scholarly journals Comparative transcriptome investigation of Nosema ceranae infecting eastern honeybee workers

2022 ◽  
Author(s):  
Fan Yuanchan ◽  
Dafu Chen ◽  
Rui Guo
Keyword(s):  
Virulence Factor ◽  
Clustering Analysis ◽  
Biological Process ◽  
Kegg Pathway ◽  
Apis Cerana ◽  
Nosema Ceranae ◽  
Kegg Pathway Analysis ◽  
Genes Encoding ◽  
Comparison Groups ◽  
Shed Light

Apis cerana is the original host for Nosema ceranae, a widespread fungal parasite resulting in bee nosemosis, which leads to severe losses for apiculture industry throughout the world. However, knowledge of N. ceranae infecting eastern honeybees is extremely limited. Currently, the mechanism underlying N. ceranae infection is still largely unknown. Based on our previously gained high-quality transcriptome datasets, comparative transcriptomic investigation was conducted in this work, with a focus on virulence factor-associated differentially expressed genes (DEGs). Microscopic observation showed that A. c. cerana workers midguts were effectively infected after inoculation with clean spores of N. ceranae. Totally, 1411, 604, and 38 DEGs were identified from NcCK vs. NcT1, NcCK vs. NcT2 and NcT1 vs. NcT2 comparison groups. Venn analysis showed that ten up-regulated genes and nine down-regulated ones were shared by aforementioned comparison groups. GO category indicated these DEGs were involved in a series of functional terms relevant to biological process, cellular component, and molecular function, such as metabolic process, cell part, and catalytic activity. Additionally, KEGG pathway analysis suggested that the DEGs were engaged in an array of pathways of great importance, such as metabolic pathway, glycolysis, and biosynthesis of secondary metabolites. Further, expression clustering analysis demonstrated that majority of genes encoding virulence factors such as ricin B lectins and polar tube proteins displayed apparent up-regulation, whereas a few virulence factor-associated genes such as hexokinase gene and 6-phosphofructokinase gene presented down-regulation during the fungal infection. Finally, the expression trend of 14 DEGs was confirmed by RT-qPCR, validating the reliability of our transcriptome datasets. These results together demonstrated that an overall alteration of the transcriptome of N. ceranae occurred during the infection of A. c. ceranae workers, and most of virulence factor-related genes were induced to activation to promote the fungal invasion. Our findings not only lay a foundation for clarifying the molecular mechanism underlying N. ceranae infection of eastern honeybee workers, but also shed light on developing novel targets for microsporidiosis control.

scholarly journals Transcriptomic inspection revealed a possible pathway regulating the formation of the high-quality brush hair in Chinese Haimen goat ( Capra hircus )

2018 ◽  
Vol 5 (1) ◽  
pp. 170907 ◽  
Author(s):  
Dejun Ji ◽  
Bo Yang ◽  
Yongjun Li ◽  
Miaoying Cai ◽  
Wei Zhang ◽  
...  
Keyword(s):  
Biological Process ◽  
Kegg Pathway ◽  
Cellular Component ◽  
Biological Information ◽  
Capra Hircus ◽  
Molecular Function ◽  
High Quality ◽  
Type Iii ◽  
Kegg Pathways ◽  
Kegg Pathway Analysis

The high-quality brush hair, or Type III brush hair, is coarse hair but with a tip and little medulla, which uniquely grows in the cervical carina of Chinese Haimen goat ( Capra hircus ). To unveil the mechanism of the formation of Type III brush hair in Haimen goats, transcriptomic RNAseq technology was used for screening of differentially expressed genes (DEGs) in the skin samples of the Type III and the non-Type III hair goats, and these DEGs were analysed by KEGG pathway analysis. The results showed that a total of 295 DEGs were obtained, mainly from three main functional types: cellular component, molecular function and biological process. These DEGs were mainly enriched in three KEGG pathways, such as protein processing in endoplasmic reticulum, MAPK, and complement and coagulation cascades. These DEGs gave hints to a possible mechanism, under which heat stress possibly initiated the formation. The study provided some useful biological information, which could give a new view about the roles of certain factors in hair growth and give hints on the mechanism of the formation of the Type III brush hair in Chinese Haimen goat.

Microarray Profiling of Bone Marrow Long Non-Coding RNA Expression in Multiple Myeloma

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5617-5617
Author(s):  
Ying Shen ◽  
Jing Liu ◽  
Yun Yang ◽  
Ju Bai ◽  
Yue Peng ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Bone Marrow ◽  
Gene Ontology ◽  
Iron Deficiency ◽  
Iron Deficiency Anemia ◽  
Pathway Analysis ◽  
Biological Process ◽  
Kegg Pathway ◽  
Go Analysis ◽  
Kegg Pathway Analysis

Abstract Introduction: Multiple myeloma (MM), the second most frequent hematologic malignancy, is characterized with clonal proliferation of malignant plasma cells in the bone marrow, and usually monoclonal protein in the blood and/or urine. Its clinical manifestations are associated with end-organ damage consisting of anaemia, renal insufficiency, bone lesions and hypercalcaemia. Long non-coding RNAs (lncRNAs) represent more than half of the mammalian noncoding transcriptome and are involved in many biological processes, including transcription regulation, competition with other linear RNAs and involvement in tumorigenesis or oncogenic pathways. Accumulating studies have revealed the important role of lncRNAs in the hematological tumors, especially MM. In order to investigate the further relationship between MM and lncRNAs, we performed global lncRNA profiling in both incipient MM patients and iron deficiency anemia (IDA) patients. We assumed that the bunch of deregulated lncRNAs in MM patients would broaden current understanding of progression of MM, and present a new approach to novel therapeutic targets. Methods: Bone marrow mononuclear cells were obtained from five MM patients with normal karyotype at the Department of Hematology, Second Affiliated Hospital, Xi'an Jiaotong University, in 2016. Additionally, bone marrow samples from five patients with IDA were used as controls. One sample in five MM patients was rejected because of its disqualification in clustering analysis. Arraystar Human LncRNA Array V4.0 was used to profile expression of lncRNAs, which was performed by KangChen Bio-tech (Shanghai, China). The array detects a total of 40,173 lncRNAs probes and an entire collection of 20,730 protein coding mRNAs. Gene Ontology (GO) analysis (http://david.abcc.ncifcrf.gov/summary.jsp) was used to analyze differentially expressed transcripts. Pathway analysis of differentially expressed transcripts were accomplished using Kyoto Encyclopedia of Genes and Genomes (KEGG) database (http://www.genome.jp/kegg). Results: Bioinformatic analysis of the lncRNA expression identified a total of 2445 lncRNAs were upregulated and 1519 lncRNAs were downregulated in four MM samples, among them, 199 lncRNAs were significantly upregulated and 27 lncRNAs were notably downregulated more than 10-fold in MM samples compared with IDA (Figure 1). GO analysis by Database for Annotation, Visualization and Integrated Discovery (DAVID ) showed that the top ten enriched biological process (BP) by upregulated transcripts were involved in multicellular organismal development and cell-cell adhesion, while downregulated transcripts were dragged in mitotic cell cycle and cell cycle. KEGG pathway analysis of the top ten enriched pathways included ECM-receptor interaction and protein processing in endoplasmic reticulum in upregulated transcript, while cell cycle and DNA replication were the top two enriched pathways in downregulated transcript (Figure 2). Among them, mitotic cell cycle was the most enriched pathway with p-value 3.86E-35. These results suggested that the dysregulated lncRNAs were related to MM cells adhesion and proliferation or differentiation closely. Conclusions: We have identified a group of dysregulated lncRNAs and mRNAs in bone marrow samples obtained from MM patients versus IDA controls. These lncRNAs participate in MM cell growth, migration and invasion by regulating cell adhesion and cell cycle, playing an important role in the development and progression of MM. Further investigation is still required to detect the underlying functions of these lncRNAs in MM pathogenesis and whether these lncRNAs may serve as new diagnostic biomarkers and therapeutic targets for MM. Figure 1 Clustering analysis of four mulitiple myeloma (MM) samples and five iron deficiency anemia (IDA) controls. Figure 1. Clustering analysis of four mulitiple myeloma (MM) samples and five iron deficiency anemia (IDA) controls. Figure 2 Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of dysregulated transcripts. (A) The top ten enriched biological process (BP) by upregulated transcripts. (B) The top ten enriched BP by downregulated transcripts. (C) The top ten enriched pathways in upregulated transcripts. (D) The top ten enriched pathways in downregulated transcripts. Figure 2. Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of dysregulated transcripts. (A) The top ten enriched biological process (BP) by upregulated transcripts. (B) The top ten enriched BP by downregulated transcripts. (C) The top ten enriched pathways in upregulated transcripts. (D) The top ten enriched pathways in downregulated transcripts. Disclosures No relevant conflicts of interest to declare.

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2021 ◽  
pp. 1-14
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Developmental Stages ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mythimna Separata ◽  
Kegg Pathway Analysis ◽  
Oriental Armyworm ◽  
Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

scholarly journals Potential Role of Phospholipases in Virulence and Fungal Pathogenesis

2000 ◽  
Vol 13 (1) ◽  
pp. 122-143 ◽  
Author(s):  
Mahmoud A. Ghannoum
Keyword(s):  
Virulence Factor ◽  
Cell Damage ◽  
Pathogenic Fungi ◽  
Microbial Pathogens ◽  
Immunogold Electron Microscopy ◽  
Lytic Enzymes ◽  
Fungal Virulence ◽  
Phospholipase B ◽  
Genes Encoding

SUMMARY Microbial pathogens use a number of genetic strategies to invade the host and cause infection. These common themes are found throughout microbial systems. Secretion of enzymes, such as phospholipase, has been proposed as one of these themes that are used by bacteria, parasites, and pathogenic fungi. The role of extracellular phospholipase as a potential virulence factor in pathogenic fungi, including Candida albicans, Cryptococcus neoformans, and Aspergillus, has gained credence recently. In this review, data implicating phospholipase as a virulence factor in C. albicans, Candida glabrata, C. neoformans, and A. fumigatus are presented. A detailed description of the molecular and biochemical approaches used to more definitively delineate the role of phospholipase in the virulence of C. albicans is also covered. These approaches resulted in cloning of three genes encoding candidal phospholipases (caPLP1, caPLB2, and PLD). By using targeted gene disruption, C. albicans null mutants that failed to secrete phospholipase B, encoded by caPLB1, were constructed. When these isogenic strain pairs were tested in two clinically relevant murine models of candidiasis, deletion of caPLB1 was shown to lead to attenuation of candidal virulence. Importantly, immunogold electron microscopy studies showed that C. albicans secretes this enzyme during the infectious process. These data indicate that phospholipase B is essential for candidal virulence. Although the mechanism(s) through which phospholipase modulates fungal virulence is still under investigations, early data suggest that direct host cell damage and lysis are the main mechanisms contributing to fungal virulence. Since the importance of phospholipases in fungal virulence is already known, the next challenge will be to utilize these lytic enzymes as therapeutic and diagnostic targets.

scholarly journals POS0399 TMT-BASED QUANTITATIVE PROTEOMICS ANALYSIS OF SYNOVIAL FLUID-DERIVED EXOSOMES IN RHEUMATOID ARTHRITIS, AXIAL SPONDYLOARTHRITIS, GOUT AND OSTEOARTHRITIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 428.3-429
Author(s):  
Y. Liu ◽  
Y. Huang ◽  
Q. Huang ◽  
Z. Huang ◽  
Z. Li ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Cluster Analysis ◽  
Synovial Fluid ◽  
Pathway Analysis ◽  
Quantitative Proteomics ◽  
Axial Spondyloarthritis ◽  
Kegg Pathway ◽  
Hierarchical Cluster ◽  
Kegg Pathway Analysis ◽  
Differential Proteins

Background:The pathogeneses of the joint diseases rheumatoid arthritis (RA), axial spondyloarthritis (axSpA), gout, and osteoarthritis (OA) are still not fully elucidated. Exosomes in synovial fluid (SF) has a critical role in the pathogenesis of arthritis. None of study has compared the proteomics of SF-derived exosomes in RA, axSpA, gout and OA.Objectives:To compare the proteomics of SF-derived exosomes in RA, axSpA, gout and OA based on tandem mass tags (TMT) labeled quantitative proteomics technique.Methods:SF-derived exosomes was isolated from RA, axSpA, gout and OA patients by the Exoquick kit combined ultracentrifugation method. TMT labeled quantitative proteomics technique was used to compare the proteomics of SF-derived exosomes. Volcano plot, hierarchical cluster, Gene Ontologies (GO), Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted.Results:A total of 1678 credible proteins were detected. With the cut off criteria of |log2 (fold-change)| ≥1.2 and p-value <0.05, 267 (140 up-regulated and 127 down-regulated)differential proteins were found in OA vs gout, 291 (179 and 112) in axSpA vs OA, 515 (109 and 406) in RA vs axSpA, 298 (191 and 107) in axSpA vs gout, 462 (160 and 302) in RA vs gout, 536 (170 and 366) in RA vs OA. GO analysis showed that the biological progress of differential proteins were mainly enriched in the “immune response”. Regarding the molecular function, the differential proteins mainly mediated “antigen binding”. GO analysis of the cellular components indicated that most proteins were annotated as “extracellular exosomes”. KEGG pathway analysis demonstrated differential proteins were significantly enriched in “complement and coagulation cascades”. The hierarchical cluster analysis of the differential proteins in the four groups showed that Lysozyme C and Keratin were more abundant in gout, Hemoglobin and Actin-related protein 2/3 complex subunit 3 in OA, Sodium/potassium-transporting ATPase subunit alpha-1 and Immunoglobulin heavy constant delta in axSpA, Pregnancy zone protein and Stromelysin-1 in RA.Conclusion:The protein profiles of SF-derived exosomes in RA, axSpA, gout and OA patients were different. The differential proteins were the potential biomarkers of RA, axSpA, gout and OA.References:[1]Cretu D, Diamandis E P, Chandran V. Delineating the synovial fluid proteome: recent advancements and ongoing challenges in biomarker research.[J]. Critical reviews in clinical laboratory sciences, 2013,50(2):51-63.[2]McArdle A J, Menikou S. What is proteomics?[J]. Archives of disease in childhood. Education and practice edition, 2020.Figure 1.The hierarchical cluster analysis of differential proteins in axSpA, OA, Gout and RA.Disclosure of Interests:None declared

scholarly journals Identification of Pathways and Key Genes in Venous Remodeling After Arteriovenous Fistula by Bioinformatics Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Kong Jie ◽  
Wang Feng ◽  
Zhao Boxiang ◽  
Gong Maofeng ◽  
Zhang Jianbin ◽  
...  
Keyword(s):  
Arteriovenous Fistula ◽  
Pathway Analysis ◽  
Kegg Pathway ◽  
Function Analysis ◽  
Gene Set Enrichment Analysis ◽  
Control Group ◽  
Hub Genes ◽  
Molting Cycle ◽  
Kegg Pathway Analysis ◽  
First Choice

The arteriovenous fistula (AVF) is the first choice for vascular access for hemodialysis of renal failure patients. Venous remodeling after exposure to high fistula flow is important for AVF to mature but the mechanism underlying remodeling is still unknown. The objective of this study is to identify the molecular mechanisms that contribute to venous remodeling after AVF. To screen and identify the differentially expressed genes (DEGs) that may involve venous remodeling after AVF, we used bioinformatics to download the public microarray data (GSE39488) from the Gene Expression Omnibus (GEO) and screen for DEGs. We then performed gene ontology (GO) function analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and gene set enrichment analysis (GSEA) for the functional annotation of DEGs. The protein-protein interaction (PPI) network was constructed and the hub genes were carried out. Finally, we harvested 12 normal vein samples and 12 AVF vein samples which were used to confirm the expressions of the hub genes by immunohistochemistry. A total of 45 DEGs were detected, including 32 upregulated and 13 downregulated DEGs. The biological process (BP) of the GO analysis were enriched in the extrinsic apoptotic signaling pathway, cGMP-mediated pathway signaling, and molting cycle. The KEGG pathway analysis showed that the upregulated DEGs were enriched in glycosaminoglycan biosynthesis and purine metabolism, while the downregulated DEGs were mainly enriched in pathways of glycosaminoglycan biosynthesis, antifolate resistance, and ABC transporters. The GSEA analysis result showed that the top three involved pathways were oxidative phosphorylation, TNFA signaling via NF-K B, and the inflammatory response. The PPI was constructed and the hub genes found through the method of DMNC showed that INHBA and NR4A2 might play an important role in venous remodeling after AVF. The integrated optical density (DOI) examined by immunohistochemistry staining showed that the expression of both INHBA and NR4A2 increased in AVF compared to the control group. Our research contributes to the understanding of the molecular mechanism of venous remodeling after exposure to high fistula flow, which may be useful in treating AVF failure.

scholarly journals Dynamics of Nosema apis and Nosema ceranae Co-Infection Seasonally in Honey Bee (Apis mellifera L.) Colonies

2019 ◽  
Vol 63 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Asli Özkırım ◽  
Aygün Schiesser ◽  
Nevіn Keskin
Keyword(s):  
Apis Mellifera ◽  
Apis Cerana ◽  
Winter Season ◽  
Nosema Ceranae ◽  
Molecular Techniques ◽  
Winter Period ◽  
Nosema Apis ◽  
Infection Level ◽  
Seasonal Infection ◽  
Asian Honeybee

AbstractNosema apis is a pathogen spesific for the European honeybee, Apis mellifera L., while Nosema ceranae is specific for the Asian honeybee, Apis cerana. Turkey provides different environmental and host conditions for both Nosema species. The aim of the study is to determine the dynamic of N. cerenae and N. apis seasonal infection. A number of samples were collected from different apiaries between 2009-2016 years. The samples were kept at −20°C in the laboratory. Light microscopy was used for spore counting and molecular techniques were used to identify the Nosema species. The results showed that winter season had an impact on the type of Nosema as well as on infection rates. The number of N. ceranae spores decreases significantly at low temperatures (≤ 5°C). The winter period was found to be the main factor affecting nosema infection level and dominancy of Nosema ceranae. Furthermore, co-infection of both species is an indicator of the dynamics of N. apis and N. ceranae. This study suggests, that there is a dynamic prevalence among the Nosema species depending of the average winter temperature and not a replacement of N. apis by N. ceranae.

scholarly journals Gene Expression Profiling of Type 2 Diabetes Mellitus by Bioinformatics Analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Huijing Zhu ◽  
Xin Zhu ◽  
Yuhong Liu ◽  
Fusong Jiang ◽  
Miao Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Candidate Genes ◽  
Signaling Pathway ◽  
Bioinformatics Analysis ◽  
Kegg Pathway ◽  
Ppi Network ◽  
Kegg Pathway Analysis

Objective. The aim of this study was to identify the candidate genes in type 2 diabetes mellitus (T2DM) and explore their potential mechanisms. Methods. The gene expression profile GSE26168 was downloaded from the Gene Expression Omnibus (GEO) database. The online tool GEO2R was used to obtain differentially expressed genes (DEGs). Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by using Metascape for annotation, visualization, and comprehensive discovery. The protein-protein interaction (PPI) network of DEGs was constructed by using Cytoscape software to find the candidate genes and key pathways. Results. A total of 981 DEGs were found in T2DM, including 301 upregulated genes and 680 downregulated genes. GO analyses from Metascape revealed that DEGs were significantly enriched in cell differentiation, cell adhesion, intracellular signal transduction, and regulation of protein kinase activity. KEGG pathway analysis revealed that DEGs were mainly enriched in the cAMP signaling pathway, Rap1 signaling pathway, regulation of lipolysis in adipocytes, PI3K-Akt signaling pathway, MAPK signaling pathway, and so on. On the basis of the PPI network of the DEGs, the following 6 candidate genes were identified: PIK3R1, RAC1, GNG3, GNAI1, CDC42, and ITGB1. Conclusion. Our data provide a comprehensive bioinformatics analysis of genes, functions, and pathways, which may be related to the pathogenesis of T2DM.

scholarly journals Bioinformatic Analysis of Circular RNA-Associated ceRNA Network Associated with Hepatocellular Carcinoma

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Jiacheng Wu ◽  
Shui Liu ◽  
Yien Xiang ◽  
Xianzhi Qu ◽  
Yingjun Xie ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Pathway Analysis ◽  
Target Genes ◽  
Kegg Pathway ◽  
Interaction Network ◽  
Bioinformatic Analysis ◽  
Differentially Expressed ◽  
Qrt Pcr ◽  
Cerna Network ◽  
Kegg Pathway Analysis

Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and is associated with a high mortality rate and poor treatment efficacy. In an attempt to investigate the mechanisms involved in the pathogenesis of HCC, bioinformatic analysis and validation by qRT-PCR were performed. Three circRNA GEO datasets and one miRNA GEO dataset were selected for this purpose. Upon combined biological prediction, a total of 11 differentially expressed circRNAs, 15 differentially expressed miRNAs, and 560 target genes were screened to construct a circRNA-related ceRNA network. GO analysis and KEGG pathway analysis were performed for the 560 target genes. To further screen key genes, a protein-protein interaction network of the target genes was constructed using STRING, and the genes and modules with higher degree were identified by MCODE and CytoHubba plugins of Cytoscape. Subsequently, a module was screened out and subjected to GO enrichment analysis and KEGG pathway analysis. This module included eight genes, which were further screened using TCGA. Finally, UBE2L3 was selected as a key gene and the hsa_circ_0009910–miR-1261–UBE2L3 regulatory axis was established. The relative expression of the regulatory axis members was confirmed by qRT-PCR in 30 pairs of samples, including HCC tissues and adjacent nontumor tissues. The results suggested that hsa_circ_0009910, which was upregulated in HCC tissues, participates in the pathogenesis of HCC by acting as a sponge of miR-1261 to regulate the expression of UBE2L3. Overall, this study provides support for the possible mechanisms of progression in HCC.

scholarly journals Screening and Functional Prediction of Key Candidate Genes in Hepatitis B Virus-Associated Hepatocellular Carcinoma

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Xia Chen ◽  
Ling Liao ◽  
Yuwei Li ◽  
Hengliu Huang ◽  
Qing Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Pathway Analysis ◽  
Kegg Pathway ◽  
Metabolic Process ◽  
Hub Genes ◽  
Kegg Pathway Analysis ◽  
B Virus

Background. The molecular mechanism by which hepatitis B virus (HBV) induces hepatocellular carcinoma (HCC) is still unknown. The genomic expression profile and bioinformatics methods were used to investigate the potential pathogenesis and therapeutic targets for HBV-associated HCC (HBV-HCC). Methods. The microarray dataset GSE55092 was downloaded from the Gene Expression Omnibus (GEO) database. The data was analyzed by the bioinformatics software to find differentially expressed genes (DEGs). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, ingenuity pathway analysis (IPA), and protein-protein interaction (PPI) network analysis were then performed on DEGs. The hub genes were identified using Centiscape2.2 and Molecular Complex Detection (MCODE) in the Cytoscape software (Cytoscape_v3.7.2). The survival data of these hub genes was downloaded from the Gene Expression Profiling Interactive Analysis (GEPIA). Results. A total of 2264 mRNA transcripts were differentially expressed, including 764 upregulated and 1500 downregulated in tumor tissues. GO analysis revealed that these DEGs were related to the small-molecule metabolic process, xenobiotic metabolic process, and cellular nitrogen compound metabolic process. KEGG pathway analysis revealed that metabolic pathways, complement and coagulation cascades, and chemical carcinogenesis were involved. Diseases and biofunctions showed that DEGs were mainly associated with the following diseases or biological function abnormalities: cancer, organismal injury and abnormalities, gastrointestinal disease, and hepatic system disease. The top 10 upstream regulators were predicted to be activated or inhibited by Z-score and identified 25 networks. The 10 genes with the highest degree of connectivity were defined as the hub genes. Cox regression revealed that all the 10 genes (CDC20, BUB1B, KIF11, TTK, EZH2, ZWINT, NDC80, TPX2, MELK, and KIF20A) were related to the overall survival. Conclusion. Our study provided a registry of genes that play important roles in regulating the development of HBV-HCC, assisting us in understanding the molecular mechanisms that underlie the carcinogenesis and progression of HCC.

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