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Systematic approach to identify therapeutic targets and functional pathways for the cervical cancer. J Genet Eng Biotechnol 2023; 21:10. [PMID: 36723760 PMCID: PMC9892376 DOI: 10.1186/s43141-023-00469-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 01/14/2023] [Indexed: 02/02/2023]
Abstract
BACKGROUND In today's society, cancer has become a big concern. The most common cancers in women are breast cancer (BC), endometrial cancer (EC), ovarian cancer (OC), and cervical cancer (CC). CC is a type of cervix cancer that is the fourth most common cancer in women and the fourth major cause of death. RESULTS This research uses a network approach to discover genetic connections, functional enrichment, pathways analysis, microRNAs transcription factors (miRNA-TF) co-regulatory network, gene-disease associations, and therapeutic targets for CC. Three datasets from the NCBI's GEO collection were considered for this investigation. Then, using a comparison approach between the datasets, 315 common DEGs were discovered. The PPI network was built using a variety of combinatorial statistical approaches and bioinformatics tools, and the PPI network was then utilized to identify hub genes and critical modules. CONCLUSION Furthermore, we discovered that CC has specific similar links with the progression of different tumors using Gene Ontology terminology and pathway analysis. Transcription factors-gene linkages, gene-disease correlations, and the miRNA-TF co-regulatory network were revealed to have functional enrichments. We believe the candidate drugs identified in this study could be effective for advanced CC treatment.
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Exploring the Novel Computational Drug Target and Associated Key Pathways of Oral Cancer. Curr Issues Mol Biol 2022; 44:3552-3572. [PMID: 36005140 PMCID: PMC9406749 DOI: 10.3390/cimb44080244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/17/2022] Open
Abstract
Oral cancer (OC) is a serious health concern that has a high fatality rate. The oral cavity has seven kinds of OC, including the lip, tongue, and floor of the mouth, as well as the buccal, hard palate, alveolar, retromolar trigone, and soft palate. The goal of this study is to look into new biomarkers and important pathways that might be used as diagnostic biomarkers and therapeutic candidates in OC. The publicly available repository the Gene Expression Omnibus (GEO) was to the source for the collection of OC-related datasets. GSE74530, GSE23558, and GSE3524 microarray datasets were collected for analysis. Minimum cut-off criteria of |log fold-change (FC)| > 1 and adjusted p < 0.05 were applied to calculate the upregulated and downregulated differential expression genes (DEGs) from the three datasets. After that only common DEGs in all three datasets were collected to apply further analysis. Gene ontology (GO) and pathway analysis were implemented to explore the functional behaviors of DEGs. Then protein−protein interaction (PPI) networks were built to identify the most active genes, and a clustering algorithm was also implemented to identify complex parts of PPI. TF-miRNA networks were also constructed to study OC-associated DEGs in-depth. Finally, top gene performers from PPI networks were used to apply drug signature analysis. After applying filtration and cut-off criteria, 2508, 3377, and 670 DEGs were found for GSE74530, GSE23558, and GSE3524 respectively, and 166 common DEGs were found in every dataset. The GO annotation remarks that most of the DEGs were associated with the terms of type I interferon signaling pathway. The pathways of KEGG reported that the common DEGs are related to the cell cycle and influenza A. The PPI network holds 88 nodes and 492 edges, and CDC6 had the highest number of connections. Four clusters were identified from the PPI. Drug signatures doxorubicin and resveratrol showed high significance according to the hub genes. We anticipate that our bioinformatics research will aid in the definition of OC pathophysiology and the development of new therapies for OC.
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Intrapericardial Administration of Secretomes from Menstrual Blood-Derived Mesenchymal Stromal Cells: Effects on Immune-Related Genes in a Porcine Model of Myocardial Infarction. Biomedicines 2022; 10:biomedicines10051117. [PMID: 35625854 PMCID: PMC9138214 DOI: 10.3390/biomedicines10051117] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/26/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
Acute myocardial infarction (AMI) is a manifestation of ischemic heart disease where the immune system plays an important role in the re-establishment of homeostasis. We hypothesize that the anti-inflammatory activity of secretomes from menstrual blood-derived mesenchymal stromal cells (S-MenSCs) and IFNγ/TNFα-primed MenSCs (S-MenSCs*) may be considered a therapeutic option for the treatment of AMI. To assess this hypothesis, we have evaluated the effect of S-MenSCs and S-MenSCs* on cardiac function parameters and the involvement of immune-related genes using a porcine model of AMI. Twelve pigs were randomly divided into three biogroups: AMI/Placebo, AMI/S-MenSCs, and AMI/S-MenSCs*. AMI models were generated using a closed chest coronary occlusion-reperfusion procedure and, after 72 h, the different treatments were intrapericardially administered. Cardiac function parameters were monitored by magnetic resonance imaging before and 7 days post-therapy. Transcriptomic analyses in the infarcted tissue identified 571 transcripts associated with the Gene Ontology term Immune response, of which 57 were differentially expressed when different biogroups were compared. Moreover, a prediction of the interactions between differentially expressed genes (DEGs) and miRNAs from secretomes revealed that some DEGs in the infarction area, such as STAT3, IGFR1, or BCL6 could be targeted by previously identified miRNAs in secretomes from MenSCs. In conclusion, the intrapericardial administration of secretome early after infarction has a significant impact on the expression of immune-related genes in the infarcted myocardium. This confirms the immunomodulatory potential of intrapericardially delivered secretomes and opens new therapeutic perspectives in myocardial infarction treatment.
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Discovering Common Pathophysiological Processes between COVID-19 and Cystic Fibrosis by Differential Gene Expression Pattern Analysis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8078259. [PMID: 35528173 PMCID: PMC9076317 DOI: 10.1155/2022/8078259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/04/2022] [Indexed: 12/12/2022]
Abstract
Coronaviruses are a family of viruses that infect mammals and birds. Coronaviruses cause infections of the respiratory system in humans, which can be minor or fatal. A comparative transcriptomic analysis has been performed to establish essential profiles of the gene expression of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) linked to cystic fibrosis (CF). Transcriptomic studies have been carried out in relation to SARS-CoV-2 since a number of people have been diagnosed with CF. The recognition of differentially expressed genes demonstrated 8 concordant genes shared between the SARS-CoV-2 and CF. Extensive gene ontology analysis and the discovery of pathway enrichment demonstrated SARS-CoV-2 response to CF. The gene ontological terms and pathway enrichment mechanisms derived from this research may affect the production of successful drugs, especially for the people with the following disorder. Identification of TF-miRNA association network reveals the interconnection between TF genes and miRNAs, which may be effective to reveal the other influenced disease that occurs for SARS-CoV-2 to CF. The enrichment of pathways reveals SARS-CoV-2-associated CF mostly engaged with the type of innate immune system, Toll-like receptor signaling pathway, pantothenate and CoA biosynthesis, allograft rejection, graft-versus-host disease, intestinal immune network for IgA production, mineral absorption, autoimmune thyroid disease, legionellosis, viral myocarditis, inflammatory bowel disease (IBD), etc. The drug compound identification demonstrates that the drug targets of IMIQUIMOD and raloxifene are the most significant with the significant hub DEGs.
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Bima AI, Elsamanoudy AZ, Alamri AS, Felimban R, Felemban M, Alghamdi KS, Kaipa PR, Elango R, Shaik NA, Banaganapalli B. Integrative global co-expression analysis identifies Key MicroRNA-target gene networks as key blood biomarkers for obesity. Minerva Med 2022; 113:532-541. [PMID: 35266657 DOI: 10.23736/s0026-4806.21.07478-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Obesity is associated with the quantitative changes in miRNAs and their target genes. However, the molecular basis of their dysregulation and expression status correlations is incompletely understood. Therefore, this study aims to examine the shared differentially expressed miRNAs and their target genes between blood and adipose tissues of obese individuals to identify potential blood-based biomarkers. In this study, 3 gene expression datasets (two mRNA and one miRNA), generated from blood and adipose tissues of 68 obese and 39 lean individuals, were analyzed by a series of robust computational concepts, like protein interactome mapping, functional enrichment of biological pathways and construction of miRNA-mRNA and transcription factor gene networks. The comparison of blood versus tissue datasets has revealed the shared differential expression of 210 genes (59.5% upregulated) involved in lipid metabolism and inflammatory reactions. The blood miRNA (GSE25470) analysis has identified 79 differentially expressed miRNAs (71% downregulated). The miRNA-target gene scan identified regulation of 30 shared genes by 22miRNAs. The gene network analysis has identified the inverse expression correlation between 8 target genes (TP53, DYSF, GAB2, GFRA2, NACC2, FAM53C, JNK and GAB2) and 3 key miRNAs (hsa-mir-940, hsa-mir-765, hsa-mir-612), which are further regulated by 24 key transcription factors. This study identifies potential obesity related blood biomarkers from largescale gene expression data by computational miRNA-target gene interactome and transcription factor network construction methods.
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Affiliation(s)
- Abdulhadi I Bima
- Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ayman Z Elsamanoudy
- Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Medical Biochemistry and Molecular Biology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Abdulhakeem S Alamri
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia.,Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Raed Felimban
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,3D Bioprinting Unit, Center of Innovation in Personalised Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majed Felemban
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kawthar S Alghamdi
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Prabhakar R Kaipa
- Department of Genetics, College of science, Osmania University, Hyderabad, India
| | - Ramu Elango
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor A Shaik
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia - .,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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Wang Q, Tang Q, Zhao L, Zhang Q, Wu Y, Hu H, Liu L, Liu X, Zhu Y, Guo A, Yang X. Time serial transcriptome reveals Cyp2c29 as a key gene in hepatocellular carcinoma development. Cancer Biol Med 2021; 17:401-417. [PMID: 32587777 PMCID: PMC7309465 DOI: 10.20892/j.issn.2095-3941.2019.0335] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022] Open
Abstract
Objective: Hepatocellular carcinoma (HCC) is a severely lethal cancer that usually originates from chronic liver injury and inflammation. Although progress on diagnosis and treatment is obvious, the cause of HCC remains unclear. In this study, we sought to determine key genes in HCC development. Methods: To identify key regulators during HCC progression, we performed transcriptome sequencing to obtain time series gene expression data from a mouse model with diethylnitrosamine-induced liver tumors and further verified gene expression and function in vitro and in vivo. Results: Among the differentially expressed genes, Cyp2c29 was continuously downregulated during HCC progression. Overexpression of Cyp2c29 suppressed NF-κB activation and proinflammatory cytokine production by increasing the production of 14,15-epoxyeicosatrienoic acid in vitro. Furthermore, overexpression of Cyp2c29 in vivo protected against liver inflammation in mouse models of liver injury induced by both acetaminophen and CCl4. Two human homologs of mouse Cyp2c29, CYP2C8 and CYP2C9, were found to be downregulated in human HCC progression, and their expression was positively correlated with overall survival in patients with HCC (significance: P = 0.046 and 0.0097, respectively). Conclusions: Collectively, through systematic analysis and verification, we determined that Cyp2c29 is a novel gene involved in liver injury and inflammation, which may be a potential biomarker for HCC prevention and prognosis determination.
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Affiliation(s)
- Qi Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qin Tang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lijun Zhao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qiong Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuxin Wu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hui Hu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lanlan Liu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiang Liu
- Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yanhong Zhu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Anyuan Guo
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiangliang Yang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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Tan S, Zhou Y, Zhao H, Wu J, Yu H, Yang Y, Yang Y, Zhao H, Li H. Comprehensive transcriptome analysis of hypothalamus reveals genes associated with disorders of sex development in pigs. J Steroid Biochem Mol Biol 2021; 210:105875. [PMID: 33746111 DOI: 10.1016/j.jsbmb.2021.105875] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/14/2022]
Abstract
XX sex reversal, also called XX disorders of sex development (XX-DSD), is a condition affecting the development of the gonads or genitalia, and is relatively common in pigs. However, its genetic etiology and transcriptional regulation mechanism in the hypothalamic-pituitary-gonadal axis (HPGA) remain mostly unknown. XX-DSD (SRY-negative) pigs and normal sows were selected by external genitalia observation. The hypothalamus, which is the integrated center of the HPGA was sampled for whole-transcriptome RNA-seq. The role of DEmiRNA was validated by its overexpression and knockdown in vitro. A total of 1,258 lncRNAs, 1,086 mRNAs, and 61 microRNAs differentially expressed in XX-DSD pigs compared with normal female pigs. Genes in the hormone biosynthesis and secretion pathway significantly up-regulated, and the up-regulation of GNRH1, KISS1 and AVP may associate with the abnormal secretion of GnRH. We also predicted the lncRNA-miRNA-mRNA co-expression triplets and constructed three competing endogenous RNA (ceRNA) potentially associated with XX-DSD. Functional enrichment studies suggested that TCONS_00340886, TCONS_00000204 and miR-181a related to GnRH secretion. Further, miR-181a inhibitor up-regulated GNRH1, PAK6, and CAMK4 in the GT1-7 cells. Conversely, transfection of miR-181a mimics obtained the opposite trends. The expression levels of FSHR, LHR, ESR1 and ESR2 were significantly higher in XX-DSD gondas than those in normal sows. Taken together, we proposed that the balance of endocrine had broken in XX-DSD pigs. The current study is the first to examine the transcriptomic profile in the hypothalamus of XX-DSD pigs. It provides new insight into coding and non-coding RNAs that may be associated with DSD in pigs.
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Affiliation(s)
- Shuwen Tan
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan 430072, China; Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Yi Zhou
- College of Basic Medicine, Zunyi Medical University, Zunyi 563006, China
| | - Haiquan Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jinhua Wu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Hui Yu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Yin Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Yalan Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan 430072, China; College of Science, Tibet University, Lhasa 850000, China.
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China.
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Feiz Haddad MH, Rezvan H, Nourian A, Habibpour H. Expression of MicroRNA of Macrophages Infected with Attenuated Leishmania major Parasite. J PEDIAT INF DIS-GER 2021. [DOI: 10.1055/s-0041-1724021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Objective Leishmaniasis has been proposed as one of the neglected vector-borne diseases due to an obligate intracellular parasite of the genus Leishmania. MicroRNAs (miRNAs) with a length of 22-nucleotide are known as the noncoding small RNAs. MiRNAs contribute to many biological and cellular approaches. Therefore, the present study evaluated expressing mmu-miR-721, mmu-miR-294–3p, mmu-miR-155–3p, and mmu-miR-30a in murine macrophages infected with attenuated Leishmania major parasites on 3 days after infection.
Methods Attenuated promastigotes have been achieved after 20 passages of Leishmania major parasites. Cell line J774A.1 (murine macrophage) has been used for in vitro experiments. The stationary phase of attenuated L. major promastigotes has been chosen to infect the cells, and then their incubation has been performed with 5% CO2 at 37°C for 3 days. The real-time polymerase chain reaction (PCR) has also been performed with SYBR Green master-mix Kit for measuring the level of mmu-miR-721, mmu-miR-294–3p, mmu-miR-30a, and mmu-miR-155-3p expression. Uninfected macrophages have been considered as a control group.
Results Real-time PCR demonstrated overexpression of mmu-miR-155-3p, mmu-miR-294–3p, and, mmu-miR-721 in the infected cells with Leishmania parasites after 3 days. Results showed no statistically significant difference in the mmu-miR-30a expression between infected macrophages and the uninfected control group.
Conclusion Our findings suggested the significant contribution of the alterations in the miRNA levels to the regulation of macrophage functions following the creation of intracellular parasites like Leishmania. These data could help to understand better the genes' expression in the host cells in the course of leishmaniasis.
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Affiliation(s)
- Mohammad Hossein Feiz Haddad
- Cellular and Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Parasitology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hossein Rezvan
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
| | - Alireza Nourian
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
| | - Habib Habibpour
- Cellular and Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Parasitology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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9
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Huo Q, Ma Y, Yin Y, Qin G. Biomarker Identification for Liver Hepatocellular Carcinoma and Cholangiocarcinoma Based on Gene Regulatory Network Analysis. Curr Bioinform 2021. [DOI: 10.2174/1574893615666200317115609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Background:
Liver hepatocellular carcinoma (LIHC) and cholangiocarcinoma (CHOL)
are two main histological subtypes of primary liver cancer with a unified molecular landscape, and
feed-forward loops (FFLs) have been shown to be relevant in these complex diseases.
Objective:
To date, there has been no comparative analysis of the pathogenesis of LIHC and CHOL
based on regulatory relationships. Therefore, we investigated the common and distinct regulatory
properties of LIHC and CHOL in terms of gene regulatory networks.
Method:
Based on identified FFLs and an analysis of pathway enrichment, we constructed pathway-specific co-expression networks and further predicted biomarkers for these cancers by network clustering.
Resul:
We identified 20 and 36 candidate genes for LIHC and CHOL, respectively. The literature
from PubMed supports the reliability of our results.
Conclusion:
Our results indicated that the hsa01522-Endocrine resistance pathway was associated
with both LIHC and CHOL. Additionally, six genes (SPARC, CTHRC1, COL4A1, EDIL3, LAMA4
and OLFML2B) were predicted to be highly associated with both cancers, and COL4A2, CSPG4,
GJC1 and ADAMTS7 were predicted to be potential biomarkers of LIHC, and COL6A3, COL1A2,
FAP and COL8A1 were predicted to be potential biomarkers of CHOL. In addition, we inferred that
the Collagen gene family, which appeared more frequently in our overall prediction results, might be
closely related to cancer development.
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Affiliation(s)
- Qiuyan Huo
- School of Computer Science and Technology, Xidian University, Xi’an,China
| | - Yuying Ma
- School of Computer Science and Technology, Xidian University, Xi’an,China
| | - Yu Yin
- School of Computer Science and Technology, Xidian University, Xi’an,China
| | - Guimin Qin
- School of Computer Science and Technology, Xidian University, Xi’an,China
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10
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Khurana P, Gupta A, Sugadev R, Sharma YK, Kumar B. HAHmiR.DB: a server platform for high-altitude human miRNA-gene coregulatory networks and associated regulatory circuits. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:6015264. [PMID: 33259604 PMCID: PMC7706787 DOI: 10.1093/database/baaa101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/27/2020] [Accepted: 11/15/2020] [Indexed: 12/12/2022]
Abstract
Around 140 million people live in high-altitude (HA) conditions! and even a larger number visit such places for tourism, adventure-seeking or sports training. Rapid ascent to HA can cause severe damage to the body organs and may lead to many fatal disorders. During induction to HA, human body undergoes various physiological, biochemical, hematological and molecular changes to adapt to the extreme environmental conditions. Several literature references hint that gene-expression-regulation and regulatory molecules like miRNAs and transcription factors (TFs) control adaptive responses during HA stress. These biomolecules are known to interact in a complex combinatorial manner to fine-tune the gene expression and help in controlling the molecular responses during this stress and ultimately help in acclimatization. High-Altitude Human miRNA Database (HAHmiR.DB) is a unique, comprehensive and curated collection of miRNAs that have been experimentally validated to be associated with HA stress, their level of expression in different altitudes, fold change, experiment duration, biomarker association, disease and drug association, tissue-specific expression level, Gene Ontology (GO) and Kyoto Encyclopaedia of Gene and Genomes (KEGG) pathway associations. As a server platform, it also uniquely constructs and analyses interactive miRNA-TF-gene coregulatory networks and extracts regulatory circuits/feed-forward loops (FFLs). These regulatory circuits help to offer mechanistic insights into complex regulatory mechanisms during HA stress. The server can also build these regulatory networks between two and more miRNAs of the database and also identify the regulatory circuits from this network. Hence, HAHmiR.DB is the first-of-its-kind database in HA research, which is a reliable platform to explore, compare, analyse and retrieve miRNAs associated with HA stress, their coregulatory networks and FFL regulatory-circuits. HAHmiR.DB is freely accessible at http://www.hahmirdb.in.
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Affiliation(s)
- Pankaj Khurana
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Apoorv Gupta
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Ragumani Sugadev
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Yogendra Kumar Sharma
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Bhuvnesh Kumar
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
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11
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Khurana P, Gupta A, Sugadev R, Sharma YK, Varshney R, Ganju L, Kumar B. nSARS-Cov-2, pulmonary edema and thrombosis: possible molecular insights using miRNA-gene circuits in regulatory networks. ACTA ACUST UNITED AC 2020; 2:16. [PMID: 33209992 PMCID: PMC7596315 DOI: 10.1186/s41544-020-00057-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/18/2020] [Indexed: 12/11/2022]
Abstract
Background Given the worldwide spread of the novel Severe Acute Respiratory Syndrome Coronavirus 2 (nSARS-CoV-2) infection pandemic situation, research to repurpose drugs, identify novel drug targets, vaccine candidates have created a new race to curb the disease. While the molecular signature of nSARS-CoV-2 is still under investigation, growing literature shows similarity among nSARS-CoV-2, pulmonary edema, and thromboembolic disorders due to common symptomatic features. A network medicine approach is used to to explore the molecular complexity of the disease and to uncover common molecular trajectories of edema and thrombosis with nSARS-CoV-2. Results and conclusion A comprehensive nSARS-CoV-2 responsive miRNA: Transcription Factor (TF): gene co-regulatory network was built using host-responsive miRNAs and it’s associated tripartite, Feed-Forward Loops (FFLs) regulatory circuits were identified. These regulatory circuits regulate signaling pathways like virus endocytosis, viral replication, inflammatory response, pulmonary vascularization, cell cycle control, virus spike protein stabilization, antigen presentation, etc. A unique miRNA-gene regulatory circuit containing a consortium of four hub FFL motifs is proposed to regulate the virus-endocytosis and antigen-presentation signaling pathways. These regulatory circuits also suggest potential correlations/similarity in the molecular mechanisms during nSARS-CoV-2 infection, pulmonary diseases and thromboembolic disorders and thus could pave way for repurposing of drugs. Some important miRNAs and genes have also been proposed as potential candidate markers. A detailed molecular snapshot of TGF signaling as the common pathway, that could play an important role in controlling common pathophysiologies among diseases, is also put forth. Supplementary information Supplementary information accompanies this paper at 10.1186/s41544-020-00057-y.
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Affiliation(s)
- P Khurana
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - A Gupta
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - R Sugadev
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - Y K Sharma
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - R Varshney
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - L Ganju
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
| | - B Kumar
- Defence Institute of Physiology and Allied Sciences, Defence R&D Organization, Lucknow Road, Timarpur, New Delhi, India
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12
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Ogbu SC, Musich PR, Zhang J, Yao ZQ, Howe PH, Jiang Y. The role of disabled-2 (Dab2) in diseases. Gene 2020; 769:145202. [PMID: 33059028 DOI: 10.1016/j.gene.2020.145202] [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: 08/03/2020] [Revised: 09/16/2020] [Accepted: 09/29/2020] [Indexed: 12/16/2022]
Abstract
Disabled-2 (Dab2/DOC-2) is a mitogen-responsive adaptor protein required for multiple cellular functions. It is involved in many signaling pathways and plays an integral role in vesicular uptake and trafficking, modulating immune function, protein-protein interactions, cellular homeostasis and differentiation, oncogenesis, and inflammatory processes in organ systems. It contains domains for binding to NPXY motif-containing and SH3 domain-containing adapter proteins, phosphoinositides, glycoprotein 100 (gp100, or megalin), integrins, clathrin, and myosin VI. However, the molecular mechanism(s) of Dab2's biological function still remain to be elucidated. In this review, we provide an extensive up-to-date understanding of the function of Dab2 and its regulation in cardiovascular diseases, immune disorders, tumorigenesis, and central nervous system disorders.
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Affiliation(s)
- Stella C Ogbu
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Phillip R Musich
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jinyu Zhang
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Zhi Q Yao
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Yong Jiang
- Department of Biomedical Sciences, J. H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA.
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13
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MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons. Sci Rep 2020; 10:8593. [PMID: 32451429 PMCID: PMC7248120 DOI: 10.1038/s41598-020-65319-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 04/28/2020] [Indexed: 12/14/2022] Open
Abstract
Muscular atrophy or muscle loss is a multifactorial clinical condition during many critical illnesses like cancer, cardiovascular diseases, diabetes, pulmonary diseases etc. leading to fatigue and weakness and contributes towards a decreased quality of life. The proportion of older adults (>65 y) in the overall population is also growing and aging is another important factor causing muscle loss. Some muscle miRNAs (myomiRs) and their target genes have even been proposed as potential diagnostic, therapeutic and predictive markers for muscular atrophy. MyomirDB (http://www.myomirdb.in/) is a unique resource that provides a comprehensive, curated, user- friendly and detailed compilation of various miRNA bio-molecular interactions; miRNA-Transcription Factor-Target Gene co-regulatory networks and ~8000 tripartite regulons associated with 247 myomiRs which have been experimentally validated to be associated with various muscular atrophy conditions. For each database entry, MyomirDB compiles source organism, muscle atrophic condition, experiment duration, its level of expression, fold change, tissue of expression, experimental validation, disease and drug association, tissue-specific expression level, Gene Ontology and KEGG pathway associations. The web resource is a unique server platform which uses in-house scripts to construct miRNA-Transcription Factor-Target Gene co-regulatory networks and extract tri-partite regulons also called Feed Forward Loops. These unique features helps to offer mechanistic insights in disease pathology. Hence, MyomirDB is a unique platform for researchers working in this area to explore, fetch, compare and analyse atrophy associated miRNAs, their co-regulatory networks and FFL regulons.
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14
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Chiang MH, Liang CJ, Lin LC, Yang YF, Huang CC, Chen YH, Kao HL, Chen YC, Ke SR, Lee CW, Lin MS, Chen YL. miR-26a attenuates cardiac apoptosis and fibrosis by targeting ataxia-telangiectasia mutated in myocardial infarction. J Cell Physiol 2020; 235:6085-6102. [PMID: 31990056 DOI: 10.1002/jcp.29537] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/08/2020] [Indexed: 12/16/2022]
Abstract
Apoptosis and fibrosis play a vital role in myocardial infarction (MI) induced tissue injury. Although microRNAs have been the focus of many studies on cardiac apoptosis and fibrosis in MI, the detailed effects of miR-26a is needed to further understood. The present study demonstrated that miR-26a was downregulated in ST-elevation MI (STEMI) patients and oxygen-glucose deprivation (OGD)-treated H9c2 cells. Downregulation of miR-26a was closely correlated with the increased expression of creatine kinase, creatine kinase-MB and troponin I in STEMI patients. Further analysis identified that ataxia-telangiectasia mutated (ATM) was a target gene for miR-26a based on a bioinformatics analysis. miR-26a overexpression effectively reduced ATM expression, apoptosis, and apoptosis-related proteins in OGD-treated H9c2 cells. In a mouse model of MI, the expression of miR-26a was significantly decreased in the infarct zone of the heart, whereas apoptosis and ATM expression were increased. miR-26a overexpression effectively reduced ATM expression and cardiac apoptosis at Day 1 after MI. Furthermore, we demonstrated that overexpression of miR-26a improved cardiac function and reduced cardiac fibrosis by the reduced expression of collagen type I and connective tissue growth factor (CTGF) in mice at Day 14 after MI. Overexpression of miR-26a or ATM knockdown decreased collagen I and CTGF expression in cultured OGD-treated cardiomyocytes. Taken together, these data demonstrate a prominent role for miR-26a in linking ATM expression to ischemia-induced apoptosis and fibrosis, key features of MI progression. miR-26a reduced MI development by affecting ATM expression and could be targeted in the treatment of MI.
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Affiliation(s)
- Ming-Hsien Chiang
- Department of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chan-Jung Liang
- Lipid Science and Aging Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Lung-Chun Lin
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Fan Yang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ching-Chang Huang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ying-Hsien Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsien-Li Kao
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Chen Chen
- Department of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shin-Rong Ke
- Cardiology Division of Cardiovascular Medical Center, Far Eastern Memorial Hospital, Taipei, Taiwan
| | - Chiang-Wen Lee
- Division of Basic Medical Sciences, Department of Nursing, and Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chiayi, Taiwan.,Department of Rehabilitation, Chang Gung Memorial Hospital, Chiayi, Taiwan.,Research Center for Industry of Human Ecology and Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Mao-Shin Lin
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yuh-Lien Chen
- Department of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
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15
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Qin G, Mallik S, Mitra R, Li A, Jia P, Eischen CM, Zhao Z. MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. Sci Rep 2020; 10:852. [PMID: 31965022 PMCID: PMC6972857 DOI: 10.1038/s41598-020-57834-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/24/2019] [Indexed: 12/11/2022] Open
Abstract
Recent studies have revealed that feed-forward loops (FFLs) as regulatory motifs have synergistic roles in cellular systems and their disruption may cause diseases including cancer. FFLs may include two regulators such as transcription factors (TFs) and microRNAs (miRNAs). In this study, we extensively investigated TF and miRNA regulation pairs, their FFLs, and TF-miRNA mediated regulatory networks in two major types of testicular germ cell tumors (TGCT): seminoma (SE) and non-seminoma (NSE). Specifically, we identified differentially expressed mRNA genes and miRNAs in 103 tumors using the transcriptomic data from The Cancer Genome Atlas. Next, we determined significantly correlated TF-gene/miRNA and miRNA-gene/TF pairs with regulation direction. Subsequently, we determined 288 and 664 dysregulated TF-miRNA-gene FFLs in SE and NSE, respectively. By constructing dysregulated FFL networks, we found that many hub nodes (12 out of 30 for SE and 8 out of 32 for NSE) in the top ranked FFLs could predict subtype-classification (Random Forest classifier, average accuracy ≥90%). These hub molecules were validated by an independent dataset. Our network analysis pinpointed several SE-specific dysregulated miRNAs (miR-200c-3p, miR-25-3p, and miR-302a-3p) and genes (EPHA2, JUN, KLF4, PLXDC2, RND3, SPI1, and TIMP3) and NSE-specific dysregulated miRNAs (miR-367-3p, miR-519d-3p, and miR-96-5p) and genes (NR2F1 and NR2F2). This study is the first systematic investigation of TF and miRNA regulation and their co-regulation in two major TGCT subtypes.
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Affiliation(s)
- Guimin Qin
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.,School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ramkrishna Mitra
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.,School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Christine M Eischen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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16
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Lin CM, Fang WJ, Wang BW, Pan CM, Chua SK, Hou SW, Shyu KG. (-)-Epigallocatechin Gallate Promotes MicroRNA 145 Expression against Myocardial Hypoxic Injury through Dab2/Wnt3a/β-catenin. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2020; 48:341-356. [DOI: 10.1142/s0192415x20500172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
MicroRNA 145 (miR-145) is a critical modulator of cardiovascular diseases. The downregulation of myocardial miR-145 is followed by an increase in disabled-2 (Dab2) expression in cardiomyocytes. (-)-epigallocatechin gallate (EGCG) is a flavonoid that has been evaluated extensively due to its diverse pharmacological properties including anti-inflammatory effects. The aim of this study was to investigate the cardioprotective effects of EGCG under hypoxia-induced stress in vitro and in vivo. The hypoxic insult led to the suppression of miR-145 expression in cultured rat cardiomyocytes in a concentration-dependent manner. Western blotting and real-time PCR were performed. In rat myocardial infarction study, in situ hybridization, and immunofluorescent analyses were adopted. The western blot and real-time PCR data revealed that hypoxic stress with 2.5% O2 suppressed the expression of miR-145 and Wnt3a/[Formula: see text]-catenin in cultured rat cardiomyocytes but augmented Dab2. Treatment with EGCG attenuated Dab2 expression, but increased Wnt3a and [Formula: see text]-catenin in hypoxic cultured cardiomyocytes. Following in vivo myocardial infarction (MI) study, the data revealed the myocardial infarct area reduced by 48.5%, 44.6%, and 48.5% in EGCG (50[Formula: see text]mg/kg) or miR-145 dominant or Dab2 siRNA groups after myocardial infarction for 28 days, respectively. This study demonstrated that EGCG increased miR-145, Wnt3a, and [Formula: see text]-catenin expression but attenuated Dab2 expression. Moreover, EGCG ameliorated myocardial ischemia in vivo. The novel suppressive effect was mediated through the miR-145 and Dab2/Wnt3a/[Formula: see text]-catenin pathways.
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Affiliation(s)
- Chiu-Mei Lin
- Department of Emergency Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
- Faculty of Medicine, School of Medicine, Fu Jen Catholic University, Taipei City, Taiwan
- Institute of Injury Prevention and Control, College of Public Health, Taipei Medical University, Taipei City, Taiwan
| | - Wei-Jen Fang
- Department of Medical Education and Research, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Bao-Wei Wang
- Department of Medical Education and Research, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Chun-Ming Pan
- Department of Medical Education and Research, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Su-Kiat Chua
- Division of Cardiology, Department of Internal Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
- Faculty of Medicine, School of Medicine, Fu Jen Catholic University, Taipei City, Taiwan
| | - Sheng-Wen Hou
- Department of Emergency Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
- Division of Cardiology, Department of Internal Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
- Faculty of Medicine, School of Medicine, Fu Jen Catholic University, Taipei City, Taiwan
| | - Kou-Gi Shyu
- Department of Emergency Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
- Division of Cardiology, Department of Internal Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
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17
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Zhao Z, Du S, Shen S, Wang L. microRNA‐132 inhibits cardiomyocyte apoptosis and myocardial remodeling in myocardial infarction by targeting IL‐1β. J Cell Physiol 2019; 235:2710-2721. [PMID: 31621911 DOI: 10.1002/jcp.29175] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Zonglei Zhao
- Department of Cardiology Henan Provincial People's Hospital (Zhengzhou University People's Hospital) Zhengzhou China
| | - Song Du
- Department of Cardiology Henan Provincial People's Hospital (Zhengzhou University People's Hospital) Zhengzhou China
| | - Shuxin Shen
- Department of Cardiology Henan Provincial People's Hospital (Zhengzhou University People's Hospital) Zhengzhou China
| | - Lixia Wang
- Department of Cardiology Henan Provincial People's Hospital (Zhengzhou University People's Hospital) Zhengzhou China
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18
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Huang W, Hu H, Zhang Q, Wu X, Wei F, Yang F, Gan L, Wang N, Yang X, Guo AY. Regulatory networks in mechanotransduction reveal key genes in promoting cancer cell stemness and proliferation. Oncogene 2019; 38:6818-6834. [PMID: 31406247 PMCID: PMC6988105 DOI: 10.1038/s41388-019-0925-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 06/21/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022]
Abstract
Tumor-repopulating cells (TRCs) are cancer stem cell (CSC)-like cells with highly tumorigenic and self-renewing abilities, which were selected from tumor cells in soft three-dimensional (3D) fibrin gels with unidentified mechanisms. Here we evaluated the transcriptome alteration during TRCs generation in 3D culture and revealed that a variety of molecules related with integrin/membrane and stemness were continuously altered by mechanical environment. Some key regulators such as MYC/STAT3/hsa-miR-199a-5p, were changed in the TRCs generation. They regulated membrane genes and the downstream mechanotransduction pathways such as Hippo/WNT/TGF-β/PI3K-AKT pathways, thus further affecting the expression of downstream cancer-related genes. By integrating networks for membrane proteins, the WNT pathway and cancer-related genes, we identified key molecules in the selection of TRCs, such as ATF4, SLC3A2, CCT3, and hsa-miR-199a-5p. Silencing ATF4 or CCT3 inhibited the selection and growth of TRCs whereas reduction of SLC3A2 or hsa-miR-199a-5p promoted TRCs growth. Further studies showed that CCT3 promoted cell proliferation and stemness in vitro, while its suppression inhibited TRCs-induced tumor formation. We also contemplated CCT3 as a stemness-related gene. Our findings provide insights in the mechanism of TRCs selection through transcriptome analysis.
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Affiliation(s)
- Wei Huang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Hui Hu
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Qiong Zhang
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Xian Wu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Fuxiang Wei
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Fang Yang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Lu Gan
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China
| | - Ning Wang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
- Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China.
| | - An-Yuan Guo
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China.
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19
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MiR-466h-5p induces expression of myocardin with complementary promoter sequences. Biochem Biophys Res Commun 2019; 514:187-193. [PMID: 31029421 DOI: 10.1016/j.bbrc.2019.04.133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/18/2019] [Indexed: 11/22/2022]
Abstract
A number of studies microRNAs (miRNA) play an important role in cardiac physiological and pathological processes. In these studies, miRNA regulates gene expression by repressing translation or directing sequence-specific degradation of complementary mRNA. Here, we reveal a new regulatory mechanism in the process of cardiac hypertrophy which miRNA may also regulate the promoter activity of target genes. In the course of the study, we find that miR-466h-5p regulates the occurrence of myocardial hypertrophy via myocardin and it can upregulate the expression of myocardin through directly binding to the promoter region of myocardin. Meanwhile, we also find that myocardin can reverse-activate miR-466h-5p expression through binding to the CarG box. Thus, miR-466h-5p and myocardin form a positive regulation loop in the process of cardiac hypertrophy. These findings reveal a new mode by which miRNAs may regulate gene expression and may play a positive role in revealing the complete mechanisms of cardiac hypertrophy.
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20
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Systems biology approach identifies key regulators and the interplay between miRNAs and transcription factors for pathological cardiac hypertrophy. Gene 2019; 698:157-169. [DOI: 10.1016/j.gene.2019.02.056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/31/2019] [Accepted: 02/20/2019] [Indexed: 12/16/2022]
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21
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Mohamed RH, Abu-Shahba N, Mahmoud M, Abdelfattah AMH, Zakaria W, ElHefnawi M. Co-regulatory Network of Oncosuppressor miRNAs and Transcription Factors for Pathology of Human Hepatic Cancer Stem Cells (HCSC). Sci Rep 2019; 9:5564. [PMID: 30944375 PMCID: PMC6447552 DOI: 10.1038/s41598-019-41978-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/21/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatic cancer stem cells (HCSCs) are considered as main players for the hepatocellular carcinoma (HCC) initiation, metastasis, drug resistance and recurrence. There is a growing evidence supporting the down-regulated miRNAs in HCSCs as key suppressors for the stemness traits, but still more details are vague about how these miRNAs modulate the HCC development. To uncover some of these miRNA regulatory aspects in HCSC, we compiled 15 down-regulated miRNA and their validated and predicted up-regulated targets in HCSC. The targets were enriched for several cancer cell stemness hallmarks and CSC pre-metastatic niche, which support these miRNAs role in suppression of HCSCs neoplastic transformation. Further, we constructed miRNA-Transcription factor (TF) regulatory networks, which provided new insights on the role of the proposed miRNA-TF co-regulation in the cancer stemness axis and its cross talk with the surrounding microenvironment. Our analysis revealed HCSC important hubs as candidate regulators for targeting hepatic cancer stemness such as, miR-148a, miR-214, E2F family, MYC and SLC7A5. Finally, we proposed a possible model for miRNA and TF co-regulation of HCSC signaling pathways. Our study identified an HCSC signature and set bridges between the reported results to give guide for future validation of HCC therapeutic strategies avoiding drug resistance.
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Affiliation(s)
- Rania Hassan Mohamed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Nourhan Abu-Shahba
- Stem Cell Research Group, Centre of Excellence for Advanced Sciences, Department of Medical Molecular Genetics, National Research Centre, Cairo, Egypt
| | - Marwa Mahmoud
- Stem Cell Research Group, Centre of Excellence for Advanced Sciences, Department of Medical Molecular Genetics, National Research Centre, Cairo, Egypt
| | - Ahmed M H Abdelfattah
- Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, Egypt.,VAP, CS Department, SUNY, Oswego, NY, USA
| | - Wael Zakaria
- Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mahmoud ElHefnawi
- Biomedical informatics and Chemoinformatics group, Centre of Excellence for Advanced Sciences, Informatics and Systems Department, National Research Centre, Cairo, Egypt. .,Informatics and systems Department, Division of Engineering research, National Research Centre, Cairo, Egypt.
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22
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Wu HY, Wu JL, Ni ZL. Overexpression of microRNA-202-3p protects against myocardial ischemia-reperfusion injury through activation of TGF-β1/Smads signaling pathway by targeting TRPM6. Cell Cycle 2019; 18:621-637. [PMID: 30810438 PMCID: PMC6464590 DOI: 10.1080/15384101.2019.1580494] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) have been found to act as key regulators in the pathogenesis of myocardial ischemic-reperfusion (I/R) injury. In this study, we explore the role and mechanism of microRNA-202-3p (miR-202-3p) in regulating cardiomyocyte apoptosis, in respective of the TGF-β1/Smads signaling pathway by targeting the transient receptor potential cation channel, subfamily M, member 6 (TRPM6). The targeting relationship between miR-202-3p and TRPM6 was verified by a dual-luciferase reporter gene assay. Sprague-Dawley rat models of myocardial I/R injury were initially established and treated with different mimics, inhibitors and siRNAs to test the effects of miR-202-3p and TRPM6 on myocardial I/R injury. The levels of inflammatory factors; IL-1β, IL-6, TNF-α as well as the degree of myocardial fibrosis and cardiomyocyte apoptosis were determined in rats transfected with different plasmids. TRPM6 was found to be the target of miR-202-3p. Up-regulated miR-202-3p or knockdown of TRPM-6 alleviated oxidative stress and inflammatory response, reduced ventricular mass, altered cardiac hemodynamics, suppressed myocardial infarction, attenuated cell apoptosis, and inhibited myocardial fibrosis. MiR-202-3p overexpression activates the TGF-β1/Smads signaling pathway by negatively regulating TRPM6 expression. Taken together, these findings suggest that miR-202-3p offers protection against ventricular remodeling after myocardial I/R injury via activation of the TGF-β1/Smads signaling pathway.
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Affiliation(s)
- Hui-Ying Wu
- a Department of Cardiovascular Medicine , Fuwai Central China Cardiovascular Hospital , Zhengzhou , P.R. China
| | - Jian-Li Wu
- b Medical School , Huanghe S & T University , Zhengzhou , P.R. China
| | - Zhan-Ling Ni
- a Department of Cardiovascular Medicine , Fuwai Central China Cardiovascular Hospital , Zhengzhou , P.R. China
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23
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Xia M, Zhang Q, Luo M, Li P, Wang Y, Lei Q, Guo AY. Regulatory network analysis reveals the oncogenesis roles of feed-forward loops and therapeutic target in T-cell acute lymphoblastic leukemia. BMC Med Genomics 2019; 12:8. [PMID: 30646895 PMCID: PMC6332896 DOI: 10.1186/s12920-018-0469-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/26/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy. Aberrant expressed genes contribute to the development and progression of T-ALL. However, the regulation underlying their aberrant expression remains elusive. Dysregulated expression of transcription factors and miRNAs played important regulatory roles in the pathogenesis of T-ALL. METHODS In this study, we analyzed the alteration of transcriptome profiling and regulatory networks between T-ALL sample and normal T cell samples at transcriptional and post-transcriptional levels. RESULTS Our results demonstrated that genes related to cell cycle and cell proliferation processes were significantly upregulated in T-ALL comparing to normal samples. Meanwhile, regulatory network analyses revealed that FOXM1, MYB, SOX4 and miR-21/19b as core regulators played vital roles in the development of T-ALL. FOXM1-miR-21-5p-CDC25A and MYB/SOX4-miR-19b-3p-RBBP8 were identified as important feed-forward loops involved in the oncogenesis of T-ALL. Drug-specific analyses showed that GSK-J4 may be an effective drug, and CDC25A/CAPN2/MCM2 could serve as potential therapeutic targets for T-ALL. CONCLUSIONS This study may provide novel insights for the regulatory mechanisms underlying the development of T-ALL and potential therapeutic targets.
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Affiliation(s)
- Mengxuan Xia
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 China
| | - Qiong Zhang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 China
| | - Mei Luo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 China
| | - Pan Li
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 China
| | - Yingxue Wang
- Department of Hematology, the Second Hospital of Shandong University, Jinan, 250033 Shandong China
| | - Qian Lei
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 China
| | - An-Yuan Guo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 China
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Zhou Y, Xu Z, Yu Y, Cao J, Qiao Y, Qiao H, Suo G. Comprehensive analysis of the lncRNA-associated ceRNA network identifies neuroinflammation biomarkers for Alzheimer's disease. Mol Omics 2019; 15:459-469. [DOI: 10.1039/c9mo00129h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accumulating evidence has highlighted the important roles of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in Alzheimer's disease (AD).
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Affiliation(s)
- Yuanshuai Zhou
- Jiangsu Key Lab of Medical Optics
- Suzhou Institute of Biomedical Engineering and Technology
- Chinese Academy of Sciences
- Jiangsu
- China
| | - Zhongjuan Xu
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Jiangsu 215123
- China
| | - Yanzhen Yu
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Jiangsu 215123
- China
| | - Junjun Cao
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Jiangsu 215123
- China
| | - Yong Qiao
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Jiangsu 215123
- China
| | - Hong Qiao
- Department of Molecular Biosciences
- the University of Texas at Austin
- Austin
- USA
| | - Guangli Suo
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Jiangsu 215123
- China
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25
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Muxel SM, Acuña SM, Aoki JI, Zampieri RA, Floeter-Winter LM. Toll-Like Receptor and miRNA-let-7e Expression Alter the Inflammatory Response in Leishmania amazonensis-Infected Macrophages. Front Immunol 2018; 9:2792. [PMID: 30555476 PMCID: PMC6283264 DOI: 10.3389/fimmu.2018.02792] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022] Open
Abstract
Parasite recognition by Toll-like receptors (TLRs) contributes to macrophage activation and subsequent control of Leishmania infection through the coordinated production of pro-inflammatory and microbicidal effector molecules. The modulation of microRNA (miRNA) expression by Leishmania infection potentially mediates the post-transcriptional regulation of the expression of genes involved in leishmanicidal activity. Here, the contribution of TLR signaling to the miRNA profile and gene expression was evaluated in Leishmania amazonensis-infected murine macrophages. The infectivity of L. amazonensis was higher in murine bone marrow-derived macrophages from mice knockout for myeloid differentiation factor 88 (MyD88−/−), TLR2 (TLR2−/−), or TLR4 (TLR4−/−) than wild type C57BL/6 (WT). L. amazonensis infection of WT macrophages modulated the expression of 32% of the miRNAs analyzed, while 50% were upregulated. The absence of MyD88, TLR2, and TLR4 altered the percentage of miRNAs modulated during L. amazonensis infection, including the downregulation of let-7e expression. Moreover, the absence of signals mediated by MyD88, TLR2, or TLR4 reduced nitric oxide synthase 2 (Nos2) mRNA expression during infection. Indeed, the inhibition of let-7e increased levels of the Nos2 mRNA and NOS2 (or iNOS) protein and nitric oxide (NO) production in L. amazonensis-infected macrophages (4–24 h). The absence of TLR2 and inhibition of let-7e increased the expression of the arginase 1 (Arg1) mRNA but did not alter the protein level during infection. However, higher levels of the L-arginine transporters Cat2B and Cat1 were detected in the absence of Myd88 signaling during infection but were not altered following let-7e inhibition. The inhibition of let-7e impacted the global expression of genes in the TLR pathway by upregulating the expression of recognition and adaptors molecules, such as Tlr6, Tlr9, Ly96, Tirap, Traf 6, Ticam1, Tollip, Casp8, Map3k1, Mapk8, Nfkbib, Nfkbil1, Ppara, Mapk8ip3, Hspd1, and Ube2n, as well as immunomodulators, such as Ptgs2/Cox2, Csf 2, Csf 3, Ifnb1, Il6ra, and Ilr1, impacting NOS2 expression, NO production and parasite infectiveness. In conclusion, L. amazonensis infection alters the TLR signaling pathways by modulating the expression of miRNAs in macrophages to subvert the host immune responses.
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Affiliation(s)
- Sandra Marcia Muxel
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Stephanie Maia Acuña
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Juliana Ide Aoki
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ricardo Andrade Zampieri
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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26
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Characterization of dysregulated lncRNA-mRNA network based on ceRNA hypothesis to reveal the occurrence and recurrence of myocardial infarction. Cell Death Discov 2018. [PMID: 29531832 PMCID: PMC5841419 DOI: 10.1038/s41420-018-0036-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) play important roles in initiation and development of human diseases. However, the mechanism of ceRNA regulated by lncRNA in myocardial infarction (MI) remained unclear. In this study, we performed a multi-step computational method to construct dysregulated lncRNA-mRNA networks for MI occurrence (DLMN_MI_OC) and recurrence (DLMN_MI_Re) based on “ceRNA hypothesis”. We systematically integrated lncRNA and mRNA expression profiles and miRNA-target regulatory interactions. The constructed DLMN_MI_OC and DLMN_MI_Re both exhibited biological network characteristics, and functional analysis demonstrated that the networks were specific for MI. Additionally, we identified some lncRNA-mRNA ceRNA modules involved in MI occurrence and recurrence. Finally, two new panel biomarkers defined by four lncRNAs (RP1-239B22.5, AC135048.13, RP11-4O1.2, RP11-285F7.2) from DLMN_MI_OC and three lncRNAs (RP11-363E7.4, CTA-29F11.1, RP5-894A10.6) from DLMN_MI_Re with high classification performance were, respectively, identified in distinguishing controls from patients, and patients with recurrent events from those without recurrent events. This study will provide us new insight into ceRNA-mediated regulatory mechanisms involved in MI occurrence and recurrence, and facilitate the discovery of candidate diagnostic and prognosis biomarkers for MI.
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27
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Soliman M, Andreeva K, Nasraoui O, Cooper NGF. A causal mediation model of ischemia reperfusion injury in the retina. PLoS One 2017; 12:e0187426. [PMID: 29121052 PMCID: PMC5679526 DOI: 10.1371/journal.pone.0187426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/19/2017] [Indexed: 11/30/2022] Open
Abstract
The goal of this study is to develop a model that explains the relationship between microRNAs, transcription factors, and their co-target genes. This relationship was previously reported in gene regulatory loops associated with 24 hour (24h) and 7 day (7d) time periods following ischemia-reperfusion injury in a rat's retina. Using a model system of retinal ischemia-reperfusion injury, we propose that microRNAs first influence transcription factors, which in turn act as mediators to influence transcription of genes via triadic regulatory loops. Analysis of the relative contributions of direct and indirect regulatory influences on genes revealed that a substantial fraction of the regulatory loops (69% for 24 hours and 77% for 7 days) could be explained by causal mediation. Over 40% of the mediated loops in both time points were regulated by transcription factors only, while about 20% of the loops were regulated entirely by microRNAs. The remaining fractions of the mediated regulatory loops were cooperatively mediated by both microRNAs and transcription factors. The results from these analyses were supported by the patterns of expression of the genes, transcription factors, and microRNAs involved in the mediated loops in both post-ischemic time points. Additionally, network motif detection for the mediated loops showed a handful of time specific motifs related to ischemia-reperfusion injury in a rat's retina. In summary, the effects of microRNAs on genes are mediated, in large part, via transcription factors.
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Affiliation(s)
- Maha Soliman
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States of America
| | - Kalina Andreeva
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States of America
| | - Olfa Nasraoui
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, United States of America
| | - Nigel G. F. Cooper
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States of America
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28
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Lei Q, Liu T, Gao F, Xie H, Sun L, Zhao A, Ren W, Guo H, Zhang L, Wang H, Chen Z, Guo AY, Li Q. Microvesicles as Potential Biomarkers for the Identification of Senescence in Human Mesenchymal Stem Cells. Am J Cancer Res 2017; 7:2673-2689. [PMID: 28819455 PMCID: PMC5558561 DOI: 10.7150/thno.18915] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 04/12/2017] [Indexed: 12/13/2022] Open
Abstract
Senescence in human mesenchymal stem cells (MSCs) not only contributes to organism aging and the development of a variety of diseases but also severely impairs their therapeutic properties as a promising cell therapy. Studies searching for efficient biomarkers that represent cellular senescence have attracted much attention; however, no single marker currently provides an accurate cell-free representation of cellular senescence. Here, we studied characteristics of MSC-derived microvesicles (MSC-MVs) that may reflect the senescence in their parental MSCs. We found that senescent late passage (LP) MSCs secreted higher levels of MSC-MVs with smaller size than did early passage (EP) MSCs, and the level of CD105+ MSC-MVs decreased with senescence in the parental MSCs. Also, a substantially weaker ability to promote osteogenesis in MSCs was observed in LP than EP MSC-MVs. Comparative analysis of RNA sequencing showed the same trend of decreasing number of highly-expressed miRNAs with increasing number of passages in both MSCs and MSC-MVs. Most of the highly-expressed genes in LP MSCs and the corresponding MSC-MVs were involved in the regulation of senescence-related diseases, such as Alzheimer's disease. Furthermore, based on the miRNA profiling, transcription factors (TF) and genes regulatory networks of MSC senescence, and the datasets from GEO database, we confirmed that expression of miR-146a-5p in MSC-MVs resembled the senescent state of their parental MSCs. Our findings provide evidence that MSC-MVs are a key factor in the senescence-associated secretory phenotype of MSCs and demonstrate that their integrated characteristics can dynamically reflect the senescence state of MSCs representing a potential biomarker for monitoring MSC senescence.
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29
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Shi H, Zhang G, Wang J, Wang Z, Liu X, Cheng L, Li W. Studying Dynamic Features in Myocardial Infarction Progression by Integrating miRNA-Transcription Factor Co-Regulatory Networks and Time-Series RNA Expression Data from Peripheral Blood Mononuclear Cells. PLoS One 2016; 11:e0158638. [PMID: 27367417 PMCID: PMC4930172 DOI: 10.1371/journal.pone.0158638] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/20/2016] [Indexed: 12/22/2022] Open
Abstract
Myocardial infarction (MI) is a serious heart disease and a leading cause of mortality and morbidity worldwide. Although some molecules (genes, miRNAs and transcription factors (TFs)) associated with MI have been studied in a specific pathological context, their dynamic characteristics in gene expressions, biological functions and regulatory interactions in MI progression have not been fully elucidated to date. In the current study, we analyzed time-series RNA expression data from peripheral blood mononuclear cells. We observed that significantly differentially expressed genes were sharply up- or down-regulated in the acute phase of MI, and then changed slowly until the chronic phase. Biological functions involved at each stage of MI were identified. Additionally, dynamic miRNA–TF co-regulatory networks were constructed based on the significantly differentially expressed genes and miRNA–TF co-regulatory motifs, and the dynamic interplay of miRNAs, TFs and target genes were investigated. Finally, a new panel of candidate diagnostic biomarkers (STAT3 and ICAM1) was identified to have discriminatory capability for patients with or without MI, especially the patients with or without recurrent events. The results of the present study not only shed new light on the understanding underlying regulatory mechanisms involved in MI progression, but also contribute to the discovery of true diagnostic biomarkers for MI.
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Affiliation(s)
- Hongbo Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, PR China
| | - Guangde Zhang
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, PR China
| | - Jing Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, PR China
| | - Zhenzhen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, PR China
| | - Xiaoxia Liu
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, PR China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, PR China
| | - Weimin Li
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, PR China
- * E-mail:
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30
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Zhou M, Wang X, Shi H, Cheng L, Wang Z, Zhao H, Yang L, Sun J. Characterization of long non-coding RNA-associated ceRNA network to reveal potential prognostic lncRNA biomarkers in human ovarian cancer. Oncotarget 2016; 7:12598-611. [PMID: 26863568 PMCID: PMC4914307 DOI: 10.18632/oncotarget.7181] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/24/2016] [Indexed: 12/14/2022] Open
Abstract
Accumulating evidence has underscored the important roles of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in cancer initiation and progression. In this study, we used an integrative computational method to identify miRNA-mediated ceRNA crosstalk between lncRNAs and mRNAs, and constructed global and progression-related lncRNA-associated ceRNA networks (LCeNETs) in ovarian cancer (OvCa) based on "ceRNA hypothesis". The constructed LCeNETs exhibited small world, modular architecture and high functional specificity for OvCa. Known OvCa-related genes tended to be hubs and occurred preferentially in the functional modules. Ten lncRNA ceRNAs were identified as potential candidates associated with stage progression in OvCa using ceRNA-network driven method. Finally, we developed a ten-lncRNA signature which classified patients into high- and low-risk subgroups with significantly different survival outcomes. Our study will provide novel insight for better understanding of ceRNA-mediated gene regulation in progression of OvCa and facilitate the identification of novel diagnostic and therapeutic lncRNA ceRNAs for OvCa.
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Affiliation(s)
- Meng Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Xiaojun Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Hongbo Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Zhenzhen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Hengqiang Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
| | - Jie Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
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31
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Transcription factor and miRNA co-regulatory network reveals shared and specific regulators in the development of B cell and T cell. Sci Rep 2015; 5:15215. [PMID: 26487345 PMCID: PMC4613730 DOI: 10.1038/srep15215] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022] Open
Abstract
The maturation process of lymphocyte was related to many blood diseases, such as lymphoma and lymphoid leukemia. Many TFs and miRNAs were separately studied in the development of B and T cells. In this study, we aim to discover the TF and miRNA co-regulation and identify key regulators in the B and T cells maturation. We obtained the candidate genes, miRNAs and TFs for each stage of their maturation, then constructed the TF-miRNA-gene feed-forward loops (FFLs) for each stage by our previous methods. Statistical test for FFLs indicated their enrichment and significance. TF-miRNA co-regulatory networks for each stage were constructed by combining their FFLs. Hub analysis revealed the key regulators in each stage, for example, MYC, STAT5A, PAX5 and miR-17 ~ 92 in the transition of pro-B cells into pre-B cells. We also identified a few common regulators and modules in two stages of B cell maturation (e.g. miR-146a/NFKB1/BCL11A) and two stages of T cell maturation (e.g. miR-20/CCND2/SORL1), as well as some shared regulators in the early stages of both B and T cell development. Our network will help to increase understanding of mature process of B and T cell, as well as the related blood diseases.
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