scholarly journals CLDN1 regulates trophoblast apoptosis and proliferation in preeclampsia

Reproduction ◽  
2021 ◽  
Author(s):  
Yu Chen Zhang ◽  
Xiaoli Qin ◽  
Xiao Ling Ma ◽  
Hui-qin Mo ◽  
Shi Qin ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Bioinformatics Analysis ◽  
Healthy Controls ◽  
Rna Seq ◽  
Hypertensive Disease ◽  
Inhibition Of Proliferation ◽  
Chorionic Villi ◽  
Qrt Pcr ◽  
Apoptotic Effect ◽  
Induction Of Apoptosis

Preeclampsia is a gestational hypertensive disease; however, preeclampsia remains poorly understood. Bioinformatics analysis was applied to find novel genes involved in the pathogenesis of preeclampsia and identified CLDN1 as one of the most differentially expressed genes when comparing patients with preeclampsia and healthy controls. The results of the qRT-PCR, western blotting and immunohistochemistry experiments demonstrated that CLDN1 was significantly downregulated in the chorionic villi in samples from patients with preeclampsia. Furthermore, knockdown of CLDN1 in HTR-8/SVneo cells resulted in the inhibition of proliferation and induction of apoptosis, and overexpression of CLDN1 reversed these effects. In addition, RNA-seq assays demonstrated that the gene BIRC3 is potentially downstream of CLDN1 and is involved in the regulation of apoptosis. Knockdown of CLDN1 confirmed that the expression level of BIRC3 was obviously decreased and was associated with a significant increase in cleaved PARP. Interestingly, the apoptotic effect in CLDN1 knockdown cells was rescued after BIRC3 overexpression. Overall, these results indicate that a decrease in CLDN1 inhibits BIRC3 expression and increases cleaved PARP levels thus participating in the pathogenesis of preeclampsia.

scholarly journals Transcriptome Analysis of Responses to Dengue Virus 2 Infection in Aedes albopictus (Skuse) C6/36 Cells

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 343
Author(s):  
Manjin Li ◽  
Dan Xing ◽  
Duo Su ◽  
Di Wang ◽  
Heting Gao ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Aedes Albopictus ◽  
Bioinformatics Analysis ◽  
Interaction Mechanism ◽  
Transcriptional Analysis ◽  
Functional Verification ◽  
Mosquito Vector ◽  
Rna Seq ◽  
Sequencing Data ◽  
Qrt Pcr

Dengue virus (DENV), a member of the Flavivirus genus of the Flaviviridae family, can cause dengue fever (DF) and more serious diseases and thus imposes a heavy burden worldwide. As the main vector of DENV, mosquitoes are a serious hazard. After infection, they induce a complex host–pathogen interaction mechanism. Our goal is to further study the interaction mechanism of viruses in homologous, sensitive, and repeatable C6/36 cell vectors. Transcriptome sequencing (RNA-Seq) technology was applied to the host transcript profiles of C6/36 cells infected with DENV2. Then, bioinformatics analysis was used to identify significant differentially expressed genes and the associated biological processes. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed to verify the sequencing data. A total of 1239 DEGs were found by transcriptional analysis of Aedes albopictus C6/36 cells that were infected and uninfected with dengue virus, among which 1133 were upregulated and 106 were downregulated. Further bioinformatics analysis showed that the upregulated DEGs were significantly enriched in signaling pathways such as the MAPK, Hippo, FoxO, Wnt, mTOR, and Notch; metabolic pathways and cellular physiological processes such as autophagy, endocytosis, and apoptosis. Downregulated DEGs were mainly enriched in DNA replication, pyrimidine metabolism, and repair pathways, including BER, NER, and MMR. The qRT-PCR results showed that the concordance between the RNA-Seq and RT-qPCR data was very high (92.3%). The results of this study provide more information about DENV2 infection of C6/36 cells at the transcriptome level, laying a foundation for further research on mosquito vector–virus interactions. These data provide candidate antiviral genes that can be used for further functional verification in the future.

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

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.

scholarly journals RNA-Seq profiling revealed PBMC RNA as potential biomarker for hepatocellular carcinoma

2020 ◽  
Author(s):  
Zhiyi Han ◽  
Wenxing Feng ◽  
Rui Hu ◽  
Qinyu Ge ◽  
Wenfeng Ma ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Mononuclear Cells ◽  
Healthy Controls ◽  
Rna Seq ◽  
Sequencing Data ◽  
Peripheral Blood Mononuclear ◽  
Qrt Pcr ◽  
Potential Biomarker ◽  
Incidence And Mortality ◽  
Differential Expressed Gene

Abstract Background Hepatocellular carcinoma is one of the most common malignancies with extremely high incidence and mortality rates. Although there have been many studies focus on biomarkers study, few have been reported on PBMC RNA profiles of hepatocellular carcinoma. Methods In this study, we attempted to profile the expression of Peripheral Blood Mononuclear Cells (PBMCs) RNA by using RNA-seq technology and compared the transcriptome between hepatocellular carcinoma patients and the healthy controls. 17 patients and 17 healthy controls involved in this study, PBMCs RNA were sequenced. The sequencing data were analyzed with bioinformatics tools and qRT-PCR was used for selected differential expressed gene validation. Results It is showed that 1578 dysregulated genes found including 1334 upregulated genes and 244 downregulated genes. GO enrichment and KEGG analysis denoted most of the differential expressed genes (DEGs) involved in immune response are closely related to hepatocellular carcinoma. Expression of the 6 selected genes (DEGs, SELENBP1, SLC4A1, SLC26A8, HSPA8P4, CALM1, and RPL7p24) were confirmed by qRT-PCR, and higher sensitivity and specificity obtained by ROC analysis of the 6 genes. CALM1 was found gradually decreasing along with the tumor enlarged. Conclusions It is suggested potential biomarker for diagnosis, classification and therapeutic target of hepatocellular carcinomas. This study provided new visions into development of liver cancer and potential efficient clinical diagnosis in the future.

Comparing the mRNA Expression Profile of Psoas Major and Longissimus Dorsi Muscles in Pig

2020 ◽  
Author(s):  
Yuanyuan Zhao ◽  
Guoqing Cao ◽  
Pengfei Gao ◽  
Guifang Jia ◽  
Fei Yang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Longissimus Dorsi ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Longissimus Dorsi Muscle ◽  
Qrt Pcr ◽  
Psoas Major Muscle ◽  
Types Of Muscle Fibers ◽  
Psoas Major

To explore the differentially expressed mRNAs between oxidative and glycolytic muscles, Qianbei black pigs were slaughtered and longissimus dorsi muscle (LDM) and psoas major muscle (PMM) were selected and sequenced using Illumina Hiseq TM 4000. Bioinformatics analysis and differentially expressed genes were analyzed by GO and KEGG. qRT-PCR was used to validate the RNA-seq result. As a result, 69 differentially expressed genes were identified, with 46 down regulated genes and 23 up regulated genes in LDM versus PMM, which were categorized into 44 functional groups under three GO classifications. KEGG pathway analysis revealed 20 pathways were enriched. qRT-PCR shows the expression trends of ND6, MYH7, TBX1, FOS and SLC7A5 are consist with the RNA-seq result. We speculated these five genes may involve in differentiation of muscle cells, metabolism of carbohydrate and lipid, deposits of intramuscular fat and transformation of different types of muscle fibers.

scholarly journals Transcriptome Analysis of Orbital Adipose Tissue in Active Thyroid Eye Disease Using Next Generation RNA Sequencing Technology

2018 ◽  
Vol 12 (1) ◽  
pp. 41-52 ◽  
Author(s):  
Bradford W. Lee ◽  
Virender B. Kumar ◽  
Pooja Biswas ◽  
Audrey C. Ko ◽  
Ramzi M. Alameddine ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Differential Expression ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Thyroid Eye Disease ◽  
Differentially Expressed ◽  
Eye Disease ◽  
Healthy Controls ◽  
Rna Seq ◽  
Next Generation

Objective: This study utilized Next Generation Sequencing (NGS) to identify differentially expressed transcripts in orbital adipose tissue from patients with active Thyroid Eye Disease (TED) versus healthy controls. Method: This prospective, case-control study enrolled three patients with severe, active thyroid eye disease undergoing orbital decompression, and three healthy controls undergoing routine eyelid surgery with removal of orbital fat. RNA Sequencing (RNA-Seq) was performed on freshly obtained orbital adipose tissue from study patients to analyze the transcriptome. Bioinformatics analysis was performed to determine pathways and processes enriched for the differential expression profile. Quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) was performed to validate the differential expression of selected genes identified by RNA-Seq. Results: RNA-Seq identified 328 differentially expressed genes associated with active thyroid eye disease, many of which were responsible for mediating inflammation, cytokine signaling, adipogenesis, IGF-1 signaling, and glycosaminoglycan binding. The IL-5 and chemokine signaling pathways were highly enriched, and very-low-density-lipoprotein receptor activity and statin medications were implicated as having a potential role in TED. Conclusion: This study is the first to use RNA-Seq technology to elucidate differential gene expression associated with active, severe TED. This study suggests a transcriptional basis for the role of statins in modulating differentially expressed genes that mediate the pathogenesis of thyroid eye disease. Furthermore, the identification of genes with altered levels of expression in active, severe TED may inform the molecular pathways central to this clinical phenotype and guide the development of novel therapeutic agents.

scholarly journals Exploration of the effects of a degS mutant on the growth of Vibrio cholerae and the global regulatory function of degS by RNA sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7959
Author(s):  
Jian Huang ◽  
Yuxi Chen ◽  
Jie Chen ◽  
Changjin Liu ◽  
Tao Zhang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Regulatory Network ◽  
Metabolic Pathways ◽  
Wild Type Strain ◽  
Mutant Phenotype ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Wild Type ◽  
Qrt Pcr ◽  
Small Colony

Background DegS is a periplasmic serine protease that is considered to be the initiator of the σE stress response pathway, and this protein plays an important role in the regulation of the stress response in E. coli. However, knowledge of the biological function and global regulatory network of DegS in Vibrio cholerae remains limited. In this study, we aimed to characterize the molecular functions and further investigate the regulatory network of degS in V. cholerae. Methods A deletion mutant of degS was constructed in the V. cholerae HN375 strain. Bacterial colony morphology was observed by a plate-based growth experiment, and bacterial growth ability was observed by a growth curve experiment. High-throughput RNA sequencing (RNA-Seq) technology was used to analyze the differential transcriptomic profiles between the wild-type and degS mutant strains. Gene ontology (GO), pathway analysis and Gene-Act-network analysis were performed to explore the main functions of the differentially expressed genes. Quantitative real-time PCR (qRT-PCR) was performed to validate the reliability and accuracy of the RNA-Seq analysis. The complementation experiments were used to test the roles of degS and ropS in the small colony degS mutant phenotype. Results When degS was deleted, the degS mutant exhibited smaller colonies on various media and slower growth than the wild-type strain. A total of 423 differentially expressed genes were identified, including 187 genes that were upregulated in the degS mutant compared to the wild-type strain and 236 genes that were relatively downregulated. GO categories and pathway analysis showed that many differentially expressed genes were associated with various cellular metabolic pathways and the cell cycle. Furthermore, Gene-Act network analysis showed that many differentially expressed genes were involved in cellular metabolic pathways and bacterial chemotaxis. The cAMP-CRP-RpoS signaling pathway and the LuxPQ signal transduction system were also affected by the degS mutant. The expression patterns of nine randomly selected differentially expressed genes were consistent between the qRT-PCR and RNA-seq results. The complementation experiments showed that the small colony degS mutant phenotype could be partially restored by complementation with the pBAD24-degS or pBAD24-rpoS plasmid. Discussion These results suggest that the degS gene is important for normal growth of V. cholerae. Some of the differentially expressed genes were involved in various cellular metabolic processes and the cell cycle, which may be associated with bacterial growth. Several new degS-related regulatory networks were identified. In addition, our results suggested that the cAMP-CRP-RpoS signaling pathway may be involved in the small colony degS mutant phenotype. Overall, we believe that these transcriptomic data will serve as useful genetic resources for research on the functions of degS in V. cholerae.

scholarly journals Transcriptome Sequencing of the Spleen Reveals Antiviral Response Genes in Chickens Infected with CAstV

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2374
Author(s):  
Joanna Sajewicz-Krukowska ◽  
Jan Paweł Jastrzębski ◽  
Maciej Grzybek ◽  
Katarzyna Domańska-Blicharz ◽  
Karolina Tarasiuk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Egg Production ◽  
Global Analysis ◽  
Antiviral Response ◽  
Differentially Expressed ◽  
P Value ◽  
Rna Seq ◽  
Qrt Pcr

Astrovirus infections pose a significant problem in the poultry industry, leading to multiple adverse effects such as a decreased egg production, breeding disorders, poor weight gain, and even increased mortality. The commonly observed chicken astrovirus (CAstV) was recently reported to be responsible for the “white chicks syndrome” associated with an increased embryo/chick mortality. CAstV-mediated pathogenesis in chickens occurs due to complex interactions between the infectious pathogen and the immune system. Many aspects of CAstV–chicken interactions remain unclear, and there is no information available regarding possible changes in gene expression in the chicken spleen in response to CAstV infection. We aim to investigate changes in gene expression triggered by CAstV infection. Ten 21-day-old SPF White Leghorn chickens were divided into two groups of five birds each. One group was inoculated with CAstV, and the other used as the negative control. At 4 days post infection, spleen samples were collected and immediately frozen at −70 °C for RNA isolation. We analyzed the isolated RNA, using RNA-seq to generate transcriptional profiles of the chickens’ spleens and identify differentially expressed genes (DEGs). The RNA-seq findings were verified by quantitative reverse-transcription PCR (qRT-PCR). A total of 31,959 genes was identified in response to CAstV infection. Eventually, 45 DEGs (p-value < 0.05; log2 fold change > 1) were recognized in the spleen after CAstV infection (26 upregulated DEGs and 19 downregulated DEGs). qRT-PCR performed on four genes (IFIT5, OASL, RASD1, and DDX60) confirmed the RNA-seq results. The most differentially expressed genes encode putative IFN-induced CAstV restriction factors. Most DEGs were associated with the RIG-I-like signaling pathway or more generally with an innate antiviral response (upregulated: BLEC3, CMPK2, IFIT5, OASL, DDX60, and IFI6; downregulated: SPIK5, SELENOP, HSPA2, TMEM158, RASD1, and YWHAB). The study provides a global analysis of host transcriptional changes that occur during CAstV infection in vivo and proves that, in the spleen, CAstV infection in chickens predominantly affects the cell cycle and immune signaling.

scholarly journals RNA-Seq Profiling Revealed PBMC RNA as Potential Biomarker for Hepatocellular Carcinoma

2021 ◽  
Author(s):  
Zhiyi Han ◽  
Wenxing Feng ◽  
Rui Hu ◽  
Qinyu Ge ◽  
Wenfeng Ma ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Mononuclear Cells ◽  
Malignant Tumors ◽  
High Morbidity ◽  
Healthy Controls ◽  
Rna Seq ◽  
Sequencing Data ◽  
Qrt Pcr ◽  
Potential Biomarker ◽  
Response Expression

Abstract Background: Hepatocellular carcinoma with extremely high morbidity and mortality is one of the most common malignant tumors. Although many existing studies focus on the study of its biomarkers, little information has been released on the PBMC RNA profile of hepatocellular carcinoma. Methods: We tried to make a profile throughout this analysis with the expression of Peripheral Blood Mononuclear Cells (PBMCs) RNA by using RNA-seq technology and compared the transcriptome between hepatocellular carcinoma patients and the healthy controls. 17 patients and 17 healthy controls involved in this study, PBMCs RNA were sequenced. The sequencing data were analyzed with bioinformatics tools and qRT-PCR was used for selected differential expressed gene validation. Results: It is showed that 1578 dysregulated genes found including 1334 upregulated genes and 244 downregulated genes. GO enrichment and KEGG studies showed that hepatocellular carcinoma is a closely linked source of the most differentially expressed genes (DEGs), implicated in the immune response. Expression of the 6 selected genes (SELENBP1, SLC4A1, SLC26A8, HSPA8P4, CALM1, and RPL7p24) were confirmed by qRT-PCR, and higher sensitivity and specificity obtained by ROC analysis of the 6 genes. CALM1 was found gradually decreasing along with the tumor enlarged. Conclusions: It is suggested potential biomarker for diagnosis of hepatocellular carcinomas. This study provided new perspectives for liver cancer development and possible future successful clinical diagnosis.

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

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.

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

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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