Bioinformatic analysis identifies potential key genes in the pathogenesis of age-related macular degeneration

Purpose: Age?related macular degeneration (AMD) is the leading cause of irreversible blindness in older individuals. More studies focused on screening the genes, which may be correlated with the development of AMD. With advances in various technologies like multiple microarray datasets, researchers could identify differentially expressed genes (DEGs) more accurately. Exploring abnormal gene expression in disease status can help to understand pathophysiological changes in complex diseases. This study aims to identify the key genes and upstream regulators in AMD and reveal factors, especially genetic association, and the prognosis of the development of this disease. Methods: Data from expression profile GSE125564 and profile GSE29801 were obtained from the Gene Expression Omnibus (GEO) database. We analyzed DEGs using R software (version 3.6.3). Functional enrichment and PPI network analysis were performed using the R package and online database STRING (version 11.0). Results: We compared AMD with normal and found 68 up?regulated genes (URGs) and 25 down?regulated genes (DRGs). We also compared wet AMD with dry AMD and found 41 DRGs in dry AMD. Further work including PPI network analysis, GO classification, and KEGG analysis was done to find connections with AMD. The URGs were mainly enriched in the biological process such as DNA replication, nucleoplasm, extracellular exosome, and cadherin binding. Besides, DRGs were mainly enriched in these functions such as an integral component of membrane and formation of the blood?aqueous barrier (BAB). Conclusion: This study implied that core genes might involve in the process of AMD. Our findings may contribute to revealing the pathogenesis, developing new biomarkers, and raising strategies of treatment for AMD

Prognostic implications and functional enrichment analysis of LTB4R in patients with acute myeloid leukemia / 南方医科大学学报

OBJECTIVE@#To explore the expression patterns, prognostic implications, and biological role of leukotriene B4 receptor (LTB4R) in patients with acute myeloid leukemia (AML).@*METHODS@#We collected the data of mRNA expression levels and clinical information of patients with AML from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database for mRNA expression analyses, survival analyses, Cox regression analyses and correlation analyses using R studio to assess the expression patterns and prognostic value of LTB4R. The correlation of LTB4R expression levels with clinical characteristics of the patients were analyzed using UALCAN. The co-expressed genes LTB4R were screened from Linkedomics and subjected to functional enrichment analysis. A protein-protein interaction network was constructed using STRING. GSEA analyses of the differentially expressed genes (DEGs) were performed based on datasets from TCGA-LAML stratified by LTB4R expression level. We also collected peripheral blood mononuclear cells (PBMCs) from AML patients and healthy donors for examination of the mRNA expression levels of LTB4R and immune checkpoint genes using qRT-PCR. We also examined serum LTB4R protein levels in the patients using ELISA.@*RESULTS@#The mRNA expression level of LTB4R was significantly increased in AML patients (4.898±1.220 vs 2.252±0.215, P < 0.001), and an elevated LTB4R expression level was correlated with a poor overall survival (OS) of the patients (P=0.004, HR=1.74). LTB4R was identified as an independent prognostic factor for OS (P=0.019, HR=1.66) and was associated with FAB subtypes, cytogenetic risk, karyotype abnormalities and NPM1 mutations. The co- expressed genes of LTB4R were enriched in the functional pathways closely associated with AML leukemogenesis, including neutrophil inflammation, lymphocyte activation, signal transduction, and metabolism. The DEGs were enriched in differentiation, activation of immune cells, and cytokine signaling. Examination of the clinical serum samples also demonstrated significantly increased expressions of LTB4R mRNA (P=0.044) and protein (P=0.008) in AML patients, and LTB4R mRNA expression was positively correlated with the expression of the immune checkpoint HAVCR2 (r= 0.466, P=0.040).@*CONCLUSION@#LTB4R can serve as a novel biomarker and independent prognostic indicator of AML and its expression patterns provide insights into the crosstalk of leukemogenesis signaling pathways involving tumor immunity and metabolism.

Analysis of sepsis-related genes through weighted gene co-expression network / 中华危重病急救医学

Objective:To identify the Key genes in the development of sepsis through weighted gene co-expression network analysis (WGCNA).Methods:The gene expression dataset GSE154918 was downloaded from the public database Gene Expression Omnibus (GEO) database, which containes data from 105 microarrays of 40 control cases, 12 cases of asymptomatic infection, 39 cases of sepsis, and 14 cases of follow-up sepsis. The R software was used to screen out differentially expressed genes (DEG) in sepsis, and the distributed access view integrated database (DAVID), search tool for retrieval of interacting neighbouring genes (STRING) and visualization software Cytoscape were used to perform gene function and pathway enrichment analysis, Protein-protein interaction (PPI) network analysis and key gene analysis to screen out the key genes in the development of sepsis.Results:Forty-six candidate genes were obtained by WGCNA and combined with DEG expression analysis, and these 46 genes were analyzed by gene ontology (GO) and Kyoto City Encyclopedia of Genes and Genomes (KEGG) pathway enrichment to obtain gene functions and involved signaling pathways. The PPI network was further constructed using the STRING database, and 5 key genes were selected by the PPI network visualization software Cytoscape, including the mast cell expressed membrane protein 1 gene (MCEMP1), the S100 calcium-binding protein A12 gene (S100A12), the adipokine resistance factor gene (RETN), the c-type lectin structural domain family 4 member gene (CLEC4D), and peroxisome proliferator-activated receptor gene (PPARG), and differential expression analysis of each of these 5 genes showed that the expression levels of the above 5 genes were significantly upregulated in sepsis patients compared with healthy controls.Conclusion:In this study, 5 key genes related to sepsis were screened by constructing WGCNA method, which may be potential candidate targets related to sepsis diagnosis and treatment.

Identification of PTPRR and JAG1 as key genes in castration-resistant prostate cancer by integrated bioinformatics methods / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

To identify novel genes in castration-resistant prostate cancer (CRPC), we downloaded three microarray datasets containing CRPC and primary prostate cancer in Gene Expression Omnibus (GEO). R packages affy and limma were performed to identify differentially expressed genes (DEGs) between primary prostate cancer and CRPC. After that, we performed functional enrichment analysis including gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway. In addition, protein-protein interaction (PPI) analysis was used to search for hub genes. Finally, to validate the significance of these genes, we performed survival analysis. As a result, we identified 53 upregulated genes and 58 downregulated genes that changed in at least two datasets. Functional enrichment analysis showed significant changes in the positive regulation of osteoblast differentiation pathway and aldosterone-regulated sodium reabsorption pathway. PPI network identified hub genes like cortactin-binding protein 2 (CTTNBP2), Rho family guanosine triphosphatase (GTPase) 3 (RND3), protein tyrosine phosphatase receptor-type R (PTPRR), Jagged1 (JAG1), and lumican (LUM). Based on PPI network analysis and functional enrichment analysis, we identified two genes (PTPRR and JAG1) as key genes. Further survival analysis indicated a relationship between high expression of the two genes and poor prognosis of prostate cancer. In conclusion, PTPRR and JAG1 are key genes in the CRPC, which may serve as promising biomarkers of diagnosis and prognosis of CRPC.

Identification of PTPRR and JAG1 as key genes in castration-resistant prostate cancer by integrated bioinformatics methods / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

To identify novel genes in castration-resistant prostate cancer (CRPC), we downloaded three microarray datasets containing CRPC and primary prostate cancer in Gene Expression Omnibus (GEO). R packages affy and limma were performed to identify differentially expressed genes (DEGs) between primary prostate cancer and CRPC. After that, we performed functional enrichment analysis including gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway. In addition, protein-protein interaction (PPI) analysis was used to search for hub genes. Finally, to validate the significance of these genes, we performed survival analysis. As a result, we identified 53 upregulated genes and 58 downregulated genes that changed in at least two datasets. Functional enrichment analysis showed significant changes in the positive regulation of osteoblast differentiation pathway and aldosterone-regulated sodium reabsorption pathway. PPI network identified hub genes like cortactin-binding protein 2 (CTTNBP2), Rho family guanosine triphosphatase (GTPase) 3 (RND3), protein tyrosine phosphatase receptor-type R (PTPRR), Jagged1 (JAG1), and lumican (LUM). Based on PPI network analysis and functional enrichment analysis, we identified two genes (PTPRR and JAG1) as key genes. Further survival analysis indicated a relationship between high expression of the two genes and poor prognosis of prostate cancer. In conclusion, PTPRR and JAG1 are key genes in the CRPC, which may serve as promising biomarkers of diagnosis and prognosis of CRPC.

Identification of the molecular mechanisms associated with acute type A aortic dissection through bioinformatics methods

Aortic dissection is characterized by the redirection of blood flow, which flows through an intimal tear into the aortic media. The purpose of this study was to find potential acute type A aortic dissection (AAAD)-related genes and molecular mechanisms by bioinformatics. The gene expression profiles of GSE52093 were obtained from Gene Expression Omnibus (GEO) database, including 7 AAAD samples and 5 normal samples. The differentially expressed genes (DEGs) were detected between AAAD and normal samples. The functional annotation and pathway enrichment analysis were conducted through the Database for Annotation, Visualization and Integration Discovery (DAVID). A protein-protein interaction network was established by the Search Tool for the Retrieval of Interacting Genes (STRING) software. The microRNAs (miRNAs) of these differentially expressed genes were predicted using <microRNA.org> database. Moreover, DEGs were analyzed in the comparative toxicogenomics (CTD) database to screen out the potential therapeutic small molecules. As a result, there were 172 DEGs identified in patients with AAAD. These DEGs were significantly enriched in 6 pathways, including cell cycle, oocyte meiosis, DNA replication, extracellular matrix-receptor interaction, and mineral absorption pathway. Notably, CDC20, CDK1, CHEK1, KIF20A, MCM10, PBK, PTTG1, RACGAP, and TOP2A were crucial genes with a high degree in the protein-protein interaction network. Furthermore, potential miRNAs (miR-301, miR-302 family, and miR-130 family) were identified. In addition, small molecules like azathioprine and zoledronic acid were identified to be potential drugs for AAAD.

Screening of colorectal cancer associated lncRNA, miRNA and mRNA based on bioinformatics technology and analysis of their biological functions / 中国肿瘤生物治疗杂志

@# Objective: To screen differentially expressed lncRNA, miRNA and mRNA in colorectal cancer (CRC) in TCGA database, and to explore their relationship with CRC prognosis and related biological functions. Methods: RNA sequencing (RNA-Seq) data and miRNA-Seq data of CRC samples were downloaded from the TCGAdatabase and analyzed, and differentially expressed lncRNA, miRNA and mRNA were screened by R program. The lncRNA-miRNA-mRNA ceRNA network in CRC was constructed by analyzing and integrating the relationships between differentially expressed RNAs through miRcode, TargetScan and miRTarbase databases.KaplanMeier method was used to analyze the relationship between the expression of lncRNA, miRNA, mRNA in ceRNA network and the survival prognosis of patients.Finally, the signal pathways involved in the occurrence and development of CRC were analyzed by GSEA functional enrichment analysis software. Results: A total of 614 differentially expressed lncRNAs, 244 differentially expressed miRNAs, and 12 672 differentially expressed mRNAs in CRC were identified; a ceRNA network consisting of 139 lncRNAs, 37 miRNAs and 228 mRNAs was constructed;It was found that 58 lncRNAs, 23 miRNAs, and 150 mRNAs were associated with the prognosis of CRC.The results of GSEA enrichment analysis showed that mRNA was mainly involved in signaling pathways such as Notch, Hedgehog and TGF-β. Conclusion: CRC-related ceRNA network was successfully constructed and lncRNAs, miRNAs and mRNAs associated with CRC prognosis were screened. It provides a valuable preliminary basis for further in-depth clinical research and basic experimental research on CRC.

Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile

BACKGROUND: Acute respiratory distress syndrome (ARDS) is a potentially devastating form of acute inflammatory lung injury as well as a major cause of acute respiratory failure. Although researchers have made significant progresses in elucidating the pathophysiology of this complex syndrome over the years, the absence of a universal detail disease mechanism up until now has led to a series of practical problems for a definitive treatment. This study aimed to predict some genes or pathways associated with sepsis-related ARDS based on a public microarray dataset and to further explore the molecular mechanism of ARDS. RESULTS: A total of 122 up-regulated DEGs and 91 down-regulated differentially expressed genes (DEGs) were obtained. The up- and down-regulated DEGs were mainly involved in functions like mitotic cell cycle and pathway like cell cycle. Protein-protein interaction network of ARDS analysis revealed 20 hub genes including cyclin B1 (CCNB1), cyclin B2 (CCNB2) and topoisomerase II alpha (TOP2A). A total of seven transcription factors including forkhead box protein M1 (FOXM1) and 30 target genes were revealed in the transcription factor-target gene regulation network. Furthermore, co-cited genes including CCNB2-CCNB1 were revealed in literature mining for the relations ARDS related genes. CONCLUSIONS: Pathways like mitotic cell cycle were closed related with the development of ARDS. Genes including CCNB1, CCNB2 and TOP2A, as well as transcription factors like FOXM1 might be used as the novel gene therapy targets for sepsis related ARDS

Graph-based unsupervised feature selection and multiview clustering for microarray data.

A challenge in bioinformatics is to analyse volumes of gene expression data generated through microarray experiments and obtain useful information. Consequently, most microarray studies demand complex data analysis to infer biologically meaningful information from such high-throughput data. Selection of informative genes is an important data analysis step to identify a set of genes which can further help in finding the biological information embedded in microarray data, and thus assists in diagnosis, prognosis and treatment of the disease. In this article we present an unsupervised feature selection technique which attempts to address the goal of explorative data analysis, unfolding the multi-faceted nature of data. It focuses on extracting multiple clustering views considering the diversity of each view from high-dimensional data. We evaluated our technique on benchmark data sets and the experimental results indicates the potential and effectiveness of the proposed model in comparison to the traditional single view clustering models, as well as other existing methods used in the literature for the studied datasets.

Perfil de transcrição gênica de células humanas estimuladas com a saliva de Lu. intermedia ou de Lu / Gene transcription profile of human cells stimulated with Lu saliva. Intermedia or Lu

A saliva dos flebotomíneos transmissores do parasita Leishmania possui uma variedade de agentes farmacológicos, como anticoagulantes, vasodilatadores além de moléculas imunomoduladoras e anti-inflamatórias. A saliva de Lu. intermedia e de Lu. longipalpis provocam o aumentam da infecção por diferentes espécies de Leishmania, em modelos experimentais.Entretanto a pré-exposição à saliva de Lu. longipalpis confere proteção a infecção, enquanto a pré-exposição à saliva de Lu. intermedia causa exacerbação da doença. Neste trabalho estimulamos as células do sangue de voluntários sadios com a saliva de Lu. intermedia ou de Lu. longipalpis e, posteriormente, o RNA foi extraído e utilizado no sequenciamento em larga escala (RNAseq). O estudo demonstrou que a saliva de Lu. intermedia e de Lu.longipalpismodula a expressão de uma série de genes e os processos biológicos mais requentes são semelhantes após a estimulação com as duas diferentes salivas. Identificamos seis processos biológicos comuns às salivas dos dois lebotomineos:Taxis,Chemotaxis,Locomotory behavior, Positive regulation of immune system process, Regulation of cytokine production e Regulation of cell activation. Dentre os genes que caracterizam esses seis processos,detectamosgenes que codificam quimiocinas, citocinas além de moléculas de superfície tais como CCL19, CCL2, CCL3, CCL4, CD80, CD83, IL10, IL1B, IL4, IL6.Definimos um conjunto de genes encontrados exclusivamente na amostra estimulada com a saliva de Lu. intermedia (ADA, CCL23, CCL3, CCL3L1, CXCL11, PDGFB, PDPN, PLAU e TNFSF15). Da mesma forma, encontramos um outro conjunto de genes expresso exclusivamenteem células estimuladas com a saliva de Lu. longipalpis(ENPP2, EREG, IDO1,IL1A e VEGFA). Essas diferenças podem fornecer pistas para o desenvolvimento da leishmaniose em indivíduos continuamente expostos à saliva de Lu. intermedia.

The saliva of sand flies, vectors of leishmania parasite, has a variety of pharmacological agents, such as anticoagulants, vasodilators as well as immunomodulatory and antiinflammatory molecules. Lu. intermedia and Lu. longipalpis increase the infection by different species of leishmania in experimental models. However, the pre-exposure to Lu. longipalpis saliva provides protection to infection, while the pre-exposure Lu. intermedia saliva causes exacerbation of the disease. In this work, we stimulated peripheral blood cells from healthy volunteers with salivary glands from Lu. intermedia or Lu. longipalpis and later RNA was extracted and used in large-scale sequencing (RNAseq). This study demonstrated that Lu. intermedia and Lu. longipalpis saliva modulate the expression of a number of genes and the most frequent biological processes are similar in cells stimulated with both saliva. We identified six biological processes commonly upregulated following stimulation with saliva of the two sand flies: taxis, chemotaxis, locomotory behavior, positive regulation of immune system process, regulation of cytokine production and regulation of cell activation. Among the genes that characterize these six biological processes, we detected genes encoding chemokines, cytokines plus surface molecules such as:CCL19, CCL2, CCL3, CCL4, CD80, CD83, IL10, IL1B, IL4 and IL6. We found a set of genes upregulated exclusively in cells stimulated with Lu. intermedia saliva (ADA, CCL23, CCL3, CCL3L1, CXCL11, PDGFB, PDPN, PLAU and TNFSF15). Similarly, another set of genes was expressed only in cells stimulated Lu. longipalpis saliva (ENPP2, EREG, IDO1,IL1A and VEGFA). These differences may provide clues for the development of leishmaniasis in individuals continuously exposed to Lu. intermedia saliva.

Analysis of the transcriptome in a multi-drug resistant uropathogenic Escherichia coli strain treated with water decoction of rhizoma coptidis by using RNA-seq / 中华微生物学和免疫学杂志

Objective To investigate the molecular mechanism of the inhibitory effects of rhizoma coptidis on multi-drug resistant uropathogenic Escherichia coli.Methods High-throughput RNA sequencing ( RNA-seq ) was performed to investigate the transcriptome in a multi-drug resistant uropathogenic Escherichia coli strain (NB8) treated with water decoction of rhizoma coptidis .Agar dilution test was used to determine the minimal inhibitory concentration ( MIC) of water decoction of rhizoma coptidis against the NB 8 strain.A growth curve was drawn to evaluate the effects of water decoction of rhizoma coptidis on the growth of NB8 strain.Total RNAs were extracted from the NB 8 strain after treated with the water decoction of rhizo-ma coptidis for 30 minutes and then synthetized to cDNA by reverse transcription after screening out the rRNAs.The HiSeq 2000 sequencing system was used for transcriptome sequencing .The TopHat software was used to map and analyze the RNA-Seq reads, and then Cufflinks was run to assemble transcripts and es-timate their abundances .The differential expression , GO enrichment and KEGG metabolic pathway were fur-ther analyzed .The NB8 strain dealt with normal saline was used as negative control .Results The MIC of water decoction of rhizoma coptidis to NB 8 strain was 12.5 mg/ml.There were 3665 genes expressed in NB8 strain treated with water decoction of rhizoma coptidis and 3430 genes expressed in NB8 strain treated with normal saline .The number of differentially expressed genes was 1428 including 921 up-regulated genes and 507 down-regulated genes .Those differentially expressed genes mainly enriched in the modules of binding and catalysis.The genes concerning cell adhesion , apoptosis and multicellular process were up-regulated, while those concerning the regulation of enzyme activities were down-regulated.Results of the KEGG meta-bolic pathway enrichment analysis showed that the genes concerning synthetic pathway of LPS were signifi -cantly up-regulated as well as those encoding the repair polymerase Ⅲthat was involved in DNA replication . However , the genes concerning fatty acid metabolism , histidine metabolism , thiamine metabolism , folate metabolism and iron carrier in ribosome synthesis showed overall down-regulation.Conclusion The tran-scriptome in uropathogenic Escherichia coli strain treated with rhizoma coptidis was profiled .The main mo-lecular mechanism of the inhibitory effects of rhizoma coptidis on uropathogenic Escherichia coli was to de-stroy the cell wall of Escherichia coli, affect the replication of DNA and regulate the transcription and transla-tion of proteins .This study illustrated that the inhibitory effects of rhizoma coptidis on uropathogenic Esche-richia coli were achieved in multiple levels .

Identification of molecular targets in the response of triple negative breast cancer to chemotherapy / 国际生物医学工程杂志

Objective To explore the molecular targets and mechanisms that could influence the sensitivity of triple negative breast cancer (TNBC) to chemotherapy,to provide important references for the chemotherapy based on gene detection.Methods The gene expression dataset GSE43502 was downloaded from the Gene Expression Omnibus in National Center for Biotechnology Information (NCBI).Gene expression data preprocessing was conducted by R Programming.The differentially expressed genes in the TNBC patients that relapsed after chemotherapy compared with the non-relapsed ones were obtained.Besides,the Database for Annotation Visualization and Integrated analysis (DAVID) was used for functional analysis of those genes.The microRNA (miRNA) that might regulate the differentially expressed genes was obtained from the starBase database.Furthermore,Cytoscape was used for the construction of miRNA-gene regulation network.Results Three hundred and twelve differentially expressed genes were obtained.Some biological process related to cell membrane,metal ion homeostasis and pathways involved in immune and inflammatory were found to be enriched in those genes.Furthermore,171 miRNA that might regulate the differentially expressed genes were obtained and 553 miRNA-gene regulation pairs were formed.Conclusions hsa-miR-30d-5p,SIX4,etc.might influence the sensitivity of TNBC to chemotherapy through cell structure or immune system.

CDH13 and HCRTR2 May Be Associated with Hypersomnia Symptom of Bipolar Depression: A Genome-Wide Functional Enrichment Pathway Analysis

Although bipolar disorder is highly heritable, the identification of specific genetic variations is limited because of the complex traits underlying the disorder. We performed a genome-wide association study of bipolar disorder using a subphenotype that shows hypersomnia symptom during a major depressive episode. We investigated a total of 2,191 cases, 1,434 controls, and 703,012 single nucleotide polymorphisms (SNPs) in the merged samples obtained from the Translational Genomics Institute and the Genetic Association Information Network. The gene emerging as the most significant by statistical analysis was rs1553441 (odds ratio=0.4093; p=1.20x10-5; Permuted p=6.0x10-6). However, the 5x0-8 threshold for statistical significance required in a genome-wide association study was not achieved. The functional enrichment pathway analysis showed significant enrichments in the adhesion, development-related, synaptic transmission-related, and cell recognition-related pathways. For further evaluation, each gene of the enriched pathways was reviewed and matched with genes that were suggested to be associated with psychiatric disorders by previous genetic studies. We found that the cadherin 13 and hypocretin (orexin) receptor 2 genes may be involved in the hypersomnia symptom during a major depressive episode of bipolar disorder.