1
|
Gambari R, Waziri AD, Goonasekera H, Peprah E. Pharmacogenomics of Drugs Used in β-Thalassemia and Sickle-Cell Disease: From Basic Research to Clinical Applications. Int J Mol Sci 2024; 25:4263. [PMID: 38673849 PMCID: PMC11050010 DOI: 10.3390/ijms25084263] [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: 03/04/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
In this short review we have presented and discussed studies on pharmacogenomics (also termed pharmacogenetics) of the drugs employed in the treatment of β-thalassemia or Sickle-cell disease (SCD). This field of investigation is relevant, since it is expected to help clinicians select the appropriate drug and the correct dosage for each patient. We first discussed the search for DNA polymorphisms associated with a high expression of γ-globin genes and identified this using GWAS studies and CRISPR-based gene editing approaches. We then presented validated DNA polymorphisms associated with a high HbF production (including, but not limited to the HBG2 XmnI polymorphism and those related to the BCL11A, MYB, KLF-1, and LYAR genes). The expression of microRNAs involved in the regulation of γ-globin genes was also presented in the context of pharmacomiRNomics. Then, the pharmacogenomics of validated fetal hemoglobin inducers (hydroxyurea, butyrate and butyrate analogues, thalidomide, and sirolimus), of iron chelators, and of analgesics in the pain management of SCD patients were considered. Finally, we discuss current clinical trials, as well as international research networks focusing on clinical issues related to pharmacogenomics in hematological diseases.
Collapse
Affiliation(s)
- Roberto Gambari
- Center “Chiara Gemmo and Elio Zago” for the Research on Thalassemia, Department of Life Sciences and Biotechnology, Ferrara University, 40124 Ferrara, Italy
| | - Aliyu Dahiru Waziri
- Department of Hematology and Blood Transfusion, Ahmadu Bello University Teaching Hospital Zaria, Kaduna 810001, Nigeria;
| | - Hemali Goonasekera
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo P.O. Box 271, Sri Lanka;
| | - Emmanuel Peprah
- Implementing Sustainable Evidence-Based Interventions through Engagement (ISEE) Lab, Department of Global and Environmental Health, School of Global Public Health, New York University, New York, NY 10003, USA;
| |
Collapse
|
2
|
Papi C, Gasparello J, Zurlo M, Cosenza LC, Gambari R, Finotti A. The Cystic Fibrosis Transmembrane Conductance Regulator Gene (CFTR) Is under Post-Transcriptional Control of microRNAs: Analysis of the Effects of agomiRNAs Mimicking miR-145-5p, miR-101-3p, and miR-335-5p. Noncoding RNA 2023; 9:ncrna9020029. [PMID: 37104011 PMCID: PMC10146138 DOI: 10.3390/ncrna9020029] [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: 03/06/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023] Open
Abstract
(1) Background: MicroRNAs are involved in the expression of the gene encoding the chloride channel CFTR (Cystic Fibrosis Transmembrane Conductance Regulator); the objective of this short report is to study the effects of the treatment of bronchial epithelial Calu-3 cells with molecules mimicking the activity of pre-miR-145-5p, pre-miR-335-5p, and pre-miR-101-3p, and to discuss possible translational applications of these molecules in pre-clinical studies focusing on the development of protocols of possible interest in therapy; (2) Methods: CFTR mRNA was quantified by Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR). The production of the CFTR protein was assessed by Western blotting; (3) Results: The treatment of Calu-3 cells with agomiR-145-5p caused the highest inhibition of CFTR mRNA accumulation and CFTR production; (4) Conclusions: The treatment of target cells with the agomiR pre-miR-145-5p should be considered when CFTR gene expression should be inhibited in pathological conditions, such as polycystic kidney disease (PKD), some types of cancer, cholera, and SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Chiara Papi
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, 44121 Ferrara, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, 44121 Ferrara, Italy
| | - Matteo Zurlo
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, 44121 Ferrara, Italy
| | - Lucia Carmela Cosenza
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, 44121 Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, 44121 Ferrara, Italy
- Research Center on Innovative Therapies for Cystic Fibrosis, University of Ferrara, 44121 Ferrara, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, University of Ferrara, 44121 Ferrara, Italy
- Research Center on Innovative Therapies for Cystic Fibrosis, University of Ferrara, 44121 Ferrara, Italy
| |
Collapse
|
3
|
Abdullah AL-maskri AA, Jin G, Li Y, Talap J, Almoiliqy M, Apu C, Zeng S, Zhou Y, Cai S. A self-assembly amplification strategy for ultra-sensitive detection of microRNA based on phosphorothioated probes. Talanta 2022; 249:123618. [DOI: 10.1016/j.talanta.2022.123618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 11/26/2022]
|
4
|
Li Y, Li F, Wang Y, Song F, Qi L, Hu Q. circ-LIMK1 regulates cisplatin resistance in lung adenocarcinoma by targeting miR-512-5p/HMGA1 axis. Open Med (Wars) 2022; 17:1568-1583. [PMID: 36304135 PMCID: PMC9547352 DOI: 10.1515/med-2022-0542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/12/2022] Open
Abstract
This study aimed to unveil the detailed role and new mechanism of circ-LIMK1 in lung adenocarcinoma. Real-time quantitative polymerase chain reaction was performed to analyze the expression of circ-LIMK1, miR-512-5p, and HMGA1. 3-(4,5)-Dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumromide assay was employed to test the half maximal inhibitory concentration of cisplatin (DDP). Western blot was used to measure the expression of HMGA1, multidrug resistance protein 1, mitochondrial 37S ribosomal protein, and vascular endothelial growth factor A. Colony formation assay, flow cytometry, transwell assay, and tube formation assay were performed to analyze cell functions. Animal models were established to assay the role of circ-LIMK1 in vivo. The expression of circ-LIMK1 was up-regulated in DDP-resistant tumor tissues and cells. Knockdown of circ-LIMK1 reduced DDP resistance, impaired cancer cell growth, migration, invasion, and angiogenesis. circ-LIMK1 targeted miR-512-5p, and HMGA1 was targeted by miR-512-5p. MiR-512-5p absence could restore the repressive effects of circ-LIMK1 knockdown on lung adenocarcinoma cell phenotypes. Overexpression of HMGA1 could restore the inhibitory effects of miR-512-5p enrichment on lung adenocarcinoma cell malignant phenotypes. Knockdown of circ-LIMK1 could reduce growth of DDP-resistant tumors in vivo. Collectively, circ-LIMK1 regulated DDP resistance in lung adenocarcinoma by targeting miR-512-5p/HMGA1 axis.
Collapse
Affiliation(s)
- Ya Li
- Department of Respiratory and Critical Care Medicine, Xi’an Gaoling District Hospital, Xi’an, China
| | - Fangfang Li
- Department of Respiratory and Critical Care Medicine, Xi’an Gaoling District Hospital, Xi’an, China
| | - Yaya Wang
- Department of Respiratory and Critical Care Medicine, Xi’an Gaoling District Hospital, Xi’an, China
| | - Fangyu Song
- Department of Respiratory and Critical Care Medicine, Xi’an Gaoling District Hospital, Xi’an, China
| | - Lin Qi
- Department of Respiratory and Critical Care Medicine, Xi’an Gaoling District Hospital, Xi’an, China
| | - Qiang Hu
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Xi’an Medical College, No. 277 Youyi West Road, Beilin District, Xi’an 710068, China
| |
Collapse
|
5
|
Combined Treatment of Bronchial Epithelial Calu-3 Cells with Peptide Nucleic Acids Targeting miR-145-5p and miR-101-3p: Synergistic Enhancement of the Expression of the Cystic Fibrosis Transmembrane Conductance Regulator ( CFTR) Gene. Int J Mol Sci 2022; 23:ijms23169348. [PMID: 36012615 PMCID: PMC9409490 DOI: 10.3390/ijms23169348] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene encodes for a chloride channel defective in Cystic Fibrosis (CF). Accordingly, upregulation of its expression might be relevant for the development of therapeutic protocols for CF. MicroRNAs are deeply involved in the CFTR regulation and their targeting with miRNA inhibitors (including those based on Peptide Nucleic Acids, PNAs)is associated with CFTR upregulation. Targeting of miR-145-5p, miR-101-3p, and miR-335-5p with antisense PNAs was found to be associated with CFTR upregulation. The main objective of this study was to verify whether combined treatments with the most active PNAs are associated with increased CFTR gene expression. The data obtained demonstrate that synergism of upregulation of CFTR production can be obtained by combined treatments of Calu-3 cells with antisense PNAs targeting CFTR-regulating microRNAs. In particular, highly effective combinations were found with PNAs targeting miR-145-5p and miR-101-3p. Content of mRNAs was analyzed by RT-qPCR, the CFTR production by Western blotting. Combined treatment with antagomiRNAs might lead to maximized upregulation of CFTR and should be considered in the development of protocols for CFTR activation in pathological conditions in which CFTR gene expression is lacking, such as Cystic Fibrosis.
Collapse
|
6
|
Identification of MiRNA–Disease Associations Based on Information of Multi-Module and Meta-Path. Molecules 2022; 27:molecules27144443. [PMID: 35889314 PMCID: PMC9321348 DOI: 10.3390/molecules27144443] [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: 05/17/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 12/10/2022] Open
Abstract
Cumulative research reveals that microRNAs (miRNAs) are involved in many critical biological processes including cell proliferation, differentiation and apoptosis. It is of great significance to figure out the associations between miRNAs and human diseases that are the basis for finding biomarkers for diagnosis and targets for treatment. To overcome the time-consuming and labor-intensive problems faced by traditional experiments, a computational method was developed to identify potential associations between miRNAs and diseases based on the graph attention network (GAT) with different meta-path mode and support vector (SVM). Firstly, we constructed a multi-module heterogeneous network based on the meta-path and learned the latent features of different modules by GAT. Secondly, we found the average of the latent features with weight to obtain a final node representation. Finally, we characterized miRNA–disease-association pairs with the node representation and trained an SVM to recognize potential associations. Based on the five-fold cross-validation and benchmark datasets, the proposed method achieved an area under the precision–recall curve (AUPR) of 0.9379 and an area under the receiver–operating characteristic curve (AUC) of 0.9472. The results demonstrate that our method has an outstanding practical application performance and can provide a reference for the discovery of new biomarkers and therapeutic targets.
Collapse
|
7
|
Kim S, Ji S, Koh HR. CRISPR as a Diagnostic Tool. Biomolecules 2021; 11:1162. [PMID: 34439828 PMCID: PMC8391464 DOI: 10.3390/biom11081162] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has recently gained growing attention as a diagnostic tool due to its capability of specific gene targeting. It consists of Cas enzymes and a guide RNA (gRNA) that can cleave the target DNA or RNA based on the sequence of the gRNA, making it an attractive genetic engineering technique. In addition to the target-specific binding and cleavage, the trans-cleavage activity was reported for some Cas proteins, including Cas12a and Cas13a, which is to cleave the surrounding single-stranded DNA or RNA upon the target binding of Cas-gRNA complex. All these activities of the CRISPR-Cas system are based on its target-specific binding, making it applied to develop diagnostic methods by detecting the disease-related gene as well as microRNAs and the genetic variations such as single nucleotide polymorphism and DNA methylation. Moreover, it can be applied to detect the non-nucleic acids target such as proteins. In this review, we cover the various CRISPR-based diagnostic methods by focusing on the activity of the CRISPR-Cas system and the form of the target. The CRISPR-based diagnostic methods without target amplification are also introduced briefly.
Collapse
Affiliation(s)
| | | | - Hye Ran Koh
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea; (S.K.); (S.J.)
| |
Collapse
|
8
|
Matamala N, Lara B, Gómez-Mariano G, Martínez S, Vázquez-Domínguez I, Otero-Sobrino Á, Muñoz-Callejas A, Sánchez E, Esquinas C, Bustamante A, Cadenas S, Curi S, Lázaro L, Martínez MT, Rodríguez E, Miravitlles M, Torres-Duran M, Herrero I, Michel FJ, Castillo S, Hernández-Pérez JM, Blanco I, Casas F, Martínez-Delgado B. miR-320c Regulates SERPINA1 Expression and Is Induced in Patients With Pulmonary Disease. Arch Bronconeumol 2021; 57:457-463. [PMID: 35698951 DOI: 10.1016/j.arbr.2020.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 03/11/2020] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Alpha-1 antitrypsin deficiency (AATD) is a genetic condition resulting in lung and liver disease with a great clinical variability. MicroRNAs have been identified as disease modifiers; therefore miRNA deregulation could play an important role in disease heterogeneity. Members of miR-320 family are involved in regulating of multiple processes including inflammation, and have potential specific binding sites in the 3'UTR region of SERPINA1 gene. In this study we explore the involvement of miR-320c, a member of this family, in this disease. METHODS Firstly in vitro studies were carried out to demonstrate regulation of SERPINA1 gene by miR-320. Furthermore, the expression of miR-320c was analyzed in the blood of 98 individuals with different AAT serum levels by using quantitative PCR and expression was correlated to clinical parameters of the patients. Finally, HL60 cells were used to analyze induction of miR-320c in inflammatory conditions. RESULTS Overexpression of miR-320 members in human HepG2 cells led to inhibition of SERPINA1 expression. Analysis of miR-320c expression in patient's samples revealed significantly increased expression of miR-320c in individuals with pulmonary disease. Additionally, HL60 cells treated with the pro-inflammatory factor lipopolysaccharide (LPS) showed increase in miR-320c expression, suggesting that miR-320c responds to inflammation. CONCLUSION Our findings demonstrate that miR-320c inhibits SERPINA1 expression in a hepatic cell line and its levels in blood are associated with lung disease in a cohort of patients with different AAT serum levels. These results suggest that miR-320c can play a role in AAT regulation and could be a biomarker of inflammatory processes in pulmonary diseases.
Collapse
Affiliation(s)
- Nerea Matamala
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Beatriz Lara
- Respiratory Medicine Department, Coventry University Hospital, Coventry, UK
| | - Gema Gómez-Mariano
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Selene Martínez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Irene Vázquez-Domínguez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Álvaro Otero-Sobrino
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Antonio Muñoz-Callejas
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Elena Sánchez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Cristina Esquinas
- Registro Español de pacientes con déficit de alfa-1 antitripsina (REDAAT), Fundación Española de Pulmón, Respira, SEPAR, Barcelona, Spain; Servicio de Neumología, Hospital Universitari Vall d'Hebron/Vall d'Hebron Institut de Recerca (VHIR), CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Ana Bustamante
- Servicio de Neumología, Hospital de Sierrallana, Torrelavega, Cantabria, Spain
| | - Sergio Cadenas
- Servicio de Neumología, Hospital Clínico Universitario de Salamanca, Spain
| | - Sergio Curi
- Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Lourdes Lázaro
- Servicio de Neumología, Complejo Asistencial Universitario de Burgos, Spain
| | | | - Esther Rodríguez
- Servicio de Neumología, Hospital Universitari Vall d'Hebron/Vall d'Hebron Institut de Recerca (VHIR), CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Marc Miravitlles
- Servicio de Neumología, Hospital Universitari Vall d'Hebron/Vall d'Hebron Institut de Recerca (VHIR), CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - María Torres-Duran
- Servicio de Neumología, Hospital Álvaro Cunqueiro, EOXI Vigo, Pneumovigo I+i, IIS Galicia Sur, Spain
| | - Inés Herrero
- Hospital Universitario Miguel Servet, Zaragoza, Spain
| | | | - Silvia Castillo
- Unidad de Neumología infantil y Fibrosis quística, Hospital Clínico Universitario de Valencia, Spain
| | | | - Ignacio Blanco
- Registro Español de pacientes con déficit de alfa-1 antitripsina (REDAAT), Fundación Española de Pulmón, Respira, SEPAR, Barcelona, Spain
| | - Francisco Casas
- Servicio de Neumología, Hospital Universitario San Cecilio, Granada, Spain
| | - Beatriz Martínez-Delgado
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain.
| |
Collapse
|
9
|
Tang M, Liu C, Liu D, Liu J, Liu J, Deng L. PMDFI: Predicting miRNA-Disease Associations Based on High-Order Feature Interaction. Front Genet 2021; 12:656107. [PMID: 33897768 PMCID: PMC8063614 DOI: 10.3389/fgene.2021.656107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/18/2021] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNA molecules that make a significant contribution to diverse biological processes, and their mutations and dysregulations are closely related to the occurrence, development, and treatment of human diseases. Therefore, identification of potential miRNA–disease associations contributes to elucidating the pathogenesis of tumorigenesis and seeking the effective treatment method for diseases. Due to the expensive cost of traditional biological experiments of determining associations between miRNAs and diseases, increasing numbers of effective computational models are being used to compensate for this limitation. In this study, we propose a novel computational method, named PMDFI, which is an ensemble learning method to predict potential miRNA–disease associations based on high-order feature interactions. We initially use a stacked autoencoder to extract meaningful high-order features from the original similarity matrix, and then perform feature interactive learning, and finally utilize an integrated model composed of multiple random forests and logistic regression to make comprehensive predictions. The experimental results illustrate that PMDFI achieves excellent performance in predicting potential miRNA–disease associations, with the average area under the ROC curve scores of 0.9404 and 0.9415 in 5-fold and 10-fold cross-validation, respectively.
Collapse
Affiliation(s)
- Mingyan Tang
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Chenzhe Liu
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Dayun Liu
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Junyi Liu
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Jiaqi Liu
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha, China
| |
Collapse
|
10
|
Zhang L, Liu B, Li Z, Zhu X, Liang Z, An J. Predicting MiRNA-disease associations by multiple meta-paths fusion graph embedding model. BMC Bioinformatics 2020; 21:470. [PMID: 33087064 PMCID: PMC7579830 DOI: 10.1186/s12859-020-03765-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/17/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Many studies prove that miRNAs have significant roles in diagnosing and treating complex human diseases. However, conventional biological experiments are too costly and time-consuming to identify unconfirmed miRNA-disease associations. Thus, computational models predicting unidentified miRNA-disease pairs in an efficient way are becoming promising research topics. Although existing methods have performed well to reveal unidentified miRNA-disease associations, more work is still needed to improve prediction performance. RESULTS In this work, we present a novel multiple meta-paths fusion graph embedding model to predict unidentified miRNA-disease associations (M2GMDA). Our method takes full advantage of the complex structure and rich semantic information of miRNA-disease interactions in a self-learning way. First, a miRNA-disease heterogeneous network was derived from verified miRNA-disease pairs, miRNA similarity and disease similarity. All meta-path instances connecting miRNAs with diseases were extracted to describe intrinsic information about miRNA-disease interactions. Then, we developed a graph embedding model to predict miRNA-disease associations. The model is composed of linear transformations of miRNAs and diseases, the means encoder of a single meta-path instance, the attention-aware encoder of meta-path type and attention-aware multiple meta-path fusion. We innovatively integrated meta-path instances, meta-path based neighbours, intermediate nodes in meta-paths and more information to strengthen the prediction in our model. In particular, distinct contributions of different meta-path instances and meta-path types were combined with attention mechanisms. The data sets and source code that support the findings of this study are available at https://github.com/dangdangzhang/M2GMDA . CONCLUSIONS M2GMDA achieved AUCs of 0.9323 and 0.9182 in global leave-one-out cross validation and fivefold cross validation with HDMM V2.0. The results showed that our method outperforms other prediction methods. Three kinds of case studies with lung neoplasms, breast neoplasms, prostate neoplasms, pancreatic neoplasms, lymphoma and colorectal neoplasms demonstrated that 47, 50, 49, 48, 50 and 50 out of the top 50 candidate miRNAs predicted by M2GMDA were validated by biological experiments. Therefore, it further confirms the prediction performance of our method.
Collapse
Affiliation(s)
- Lei Zhang
- Engineering Research Center of Mine Digitalization of Ministry of Education, China University of Mining and Technology, Xuzhou, China
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
| | - Bailong Liu
- Engineering Research Center of Mine Digitalization of Ministry of Education, China University of Mining and Technology, Xuzhou, China.
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China.
| | - Zhengwei Li
- Engineering Research Center of Mine Digitalization of Ministry of Education, China University of Mining and Technology, Xuzhou, China.
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China.
| | - Xiaoyan Zhu
- Engineering Research Center of Mine Digitalization of Ministry of Education, China University of Mining and Technology, Xuzhou, China
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
| | - Zhizhen Liang
- Engineering Research Center of Mine Digitalization of Ministry of Education, China University of Mining and Technology, Xuzhou, China
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
| | - Jiyong An
- Engineering Research Center of Mine Digitalization of Ministry of Education, China University of Mining and Technology, Xuzhou, China
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
| |
Collapse
|
11
|
Gabr MT, Brogi S. MicroRNA-Based Multitarget Approach for Alzheimer's Disease: Discovery of the First-In-Class Dual Inhibitor of Acetylcholinesterase and MicroRNA-15b Biogenesis. J Med Chem 2020; 63:9695-9704. [PMID: 32787143 DOI: 10.1021/acs.jmedchem.0c00756] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The multitarget approach in drug design is a powerful strategy in tackling the multifactorial nature of Alzheimer's disease (AD). Herein, we report a novel strategy in the design of multitargeted therapeutics for AD through dual inhibition of acetylcholinesterase (AChE) and microRNA-15b biogenesis. We performed high-throughput screening (HTS) of a chemical library to identify binders of mircoRNA-15b which is identified as a biomarker and potential therapeutic target of AD. The hits from HTS were further screened for their AChE inhibitory activity, the most widely investigated target for the development of AD therapeutics. MG-6267 was identified as the first dual inhibitor of AChE and microRNA-15b biogenesis. Cellular assays revealed the superiority of MG-6267 to single-targeted inhibitors of AChE and microRNA-15b in protecting SH-SY5Y neuroblastoma cells from amyloid-beta (Aβ)-induced cytotoxicity. This work paves the way for future research efforts aiming at the development of microRNA-based multitargeted therapeutics for AD.
Collapse
Affiliation(s)
- Moustafa T Gabr
- Department of Radiology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| |
Collapse
|
12
|
Boubaker G, Strempel S, Hemphill A, Müller N, Wang J, Gottstein B, Spiliotis M. Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice. PLoS Negl Trop Dis 2020; 14:e0007640. [PMID: 32442168 PMCID: PMC7244097 DOI: 10.1371/journal.pntd.0007640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/05/2020] [Indexed: 12/15/2022] Open
Abstract
We present a comprehensive analysis of the hepatic miRNA transcriptome at one month post-infection of experimental primary alveolar echinococcosis (AE), a parasitic infection caused upon ingestion of E. multilocularis eggs. Liver tissues were collected from infected and non-infected C57BL/6 mice, then small RNA libraries were prepared for next-generation sequencing (NGS). We conducted a Stem-loop RT-qPCR for validation of most dysregulated miRNAs. In infected mice, the expression levels of 28 miRNAs were significantly altered. Of these, 9 were up-regulated (fold change (FC) ≥ 1.5) and 19 were down-regulated (FC ≤ 0.66) as compared to the non-infected controls. In infected livers, mmu-miR-148a-3p and mmu-miR-101b-3p were 8- and 6-fold down-regulated, respectively, and the expression of mmu-miR-22-3p was reduced by 50%, compared to non-infected liver tissue. Conversely, significantly higher hepatic levels were noted for Mus musculus (mmu)-miR-21a-5p (FC = 2.3) and mmu-miR-122-5p (FC = 1.8). In addition, the relative mRNA expression levels of five genes (vegfa, mtor, hif1-α, fasn and acsl1) that were identified as targets of down-regulated miRNAs were significantly enhanced. All the five genes exhibited a higher expression level in livers of E. multilocularis infected mice compared to non-infected mice. Finally, we studied the issue related to functionally mature arm selection preference (5p and/or 3p) from the miRNA precursor and showed that 9 pre-miRNAs exhibited different arm selection preferences in normal versus infected liver tissues. In conclusion, this study provides first evidence that miRNAs are regulated early in primary murine AE. Our findings raise intriguing questions such as (i) how E. multilocularis affects hepatic miRNA expression;(ii) what are the alterations in miRNA expression patterns in more advanced AE-stages; and (iii) which hepatic cellular, metabolic and/or immunologic processes are modulated through altered miRNAs in AE. Thus, further research on the regulation of miRNAs during AE is needed, since miRNAs constitute an attractive potential option for development of novel therapeutic approaches against AE. Various infectious diseases in humans have been associated with altered expression patterns of microRNAs (miRNAs), a class of small non-coding RNAs involved in negative regulation of gene expression. Herein, we revealed that significant alteration of miRNAs expression occurred in murine liver subsequently to experimental infection with E. multilocularis eggs when compared to non-infected controls. At the early stage of murine AE, hepatic miRNAs were mainly down-regulated. Respective target genes of the most extensively down-regulated miRNAs were involved in angiogenesis and fatty acid synthesis. Furthermore, we found higher mRNA levels of three angiogenic and two lipogenic genes in E. multilocularis infected livers compared to non-infected controls. Angiogenesis and fatty acid biosynthesis may be beneficial for development of the E. multilocularis metacestodes. In fact the formation of new blood vessels in the periparasitic area may ensure that parasites are supplied with oxygen and nutrients and get rid of waste products. Additionally, E. multilocularis is not able to undertake de novo fatty acid synthesis, thus lipids must be scavenged from its host. More research on the regulation of the hepatic miRNA transcriptome at more advanced stages of AE is needed.
Collapse
Affiliation(s)
- Ghalia Boubaker
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
- Department of Clinical Biology B, Laboratory of Parasitology and Mycology, University of Monastir, Monastir, Tunisia
- * E-mail: (GB); (BG)
| | | | - Andrew Hemphill
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Norbert Müller
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Junhua Wang
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Bruno Gottstein
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
- Institute of Infectious Diseases, Faculty of Medicine, University of Berne, Berne, Switzerland
- * E-mail: (GB); (BG)
| | - Markus Spiliotis
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| |
Collapse
|
13
|
Matamala N, Lara B, Gómez-Mariano G, Martínez S, Vázquez-Domínguez I, Otero-Sobrino Á, Muñoz-Callejas A, Sánchez E, Esquinas C, Bustamante A, Cadenas S, Curi S, Lázaro L, Martínez MT, Rodríguez E, Miravitlles M, Torres-Duran M, Herrero I, Michel FJ, Castillo S, Hernández-Pérez JM, Blanco I, Casas F, Martínez-Delgado B. miR-320c Regulates SERPINA1 Expression and Is Induced in Patients With Pulmonary Disease. Arch Bronconeumol 2020; 57:S0300-2896(20)30084-3. [PMID: 32439252 DOI: 10.1016/j.arbres.2020.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Alpha-1 antitrypsin deficiency (AATD) is a genetic condition resulting in lung and liver disease with a great clinical variability. MicroRNAs have been identified as disease modifiers; therefore miRNA deregulation could play an important role in disease heterogeneity. Members of miR-320 family are involved in regulating of multiple processes including inflammation, and have potential specific binding sites in the 3'UTR region of SERPINA1 gene. In this study we explore the involvement of miR-320c, a member of this family, in this disease. METHODS Firstly in vitro studies were carried out to demonstrate regulation of SERPINA1 gene by miR-320. Furthermore, the expression of miR-320c was analyzed in the blood of 98 individuals with different AAT serum levels by using quantitative PCR and expression was correlated to clinical parameters of the patients. Finally, HL60 cells were used to analyze induction of miR-320c in inflammatory conditions. RESULTS Overexpression of miR-320 members in human HepG2 cells led to inhibition of SERPINA1 expression. Analysis of miR-320c expression in patient's samples revealed significantly increased expression of miR-320c in individuals with pulmonary disease. Additionally, HL60 cells treated with the pro-inflammatory factor lipopolysaccharide (LPS) showed increase in miR-320c expression, suggesting that miR-320c responds to inflammation. CONCLUSION Our findings demonstrate that miR-320c inhibits SERPINA1 expression in a hepatic cell line and its levels in blood are associated with lung disease in a cohort of patients with different AAT serum levels. These results suggest that miR-320c can play a role in AAT regulation and could be a biomarker of inflammatory processes in pulmonary diseases.
Collapse
Affiliation(s)
- Nerea Matamala
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Beatriz Lara
- Respiratory Medicine Department, Coventry University Hospital, Coventry, UK
| | - Gema Gómez-Mariano
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Selene Martínez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Irene Vázquez-Domínguez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), Madrid, Spain
| | - Álvaro Otero-Sobrino
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Antonio Muñoz-Callejas
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Elena Sánchez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Cristina Esquinas
- Registro Español de pacientes con déficit de alfa-1 antitripsina (REDAAT), Fundación Española de Pulmón, Respira, SEPAR, Barcelona, Spain; Servicio de Neumología, Hospital Universitari Vall d'Hebron/Vall d'Hebron Institut de Recerca (VHIR), CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Ana Bustamante
- Servicio de Neumología, Hospital de Sierrallana, Torrelavega, Cantabria, Spain
| | - Sergio Cadenas
- Servicio de Neumología, Hospital Clínico Universitario de Salamanca, Spain
| | - Sergio Curi
- Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Lourdes Lázaro
- Servicio de Neumología, Complejo Asistencial Universitario de Burgos, Spain
| | | | - Esther Rodríguez
- Servicio de Neumología, Hospital Universitari Vall d'Hebron/Vall d'Hebron Institut de Recerca (VHIR), CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - Marc Miravitlles
- Servicio de Neumología, Hospital Universitari Vall d'Hebron/Vall d'Hebron Institut de Recerca (VHIR), CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| | - María Torres-Duran
- Servicio de Neumología, Hospital Álvaro Cunqueiro, EOXI Vigo, Pneumovigo I+i, IIS Galicia Sur, Spain
| | - Inés Herrero
- Hospital Universitario Miguel Servet, Zaragoza, Spain
| | | | - Silvia Castillo
- Unidad de Neumología infantil y Fibrosis quística, Hospital Clínico Universitario de Valencia, Spain
| | | | - Ignacio Blanco
- Registro Español de pacientes con déficit de alfa-1 antitripsina (REDAAT), Fundación Española de Pulmón, Respira, SEPAR, Barcelona, Spain
| | - Francisco Casas
- Servicio de Neumología, Hospital Universitario San Cecilio, Granada, Spain
| | - Beatriz Martínez-Delgado
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), CIBER de Enfermedades Raras (CIBERER), Madrid, Spain.
| |
Collapse
|
14
|
miR-1224-5p inhibits the proliferation and invasion of ovarian cancer via targeting SND1. Hum Cell 2020; 33:780-789. [PMID: 32409958 DOI: 10.1007/s13577-020-00364-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/16/2020] [Indexed: 01/22/2023]
Abstract
Emerging evidences have indicated that abnormal expression of microRNAs (miRNAs) contributed to carcinogenesis of ovarian cancer. However, the molecular mechanism of many aberrant expressed miRNAs was not known. Here, we discovered that miR-1224-5p was a downregulated miRNA in ovarian cancer via bioinformatic analysis and RT-qPCR. It was found that upregulation of miR-1224-5p inhibited cell proliferation and invasion ability of ovarian cancer cells. SND1, a well-characterized oncogene, was predicted as a target gene of miR-1224-5p. The western blotting, dual luciferase reporter assay, RNA-binding protein immunoprecipitation assay, and RT-qPCR demonstrated SND1 as a target gene of miR-1224-5p in ovarian cancer. MiR-1224-5p inhibited the expression of mesenchymal markers and increased the expression of epithelial markers in ovarian cancer cells via targeting SND1, indicating miR-1224-5p was involved in epithelial mesenchymal transition. The rescue assay manifested that miR-1224-5p-regulated cell proliferation and invasion mainly rely on downregulation of SND1 in ovarian cancer cells. In conclusion, our study revealed a direct regulatory association between miR-1224-5p and SND1 and their involvement in ovarian carcinogenesis.
Collapse
|
15
|
Bartoszewski R, Sikorski AF. Editorial focus: understanding off-target effects as the key to successful RNAi therapy. Cell Mol Biol Lett 2019; 24:69. [PMID: 31867046 PMCID: PMC6902517 DOI: 10.1186/s11658-019-0196-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022] Open
Abstract
With the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
Collapse
Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F. Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| |
Collapse
|
16
|
Fadaka AO, Pretorius A, Klein A. MicroRNA Assisted Gene Regulation in Colorectal Cancer. Int J Mol Sci 2019; 20:E4899. [PMID: 31623294 PMCID: PMC6801675 DOI: 10.3390/ijms20194899] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second-leading cause of cancer death and a major public health problem. Nearly 80% CRC cases are diagnosed after the disease have metastasized and are often too advanced for treatment. Small non-coding RNA guides argonaute protein to their specific target for regulation as the sole of RNA induced silencing complex for gene silencing. These non-coding RNA for example microRNA, are thought to play a key role in affecting the efficiency of gene regulation in cancer, especially CRC. Understanding the mechanism at the molecular level could lead to improved diagnosis, treatment, and management decisions for CRC. The study aimed to predict the molecular mechanism of gene regulation based microRNA-mRNA duplex as a lead in the silencing mechanism. Five candidate microRNAs were identified through the in silico approach. The MicroRNA target prediction and subsequent correlation, and prioritization were performed using miRTarBase, gbCRC and CoReCG, and DAVID databases respectively. Protein selection and preparation were carried out using PDB and Schrödinger suits. The molecular docking analysis was performed using PATCHDOCK webserver and visualized by discovery studio visualizer. The results of the study reveal that the candidate microRNAs have strong binding affinity towards their targets suggesting a crucial factor in the silencing mechanism. Furthermore, the molecular docking of the receptor to both the microRNA and microRNA-mRNA duplex were analyzed computationally to understand their interaction at the molecular level. Conclusively, the study provides an explanation for understanding the microRNAs-based gene regulation (silencing mechanism) in CRC.
Collapse
Affiliation(s)
- Adewale O Fadaka
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535 Cape Town, South Africa.
| | - Ashley Pretorius
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535 Cape Town, South Africa.
| | - Ashwil Klein
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535 Cape Town, South Africa.
| |
Collapse
|
17
|
Gulei D, Raduly L, Broseghini E, Ferracin M, Berindan-Neagoe I. The extensive role of miR-155 in malignant and non-malignant diseases. Mol Aspects Med 2019; 70:33-56. [PMID: 31558293 DOI: 10.1016/j.mam.2019.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) have rapidly emerged as key molecules in cancer initiation and development, showing the capability to regulate pivotal oncogenic pathways. MiR-155 has gathered an increased attention especially in oncology, but also in non-malignanat pathologies. Nowadays, this noncoding RNA is one of the most important miRNAs in cancer, due to the extensive signaling network associated with it, implication in immune system regulation and also deregulation in disease states. Therefore, numerous research protocols are focused on preclinical modulation of miR-155 for therapeutic purposes, or investigation of its dynamic expression for diagnostic/prognostic assessments, with the final intention of bringing this miRNA into the clinical setting. This review comprehensively presents the extended role of miR-155 in cancer and other pathologies, where its expression is dysregulated. Finally, we assess the future steps toward miR-155 based therapeutics.
Collapse
Affiliation(s)
- Diana Gulei
- MEDFUTURE - Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, Marinescu 23 Street, Cluj-Napoca, Romania.
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Marinescu 23 Street, No. 23, 400337, Cluj-Napoca, Romania
| | - Elisabetta Broseghini
- Department of Experimental, Diagnostic and Specialty Medicine, DIMES, University of Bologna, Bologna, Italy
| | - Manuela Ferracin
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Marinescu 23 Street, No. 23, 400337, Cluj-Napoca, Romania; Department of Experimental, Diagnostic and Specialty Medicine, DIMES, University of Bologna, Bologna, Italy
| | - Ioana Berindan-Neagoe
- MEDFUTURE - Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, Marinescu 23 Street, Cluj-Napoca, Romania; Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Marinescu 23 Street, No. 23, 400337, Cluj-Napoca, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuţă", Cluj-Napoca, 400015, Romania.
| |
Collapse
|
18
|
Wiczling P, Daghir-Wojtkowiak E, Kaliszan R, Markuszewski MJ, Limon J, Koczkowska M, Stukan M, Kuźniacka A, Ratajska M. Bayesian multilevel model of micro RNA levels in ovarian-cancer and healthy subjects. PLoS One 2019; 14:e0221764. [PMID: 31465488 PMCID: PMC6715278 DOI: 10.1371/journal.pone.0221764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
Abstract
In transcriptomics, micro RNAs (miRNAs) has gained much interest especially as potential disease indicators. However, apart from holding a great promise related to their clinical application, a lot of inconsistent results have been published. Our aim was to compare the miRNA expression levels in ovarian cancer and healthy subjects using the Bayesian multilevel model and to assess their potential usefulness in diagnosis. We have analyzed a case-control observational data on expression profiling of 49 preselected miRNA-based ovarian cancer indicators in 119 controls and 59 patients. A Bayesian multilevel model was used to characterize the effect of disease on miRNA levels controlling for differences in age and body weight. The difference between the miRNA level and health status of the patient on the scale of the data variability were discussed in the context of their potential usefulness in diagnosis. Additionally, the cross-validated area under the ROC curve (AUC) was used to assess the expected out-of-sample discrimination index of a different sets of miRNAs. The proposed model allowed us to describe the set of miRNA levels in patients and controls. Three highly correlated miRNAs: miR-101-3p, miR-142-5p, miR-148a-3p rank the highest with almost identical effect sizes that ranges from 0.45 to 1.0. For those miRNAs the credible interval for AUC ranged from 0.63 to 0.67 indicating their limited discrimination potential. A little benefit in adding information from other miRNAs was observed. There were several miRNAs in the dataset (miR-604, hsa-miR-221-5p) for which inferences were uncertain. For those miRNAs more experimental effort is needed to fully assess their effect in the context of new hits discovery and usefulness as disease indicators. The proposed multilevel Bayesian model can be used to characterize the panel of miRNA profile and to assess the difference in expression levels between healthy and cancer individuals.
Collapse
Affiliation(s)
- Paweł Wiczling
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera, Gdańsk, Poland
| | - Emilia Daghir-Wojtkowiak
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera, Gdańsk, Poland
| | - Roman Kaliszan
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera, Gdańsk, Poland
| | - Michał Jan Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera, Gdańsk, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdańsk, Dębinki, Gdańsk, Poland
| | - Magdalena Koczkowska
- Department of Biology and Genetics, Medical University of Gdańsk, Dębinki, Gdańsk, Poland
| | - Maciej Stukan
- Department of Gynecological Oncology, Gdynia Oncology Centre, Powstania Styczniowego, Gdynia, Poland
| | - Alina Kuźniacka
- Department of Biology and Genetics, Medical University of Gdańsk, Dębinki, Gdańsk, Poland
| | - Magdalena Ratajska
- Department of Biology and Genetics, Medical University of Gdańsk, Dębinki, Gdańsk, Poland
| |
Collapse
|
19
|
Tafrihi M, Hasheminasab E. MiRNAs: Biology, Biogenesis, their Web-based Tools, and Databases. Microrna 2019; 8:4-27. [PMID: 30147022 DOI: 10.2174/2211536607666180827111633] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 07/11/2018] [Accepted: 08/20/2018] [Indexed: 05/25/2023]
Abstract
INTRODUCTION MicroRNAs (miRNAs), which are evolutionarily conserved, and endogenous non-coding RNAs, participate in the post-transcriptional regulation of eukaryotic genes. The biogenesis of miRNAs occurs in the nucleus. Then, in the cytoplasm, they are assembled along with some proteins in a ribonucleoprotein complex called RISC. miRNA component of the RISC complex binds to the complementary sequence of mRNA target depending on the degree of complementarity, and leads to mRNA degradation and/or inhibition of protein synthesis. miRNAs have been found in eukaryotes and some viruses play a role in development, metabolism, cell proliferation, growth, differentiation, and death. OBJECTIVE A large number of miRNAs and their targets were identified by different experimental techniques and computational approaches. The principal aim of this paper is to gather information about some miRNA databases and web-based tools for better and quicker access to relevant data. RESULTS Accordingly, in this paper, we collected and introduced miRNA databases and some webbased tools that have been developed by various research groups. We have categorized them into different classes including databases for viral miRNAs, and plant miRNAs, miRNAs in human beings, mice and other vertebrates, miRNAs related to human diseases, and target prediction, and miRNA expression. Also, we have presented relevant statistical information about these databases.
Collapse
Affiliation(s)
- Majid Tafrihi
- Molecular & Cell Biology Research Lab. 2, Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Mazandaran, Iran
| | - Elham Hasheminasab
- Molecular & Cell Biology Research Lab. 2, Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Mazandaran, Iran
| |
Collapse
|
20
|
Bartoszewski R, Sikorski AF. Editorial focus: entering into the non-coding RNA era. Cell Mol Biol Lett 2018; 23:45. [PMID: 30250489 PMCID: PMC6145373 DOI: 10.1186/s11658-018-0111-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Recent developments in high-throughput genotyping technologies have revealed the existence of several new classes of RNA that do not encode proteins but serve other cellular roles. To date, these non-coding RNAs (ncRNAs) have been shown to modulate both gene expression and genome remodeling, thus contributing to the control of both normal and disease-related cellular processes. The attraction of this research topic can be seen in the increasing number of submissions on ncRNAs to molecular biology journals, including Cellular Molecular Biology Letters (CMBL). As researchers attempt to deepen the understanding of the role of ncRNAs in cell biology, it is worth discussing the broader importance of this research.
Collapse
Affiliation(s)
- Rafal Bartoszewski
- 1Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F Sikorski
- 2Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| |
Collapse
|
21
|
De Paepe B, Lefever S, Mestdagh P. How long noncoding RNAs enforce their will on mitochondrial activity: regulation of mitochondrial respiration, reactive oxygen species production, apoptosis, and metabolic reprogramming in cancer. Curr Genet 2017; 64:163-172. [DOI: 10.1007/s00294-017-0744-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/17/2017] [Accepted: 08/31/2017] [Indexed: 12/13/2022]
|
22
|
Liu Y, Zeng X, He Z, Zou Q. Inferring microRNA-disease associations by random walk on a heterogeneous network with multiple data sources. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:905-915. [PMID: 27076459 DOI: 10.1109/tcbb.2016.2550432] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Since the discovery of the regulatory function of microRNA (miRNA), increased attention has focused on identifying the relationship between miRNA and disease. It has been suggested that computational method are an efficient way to identify potential disease-related miRNAs for further confirmation using biological experiments. In this paper, we first highlighted three limitations commonly associated with previous computational methods. To resolve these limitations, we established disease similarity subnetwork and miRNA similarity subnetwork by integrating multiple data sources, where the disease similarity is composed of disease semantic similarity and disease functional similarity, and the miRNA similarity is calculated using the miRNA-target gene and miRNA-lncRNA (long non-coding RNA) associations. Then, a heterogeneous network was constructed by connecting the disease similarity subnetwork and the miRNA similarity subnetwork using the known miRNA-disease associations. We extended random walk with restart to predict miRNA-disease associations in the heterogeneous network. The leave-one-out cross-validation achieved an average area under the curve (AUC) of 0:8049 across 341 diseases and 476 miRNAs. For five-fold cross-validation, our method achieved an AUC from 0:7970 to 0:9249 for 15 human diseases. Case studies further demonstrated the feasibility of our method to discover potential miRNA-disease associations. An online service for prediction is freely available at http://ifmda.aliapp.com.
Collapse
|
23
|
Shi L, Zhang L, Wang C, Sun S, Cao X, Zhang X. Expression of serum microRNA-378 and its clinical significance in renal cell carcinoma. Genet Mol Biol 2017. [PMID: 28644508 PMCID: PMC5488467 DOI: 10.1590/1678-4685-gmb-2016-0121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Studies have demonstrated that miRNA-378 is expressed in various malignant tumors. In
the present study, we aimed to explore the expression of serum miRNA-378 and its
clinical significance in renal cell carcinoma (RCC) patients. A total of 75 RCC
patients, 63 renal cysts (RC) patients and 75 healthy controls were selected. The
miRNA-378 level in RCC and RC groups was significantly higher than in healthy control
group, with RCC group having the highest level. The miRNA-378 levels were
significantly decreased within the same group after surgery. When compared with
healthy controls, RC group had higher levels but not significantly (p > 0.05)
while levels in RCC group were significantly higher (p < 0.05). miRNA-378
expression was correlated with clinical stage and differentiation degree, but not
correlated with patient's age, gender, surgical strategy and tumor diameter. The AUC
of miRNA-378 was 0.896, 95% confidence interval was 0.847 to 0.945, and AUC
hypothesis testing was statistically significant (p < 0.001, RCC vs healthy
control). miRNA-378 shows potential in the diagnosis and prediction of postoperative
curative effect of renal cell carcinoma, but further studies with lager samples are
needed.
Collapse
Affiliation(s)
- Lixin Shi
- Department of Urology, PLA General Hospital, Beijing, China
| | - Lei Zhang
- Department of Urology, PLA General Hospital, Beijing, China
| | - Chunyang Wang
- Department of Urology, PLA General Hospital, Beijing, China
| | - Shengkun Sun
- Department of Urology, PLA General Hospital, Beijing, China
| | - Xiyuan Cao
- Institute of Basic Medicine, Military Medical Science Academy of the PLA, Beijing, China
| | - Xu Zhang
- Department of Urology, PLA General Hospital, Beijing, China
| |
Collapse
|
24
|
Genetic and epigenetic changes in host ABCB1 influences malaria susceptibility to Plasmodium falciparum. PLoS One 2017; 12:e0175702. [PMID: 28422980 PMCID: PMC5397027 DOI: 10.1371/journal.pone.0175702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/30/2017] [Indexed: 01/20/2023] Open
Abstract
Multiple mechanisms such as genetic and epigenetic variations within a key gene may play a role in malarial susceptibility and response to anti-malarial drugs in the population. ABCB1 is one of the well-studied membrane transporter genes that code for the P-glycoprotein (an efflux protein) and whose effect on malaria disease predisposition and susceptibility to drugs remains to be understood. We studied the association of single nucleotide variations in human ABCB1 that influences its function in subjects with uncomplicated and complicated malaria caused by Plasmodium falciparum (Pf). Global DNA methylation and ABCB1 DNA promoter methylation levels were performed along with transcriptional response and protein expression in subjects with malaria and healthy controls. The rs2032582 locus was significantly associated with complicated and combined malaria groups when compared to controls (p < 0.05). Significant DNA methylation difference was noticed between case and control (p < 0.05). In addition, global DNA methylation levels of the host DNA were inversely proportional to parasitemia in individuals with Pf infection. Our study also revealed the correlation between ABCB1 DNA promoter methylation with rs1128503 and rs2032582 polymorphisms in malaria and was related to increased expression of ABCB1 protein levels in complicated malaria group (p < 0.05) when compared to uncomplicated malaria and control groups. The study provides evidence for multiple mechanisms that may regulate the role of host ABCB1 function to mediate aetiology of malaria susceptibility, prognosis and drug response. These may have clinical implications and therapeutic application for various malarial conditions.
Collapse
|
25
|
Jiang G, Huang C, Li J, Huang H, Jin H, Zhu J, Wu XR, Huang C. Role of STAT3 and FOXO1 in the Divergent Therapeutic Responses of Non-metastatic and Metastatic Bladder Cancer Cells to miR-145. Mol Cancer Ther 2017; 16:924-935. [PMID: 28223425 DOI: 10.1158/1535-7163.mct-16-0631] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/03/2017] [Accepted: 01/25/2017] [Indexed: 12/22/2022]
Abstract
Although miR-145 is the most frequently downregulated miRNA in bladder cancer, its exact stage association and downstream effector have not been defined. Here, we found that miR-145 was upregulated in human patients with bladder cancer with lymph node metastasis and in metastatic T24T cell line. Forced expression of miR-145 promoted anchorage-independent growth of T24T cells accompanied by the downregulation of forkhead box class O1 (FOXO1). In contrast, in non-metastatic T24 cells, miR-145 overexpression inhibited cell growth with upregulation of FOXO1, and the knockdown of FOXO1 abolished the miR-145-mediated inhibition of cell growth. Mechanistic studies revealed that miR-145 directly bound to and attenuated 3'-untranslated region (UTR) activity of foxo1 mRNA in both T24 and T24T cells. Interestingly, miR-145 suppressed STAT3 phosphorylation at Tyr705 and increased foxo1 promoter transcriptional activity in T24 cells, but not in T24T cells, suggesting a role of STAT3 in the divergent responses to miR-145. Supporting this was our finding that STAT3 knockdown mimicked miR-145-mediated upregulation of FOXO1 in T24T cells and inhibition of anchorage-independent growth. Consistently, ectopic expression of miR-145 promoted tumor formation of xenograft T24T cells, whereas such promoting effect became inhibitory due to specific knockdown of STAT3. Together, our findings demonstrate the stage-specific association and function of miR-145 in bladder cancers and provide novel insights into the therapeutic targeting of miR-145. Mol Cancer Ther; 16(5); 924-35. ©2017 AACR.
Collapse
Affiliation(s)
- Guosong Jiang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York.,Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chao Huang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York.,Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jingxia Li
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Honglei Jin
- Zhejiang Provincial Key Laboratory for Technology & Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junlan Zhu
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Xue-Ru Wu
- Departments of Urology and Pathology, New York University School of Medicine, New York; Veterans Affairs Medical Center in Manhattan, New York, New York
| | - Chuanshu Huang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York.
| |
Collapse
|
26
|
Wang Y, Li F, Wang S. MicroRNA‑93 is overexpressed and induces apoptosis in glaucoma trabecular meshwork cells. Mol Med Rep 2016; 14:5746-5750. [PMID: 27878244 DOI: 10.3892/mmr.2016.5938] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/03/2016] [Indexed: 11/05/2022] Open
Abstract
Glaucoma is an optic neuropathy and a major cause of blindness globally. Trabecular meshwork cells are important in maintaining aqueous humor flow, the dysfunction of which tends to induce glaucoma. As important regulators of gene expression, microRNAs may be crucial in regulating trabecular meshwork cells. The present study aimed to reveal the effect of microRNA‑93 (miR‑93) on glaucoma trabecular meshwork (GTM) cell apoptosis. The expression levels of miR‑93 were compared between human trabecular meshwork (HTM) cells and GTM cells. The expression of miR‑93 was inhibited and increased by transfecting the cells with a lentivirus containing its specific inhibitor sponge and expression vector to investigate changes in GTM cell viability and apoptosis. Alterations in the protein expression of nuclear factor erythroid 2‑like 2 (NFE2L2) were also examined to elucidate the possible mechanism underlying the effects of miR‑93. The results showed a marked promotion in the expression of miR‑93 in the GTM cells, compared with the HTM cells (P<0.01). GTM cell viability was increased and its apoptosis was inhibited by transfection with the miR‑93 sponge (P<0.01 and P<0.001, respectively), whereas the overexpression of miR‑93 abrogated these effects (P<0.05 and P<0.0001, respectively). The expression of NFE2L2, a possible target of miR‑93, was promoted by transfection with the miR‑93 sponge (P<0.01) and was inhibited in the cells overexpressing miR‑93 (P<0.01). Therefore, miR‑93 was capable of inhibiting viability and inducing apoptosis of the GTM cells, which was achieved via the suppression of NFE2L2. These results elucidated the pro‑apoptotic effects of miR‑93 in GTM cells and its possible functional mechanism, providing potential therapeutic targets for the treatment of glaucoma.
Collapse
Affiliation(s)
- Yansa Wang
- Department of Ophthalmology, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Fenghua Li
- Department of Ophthalmology, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Shuyun Wang
- Department of Ophthalmology, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| |
Collapse
|
27
|
Biswas K, Chakraborty S, Podder S, Ghosh TC. Insights into the dN/dS ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity. Genomics 2016; 108:11-7. [DOI: 10.1016/j.ygeno.2016.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/22/2016] [Accepted: 04/23/2016] [Indexed: 01/07/2023]
|
28
|
Chakraborty S, Panda A, Ghosh TC. Exploring the evolutionary rate differences between human disease and non-disease genes. Genomics 2015; 108:18-24. [PMID: 26562439 DOI: 10.1016/j.ygeno.2015.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/29/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
Abstract
Comparisons of evolutionary features between human disease and non-disease genes have a wide implication to understand the genetic basis of human disease genes. However, it has not yet been resolved whether disease genes evolve at slower or faster rate than the non-disease genes. To resolve this controversy, here we integrated human disease genes from several databases and compared their protein evolutionary rates with non-disease genes in both housekeeping and tissue-specific group. We noticed that in tissue specific group, disease genes evolve significantly at a slower rate than non-disease genes. However, we found no significant difference in evolutionary rates between disease and non-disease genes in housekeeping group. Tissue specific disease genes have a higher protein complex number, elevated gene expression level and are also associated with conserve biological processes. Finally, our regression analysis suggested that protein complex number followed by protein multifunctionality independently modulates the evolutionary rate of human disease genes.
Collapse
Affiliation(s)
- Sandip Chakraborty
- Bioinformatics Centre, Bose Institute, P-1/12, C.I.T. Scheme VII M, Kolkata 700 054, India
| | - Arup Panda
- Bioinformatics Centre, Bose Institute, P-1/12, C.I.T. Scheme VII M, Kolkata 700 054, India
| | - Tapash Chandra Ghosh
- Bioinformatics Centre, Bose Institute, P-1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.
| |
Collapse
|
29
|
Hong M, Wang N, Tan HY, Tsao SW, Feng Y. MicroRNAs and Chinese Medicinal Herbs: New Possibilities in Cancer Therapy. Cancers (Basel) 2015; 7:1643-57. [PMID: 26305257 PMCID: PMC4586788 DOI: 10.3390/cancers7030855] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/04/2015] [Accepted: 08/17/2015] [Indexed: 12/13/2022] Open
Abstract
In recent decades Chinese medicine has been used worldwide as a complementary and alternative medicine to treat cancer. Plenty of studies have shown that microRNAs (miRNAs) play fundamental roles in many pathological processes, including cancer, while the anti-cancer mechanisms of Chinese medicinal herbs targeting miRNAs also have been extensively explored. Our previous studies and those of others on Chinese medicinal herbs and miRNAs in various cancer models have provided a possibility of new cancer therapies, for example, up-regulating the expression of miR-23a may activate the positive regulatory network of p53 and miR-23a involved in the mechanism underlying the anti-tumor effect of berberine in hepatocellular carcinoma (HCC). In this review, we survey the role of Chinese medicinal herbal products in regulating miRNAs in cancer and the use of mediating miRNAs for cancer treatment. In addition, the controversial roles of herb-derived exogenous miRNAs in cancer treatment are also discussed. It is expected that targeting miRNAs would provide a novel therapeutic approach in cancer therapy by improving overall response and survival outcomes in cancer treatment, especially when combined with conventional therapeutics and Chinese medicinal herbal products.
Collapse
Affiliation(s)
- Ming Hong
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Ning Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Hor Yue Tan
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Sai-Wah Tsao
- Department of Anatomy, Li KaShing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Yibin Feng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
30
|
Giza DE, Vasilescu C, Calin GA. Key principles of miRNA involvement in human diseases. Discoveries (Craiova) 2014; 2:e34. [PMID: 26317116 PMCID: PMC4547364 DOI: 10.15190/d.2014.26] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 12/29/2014] [Accepted: 12/30/2014] [Indexed: 12/12/2022] Open
Abstract
Although rapid progress in our understanding of the functions of miRNA has been made by experimentation and computational approach, a considerable effort still has to be done in determining the general principles that govern the miRNA's mode of action in human diseases. We will further discuss how these principles are being progressively approached by molecular studies, as well as the importance of miRNA in regulating different target genes and functions in specific biological contexts. There is a great demand to understand the principles of context - specific miRNA target recognition in order to design future experiments and models of normal developmental and disease states.
Collapse
Affiliation(s)
- Dana Elena Giza
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Hematology, Fundeni Clinical Hospital, Bucharest, Romania
| | - Catalin Vasilescu
- Department of Surgery, Fundeni Clinical Hospital, Bucharest, Romania
- UMF Carol Davila, Bucharest, Romania
| | - George A. Calin
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|