- Correspondence: ; Tel.: +386-154-371-25
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ElShelmani H, Wride MA, Saad T, Rani S, Kelly DJ, Keegan D. The Role of Deregulated MicroRNAs in Age-Related Macular Degeneration Pathology. Transl Vis Sci Technol 2021; 10:12. [PMID: 34003896 PMCID: PMC7881277 DOI: 10.1167/tvst.10.2.12] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Purpose We previously identified three microRNAs (miRNAs) with significantly increased expression in the serum of patients with age-related macular degeneration (AMD) compared with healthy controls. Our objective was to identify potential functional roles of these upregulated miRNAs (miR-19a, miR-126, and miR-410) in AMD, using computational tools for miRNAs prediction and identification, and to demonstrate the miRNAs target genes and signaling pathways. We also aim to demonstrate the pathologic role of isolated sera-derived exosomes from patients with AMD and controls using in vitro models. Methods miR-19a, miR-126, and miR-410 were investigated using bioinformatic approaches, including DIANA-mirPath and miR TarBase. Data on the resulting target genes and signaling pathways were incorporated with the differentially expressed miRNAs in AMD. Apoptosis markers, human apoptosis miRNAs polymerase chain reaction arrays and angiogenesis/vasculogenesis assays were performed by adding serum-isolated AMD patient or control patient derived exosomes into an in vitro human angiogenesis model and ARPE-19 cell lines. Results A number of pathways known to be involved in AMD development and progression were predicted, including the vascular endothelial growth factor signaling, apoptosis, and neurodegenerative pathways. The study also provides supporting evidence for the involvement of serum-isolated AMD-derived exosomes in the pathology of AMD, via apoptosis and/or angiogenesis. Conclusions miR-19a, miR-126, miR-410 and their target genes had a significant correlation with AMD pathogenesis. As such, they could be potential new targets as predictive biomarkers or therapies for patients with AMD. Translational Relevance The functional analysis and the pathologic role of altered miRNA expression in AMD may be applicable in developing new therapies for AMD through the disruption of individual or multiple pathophysiologic pathways.
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Affiliation(s)
- Hanan ElShelmani
- Ocular Development and Neurobiology Research Group, Zoology Department, School of Natural Sciences, University of Dublin, Trinity College Dublin, Dublin 2, Ireland.,Mater Retina Research Group, Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland
| | - Michael A Wride
- Ocular Development and Neurobiology Research Group, Zoology Department, School of Natural Sciences, University of Dublin, Trinity College Dublin, Dublin 2, Ireland
| | - Tahira Saad
- Mater Retina Research Group, Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland
| | - Sweta Rani
- Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - David J Kelly
- Zoology Department, School of Natural Sciences, University of Dublin, Trinity College Dublin, Ireland
| | - David Keegan
- Mater Retina Research Group, Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland
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Ormseth MJ, Solus JF, Sheng Q, Chen SC, Ye F, Wu Q, Oeser AM, Allen R, Raggi P, Vickers KC, Stein CM. Plasma miRNAs improve the prediction of coronary atherosclerosis in patients with rheumatoid arthritis. Clin Rheumatol 2021; 40:2211-2219. [PMID: 33389220 PMCID: PMC8162679 DOI: 10.1007/s10067-020-05573-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 12/22/2022]
Abstract
OBJECTIVE MicroRNAs (miRNAs) regulate gene expression and are disease biomarkers. Rheumatoid arthritis (RA) patients have accelerated atherosclerosis leading to excess cardiovascular morbidity and mortality, but traditional risk factors for cardiovascular risk stratification are inadequate. In the general population, miRNAs improve cardiovascular risk estimation beyond traditional risk factors. Our objective was to develop a miRNA panel that predicts coronary atherosclerosis in RA patients. METHODS Plasma small RNA next-generation sequencing (NGS) was performed on 161 RA patients whose Agatston scores for coronary artery calcium were previously measured. Random forest analysis of plasma NGS miRNA expression was used to determine which miRNAs best differentiated between those patients with and without coronary artery calcium. Top predictive miRNAs were assayed by quantitative PCR (qPCR). Elastic net regression was used to develop the most parsimonious models with qPCR-measured miRNA concentrations and clinical variables (age, sex, ACC/AHA 10-year risk score, DAS28 score, and diabetes) separately to predict the presence of coronary artery calcium and high coronary artery calcium. C-statistics were used to assess performance model performance. RESULTS The top miRNAs which differentiated those with and without coronary atherosclerosis based on random forest analysis included let-7c-5p, miR-30e-5p, miR-30c-5p, miR-4446-3p, miR-126-5p, miR-3168, miR-425-5p, miR-126-3p, miR-30a-5p, and miR-125a-5p. For coronary artery calcium prediction, addition of all miRNAs except miR-126-3p to clinical factors improved the c-statistic modestly from 0.86 to 0.87. For high coronary artery calcium prediction, addition of all miRNAs except miR-30c-5p to clinical factors improved the c-statistic from 0.75 to 0.80. CONCLUSION A plasma miRNA panel improved the prediction of high coronary artery calcium beyond traditional risk factors and RA disease activity. Further evaluation of the miRNA panel for prediction of coronary events in RA is necessary. Key Point • A plasma microRNA panel including let-7c-5p, miR-30a-5p, miR-30e-5p, miR-125a-5p, miR-126-3p, miR-126-5p, miR-425-5p, miR-3168, and miR-4446-3p improved the prediction of high coronary artery calcium beyond clinical factors in patients with rheumatoid arthritis.
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Affiliation(s)
- Michelle J Ormseth
- Tennessee Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, TN, USA.
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA.
| | - Joseph F Solus
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Quanhu Sheng
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Sheau-Chiann Chen
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Fei Ye
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Qiong Wu
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Annette M Oeser
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - Ryan Allen
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | | | - Kasey C Vickers
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
| | - C Michael Stein
- Vanderbilt University Medical Center, 1161 21st Avenue South, T-3113 MCN, Nashville, TN, 37232-2681, USA
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Catanzaro G, Filardi T, Sabato C, Vacca A, Migliaccio S, Morano S, Ferretti E. Tissue and circulating microRNAs as biomarkers of response to obesity treatment strategies. J Endocrinol Invest 2021; 44:1159-1174. [PMID: 33111214 PMCID: PMC8124039 DOI: 10.1007/s40618-020-01453-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Obesity, characterized by an increased amount of adipose tissue, is a metabolic chronic alteration which has reached pandemic proportion. Lifestyle changes are the first line therapy for obesity and a large variety of dietary approaches have demonstrated efficacy in promoting weight loss and improving obesity-related metabolic alterations. Besides diet and physical activity, bariatric surgery might be an effective therapeutic strategy for morbid obese patients. Response to weight-loss interventions is characterised by high inter-individual variability, which might involve epigenetic factors. microRNAs have critical roles in metabolic processes and their dysregulated expression has been reported in obesity. AIM The aim of this review is to provide a comprehensive overview of current studies evaluating changes in microRNA expression in obese patients undergoing lifestyle interventions or bariatric surgery. RESULTS A considerable number of studies have reported a differential expression of circulating microRNAs before and after various dietary and bariatric surgery approaches, identifying several candidate biomarkers of response to weight loss. Significant changes in microRNA expression have been observed at a tissue level as well, with entirely different patterns between visceral and subcutaneous adipose tissue. Interestingly, relevant differences in microRNA expression have emerged between responders and non-responders to dietary or surgical interventions. A wide variety of dysregulated microRNA target pathways have also been identified, helping to understand the pathophysiological mechanisms underlying obesity and obesity-related metabolic diseases. CONCLUSIONS Although further research is needed to draw firm conclusions, there is increasing evidence about microRNAs as potential biomarkers for weight loss and response to intervention strategies in obesity.
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Affiliation(s)
- G Catanzaro
- Department of Experimental Medicine, Policlinico Umberto I, "Sapienza" University of Rome, Viale del Policlinico 155, 00161, Rome, Italy
| | - T Filardi
- Department of Experimental Medicine, Policlinico Umberto I, "Sapienza" University of Rome, Viale del Policlinico 155, 00161, Rome, Italy
| | - C Sabato
- Department of Experimental Medicine, Policlinico Umberto I, "Sapienza" University of Rome, Viale del Policlinico 155, 00161, Rome, Italy
| | - A Vacca
- Department of Experimental Medicine, Policlinico Umberto I, "Sapienza" University of Rome, Viale del Policlinico 155, 00161, Rome, Italy
| | - S Migliaccio
- Department of Movement, Human and Health Sciences, "Foro Italico" University of Rome, Rome, Italy
| | - S Morano
- Department of Experimental Medicine, Policlinico Umberto I, "Sapienza" University of Rome, Viale del Policlinico 155, 00161, Rome, Italy
| | - E Ferretti
- Department of Experimental Medicine, Policlinico Umberto I, "Sapienza" University of Rome, Viale del Policlinico 155, 00161, Rome, Italy.
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Zhao T, Wang J, He A, Wang S, Chen Y, Lu J, Lv J, Li S, Wang J, Qian M, Li H, Shen X. Mebhydrolin ameliorates glucose homeostasis in type 2 diabetic mice by functioning as a selective FXR antagonist. Metabolism 2021; 119:154771. [PMID: 33831422 DOI: 10.1016/j.metabol.2021.154771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/01/2021] [Accepted: 03/28/2021] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Type 2 diabetes mellitus (T2DM) is a chronic disease with hallmarks of hyperglycemia and hyperlipidemia. Long-term hyperglycemia damages the functions of multiple tissues and organs leading to a series of complications and disability or even death. Nuclear receptor farnesoid X receptor (FXR) antagonism has been recently discovered to exhibit beneficial effect on glucose metabolism in T2DM mice, although the underlying mechanisms remain unclear. Here, we performed the study on the discovery of new FXR antagonist and investigated the mechanism underlying the amelioration of FXR antagonism on glucose homeostasis in T2DM mice by using the determined FXR antagonist as a probe. METHODS FXR antagonist Mebhydrolin was discovered by screening against the lab in-house FDA approved drug library through surface plasmon resonance (SPR), microscale thermophoresis (MST), AlphaScreen, mammalian one-hybrid and transactivation assays. Activity of Mebhydrolin in improving glucose homeostasis was evaluated in db/db and HFD/STZ-induced T2DM mice, and the mechanisms governing the regulation of Mebhydrolin were investigated by assays of immunostaining, Western blot, ELISA, RT-PCR against liver tissues of both T2DM mice and the T2DM mice with liver-specific FXR knockdown injected via adeno-associated-virus AAV-FXR-RNAi and mouse primary hepatocytes. Finally, molecular docking and molecular dynamics (MD) technology-based study was performed to investigate the structural basis for the antagonistic regulation of Mebhydrolin against FXR at an atomic level. FINDINGS Mebhydrolin ameliorated blood glucose homeostasis in T2DM mice by both suppressing hepatic gluconeogenesis via FXR/miR-22-3p/PI3K/AKT/FoxO1 pathway and promoting glycogen synthesis through FXR/miR-22-3p/PI3K/AKT/GSK3β pathway. Structurally, residues L291, M332 and Y373 of FXR were required for Mebhydrolin binding to FXR-LBD, and Mebhydrolin induced H2 and H6 shifting of FXR potently affecting the regulation of the downstream target genes. CONCLUSIONS Our work has revealed a novel mode for the regulation of FXR against glucose metabolism in T2DM mice and highlighted the potential of Mebhydrolin in the treatment of T2DM.
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MESH Headings
- Animals
- Blood Glucose/drug effects
- Blood Glucose/metabolism
- Carbolines/chemistry
- Carbolines/pharmacokinetics
- Carbolines/therapeutic use
- Cells, Cultured
- Diabetes Mellitus, Experimental/chemically induced
- Diabetes Mellitus, Experimental/drug therapy
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Type 2/chemically induced
- Diabetes Mellitus, Type 2/drug therapy
- Diabetes Mellitus, Type 2/metabolism
- Gluconeogenesis/drug effects
- Gluconeogenesis/genetics
- Glucose/metabolism
- HEK293 Cells
- Homeostasis/drug effects
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Molecular Docking Simulation
- Protein Interaction Domains and Motifs
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Streptozocin
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Affiliation(s)
- Tong Zhao
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jie Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Anxu He
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shan Wang
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yidi Chen
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jian Lu
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jianlu Lv
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiaying Wang
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Minyi Qian
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Xu Shen
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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38
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Fernández-Moreno R, Torre-Cisneros J, Cantisán S. Human cytomegalovirus (HCMV)-encoded microRNAs: potential biomarkers and clinical applications. RNA Biol 2021; 18:2194-2202. [PMID: 34039247 DOI: 10.1080/15476286.2021.1930757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
HCMV-encoded microRNAs (hcmv-miRNAs) are non-coding and non-immunogenic molecules that target numerous cellular genes and allow the virus to modulate the host's signalling pathways, thus favouring viral survival and replication. Given their capacity to silence the human genes involved in various physiological processes, these hcmv-miRNAs have now emerged as a potential clinical biomarker in many human diseases. In this review, we summarize the evidence published on the diagnostic and prognostic value of hcmv-miRNAs in several human diseases and their clinical implications. Specifically, we discuss the role of hcmv-miRNAs in the development of cardiovascular diseases and cancer by silencing tumour suppressors. We also examine the current knowledge on the utility of some hcmv-miRNAs in predicting HCMV viraemia recurrence in transplant patients, as well as the interference of hcmv-miRNAs in the development of an appropriate immune response against other viral infections, which might have therapeutic implications.
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Affiliation(s)
- Raquel Fernández-Moreno
- Instituto Maimónides De Investigación Biomédica De Córdoba (Imibic)/reina Sofia University Hospital/University of Cordoba, Cordoba, Spain
| | - Julián Torre-Cisneros
- Instituto Maimónides De Investigación Biomédica De Córdoba (Imibic)/reina Sofia University Hospital/University of Cordoba, Cordoba, Spain.,Infectious Diseases Unit, Reina Sofía Hospital, Cordoba, Spain
| | - Sara Cantisán
- Instituto Maimónides De Investigación Biomédica De Córdoba (Imibic)/reina Sofia University Hospital/University of Cordoba, Cordoba, Spain
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Wang H, Wu C, Kong D. miR-140-5p Overexpression Protects Against Lipopolysaccharide-Induced Necrotizing Pneumonia via Targeting Toll-Like Receptor 4. Cell Mol Bioeng 2021; 14:339-348. [PMID: 34295443 DOI: 10.1007/s12195-021-00673-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/27/2021] [Indexed: 01/04/2023] Open
Abstract
Objective This study is to identify the effects of miRNA-140-5p on necrotizing pneumonia (NP) and its underlying mechanism. Methods The mRNA levels of miRNA-140-5p and TLR4 and secretion of IL-1β, IL-6, and TNF-α in peripheral blood from children with NP and healthy volunteers were determined using qRT-PCR and specific ELISAs. The interactions between miRNA-140-5p and TLR4 were investigated using a dual-luciferase reporter system. Cell viabilities were determined using a CCK-8 assay. qRT-PCR, western blotting, and specific ELISAs were applied to determine the expressions of genes in the cells. Peripheral blood from children with NP had significantly elevated levels of TLR4 but significantly lower levels of miR-140-5p compared to the control. Results Spearman's rank correlation analysis showed a negative correlation between TLR4 and miR-140-5p. miR-140-5p regulated the expressions of TLR4 in A549 cells. Additionally, LPS induced a significant enhancement in the levels of TLR4 but significant reduction in the levels of miR-140-5p. The overexpression of miR-140-5p suppressed cell apoptosis and induced the release of inflammatory cytokines in the LPS-induced A549 cells. Conclusion The underlying mechanisms of miR-140-5p on the regulation of TLR4 are in part by the regulation of p65. The miR-140-5p inhibits necrotizing pneumonia by regulating TLR-4 via TNF-p65 signaling pathway. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-021-00673-0.
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Affiliation(s)
- Haichao Wang
- School of Biology and Food Engineering, Suzhou University, No. 49 Bianhe Middle Road, Suzhou, 234000 Anhui China
| | - Changhao Wu
- School of Biology and Food Engineering, Suzhou University, No. 49 Bianhe Middle Road, Suzhou, 234000 Anhui China
| | - Dehui Kong
- School of Biology and Food Engineering, Suzhou University, No. 49 Bianhe Middle Road, Suzhou, 234000 Anhui China
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40
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Liu Y, Liu Z, Liu R, Wang K, Shi H, Huang J. A MnO 2 nanosheet-mediated photo-controlled DNAzyme for intracellular miRNA cleavage to suppress cell growth. Analyst 2021; 146:3391-3398. [PMID: 33876148 DOI: 10.1039/d1an00406a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Certain miRNAs, called oncomiRs, play a causal role in the onset and maintenance of cancer when overexpressed, thus, representing a potential new class of targets for therapeutic intervention. RNA-cleaving DNAzymes, mainly aimed at mRNA, have shown potential as therapeutic agents for various diseases. However, it's rarely reported that a DNAzyme was used for intracellular miRNA cleavage to suppress cell growth. Herein, we have developed a MnO2 nanosheet-mediated photo-controlled DNAzyme (NPD) for intracellular miRNA cleavage to suppress cell growth. MnO2 nanosheets adsorb photocaged DNAzymes, protect them from enzymatic digestion, and efficiently deliver them into cells. In the presence of intracellular glutathione (GSH), MnO2 nanosheets are reduced to Mn2+ ions, which serve as cofactors of the 8-17 DNAzyme for miRNA cleavage. Once the DNAzyme is activated by light, it can cyclically cleave endogenous miR-21 inside cells, which would suppress cancer cell migration and invasion, and finally induce cancer cell apoptosis.
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Affiliation(s)
- Yehua Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
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41
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Dong X, Li Y, Cao R, Xu H. MicroRNA-363-3p Inhibits the Expression of Renal Fibrosis Markers in TGF-β1-Treated HK-2 Cells by Targeting TGF-β2. Biochem Genet 2021; 59:1033-1048. [PMID: 33630202 DOI: 10.1007/s10528-021-10044-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/29/2021] [Indexed: 11/30/2022]
Abstract
This study aimed to explore the role of miR-363-3p in renal fibrosis (RF) in vitro. HK-2 cells were treated with transforming growth factor (TGF)-β1 for 72 h to establish an in vitro model of RF. Subsequently, western blot analysis and reverse transcription-quantitative PCR were used to detect the protein and mRNA expression levels of RF markers in TGF-β1-treated HK-2 cells, respectively. The results showed that the protein and mRNA expression levels of TGF-β2, α-smooth muscle actin (SMA), fibronectin, vimentin, collagen II and N-cadherin were increased, while the protein and mRNA expression levels of E-cadherin were decreased in TGF-β1-treated HK-2 cells. The level of miR-363-3p was significantly decreased in TGF-β1-treated HK-2 cells. TargetScan indicated that TGF-β2 was a direct target gene for miR-363-3p, which was further verified using dual luciferase reporter gene assays. Further analyses revealed that the increased protein and mRNA expression levels of TGF-β2, α-SMA, fibronectin, vimentin, collagen II, N-cadherin, increased phosphorylated-Smad3 protein level, and decreased E-cadherin protein and mRNA expression in TGF-β1-treated HK-2 cells were significantly reversed by miR-363-3p mimics. However, all the effects were suppressed by a TGF-β2-plasmid. The results suggested that miR-363-3p plays a protective role in RF by regulating the TGF-β2/Smad3 signaling pathway.
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Affiliation(s)
- Xiangnan Dong
- Department of Urinary Medicine, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Yang Li
- Department of Nephrology, Qingdao Municipal Hospital, 1 Jiaozhou Road, Shibei, Qingdao, 266000, Shandong, China
| | - Rui Cao
- Department of Blood Purification Center, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Honglan Xu
- Department of Nephrology, Qingdao Municipal Hospital, 1 Jiaozhou Road, Shibei, Qingdao, 266000, Shandong, China.
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Amiri A, Mahjoubin-Tehran M, Asemi Z, Shafiee A, Hajighadimi S, Moradizarmehri S, Mirzaei HR, Mirzaei H. Role of Resveratrol in Modulating microRNAs in Human Diseases: From Cancer to Inflammatory Disorder. Curr Med Chem 2021; 28:360-376. [PMID: 31830882 DOI: 10.2174/0929867326666191212102407] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 12/09/2022]
Abstract
Cancer and inflammatory disorders are two important public health issues worldwide with significant socio.economic impacts. Despite several efforts, the current therapeutic platforms are associated with severe limitations. Therefore, developing new therapeutic strategies for the treatment of these diseases is a top priority. Besides current therapies, the utilization of natural compounds has emerged as a new horizon for the treatment of cancer and inflammatory disorders as well. Such natural compounds could be used either alone or in combination with the standard cancer therapeutic modalities such as chemotherapy, radiotherapy, and immunotherapy. Resveratrol is a polyphenolic compound that is found in grapes as well as other foods. It has been found that this medicinal agent displays a wide pharmacological spectrum, including anti-cancer, anti-inflammatory, anti-microbial, and antioxidant activities. Recently, clinical and pre-clinical studies have highlighted the anti-cancer and anti-inflammatory effects of resveratrol. Increasing evidence revealed that resveratrol exerts its therapeutic effects by targeting various cellular and molecular mechanisms. Among cellular and molecular targets that are modulated by resveratrol, microRNAs (miRNAs) have appeared as key targets. MiRNAs are short non-coding RNAs that act as epigenetic regulators. These molecules are involved in many processes that are involved in the initiation and progression of cancer and inflammatory disorders. Herein, we summarized various miRNAs that are directly/indirectly influenced by resveratrol in cancer and inflammatory disorders.
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Affiliation(s)
- Atefeh Amiri
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Mahjoubin-Tehran
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Alimohammad Shafiee
- Division of General Internal Medicine, Toronto General Hospital, Toronto, Canada
| | - Sarah Hajighadimi
- Division of General Internal Medicine, Toronto General Hospital, Toronto, Canada
| | - Sanaz Moradizarmehri
- Division of General Internal Medicine, Toronto General Hospital, Toronto, Canada
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Canada
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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Cai G, Cai G, Zhou H, Zhuang Z, Liu K, Pei S, Wang Y, Wang H, Wang X, Xu S, Cui C, Sun M, Guo S, Jia K, Wang X, Zhang D. Mesenchymal stem cell-derived exosome miR-542-3p suppresses inflammation and prevents cerebral infarction. Stem Cell Res Ther 2021; 12:2. [PMID: 33407827 PMCID: PMC7786953 DOI: 10.1186/s13287-020-02030-w] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 11/16/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Cerebral infarction ranks as the second leading cause of disability and death globally, and inflammatory response of glial cells is the main cause of brain damage during cerebral infarction. METHODS Studies have shown that mesenchymal stem cells (MSCs) can secrete exosomes and contribute to cerebral disease. Here, we would explore the function of MSC-derived exosome in cerebral infarction. RESULTS Microarray indicated a decrease of miR-542-3p and an increase of Toll-Like Receptor 4 (TLR4) in middle cerebral artery occlusion (MCAO) mice comparing with sham mice. And luciferase and RIP analysis indicated a binding of miR-542-3p and TLR4. Then, we injected AAV9-miR-542-3p into paracele of sham or MCAO mice. Functional analysis showed that AAV9-miR-542-3p inhibited infarction area and the number of degenerating neurons and suppressed inflammatory factors' expression and inflammatory cell infiltration. As well, transfection of miR-542-3p mimics into HA1800 cells underwent oxygen and glucose deprivation (OGD). Similarly, overexpression of miR-542-3p alleviated OGD induced cell apoptosis, ROS, and activation of inflammation response. Moreover, miR-542-3p could be packaged into MSCs and secreted into HA1800 cells. The extractive exosome-miR-21-3p treatment relieved MCAO- or OGD-induced cerebral injury and inflammation through targeting TLR4. CONCLUSION These results confirmed that MSC-derived exosome miR-542-3p prevented ischemia-induced glial cell inflammatory response via inhibiting TLR4. These results suggest possible therapeutic strategies for using exosome delivery of miR-542-3p to cure cerebral ischemic injury.
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Affiliation(s)
- Guofeng Cai
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Guoliang Cai
- Postdoctoral Research Workstation of Harbin Sport University, Harbin, China ,Department of Sport Science and Health, Harbin Sport University, Harbin, 150008 China
| | - Haichun Zhou
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Zhe Zhuang
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Kai Liu
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Siying Pei
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Yanan Wang
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Hong Wang
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Xin Wang
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Shengnan Xu
- grid.412068.90000 0004 1759 8782Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Cheng Cui
- grid.412068.90000 0004 1759 8782Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Manchao Sun
- grid.412068.90000 0004 1759 8782Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Sihui Guo
- grid.412068.90000 0004 1759 8782Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Kunping Jia
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Xiuzhen Wang
- grid.412068.90000 0004 1759 8782Hanan Branch of Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, 150001 China
| | - Dianquan Zhang
- Department of Rehabilitation Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong Province China
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Pawluczyk IZA, Didangelos A, Barbour SJ, Er L, Becker JU, Martin R, Taylor S, Bhachu JS, Lyons EG, Jenkins RH, Fraser D, Molyneux K, Perales-Patón J, Saez-Rodriguez J, Barratt J. Differential expression of microRNA miR-150-5p in IgA nephropathy as a potential mediator and marker of disease progression. Kidney Int 2021; 99:1127-1139. [PMID: 33417998 DOI: 10.1016/j.kint.2020.12.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 01/05/2023]
Abstract
Understanding why certain patients with IgA nephropathy progress to kidney failure while others maintain normal kidney function remains a major unanswered question. To help answer this, we performed miRNome profiling by next generation sequencing of kidney biopsies in order to identify microRNAs specifically associated with the risk of IgA nephropathy progression. Following sequencing and validation in independent cohorts, four microRNAs (-150-5p, -155-5p, -146b-5p, -135a-5p) were found to be differentially expressed in IgA nephropathy progressors compared to non-progressors, and patients with thin membrane nephropathy, lupus nephritis and membranous nephropathy, and correlated with estimated glomerular filtration rate, proteinuria, and the Oxford MEST-C scores (five histological features that are independent predictors of clinical outcome). Each individual microRNA increased the discrimination score of the International IgAN Prediction Tool, although due to the small number of samples the results did not reach statistical significance. miR-150-5p exhibited the largest amplitude of expression between cohorts and displayed the best discrimination between IgA nephropathy progressors and non-progressors by receiver operating curve analysis (AUC: 0.8). However, expression was similarly upregulated in kidneys with established fibrosis and low estimated glomerular filtration rates at the time of biopsy. Consistent with a more generic role in kidney fibrosis, in situ hybridization revealed that miR-150-5p was found in lymphoid infiltrates, and areas of proliferation and fibrosis consistent with the known drivers of progression. Thus, miR-150-5p may be a potential functional mediator of kidney fibrosis that may add value in predicting risk of progression in IgA nephropathy and other kidney diseases.
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Affiliation(s)
- Izabella Z A Pawluczyk
- The Mayer IgA Nephropathy Laboratories, Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.
| | - Athanasios Didangelos
- The Mayer IgA Nephropathy Laboratories, Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Sean J Barbour
- Division of Nephrology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lee Er
- Division of Nephrology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jan U Becker
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Roberto Martin
- Bioinformatics and Biostatistics Unit, Madrid Institute for Advanced Studies (IMDEA) Food, CEI UAM+CSIS, Madrid, Spain
| | - Scott Taylor
- The Mayer IgA Nephropathy Laboratories, Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Jasraj S Bhachu
- The Mayer IgA Nephropathy Laboratories, Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Edward G Lyons
- The Mayer IgA Nephropathy Laboratories, Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Robert H Jenkins
- Wales Kidney Research Institute, Division of Infection and Immunity, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Donald Fraser
- Wales Kidney Research Institute, Division of Infection and Immunity, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Karen Molyneux
- The Mayer IgA Nephropathy Laboratories, Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Javier Perales-Patón
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Jonathan Barratt
- The Mayer IgA Nephropathy Laboratories, Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
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45
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Infante A, Gener B, Vázquez M, Olivares N, Arrieta A, Grau G, Llano I, Madero L, Bueno AM, Sagastizabal B, Gerovska D, Araúzo‐Bravo MJ, Astigarraga I, Rodríguez CI. Reiterative infusions of MSCs improve pediatric osteogenesis imperfecta eliciting a pro-osteogenic paracrine response: TERCELOI clinical trial. Clin Transl Med 2021; 11:e265. [PMID: 33463067 PMCID: PMC7805402 DOI: 10.1002/ctm2.265] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Osteogenesis imperfecta (OI) is a rare genetic disease characterized by bone fragility, with a wide range in the severity of clinical manifestations. The majority of cases are due to mutations in the COL1A1 or COL1A2 genes, which encode type I collagen. Mesenchymal stem cells (MSCs), as the progenitors of the osteoblasts, the main type I collagen secreting cell type in the bone, have been proposed and tested as an innovative therapy for OI with promising but transient outcomes. METHODS To overcome the short-term effect of MSCs therapy, we performed a phase I clinical trial based on reiterative infusions of histocompatible MSCs, administered in a 2.5-year period, in two pediatric patients affected by severe and moderate OI. The aim of this study was to assess the safety and effectiveness of this cell therapy in nonimmunosuppressed OI patients. The host response to MSCs was studied by analyzing the sera from OI patients, collected before, during, and after the cell therapy. RESULTS We first demonstrated that the sequential administration of MSCs was safe and improved the bone parameters and quality of life of OI patients along the cell treatment plus 2-year follow-up period. Moreover, the study of the mechanism of action indicated that MSCs therapy elicited a pro-osteogenic paracrine response in patients, especially noticeable in the patient affected by severe OI. CONCLUSIONS Our results demonstrate the feasibility and potential of reiterative MSCs infusion for two pediatric OI and highlight the paracrine response shown by patients as a consequence of MSCs treatment.
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Affiliation(s)
- Arantza Infante
- Stem Cells and Cell Therapy LaboratoryBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
| | - Blanca Gener
- Stem Cells and Cell Therapy LaboratoryBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
- Service of GeneticsCruces University HospitalBarakaldoSpain
| | - Miguel Vázquez
- Department of PediatricsBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
| | - Nerea Olivares
- Department of Biochemistry, Immunology UnitCruces University HospitalBarakaldoSpain
| | - Arantza Arrieta
- Department of Biochemistry, Immunology UnitCruces University HospitalBarakaldoSpain
| | - Gema Grau
- Department of PediatricsBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
| | - Isabel Llano
- Service of GeneticsCruces University HospitalBarakaldoSpain
| | - Luis Madero
- Department of Pediatric Hematology, Oncology and Stem CellsNiño Jesús University Children´s HospitalMadridSpain
| | - Ana Maria Bueno
- Department of Orthopedic SurgeryGetafe University HospitalMadridSpain
| | | | - Daniela Gerovska
- Computational Biology and Systems Biomedicine Research GroupBiodonostia Health Research InstituteDonostiaSpain
| | - Marcos J Araúzo‐Bravo
- Computational Biology and Systems Biomedicine Research GroupBiodonostia Health Research InstituteDonostiaSpain
| | - Itziar Astigarraga
- Department of PediatricsBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
- Department of PediatricsBasque Country University UPV/EHULeioaSpain
| | - Clara I. Rodríguez
- Stem Cells and Cell Therapy LaboratoryBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
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Abstract
PURPOSE OF REVIEW MiRNAs are critical regulators for gene expression. Numerous studies have revealed how miRNAs contribute to the pathogenesis of hematologic malignancies. RECENT FINDINGS The identification of novel miRNA regulatory factors and pathways crucial for miRNA dysregulation has been linked to hematologic malignancies. miRNA expression profiling has shown their potential to predict outcomes and treatment responses. Recently, targeting miRNA biogenesis or pathways has become a promising therapeutic strategy with recent miRNA-therapeutics being developed. SUMMARY We provide a comprehensive overview of the role of miRNAs for diagnosis, prognosis, and therapeutic potential in hematologic malignancies.
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Domingo S, Solé C, Moliné T, Ferrer B, Cortés-Hernández J. MicroRNAs in Several Cutaneous Autoimmune Diseases: Psoriasis, Cutaneous Lupus Erythematosus and Atopic Dermatitis. Cells 2020; 9:cells9122656. [PMID: 33321931 PMCID: PMC7763020 DOI: 10.3390/cells9122656] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNA molecules that regulate the gene expression at a post-transcriptional level and participate in maintaining the correct cell homeostasis and functioning. Different specific profiles have been identified in lesional skin from autoimmune cutaneous diseases, and their deregulation cause aberrant control of biological pathways, contributing to pathogenic conditions. Detailed knowledge of microRNA-affected pathways is of crucial importance for understating their role in skin autoimmune diseases. They may be promising therapeutic targets with novel clinical implications. They are not only present in skin tissue, but they have also been found in other biological fluids, such as serum, plasma and urine from patients, and therefore, they are potential biomarkers for the diagnosis, prognosis and response to treatment. In this review, we discuss the current understanding of the role of described miRNAs in several cutaneous autoimmune diseases: psoriasis (Ps, 33 miRNAs), cutaneous lupus erythematosus (CLE, 2 miRNAs) and atopic dermatitis (AD, 8 miRNAs). We highlight their role as crucial elements implicated in disease pathogenesis and their applicability as biomarkers and as a novel therapeutic approach in the management of skin inflammatory diseases.
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Affiliation(s)
- Sandra Domingo
- Rheumatology Research Group, Lupus Unit, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
| | - Cristina Solé
- Rheumatology Research Group, Lupus Unit, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
- Correspondence: ; Tel.: +34-9-3489-4045
| | - Teresa Moliné
- Department of Pathology, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (T.M.); (B.F.)
| | - Berta Ferrer
- Department of Pathology, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (T.M.); (B.F.)
| | - Josefina Cortés-Hernández
- Rheumatology Research Group, Lupus Unit, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
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48
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Liu Y, Jin J, Chen Y, Chen C, Chen Z, Xu L. Integrative analyses of biomarkers and pathways for adipose tissue after bariatric surgery. Adipocyte 2020; 9:384-400. [PMID: 32684073 PMCID: PMC7469525 DOI: 10.1080/21623945.2020.1795434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We explored potential biomarkers and molecular mechanisms regarding multiple benefits after bariatric surgery. Differentially expressed genes (DEGs) for subcutaneous adipose tissue (AT) after bariatric surgery were identified by analyzing two expression profiles from the GEO. Subsequently, enrichment analysis, GSEA, PPI network, and gene-microRNAs and gene-TFs networks were interrogated to identify hub genes and associated pathways. Co-expressed DEGs included one that was up-regulated and 22 that were down-regulated genes. The enrichment analyses indicated that down-regulated DEGs were significantly involved in inflammatory responses. GSEA provided comprehensive evidence that most genes enriched in pro-inflammation pathways, while gene-sets after surgery enriched in metabolism. We identified nine hub genes in the PPI network, most of which were validated as highly expressed and hypomethylated in obesity by Attie Lab Diabetes and DiseaseMeth databases, respectively. DGIdb was also applied to predict potential therapeutic agents that might reverse abnormally high hub gene expression. Bariatric surgery induces a significant shift from an obese pro-inflammatory state to an anti-inflammatory state, with improvement in adipocyte metabolic function – representing key mechanisms whereby AT function improves after bariatric surgery. Our study deepens a mechanistic understanding of the benefits of bariatric surgery and provides potential biomarkers or treatment targets for further research.
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Affiliation(s)
- Yingshan Liu
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jing Jin
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yanshan Chen
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Chuna Chen
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zhenguo Chen
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Lingling Xu
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
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Pourteymourfard Tabrizi Z, Jami MS. Selection of suitable bioinformatic tools in micro-RNA research. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhou F, Liu Z, Cai H, Miao Z, Wei F, Song C. Role of microRNA-15a-5p/TNFAIP3-interacting protein 2 axis in acute lung injury induced by traumatic hemorrhagic shock. Exp Ther Med 2020; 20:2. [PMID: 32934667 PMCID: PMC7471858 DOI: 10.3892/etm.2020.9130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to investigate the role of microRNA (miR)-15a-5p in the pathogenesis of acute lung injury induced by traumatic hemorrhagic shock (THS), and to explore the underlying molecular mechanism. The expression level of miR-15a-5p was detected using reverse transcription-quantitative (RT-qPCR) and the association between miR-15a-5p and TNFAIP3-interacting protein 2 (TNIP2) was revealed using TargetScan and dual luciferase reporter assays. To investigate the effect of miR-15a-5p on THS-induced acute lung injury, a THS rat model was established. Lung capillary permeability and lung edema were then determined. Moreover, proinflammatory factors in the bronchoalveolar lavage fluid (BALF) and serum of the THS rat model were detected using ELISA. In addition, protein levels in the current study were measured via western blotting. It was revealed that miR-15a-5p was significantly upregulated in both patients with THS and samples from the THS rat model. TNIP2 represents a direct target of miR-15a-5p, and it was downregulated in both patients with THS and the THS rat model. Further analyses indicated that downregulation of miR-15a-5p significantly relieved acute lung injury induced by THS, evidenced by a decreased ratio of Evan's blue dye (EBD) in the BALF to EBD in plasma of THS rats, decreased lung permeability index and reduced lung wet/dry ratio. Inhibition of miR-15a-5p also decreased THS-induced upregulation of pro-inflammatory factors. Furthermore, the data revealed that THS-induced NF-κB activation in the lung tissues of rats was inhibited by miR-15a-5p knockdown. Moreover, it was demonstrated that all the effects of miR-15a-5p on THS rats were ablated following TNIP2 silencing. Taken together, the data of the current study indicate that miR-15a-5p downregulation serves a protective role in THS-induced acute lung injury via directly targeting TNIP2.
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Affiliation(s)
- Feng Zhou
- Department of Emergency, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Zhizhen Liu
- Department of Emergency, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Huazhong Cai
- Department of Emergency, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Zhenjun Miao
- Department of Emergency, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Faxing Wei
- Department of Emergency, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Chao Song
- Department of Emergency, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
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