1
|
Chen J, Zhao L, Zhang L, Luo Y, Jiang Y, H P. The identification of signature genes and their relationship with immune cell infiltration in age-related macular degeneration. Mol Biol Rep 2024; 51:339. [PMID: 38393419 DOI: 10.1007/s11033-023-08969-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/26/2023] [Indexed: 02/25/2024]
Abstract
BACKGROUND Age-related macular degeneration (AMD) is a prevalent source of visual impairment among the elderly population, and its incidence has risen in tandem with the increasing longevity of humans. Despite the progress made with anti-VEGF therapy, clinical outcomes have proven to be unsatisfactory. METHOD We obtained differentially expressed genes (DEGs) of AMD patients and healthy controls from the GEO database. GO and KEGG analyses were used to enrich the DEGs. Weighted gene coexpression network analysis (WGCNA) was used to identify modules related to AMD. SVM, random forest, and least absolute shrinkage and selection operator (LASSO) were employed to screen hub genes. Gene set enrichment analysis (GSEA) was used to explore the pathways in which these hub genes were enriched. CIBERSORT was utilized to analyze the relationship between the hub genes and immune cell infiltration. Finally, Western blotting and RT‒PCR were used to explore the expression of hub genes in AMD mice. RESULTS We screened 1084 DEGs in GSE29801, of which 496 genes were upregulated. These 1084 DEGs were introduced into the WGCNA, and 94 genes related to AMD were obtained. Seventy-nine overlapping genes were obtained by the Venn plot. These 79 genes were introduced into three machine-learning methods to screen the hub genes, and the genes identified by the three methods were TNC, FAP, SREBF1, and TGF-β2. We verified their diagnostic function in the GSE29801 and GSE103060 datasets. Then, the hub gene co-enrichment pathways were obtained by GO and KEGG analyses. CIBERSORT analysis showed that these hub genes were associated with immune cell infiltration. Finally, we found increased expression of TNC, FAP, SREBF1, and TGF-β2 mRNA and protein in the retinas of AMD mice. CONCLUSION We found that four hub genes, namely, FAP, TGF-β2, SREBF1, and TNC, have diagnostic significance in patients with AMD and are related to immune cell infiltration. Finally, we determined that the mRNA and protein expression of these hub genes was upregulated in the retinas of AMD mice.
Collapse
Affiliation(s)
- Jinquan Chen
- Department of Ophthalmology, The Tongnan District People's Hospital, Chongqing, China
| | - Long Zhao
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Longbin Zhang
- Department of Ophthalmology, The Tongnan District People's Hospital, Chongqing, China
| | - Yiling Luo
- Department of Ophthalmology, The Tongnan District People's Hospital, Chongqing, China
| | - Yuling Jiang
- Department of Ophthalmology, The Tongnan District People's Hospital, Chongqing, China
| | - Peng H
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| |
Collapse
|
2
|
Strzalka-Mrozik B, Paprzycka O, Gruszka O, Madej M, Kruszniewska-Rajs C, Gola JM, Turek A. Ranibizumab Modifies the Expression of Metalloproteinases and Their Tissue Inhibitors in Peripheral Blood Mononuclear Cells in Patients with Exudative Age-Related Macular Degeneration. J Clin Med 2024; 13:295. [PMID: 38202302 PMCID: PMC10780024 DOI: 10.3390/jcm13010295] [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: 11/28/2023] [Revised: 12/27/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Age-related macular degeneration (AMD) is the leading cause of vision loss in people over 60 years of age. Despite research, the causes of AMD remain unclear. Matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) are known to be involved in AMD development, and anti-vascular endothelial growth factor therapy has revolutionized its treatment. This study aims to analyze the changes in gene expression in MMPs and TIMPS in patients with neovascular AMD before and after three doses of ranibizumab. METHODS The study involved 29 patients with neovascular AMD treated with ranibizumab. Peripheral blood mononuclear cells were collected before treatment and 24 h after the third dose of ranibizumab. We assessed MMP and TIMP gene expression profiles through oligonucleotide microarrays and validated selected differential genes using RT-qPCR. RESULTS A statistically significant change in the expression of six MMP- and TIMP-related genes was observed using oligonucleotide microarray. The mRNA levels of the two genes with the most significant fold changes, MMP15 and TIMP2, were then quantified using RT-qPCR. The results confirmed a statistically significant increase in MMP15 expression and a decrease in TIMP2 levels, although this change was not statistically significant in the group before and after the third dose of ranibizumab. CONCLUSION Ranibizumab affects the systemic expression of MMP and TIMP-related genes in patients with neovascular AMD. Results from our exploratory study suggest that MMP15, in particular, may play a role in the treatment response, but further research is necessary.
Collapse
Affiliation(s)
- Barbara Strzalka-Mrozik
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (O.P.); (O.G.); (M.M.); (C.K.-R.); (J.M.G.)
| | - Olga Paprzycka
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (O.P.); (O.G.); (M.M.); (C.K.-R.); (J.M.G.)
| | - Oliwia Gruszka
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (O.P.); (O.G.); (M.M.); (C.K.-R.); (J.M.G.)
| | - Marcel Madej
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (O.P.); (O.G.); (M.M.); (C.K.-R.); (J.M.G.)
- Silesia LabMed, Centre for Research and Implementation, Medical University of Silesia, 40-752 Katowice, Poland
| | - Celina Kruszniewska-Rajs
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (O.P.); (O.G.); (M.M.); (C.K.-R.); (J.M.G.)
| | - Joanna Magdalena Gola
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (O.P.); (O.G.); (M.M.); (C.K.-R.); (J.M.G.)
| | - Artur Turek
- Department of Biopharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland;
| |
Collapse
|
3
|
Investigation of Key Signaling Pathways Associating miR-204 and Common Retinopathies. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5568113. [PMID: 34646884 PMCID: PMC8505061 DOI: 10.1155/2021/5568113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/15/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
MicroRNAs are a large group of small noncoding RNAs that work in multiple cellular pathways. miR-204, as one of the key axes in the development, maintenance, and pathogenesis of the retina, plays several roles by modulating its target genes. This study was aimed at evaluating the target genes of miR-204 involved in the development and progression of common retinopathies such as glaucoma, retinoblastoma, and age-related macular degeneration. In this study, three datasets related to retinopathies (GSE50195, GSE27276, and GSE97508) were selected from Gene Expression Omnibus. miR-204 target genes were isolated from TargeScan. The shares between retinopathy and miR-204 target genes were then categorized. Using Enrichr and STRING, we highlighted the signaling pathways and the relationships between the proteins. SHC1 events in ERBB2, adherent junction's interactions, NGF signaling via TRKA from the plasma membrane, IRF3-mediated activation of type 1 IFN, pathways in upregulated genes and G0 and early G1, RORA-activated gene expression, PERK-regulated gene expression, adherent junction's interactions, and CREB phosphorylation pathways in downregulated genes were identified in glaucoma, retinoblastoma, and age-related macular degeneration. WEE1, SMC2, HMGB1, RRM2, and POLA1 proteins were also observed to be involved in the progression and invasion of retinoblastoma; SLC24A2 and DTX4 in age-related macular degeneration; and EPHB6, EFNB3, and SHC1 in glaucoma. Continuous bioinformatics analysis has shown that miR-204 has a significant presence and expression in retinal tissue, and approximately 293 genes are controlled and regulated by miR-204 in this tissue; also, target genes of miR-204 have the potential to develop various retinopathies; thus, a study of related target genes can provide appropriate treatment strategies in the future.
Collapse
|
4
|
Hsp90-associated DNA replication checkpoint protein and proteasome-subunit components are involved in the age-related macular degeneration. Chin Med J (Engl) 2021; 134:2322-2332. [PMID: 34629418 PMCID: PMC8510006 DOI: 10.1097/cm9.0000000000001773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: Age-related macular degeneration (AMD) is the leading cause of vision loss worldwide. However, the mechanisms involved in the development and progression of AMD are poorly delineated. We aimed to explore the critical genes involved in the progression of AMD. Methods: The differentially expressed genes (DEGs) in AMD retinal pigment epithelial (RPE)/choroid tissues were identified using the microarray datasets GSE99248 and GSE125564, which were downloaded from the gene expression omnibus database. The overlapping DEGs from the two datasets were screened to identify DEG-related biological pathways using gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The hub genes were identified from these DEGs through protein-protein interaction network analyses. The expression levels of hub genes were evaluated by quantitative real-time polymerase chain reaction following the induction of senescence in ARPE-19 with FK866. Following the identification of AMD-related key genes, the potential small molecule compounds targeting the key genes were predicted by PharmacoDB. Finally, a microRNA-gene interaction network was constructed. Results: Microarray analyses identified 174 DEGs in the AMD RPE compared to the healthy RPE samples. These DEGs were primarily enriched in the pathways involved in the regulation of DNA replication, cell cycle, and proteasome-mediated protein polyubiquitination. Among the top ten hub genes, HSP90AA1, CHEK1, PSMA4, PSMD4, and PSMD8 were upregulated in the senescent ARPE-19 cells. Additionally, the drugs targeting HSP90AA1, CHEK1, and PSMA4 were identified. We hypothesize that Hsa-miR-16-5p might target four out of the five key DEGs in the AMD RPE. Conclusions: Based on our findings, HSP90AA1 is likely to be a central gene controlling the DNA replication and proteasome-mediated polyubiquitination during the RPE senescence observed in the progression of AMD. Targeting HSP90AA1, CHEK1, PSMA4, PSMD4, and/or PSMD8 genes through specific miRNAs or small molecules might potentially alleviate the progression of AMD through attenuating RPE senescence.
Collapse
|
5
|
Identification of Multiple Hub Genes and Pathways in Hepatocellular Carcinoma: A Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8849415. [PMID: 34337056 PMCID: PMC8292096 DOI: 10.1155/2021/8849415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 05/02/2021] [Accepted: 06/25/2021] [Indexed: 12/22/2022]
Abstract
Hepatocellular carcinoma (HCC) is a common malignant tumor of the digestive system, and its early asymptomatic characteristic increases the difficulty of diagnosis and treatment. This study is aimed at obtaining some novel biomarkers with diagnostic and prognostic meaning and may find out potential therapeutic targets for HCC. We screen differentially expressed genes (DEGs) from the HCC gene expression profile GSE14520 using GEO2R. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted by using the clusterProfiler software while a protein-protein interaction (PPI) network was performed based on the STRING database. Then, prognosis analysis of hub genes was conducted using The Cancer Genome Atlas (TCGA) database. Quantitative real-time polymerase chain reaction (qRT-PCR) was utilized to further verify the expression of hub genes and explore the correlation between gene expression and clinicopathological parameters. A total of 1053 DEGs were captured, containing 497 upregulated genes and 556 downregulated genes. GO and KEGG analysis indicated that the downregulated DEGs were mainly enriched in the fatty acid catabolic process while upregulated DEGs were primarily enriched in the cell cycle. Simultaneously, ten hub genes (CYP3A4, UGT1A6, AOX1, UGT1A4, UGT2B15, CDK1, CCNB1, MAD2L1, CCNB2, and CDC20) were identified by the PPI network. Five prognosis-related hub genes (CYP3A4, CDK1, CCNB1, MAD2L1, and CDC20) were uncovered by the survival analysis based on TCGA database. The ten hub genes were further validated by qRT-PCR using samples obtained from our hospital. The prognosis-related hub genes such as CYP3A4, CDK1, CCNB1, MAD2L1, and CDC20 could be considered potential diagnosis biomarkers and prognosis targets for HCC. We also use Oncomine for further verification, and we found CCNB1, CCNB2, CDK1, and CYP3A4 which were highly expressed in HCC. Meanwhile, CCNB1, CCNB2, and CDK1 are highly expressed in almost all cancer types, which may play an important role in cancer. Still, further functional study should be conducted to explore the underlying mechanism and biological effect in the near future.
Collapse
|
6
|
Hamid MA, Moustafa MT, Nashine S, Costa RD, Schneider K, Atilano SR, Kuppermann BD, Kenney MC. Anti-VEGF Drugs Influence Epigenetic Regulation and AMD-Specific Molecular Markers in ARPE-19 Cells. Cells 2021; 10:cells10040878. [PMID: 33921543 PMCID: PMC8069662 DOI: 10.3390/cells10040878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 12/16/2022] Open
Abstract
Our study assesses the effects of anti-VEGF (Vascular Endothelial Growth Factor) drugs and Trichostatin A (TSA), an inhibitor of histone deacetylase (HDAC) activity, on cultured ARPE-19 (Adult Retinal Pigment Epithelial-19) cells that are immortalized human retinal pigment epithelial cells. ARPE-19 cells were treated with the following anti-VEGF drugs: aflibercept, ranibizumab, or bevacizumab at 1× and 2× concentrations of the clinical intravitreal dose (12.5 μL/mL and 25 μL/mL, respectively) and analyzed for transcription profiles of genes associated with the pathogenesis age-related macular degeneration (AMD). HDAC activity was measured using the Fluorometric Histone Deacetylase assay. TSA downregulated HIF-1α and IL-1β genes, and upregulated BCL2L13, CASPASE-9, and IL-18 genes. TSA alone or bevacizumab plus TSA showed a significant reduction of HDAC activity compared to untreated ARPE-19 cells. Bevacizumab alone did not significantly alter HDAC activity, but increased gene expression of SOD2, BCL2L13, CASPASE-3, and IL-18 and caused downregulation of HIF-1α and IL-18. Combination of bevacizumab plus TSA increased gene expression of SOD2, HIF-1α, GPX3A, BCL2L13, and CASPASE-3, and reduced CASPASE-9 and IL-β. In conclusion, we demonstrated that anti-VEGF drugs can: (1) alter expression of genes involved in oxidative stress (GPX3A and SOD2), inflammation (IL-18 and IL-1β) and apoptosis (BCL2L13, CASPASE-3, and CASPASE-9), and (2) TSA-induced deacetylation altered transcription for angiogenesis (HIF-1α), apoptosis, and inflammation genes.
Collapse
Affiliation(s)
- Mohamed A. Hamid
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92697, USA; (M.A.H.); (M.T.M.); (S.N.); (R.D.C.); (K.S.); (S.R.A.); (B.D.K.)
- Ophthalmology Department, Faculty of Medicine, Minia University, Minia 61111, Egypt
| | - M. Tarek Moustafa
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92697, USA; (M.A.H.); (M.T.M.); (S.N.); (R.D.C.); (K.S.); (S.R.A.); (B.D.K.)
- Ophthalmology Department, Faculty of Medicine, Minia University, Minia 61111, Egypt
| | - Sonali Nashine
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92697, USA; (M.A.H.); (M.T.M.); (S.N.); (R.D.C.); (K.S.); (S.R.A.); (B.D.K.)
| | - Rodrigo Donato Costa
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92697, USA; (M.A.H.); (M.T.M.); (S.N.); (R.D.C.); (K.S.); (S.R.A.); (B.D.K.)
- Instituto Donato Oftalmologia, Poςos de Caldas, MG 37701-528, Brazil
| | - Kevin Schneider
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92697, USA; (M.A.H.); (M.T.M.); (S.N.); (R.D.C.); (K.S.); (S.R.A.); (B.D.K.)
| | - Shari R. Atilano
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92697, USA; (M.A.H.); (M.T.M.); (S.N.); (R.D.C.); (K.S.); (S.R.A.); (B.D.K.)
| | - Baruch D. Kuppermann
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92697, USA; (M.A.H.); (M.T.M.); (S.N.); (R.D.C.); (K.S.); (S.R.A.); (B.D.K.)
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA
| | - M. Cristina Kenney
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92697, USA; (M.A.H.); (M.T.M.); (S.N.); (R.D.C.); (K.S.); (S.R.A.); (B.D.K.)
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA 92697, USA
- Correspondence: ; Tel.: +1-949-824-7603
| |
Collapse
|
7
|
Zhou M, Duan PC, Liang JH, Zhang XF, Pan CW. Geographic distributions of age-related macular degeneration incidence: a systematic review and meta-analysis. Br J Ophthalmol 2020; 105:1427-1434. [PMID: 32907810 DOI: 10.1136/bjophthalmol-2020-316820] [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: 05/06/2020] [Revised: 07/16/2020] [Accepted: 08/18/2020] [Indexed: 01/17/2023]
Abstract
PURPOSE We performed a systematic review and meta-analysis to summarise the geographic distribution of age-related macular degeneration (AMD) incidence. METHODS Databases including PubMed, Embase and Web of Science were searched for publications of early and late AMD before September 2019. Studies were included if they applied a standardised photographic assessment and classification system. The proportion of participants with AMD in each eligible study was combined to obtain a pooled incidence from all studies using a random effects model. We also assessed sources of potential heterogeneity in the incidence of AMD using meta-regression analyses for both late and early AMD. RESULTS Twenty-four population-based studies (70 123 individuals aged 55 years or older) were included in the meta-analysis. The pooled global annual incidences of early and late AMD were 1.59% (95% CI 1.12% to 2.10%) and 0.19% (95% CI: 0.13% to 0.28%), respectively. Individuals of European descent had the highest annual incidence of both early (2.73%, 95% CI 1.63% to 4.57%) and late (0.36%, 95% CI 0.17% to 0.75%) AMD than other ethnic groups. Average age (p=0.001) at baseline, ethnicity (p=0.001), region (p=0.043) and gender (p=0.011) were predictors for incident late AMD, while only average age (p=0.01) at baseline and ethnicity (p=0.025) was associated with incidence of early AMD. CONCLUSIONS This meta-analysis offers an up-to-date overview of AMD globally, which may provide scientific guidance for the design and implementation of public health strategies such as screening programmes for AMD in both specific geographic locations and ethnic groups, as well as worldwide.
Collapse
Affiliation(s)
- Miao Zhou
- School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Pei-Chen Duan
- School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Jing-Hong Liang
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Xiao-Feng Zhang
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chen-Wei Pan
- School of Public Health, Medical College of Soochow University, Suzhou, China
| |
Collapse
|
8
|
Dang H, Ye Y, Zhao X, Zeng Y. Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database. BMC Cardiovasc Disord 2020; 20:320. [PMID: 32631246 PMCID: PMC7336680 DOI: 10.1186/s12872-020-01596-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Ischemic cardiomyopathy (ICM) is one of the most usual causes of death worldwide. This study aimed to find the candidate gene for ICM. METHODS We studied differentially expressed genes (DEGs) in ICM compared to healthy control. According to these DEGs, we carried out the functional annotation, protein-protein interaction (PPI) network and transcriptional regulatory network constructions. The expression of selected candidate genes were confirmed using a published dataset and Quantitative real time polymerase chain reaction (qRT-PCR). RESULTS From three Gene Expression Omnibus (GEO) datasets, we acquired 1081 DEGs (578 up-regulated and 503 down-regulated genes) between ICM and healthy control. The functional annotation analysis revealed that cardiac muscle contraction, hypertrophic cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy and dilated cardiomyopathy were significantly enriched pathways in ICM. SNRPB, BLM, RRS1, CDK2, BCL6, BCL2L1, FKBP5, IPO7, TUBB4B and ATP1A1 were considered the hub proteins. PALLD, THBS4, ATP1A1, NFASC, FKBP5, ECM2 and BCL2L1 were top six transcription factors (TFs) with the most downstream genes. The expression of 6 DEGs (MYH6, THBS4, BCL6, BLM, IPO7 and SERPINA3) were consistent with our integration analysis and GSE116250 validation results. CONCLUSIONS The candidate DEGs and TFs may be related to the ICM process. This study provided novel perspective for understanding mechanism and exploiting new therapeutic means for ICM.
Collapse
Affiliation(s)
- Haiming Dang
- Department of cardiac surgery, Capital medical university, Beijing Anzhen hospital, Beijing, China
| | - Yicong Ye
- Department of cardiology, Capital medical university, Beijing Anzhen hospital, No.2, Anzhen Road, Chaoyan District, Beijing, 100029, China
| | - Xiliang Zhao
- Department of cardiology, Capital medical university, Beijing Anzhen hospital, No.2, Anzhen Road, Chaoyan District, Beijing, 100029, China
| | - Yong Zeng
- Department of cardiology, Capital medical university, Beijing Anzhen hospital, No.2, Anzhen Road, Chaoyan District, Beijing, 100029, China.
| |
Collapse
|
9
|
Bioinformatical Analysis of miRNA-mRNA Interaction Network Underlying Macrophage Aging and Cholesterol-Responsive Difference between Young and Aged Macrophages. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9267475. [PMID: 32626771 PMCID: PMC7306864 DOI: 10.1155/2020/9267475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 05/18/2020] [Indexed: 01/28/2023]
Abstract
Purpose Macrophage aging is involved with the occurrence and progression of age-related macular degeneration (AMD). The purpose of this study was to identify the specific microRNAs (miRNA), mRNAs, and their interactions underlying macrophage aging and response to cholesterol through bioinformatical analysis in order to get a better understanding of the mechanism of AMD. Methods The microarray data were obtained from Gene Expression Omnibus (accession GSE111304 and GSE111382). The age-related differentially expressed genes in macrophages were identified using R software. Further miRNA-mRNA interactions were analyzed through miRWalk, mirTarBase, starBase, and then produced by Cytoscape. The functional annotations including Gene Ontology and KEGG pathways of the miRNA target genes were performed by the DAVID and the STRING database. In addition, protein-protein interaction network was constructed to identify the key genes in response to exogenous cholesterol. Results When comparing aged and young macrophages, a total of 14 miRNAs and 101 mRNAs were detected as differentially expressed. Besides, 19 validated and 544 predicted miRNA-mRNA interactions were detected. Lipid metabolic process was found to be associated with macrophage aging through functional annotations of the miRNA targets. After being treated with oxidized and acetylated low-density lipoprotein, miR-714 and 16 mRNAs differentially expressed in response to both kinds of cholesterol between aged and young macrophages. Among them, 6 miRNA-mRNA predicted pairs were detected. The functional annotations were mainly related to lipid metabolism process and farnesyl diphosphate farnesyl transferase 1 (FDFT1) was identified to be the key gene in the difference of response to cholesterol between aged and young macrophages. Conclusions Lipid metabolic process was critical in both macrophage aging and response to cholesterol thus was regarded to be associated with the occurrence and progression of AMD. Moreover, miR-714-FDFT1 may modulate cholesterol homeostasis in aged macrophages and have the potential to be a novel therapeutic target for AMD.
Collapse
|
10
|
Chao de la Barca JM, Rondet-Courbis B, Ferré M, Muller J, Buisset A, Leruez S, Plubeau G, Macé T, Moureauzeau L, Chupin S, Tessier L, Blanchet O, Lenaers G, Procaccio V, Mirebeau-Prunier D, Simard G, Gohier P, Miléa D, Reynier P. A Plasma Metabolomic Profiling of Exudative Age-Related Macular Degeneration Showing Carnosine and Mitochondrial Deficiencies. J Clin Med 2020; 9:jcm9030631. [PMID: 32120889 PMCID: PMC7141125 DOI: 10.3390/jcm9030631] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/11/2022] Open
Abstract
To determine the plasma metabolomic profile of exudative age-related macular degeneration (AMD), we performed a targeted metabolomics study on the plasma from patients (n = 40, mean age = 81.1) compared to an age- and sex-matched control group (n = 40, mean age = 81.8). All included patients had documented exudative AMD, causing significant visual loss (mean logMAR visual acuity = 0.63), compared to the control group. Patients and controls did not differ in terms of body mass index and co-morbidities. Among the 188 metabolites analyzed, 150 (79.8%) were accurately measured. The concentrations of 18 metabolites were significantly modified in the AMD group, but only six of them remained significantly different after Benjamini–Hochberg correction. Valine, lysine, carnitine, valerylcarnitine and proline were increased, while carnosine, a dipeptide disclosing anti-oxidant and anti-glycating properties, was, on average, reduced by 50% in AMD compared to controls. Moreover, carnosine was undetectable for 49% of AMD patients compared to 18% in the control group (p-value = 0.0035). Carnitine is involved in the transfer of fatty acids within the mitochondria; proline, lysine and valerylcarnitine are substrates for mitochondrial electrons transferring flavoproteins, and proline is one of the main metabolites supplying energy to the retina. Overall, our results reveal six new metabolites involved in the plasma metabolomic profile of exudative AMD, suggesting mitochondrial energetic impairments and carnosine deficiency.
Collapse
Affiliation(s)
- Juan M. Chao de la Barca
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (J.M.C.d.l.B.); (S.C.); (L.T.); (V.P.); (D.M.-P.); (G.S.)
- Unité Mixte de Recherche MITOVASC, équipe Mitolab, Centre National de la Recherche Scientifique 6015, Institut National de la Santé et de la Recherche Médicale U1083, Université d’Angers, 49933 Angers, France; (M.F.); (G.L.)
| | - Barnabé Rondet-Courbis
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France; (B.R.-C.); (J.M.); (A.B.); (S.L.); (G.P.); (T.M.); (L.M.); (P.G.); (D.M.)
| | - Marc Ferré
- Unité Mixte de Recherche MITOVASC, équipe Mitolab, Centre National de la Recherche Scientifique 6015, Institut National de la Santé et de la Recherche Médicale U1083, Université d’Angers, 49933 Angers, France; (M.F.); (G.L.)
| | - Jeanne Muller
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France; (B.R.-C.); (J.M.); (A.B.); (S.L.); (G.P.); (T.M.); (L.M.); (P.G.); (D.M.)
| | - Adrien Buisset
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France; (B.R.-C.); (J.M.); (A.B.); (S.L.); (G.P.); (T.M.); (L.M.); (P.G.); (D.M.)
| | - Stéphanie Leruez
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France; (B.R.-C.); (J.M.); (A.B.); (S.L.); (G.P.); (T.M.); (L.M.); (P.G.); (D.M.)
| | - Guillaume Plubeau
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France; (B.R.-C.); (J.M.); (A.B.); (S.L.); (G.P.); (T.M.); (L.M.); (P.G.); (D.M.)
| | - Thibaut Macé
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France; (B.R.-C.); (J.M.); (A.B.); (S.L.); (G.P.); (T.M.); (L.M.); (P.G.); (D.M.)
| | - Laurie Moureauzeau
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France; (B.R.-C.); (J.M.); (A.B.); (S.L.); (G.P.); (T.M.); (L.M.); (P.G.); (D.M.)
| | - Stéphanie Chupin
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (J.M.C.d.l.B.); (S.C.); (L.T.); (V.P.); (D.M.-P.); (G.S.)
| | - Lydie Tessier
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (J.M.C.d.l.B.); (S.C.); (L.T.); (V.P.); (D.M.-P.); (G.S.)
| | - Odile Blanchet
- Centre de Ressources Biologiques, BB-0033-00038, Centre Hospitalier Universitaire, 49933 Angers, France;
| | - Guy Lenaers
- Unité Mixte de Recherche MITOVASC, équipe Mitolab, Centre National de la Recherche Scientifique 6015, Institut National de la Santé et de la Recherche Médicale U1083, Université d’Angers, 49933 Angers, France; (M.F.); (G.L.)
| | - Vincent Procaccio
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (J.M.C.d.l.B.); (S.C.); (L.T.); (V.P.); (D.M.-P.); (G.S.)
- Unité Mixte de Recherche MITOVASC, équipe Mitolab, Centre National de la Recherche Scientifique 6015, Institut National de la Santé et de la Recherche Médicale U1083, Université d’Angers, 49933 Angers, France; (M.F.); (G.L.)
| | - Delphine Mirebeau-Prunier
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (J.M.C.d.l.B.); (S.C.); (L.T.); (V.P.); (D.M.-P.); (G.S.)
- Unité Mixte de Recherche MITOVASC, équipe Mitolab, Centre National de la Recherche Scientifique 6015, Institut National de la Santé et de la Recherche Médicale U1083, Université d’Angers, 49933 Angers, France; (M.F.); (G.L.)
| | - Gilles Simard
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (J.M.C.d.l.B.); (S.C.); (L.T.); (V.P.); (D.M.-P.); (G.S.)
| | - Philippe Gohier
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France; (B.R.-C.); (J.M.); (A.B.); (S.L.); (G.P.); (T.M.); (L.M.); (P.G.); (D.M.)
| | - Dan Miléa
- Département d’Ophtalmologie, Centre Hospitalier Universitaire, 49933 Angers, France; (B.R.-C.); (J.M.); (A.B.); (S.L.); (G.P.); (T.M.); (L.M.); (P.G.); (D.M.)
- Singapore Eye Research Institute, Singapore National Eye Centre, Duke-NUS Medical School, Singapore 168751, Singapore
| | - Pascal Reynier
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France; (J.M.C.d.l.B.); (S.C.); (L.T.); (V.P.); (D.M.-P.); (G.S.)
- Unité Mixte de Recherche MITOVASC, équipe Mitolab, Centre National de la Recherche Scientifique 6015, Institut National de la Santé et de la Recherche Médicale U1083, Université d’Angers, 49933 Angers, France; (M.F.); (G.L.)
- Correspondence: ; Tel.: +33-241-353-314
| |
Collapse
|
11
|
Zhang Q, Chen W, Chen S, Li S, Wei D, He W. Identification of key genes and upstream regulators in ischemic stroke. Brain Behav 2019; 9:e01319. [PMID: 31168961 PMCID: PMC6625467 DOI: 10.1002/brb3.1319] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/17/2019] [Accepted: 03/26/2019] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Ischemic stroke (IS) causes severe neurological impairments and physical disabilities and has a high economic burden. Our study aims to identify the key genes and upstream regulators in IS by integrated microarray analysis. METHODS An integrated analysis of microarray studies of IS was performed to identify the differentially expressed genes (DEGs) in IS compared to normal control. Based on these DEGs, we performed the functional annotation and transcriptional regulatory network constructions. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the expression of DEGs. RESULTS From two Gene Expression Omnibus datasets obtained, we obtained 1526 DEGs (534 up-regulated and 992 down-regulated genes) between IS and normal control. The results of functional annotation showed that Oxidative phosphorylation and Alzheimer's disease were significantly enriched pathways in IS. Top four transcription factors (TFs) with the most downstream genes including PAX4, POU2F1, ELK1, and NKX2-5. The expression of six genes (ID3, ICAM2, DCTPP1, ANTXR2, DUSP1, and RGS2) was detected by qRT-PCR. Except for DUSP1 and RGS2, the other four genes in qRT-PCR played the same pattern with that in our integrated analysis. CONCLUSIONS The dysregulation of these six genes may involve with the process of ischemic stroke (IS). Four TFs (PAX4, POU2F1, ELK1 and NKX2-5) were concluded to play a role in IS. Our finding provided clues for exploring mechanism and developing novel diagnostic and therapeutic strategies for IS.
Collapse
Affiliation(s)
- Qian Zhang
- Department of PharmacyFirst Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Wenjie Chen
- Department of NeurologyFirst Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Siqia Chen
- Department of NeurologyFirst Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Shunxian Li
- Department of NeurologyFirst Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Duncan Wei
- Department of PharmacyFirst Affiliated Hospital of Shantou University Medical CollegeShantouChina
| | - Wenzhen He
- Department of NeurologyFirst Affiliated Hospital of Shantou University Medical CollegeShantouChina
| |
Collapse
|
12
|
Liu M, Guo P, An J, Guo C, Lu F, Lei Y. Genome‑wide profiling of lncRNA and mRNA expression in CRSwNP. Mol Med Rep 2019; 19:3855-3863. [PMID: 30864741 DOI: 10.3892/mmr.2019.10005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 10/03/2018] [Indexed: 11/06/2022] Open
Abstract
Chronic rhinosinusitis with nasal polyps (CRSwNP) is one of the most prevalent chronic diseases. In patients with CRSwNP, the present study performed comprehensive bioinformatics analyses to characterize the transcriptome profiles of mRNAs and long non‑coding RNAs (lncRNAs). A total of 265 differentially expressed lncRNAs and 994 mRNAs were identified. The majority of up‑ and downregulated differentially expressed genes were significantly enriched in the biological process of 'signal transduction'. The most significantly enriched molecular function was 'protein binding' and the most significantly enriched cellular component was 'membrane'. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis led to identification of several significantly enriched pathways [false discovery rate (FDR)<0.05], including 'cytokine‑cytokine receptor interaction' (FDR=3.94x1016) and 'cell adhesion molecules' (CAMs) (FDR=1.28x10‑5). Key differentially expressed lncRNAs were identified, including lncRNA XLOC_010280, which regulates chemokine (C‑C motif) ligand 18 (CCL18) and inflammation, and RP11‑798M19.6, which regulates polypeptide N‑acetylgalactosaminyltransferase 7 (GALNT7) and cell proliferation. Based on the results of reverse transcription‑quantitative polymerase chain reaction, except for CCL8, neural precursor cell expressed developmentally downregulated gene 4‑like and GALNT7, the expression of 3 other selected genes was consistent with the results of integrated analysis. The results of the present study provide a foundation for future investigations into mRNAs and lncRNAs as diagnostic and therapeutic targets in CRSwNP.
Collapse
Affiliation(s)
- Minglei Liu
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong 272000, P.R. China
| | - Ping Guo
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong 272000, P.R. China
| | - Jun An
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong 272000, P.R. China
| | - Chao Guo
- Department of Anesthesiology, The First People's Hospital of Jining, Jining, Shandong 272000, P.R. China
| | - Fengxiang Lu
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong 272000, P.R. China
| | - Yanhua Lei
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong 272000, P.R. China
| |
Collapse
|
13
|
Gong R, Ren S, Chen M, Wang Y, Zhang G, Shi L, Zhang C, Su R, Li Y. Bioinformatics Analysis Reveals the Altered Gene Expression of Patients with Postmenopausal Osteoporosis Using Liuweidihuang Pills Treatment. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1907906. [PMID: 30809532 PMCID: PMC6369488 DOI: 10.1155/2019/1907906] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/12/2018] [Indexed: 12/15/2022]
Abstract
Postmenopausal osteoporosis (PMOP), as well as its associated increased risk for fragility fracture, is one of the most disabling consequences of aging in women. This present study aimed to identify candidate genes that involve pathogenesis of PMOP and the therapeutic mechanism of Liuweidihuang (LWDH) pills on PMOP. We integrated microarray datasets of PMOP derived from the Gene Expression Omnibus (GEO) to screen differentially expressed genes (DEGs) between PMOP and normal controls as well as patients with PMOP and patients after treatment of LWDH pills. GO and KEGG enrichment analysis for DEGs were performed. The shared DEGs, associated with both the pathogenesis of PMOP and the therapeutic mechanism of LWDH, were further analyzed by protein-protein interaction (PPI) network. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the DEGs obtained by our integrated analysis. Compared with normal controls, 1732 DEGs in PMOP were obtained with p<0.05. According to the qRT-PCR results, expression of ATF2, FBXW7, RDX, and RBBP4 was consistent with that in our integrated analysis, generally. GO and KEGG enrichment analysis showed that those DEGs were significantly enriched in regulation of transcription, DNA-dependent, cytoplasm, protein binding, and MAPK signaling pathway. A total of 58 shared DEGs in PMOP versus normal control and in patients with PMOP versus patients after LWDH treatment were identified, which had opposite expression trend in these two comparisons. In the PPI network, CSNK2A1, ATF2, and FBXW7 were three hub proteins. Three genes including ATF2, FBXW7, and RDX were speculated to be therapeutic targets of LWDH for PMOP based on BATMAN-TCM database. We speculated that three genes of ATF2, FBXW7, and RDX may play crucial roles in both pathogenesis of PMOP and therapeutic mechanism of LWDH on PMOP. Our results may provide clues for the molecular pathogenesis of PMOP and offer new possibilities for treatment of PMOP.
Collapse
Affiliation(s)
- Rui Gong
- Hebei Medical University Endocrine Research Institute, China
| | - Shan Ren
- Department of ICU, Hebei General Hospital, China
| | - Menghui Chen
- Department of Cardiothoracic Surgery, The Third Hospital of Shijiazhuang, China
| | - Yanli Wang
- Obstetrics and Gynecology, The Third Hospital of Shijiazhuang, China
| | - Guoliang Zhang
- Department of Cardiothoracic Surgery, The Third Hospital of Shijiazhuang, China
| | - Lijuan Shi
- Department of Endocrinology, The Third Hospital of Shijiazhuang, China
| | - Cuizhao Zhang
- Department of Laboratory, The Third Hospital of Shijiazhuang, China
| | - Ruihong Su
- Department of Laboratory, The Third Hospital of Shijiazhuang, China
| | - Yukun Li
- Department of Endocrinology, The Third Affiliated Hospital of Hebei Medical University, China
| |
Collapse
|
14
|
Sun L, Huang T, Xu W, Sun J, Lv Y, Wang Y. Advanced glycation end products promote VEGF expression and thus choroidal neovascularization via Cyr61-PI3K/AKT signaling pathway. Sci Rep 2017; 7:14925. [PMID: 29097668 PMCID: PMC5668426 DOI: 10.1038/s41598-017-14015-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023] Open
Abstract
Choroidal neovascularisation (CNV) causes severe vision loss among old patients, especially those with diabetes. Previously, Cyr61 has been found to play a critical role in the pathogenesis of both AMD and diabetes. In the present study, we found that increased CNV severity together with higher expression of Cyr61 and VEGF in diabetes mice compared with control mice. Moreover, knockdown of Cyr61 decreased CNV severity. In vitro mechanism study revealed that the advanced glycation end products (AGEs) significantly increased the expression of Cyr61 in retinal pigment epithelial (RPE) cells, mimicking the effects of diabetes. In turn, the increased Cyr61 enhanced VEGF expression through FAK and PI3K/Akt pathways. Chemically blocking the above pathway significantly inhibited CNV formation, providing a new strategy for clinical prevention and treatment of CNV in related diseases.
Collapse
Affiliation(s)
- Lijuan Sun
- Eye Institute of Chinese PLA and Department of Ophthalmology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Tonglie Huang
- State Key Laboratory of Cancer Biology, Department of Biopharmaceutics, School of Pharmacy, Fourth Military Medical University, Xi'an, 710032, China
| | - Wenqin Xu
- Eye Institute of Chinese PLA and Department of Ophthalmology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Jiaxing Sun
- Eye Institute of Chinese PLA and Department of Ophthalmology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Yang Lv
- Eye Institute of Chinese PLA and Department of Ophthalmology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Yusheng Wang
- Eye Institute of Chinese PLA and Department of Ophthalmology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China.
| |
Collapse
|