Integrated Metabolomics and Transcriptomic Analysis of Hepatopancreas in Different Living Status Macrobrachium nipponense in Response to Hypoxia

As the basic element of aerobic animal life, oxygen participates in most physiological activities of animals. Hypoxia stress is often the subject of aquatic animal research. Macrobrachium nipponense, an economically important aquatic animal in southern China, has been affected by hypoxia for many years and this has resulted in a large amount of economic loss due to its sensitivity to hypoxia; Metabolism and transcriptome data were combined in the analysis of the hepatopancreas of M. nipponense in different physiological states under hypoxia; A total of 108, 86, and 48 differentially expressed metabolites (DEMs) were found in three different comparisons (survived, moribund, and dead shrimps), respectively. Thirty-two common DEMs were found by comparing the different physiological states of M. nipponense with the control group in response to hypoxia. Twelve hypoxia-related genes were identified by screening and analyzing common DEMs. GTP phosphoenolpyruvate carboxykinase (PEPCK) was the only differentially expressed gene that ranked highly in transcriptome analysis combined with metabolome analysis. PEPCK ranked highly both in transcriptome analysis and in combination with metabolism analysis; therefore, it was considered to have an important role in hypoxic response. This manuscript fills the one-sidedness of the gap in hypoxia transcriptome analysis and reversely deduces several new genes related to hypoxia from metabolites. This study contributes to the clarification of the molecular process associated with M. nipponense under hypoxic stress.

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Transcriptome Analysis of Aedes aegypti Aag2 Cells in Response to Dengue Virus-2 Infection

10.21203/rs.3.rs-22807/v4 ◽

2020 ◽

Author(s):

Man-jin Li ◽

Ce-jie Lan ◽

He-ting Gao ◽

Dan Xing ◽

Zhen-yu Gu ◽

...

Keyword(s):

Aedes Aegypti ◽

Dengue Virus ◽

Cell Line ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Bioinformatics Analysis ◽

Differentially Expressed ◽

Control Group ◽

Sequencing Data ◽

Qrt Pcr

Abstract Background: Dengue virus (DENV) is a flavivirus transmitted by mosquitoes that is prevalent in tropical and subtropical countries and has four serotypes (DENV1-4). Aedes aegypti, as the main transmission vector of DENV, exhibits strong infectivity and transmission. With the aim of obtaining a better understanding of the Ae. aegypti-DENV interaction, the transcriptome changes in DENV-2-infected Aag2 cells were studied to describe the immune responses of mosquitoes using the Ae. aegypti Aag2 cell line as a model.Methods: RNAseq technology was used to sequence the transcripts of the Ae. aegypti Aag2 cell line before and after infection with DENV-2. A bioinformatics analysis was then performed to assess the biological functions of the differentially expressed genes, and the sequencing data were verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR).Results: The transcriptome analysis generated 8866 unigenes that were found in both groups, 225 unigenes that were only found in the infection group, and 683 unigenes that only existed in the control group. A total of 1199 differentially expressed genes, including 1014 upregulated and 185 downregulated genes, were identified. The bioinformatics analysis showed that the differentially expressed genes were mainly involved in the longevity regulating pathway, circadian rhythm, DNA replication, and peroxisome, purine, pyrimidine, and drug metabolism. The qRT-PCR verification results showed the same trend, which confirmed that the expression of the differentially expressed genes had changed and that the transcriptome sequencing data were reliable.Conclusions: This study investigated the changes in the transcriptome levels in the DENV-2-infected Ae. aegypti Aag2 cell line, which provides a faster and effective method for discovering genes related to Ae. aegypti pathogen susceptibility. The findings provide basic data and directions for further research on the complex mechanism underlying host-pathogen interactions.

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RNA-Seq Analysis Identifies Differentially Expressed Genes in Subcutaneous Adipose Tissue in Qaidaford Cattle, Cattle-Yak, and Angus Cattle

Animals ◽

10.3390/ani9121077 ◽

2019 ◽

Vol 9 (12) ◽

pp. 1077 ◽

Cited By ~ 2

Author(s):

Chengchuang Song ◽

Yongzhen Huang ◽

Zhaoxin Yang ◽

Yulin Ma ◽

Buren Chaogetu ◽

...

Keyword(s):

Adipose Tissue ◽

Meat Quality ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Cell Metabolism ◽

Differentially Expressed ◽

Receptor Interaction ◽

Control Group ◽

Rna Seq ◽

Angus Cattle

In the beef industry, fat tissue is closely related to meat quality. In this study, high-throughput RNA sequencing was utilized for adipose tissue transcriptome analysis between cattle-yak, Qaidamford cattle, and Angus cattle. The screening and identification of differentially expressed genes (DEGs) between different breeds of cattle would facilitate cattle breeding. Compared to Angus cattle adipose tissue, a total of 4167 DEGs were identified in cattle-yak adipose tissue and 3269 DEGs were identified in Qaidamford cattle adipose tissue. Considering cattle-yak as a control group, 154 DEGs were identified in Qaidamford cattle adipose tissue. GO analysis indicated the significant enrichment of some DEGs related to lipid metabolism. The KEGG pathway database was also used to map DEGs and revealed that most annotated genes were involved in ECM-receptor interaction and the PI3K-Akt signal pathway, which are closely related to cell metabolism. Eight selected DEGs related to adipose tissue development or metabolism were verified by RT-qPCR, indicating the reliability of the RNA-seq data. The results of this comparative transcriptome analysis of adipose tissue and screening DEGs suggest several candidates for further investigations of meat quality in different cattle breeds.

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Screening of Biomarkers for Hypertension Susceptibility in Pregnancy

Proceedings of Anticancer Research ◽

10.26689/par.v4i5.1523 ◽

2020 ◽

Vol 4 (5) ◽

Author(s):

Jian Xu ◽

Liye Fan ◽

Feng Qi ◽

Xia Xiu

Keyword(s):

Small Molecule ◽

Target Genes ◽

Gestational Hypertension ◽

Expression Profiles ◽

Differentially Expressed Gene ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Control Group ◽

Signal Pathways ◽

Small Molecule Drug

Objective: To study the differential lncRNA / mRNA expression profiles of placental tissues in patients with gestational hypertension, analyze their possible mechanisms of action, and explore their target genes and small molecule drug-related lncRNAs. Methods: Three patients with gestational hypertension who were treated in our hospital from May 2018 to May 2019 were selected as the research subjects and three healthy pregnant women who underwent a prenatal examination in the same hospital were selected as the control group. The placental tissues were taken from the patients. RNA-sequencing was performed to construct lncRNA/mRNA differential expression profiles; screening differentially expressed lncRNAs were used to predict target genes, and GO and KEGG enrichment analysis predicted the biological functions of target genes and the enriched signal pathways, respectively. Protein-protein interaction network, lncRNA-miRNA-mRNA network, and differentially expressed gene-small molecule drug association networks were constructed. Results: RNA-seq analysis revealed 19 differentially expressed lncRNA (4 up-regulated; 15 down-regulated) (P<0.05). Moreover, 423 differentially expressed genes (DEGs) (84 up-regulated; 339 down-regulated)(P<0.05). GO and KEGG enrichment analysis found that gestational hypertension is mainly related to endothelial cell damage, inflammatory response, abnormal immune regulation, and abnormal trophoblast invasion. The PPI network and lncRNA-miRNA-mRNA network were constructed. Differentially expressed gene-drug small molecule prediction results found 19 pairs of differentially gene-small drug relationship pairs, mainly including antibody, inhibitor et al. Conclusion: Differently expressed lncRNAs in the placenta of patients with gestational hypertension can participate in the regulation of multiple biological functional level-related signal pathways through targeted regulation of their target genes, and play an important role in the occurrence and development of gestational hypertension. The predicted small molecule drug can be used as a reference for clinical treatment.

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Transcriptome Analysis of Aedes aegypti Aag2 Cells in Response to Dengue Virus-2 Infection

10.21203/rs.3.rs-22807/v2 ◽

2020 ◽

Author(s):

Man-jin Li ◽

Ce-jie Lan ◽

He-ting Gao ◽

Dan Xing ◽

Zhen-yu Gu ◽

...

Keyword(s):

Aedes Aegypti ◽

Dengue Virus ◽

Cell Line ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Bioinformatics Analysis ◽

Differentially Expressed ◽

Control Group ◽

Sequencing Data ◽

Qrt Pcr

Abstract Background Dengue virus (DENV) is a flavivirus transmitted by mosquitoes that is prevalent in tropical and subtropical countries and has four serotypes (DENV1-4). Aedes aegypti, as the main transmission vector of DENV, exhibits strong infectivity and transmission. With the aim of obtaining a better understanding of the Ae. aegypti-DENV interaction, the transcriptome changes in DENV-2-infected Aag2 cells were studied to describe the immune responses of mosquitoes using the Ae. aegypti Aag2 cell line as a model.Methods RNAseq technology was used to sequence the transcripts of the Ae. aegypti Aag2 cell line before and after infection with DENV-2. A bioinformatics analysis was then performed to assess the biological functions of the differentially expressed genes, and the sequencing data were verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR).Results The transcriptome analysis generated 8,866 unigenes that were found in both groups, 225 unigenes that were only found in the infection group, and 683 unigenes that only existed in the control group. A total of 1199 differentially expressed genes, including 1014 upregulated and 185 downregulated genes, were identified. The bioinformatics analysis showed that the differentially expressed genes were mainly involved in the longevity regulating pathway, circadian rhythm, DNA replication, and peroxisome, purine, pyrimidine, and drug metabolism. The qRT-PCR verification results showed the same trend, which confirmed that the expression of the differentially expressed genes had changed and that the transcriptome sequencing data were reliable.Conclusions This study investigated the changes in the transcriptome levels in the DENV-2-infected Ae. aegypti Aag2 cell line, which provides a faster and effective method for discovering genes related to Ae. aegypti pathogen susceptibility. The findings provide basic data and directions for further research on the complex mechanism underlying host-pathogen interactions.

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Transcriptome Analysis of Aedes aegypti Aag2 Cells in Response to Dengue Virus-2 Infection

10.21203/rs.3.rs-22807/v1 ◽

2020 ◽

Author(s):

Man-jin Li ◽

Ce-jie Lan ◽

He-ting Gao ◽

Dan Xing ◽

Zhen-yu Gu ◽

...

Keyword(s):

Aedes Aegypti ◽

Dengue Virus ◽

Cell Line ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Bioinformatics Analysis ◽

Differentially Expressed ◽

Control Group ◽

Sequencing Data ◽

Qrt Pcr

Abstract Background Dengue virus (DENV) is a flavivirus transmitted by mosquitoes that is prevalent in tropical and subtropical countries and has four serotypes (DENV1-4). Aedes aegypti, as the main transmission vector of DENV, exhibits strong infectivity and transmission. With the aim of obtaining a better understanding of the Aedes aegypti-DENV interaction, the transcriptome changes in DENV-2-infected Aag2 cells were studied to describe the immune responses of mosquitoes using the Aedes aegypti Aag2 cell line as a model. Methods RNAseq technology was used to sequence the transcripts of the Aedes aegypti Aag2 cell line before and after infection with DENV-2. A bioinformatics analysis was then performed to assess the biological functions of the differentially expressed genes, and the sequencing data were verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Results The transcriptome analysis generated 8,866 unigenes that were found in both groups, 225 unigenes that were only found in the infection group, and 683 unigenes that only existed in the control group. A total of 1199 differentially expressed genes, including 1014 upregulated and 185 downregulated genes, were identified. The bioinformatics analysis showed that the differentially expressed genes were mainly involved in the longevity regulating pathway, circadian rhythm, DNA replication, and peroxisome, purine, pyrimidine, and drug metabolism. The qRT-PCR verification results showed the same trend, which confirmed that the expression of the differentially expressed genes had changed and that the transcriptome sequencing data were reliable. Conclusions This study investigated the changes in the transcriptome levels in the DENV-2-infected Aedes aegypti Aag2 cell line, which provides a faster and effective method for discovering genes related to Aedes aegypti pathogen susceptibility. The findings provide basic data and directions for further research on the complex mechanism underlying host-pathogen interactions.

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Transcriptome Analysis of Aedes aegypti Aag2 Cells in Response to Dengue Virus-2 Infection

10.21203/rs.3.rs-22807/v3 ◽

2020 ◽

Author(s):

Man-jin Li ◽

Ce-jie Lan ◽

He-ting Gao ◽

Dan Xing ◽

Zhen-yu Gu ◽

...

Keyword(s):

Aedes Aegypti ◽

Dengue Virus ◽

Cell Line ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Bioinformatics Analysis ◽

Differentially Expressed ◽

Control Group ◽

Sequencing Data ◽

Qrt Pcr

Abstract Background: Dengue virus (DENV) is a flavivirus transmitted by mosquitoes that is prevalent in tropical and subtropical countries and has four serotypes (DENV1-4). Aedes aegypti, as the main transmission vector of DENV, exhibits strong infectivity and transmission. With the aim of obtaining a better understanding of the Ae. aegypti-DENV interaction, the transcriptome changes in DENV-2-infected Aag2 cells were studied to describe the immune responses of mosquitoes using the Ae. aegypti Aag2 cell line as a model.Methods: RNAseq technology was used to sequence the transcripts of the Ae. aegypti Aag2 cell line before and after infection with DENV-2. A bioinformatics analysis was then performed to assess the biological functions of the differentially expressed genes, and the sequencing data were verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR).Results: The transcriptome analysis generated 8,866 unigenes that were found in both groups, 225 unigenes that were only found in the infection group, and 683 unigenes that only existed in the control group. A total of 1199 differentially expressed genes, including 1014 upregulated and 185 downregulated genes, were identified. The bioinformatics analysis showed that the differentially expressed genes were mainly involved in the longevity regulating pathway, circadian rhythm, DNA replication, and peroxisome, purine, pyrimidine, and drug metabolism. The qRT-PCR verification results showed the same trend, which confirmed that the expression of the differentially expressed genes had changed and that the transcriptome sequencing data were reliable.Conclusions: This study investigated the changes in the transcriptome levels in the DENV-2-infected Ae. aegypti Aag2 cell line, which provides a faster and effective method for discovering genes related to Ae. aegypti pathogen susceptibility. The findings provide basic data and directions for further research on the complex mechanism underlying host-pathogen interactions.

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Differential expression of phosphoenolpyruvate carboxykinase 1 in cancers of the breast.

10.31219/osf.io/2yd4t ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Differential Expression ◽

Survival Data ◽

Phosphoenolpyruvate Carboxykinase ◽

Molecular Subtype ◽

Differentially Expressed Gene ◽

Normal Breast ◽

Differentially Expressed ◽

Significant Differential Expression ◽

Primary Tumors

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding phosphoenolpyruvate carboxykinase 1, PCK1, when comparing primary tumors of the breast to the tissue of origin, the normal breast. PCK1 mRNA was present at significantly lower quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of PCK1 in primary tumors of the breast was correlated with overall survival in patients with normal-like subtype cancer, demonstrating a relationship between primary tumor expression of a differentially expressed gene and patient survival outcomes influenced by PAM50 molecular subtype. PCK1 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

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Identification of crucial genes involved in pathogenesis of regional weakening of the aortic wall

Hereditas ◽

10.1186/s41065-021-00200-1 ◽

2021 ◽

Vol 158 (1) ◽

Author(s):

Hong Lin Zu ◽

Hong Wei Liu ◽

Hai Yang Wang

Keyword(s):

Protein Interactions ◽

Aortic Wall ◽

Differentially Expressed Gene ◽

Microarray Dataset ◽

Smooth Muscle Contraction ◽

Differentially Expressed ◽

Coexpression Network ◽

Control Group ◽

Molecular Compound ◽

Microarray Gene Expression

Abstract Background The diameter of the abdominal aortic aneurysm (AAA) is the most commonly used parameter for the prediction of occurrence of AAA rupture. However, the most vulnerable region of the aortic wall may be different from the most dilated region of AAA under pressure. The present study is the first to use weighted gene coexpression network analysis (WGCNA) to detect the coexpressed genes that result in regional weakening of the aortic wall. Methods The GSE165470 raw microarray dataset was used in the present study. Differentially expressed genes (DEGs) were filtered using the “limma” R package. DEGs were assessed by Gene Ontology biological process (GO-BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. WGCNA was used to construct the coexpression networks in the samples with regional weakening of the AAA wall and in the control group to detect the gene modules. The hub genes were defined in the significant functional modules, and a hub differentially expressed gene (hDEG) coexpression network was constructed with the highest confidence based on protein–protein interactions (PPIs). Molecular compound detection (MCODE) was used to identify crucial genes in the hDEG coexpression network. Crucial genes in the hDEG coexpression network were validated using the GSE7084 and GSE57691 microarray gene expression datasets. Result A total of 350 DEGs were identified, including 62 upregulated and 288 downregulated DEGs. The pathways were involved in immune responses, vascular smooth muscle contraction and cell–matrix adhesion of DEGs in the samples with regional weakening in AAA. Antiquewhite3 was the most significant module and was used to identify downregulated hDEGs based on the result of the most significant modules negatively related to the trait of weakened aneurysm walls. Seven crucial genes were identified and validated: ACTG2, CALD1, LMOD1, MYH11, MYL9, MYLK, and TPM2. These crucial genes were associated with the mechanisms of AAA progression. Conclusion We identified crucial genes that may play a significant role in weakening of the AAA wall and may be potential targets for medical therapies and diagnostic biomarkers. Further studies are required to more comprehensively elucidate the functions of crucial genes in the pathogenesis of regional weakening in AAA.

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The expression of chondrogenesis-related and arthritis-related genes in human ONFH cartilage with different Ficat stages

PeerJ ◽

10.7717/peerj.6306 ◽

2019 ◽

Vol 7 ◽

pp. e6306 ◽

Cited By ~ 2

Author(s):

Gaoyang Chen ◽

Lei Zhong ◽

Qingyu Wang ◽

Zhaoyan Li ◽

Jing Shang ◽

...

Keyword(s):

Articular Cartilage ◽

Antigen Processing ◽

Molecular Mechanisms ◽

Differentially Expressed Gene ◽

Stage Iv ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Control Group ◽

Neck Fracture ◽

Insight Into

Background It has been well known that the degeneration of hip articular cartilage with osteonecrosis of the femoral head (ONFH) increases the instability of hip and accelerates the development process of ONFH. A better understanding of the expression of chondrogenesis-related and arthritis-related genes of cartilage along with the progression of ONFH seems to be essential for further insight into the molecular mechanisms of ONFH pathogenesis. Methods We analyzed the differentially expressed gene profile (GSE74089) of human hip articular cartilage with ONFH. The functions and pathway enrichments of differentially expressed genes (DEGs) were analyzed via GO and KEGG analysis. The expression of six selected critical chondrogenesis-related and four arthritis-related genes in eight human hip articular cartilage with femoral neck fracture (FNF) and 26 human hip articular cartilage with different stages ONFH (6 cases of Ficat stage II, 10 cases of Ficat stage III and 10 cases of Ficat stage IV) were detected. Results A total of 2,174 DEGs, including 1,482 up-regulated and 692 down-regulated ones, were obtained in the ONFH cartilage specimens compared to the control group. The GO and KEGG enrichment analysis indicated that the function of these DEGs mainly enriched in extracellular matrix, angiogenesis, antigen processing and presentation. The results showed a significant stepwise up-expression of chondrogenesis-related genes, including MMP13, ASPN, COL1A1, OGN, COL2A1 and BMP2, along with the progression of ONFH. The arthritis-related genes IL1β, IL6 and TNFα were only found up-expressed in Ficat IV stage which indicated that the arthritis-related molecular changes were not significant in the progression of ONFH before Ficat III stage. However, the arthritis-related gene PTGS2 was significant stepwise up-expression along with the progression of ONFH which makes it to be a sensitive arthritis-related biomarker of ONFH. Conclusion Expression changes of six chondrogenesis-related and four arthritis-related genes were found in hip articular cartilage specimens with different ONFH Ficat stages. These findings are expected to a get a further insight into the molecular mechanisms of ONFH progression.

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Decoding Psoriasis: Integrated Bioinformatics Approach to Understand Hub Genes and Involved Pathways

Current Pharmaceutical Design ◽

10.2174/1381612826666200311130133 ◽

2020 ◽

Vol 26 (29) ◽

pp. 3619-3630

Author(s):

Saumya Choudhary ◽

Dibyabhaba Pradhan ◽

Noor S. Khan ◽

Harpreet Singh ◽

George Thomas ◽

...

Keyword(s):

Gene Expression ◽

Differentially Expressed Gene ◽

Therapeutic Targets ◽

Interaction Network ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Keratinocyte Differentiation ◽

Hub Genes ◽

Lesional Skin ◽

Ncbi Gene Expression Omnibus

Background: Psoriasis is a chronic immune mediated skin disorder with global prevalence of 0.2- 11.4%. Despite rare mortality, the severity of the disease could be understood by the accompanying comorbidities, that has even led to psychological problems among several patients. The cause and the disease mechanism still remain elusive. Objective: To identify potential therapeutic targets and affecting pathways for better insight of the disease pathogenesis. Method: The gene expression profile GSE13355 and GSE14905 were retrieved from NCBI, Gene Expression Omnibus database. The GEO profiles were integrated and the DEGs of lesional and non-lesional psoriasis skin were identified using the affy package in R software. The Kyoto Encyclopaedia of Genes and Genomes pathways of the DEGs were analyzed using clusterProfiler. Cytoscape, V3.7.1 was utilized to construct protein interaction network and analyze the interactome map of candidate proteins encoded in DEGs. Functionally relevant clusters were detected through Cytohubba and MCODE. Results: A total of 1013 genes were differentially expressed in lesional skin of which 557 were upregulated and 456 were downregulated. Seven dysregulated genes were extracted in non-lesional skin. The disease gene network of these DEGs revealed 75 newly identified differentially expressed gene that might have a role in development and progression of the disease. GO analysis revealed keratinocyte differentiation and positive regulation of cytokine production to be the most enriched biological process and molecular function. Cytokines -cytokine receptor was the most enriched pathways. Among 1013 identified DEGs in lesional group, 36 DEGs were found to have altered genetic signature including IL1B and STAT3 which are also reported as hub genes. CCNB1, CCNA2, CDK1, IL1B, CXCL8, MKI 67, ESR1, UBE2C, STAT1 and STAT3 were top 10 hub gene. Conclusion: The hub genes, genomic altered DEGs and other newly identified differentially dysregulated genes would improve our understanding of psoriasis pathogenesis, moreover, the hub genes could be explored as potential therapeutic targets for psoriasis.

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