scholarly journals RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 158
Author(s):  
Li Chen ◽  
Guoqin Li ◽  
Yong Tian ◽  
Tao Zeng ◽  
Wenwu Xu ◽  
...  
Keyword(s):  
Immune Response ◽  
Influenza Virus ◽  
Rna Sequencing ◽  
Expression Profile ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Regulation Of Transcription ◽  
Infected Chicken ◽  
Positive Regulation ◽  
H5n1 Influenza

H5N1, a highly pathogenic avian influenza virus that is prevalent in Asia, seriously harms the poultry industry and global public health. However, its pathogenesis is still not well understood. Circular RNAs (circRNAs), a newly identified type of RNA, reportedly play crucial roles in various pathogenic processes. In this study, RNA sequencing was performed to analyze the expression profile of circRNAs in H5N1-infected chicken embryo fibroblast (DF1) cells. A total of 14,586 circRNAs were identified. The expression profiles of infected cells changed more significantly, relative to uninfected cells, as the infection period was extended; namely, 261, 626, and 1103 circRNAs exhibited differential expression in cells infected for 6 h, 12 h, and 20 h, respectively. GO and KEGG enrichment analysis revealed significant enrichment of the parental genes of the differentially expressed circRNAs for viral replication and immune response-related pathways, such as positive regulation of transcription from the RNA polymerase II promoter, positive regulation of I-kappaB kinase/NF-kappaB signaling, innate immune response, and ubiquitin protein ligase activity. In conclusion, we identified the expression profile of circRNAs in H5N1-infected chicken DF1 cells. Bioinformatic analyses of the dysregulated circRNAs suggest that circRNAs might play important roles in the pathogenesis of H5N1 infection, offering new insights into the mechanisms underlying H5N1–host interaction.

scholarly journals A Single-Amino-Acid Substitution in a Polymerase Protein of an H5N1 Influenza Virus Is Associated with Systemic Infection and Impaired T-Cell Activation in Mice

2009 ◽  
Vol 83 (21) ◽  
pp. 11102-11115 ◽  
Author(s):  
Jamie L. Fornek ◽  
Laura Gillim-Ross ◽  
Celia Santos ◽  
Victoria Carter ◽  
Jerrold M. Ward ◽  
...  
Keyword(s):  
Immune Response ◽  
Influenza Virus ◽  
Amino Acid ◽  
T Cell ◽  
Amino Acid Substitution ◽  
Systemic Infection ◽  
Influenza Viruses ◽  
Single Amino Acid Substitution ◽  
Single Amino Acid ◽  
H5n1 Influenza

ABSTRACT The transmission of H5N1 influenza viruses from birds to humans poses a significant public health threat. A substitution of glutamic acid for lysine at position 627 of the PB2 protein of H5N1 viruses has been identified as a virulence determinant. We utilized the BALB/c mouse model of H5N1 infection to examine how this substitution affects virus-host interactions and leads to systemic infection. Mice infected with H5N1 viruses containing lysine at amino acid 627 in the PB2 protein exhibited an increased severity of lesions in the lung parenchyma and the spleen, increased apoptosis in the lungs, and a decrease in oxygen saturation. Gene expression profiling revealed that T-cell receptor activation was impaired at 2 days postinfection (dpi) in the lungs of mice infected with these viruses. The inflammatory response was highly activated in the lungs of mice infected with these viruses and was sustained at 4 dpi. In the spleen, immune-related processes including NK cell cytotoxicity and antigen presentation were highly activated by 2 dpi. These differences are not attributable solely to differences in viral replication in the lungs but to an inefficient immune response early in infection as well. The timing and magnitude of the immune response to highly pathogenic influenza viruses is critical in determining the outcome of infection. The disruption of these factors by a single-amino-acid substitution in a polymerase protein of an influenza virus is associated with severe disease and correlates with the spread of the virus to extrapulmonary sites.

scholarly journals Microarray Expression Profile of Circular RNAs in Plasma from Primary Biliary Cholangitis Patients

2017 ◽  
Vol 44 (4) ◽  
pp. 1271-1281 ◽  
Author(s):  
Jiajia Zheng ◽  
Zhenrong Li ◽  
Tiancheng Wang ◽  
Yang Zhao ◽  
Yongfeng Wang
Keyword(s):  
Expression Profile ◽  
Expression Profiles ◽  
Characteristic Curve ◽  
Group Versus ◽  
Target Prediction ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Primary Biliary Cholangitis ◽  
Healthy Controls ◽  
Qrt Pcr

Background/Aims: Circular RNAs (circRNAs) play a crucial role in the occurrence of several diseases, including autoimmune diseases. However, their role in primary biliary cholangitis (PBC) remains unclear. Here, we aimed to determine the circRNA expression profile in plasma from PBC patients and further explore the value of circRNA in diagnosing PBC. Methods: CircRNA microarrays were used to determine circRNA expression profiles in plasma samples from 6 PBC patients and 6 healthy controls. Statistical analyses identified differentially expressed circRNAs, and these circRNAs were verified by qRT-PCR in 29 PBC patients and 30 healthy controls. MicroRNA (miRNA) target prediction software identified putative miRNA response elements (MREs), which were used to construct a map of circRNA-miRNA interactions for the differentially expressed circRNAs. Results: Our results indicated that there were 18 up-regulated and 4 down-regulated circular RNAs in the plasma from PBC patients compared with that from healthy individuals. Among the differentially expressed circRNAs, hsa_circ_402458 (P=0.0033), hsa_circ_087631 and hsa_circ_406329 (P=0.0185) were up-regulated, and hsa_circ_407176 (P=0.0066) and hsa_circ_082319 were down-regulated in the PBC group versus the healthy group as demonstrated by qRT-PCR. In particular, hsa_circ_402458 was significantly higher in PBC patients not receiving UDCA treatment than in PBC patients receiving UDCA treatment (P=0.0338). The area under the receiver operating characteristic curve for hsa_circ_402458 for diagnosing PBC was 0.710 (P=0.005). For hsa_circ_402458, two putative miRNA targets, hsa-miR-522-3p and hsa-miR-943, were predicted. Conclusions: circRNA dysregulation may play a role in PBC pathogenesis, and hsa_circ_402458 shows promise as a candidate biomarker for PBC.

scholarly journals Expression Profile of Circular RNAs in Epicardial Adipose Tissue in Heart Failure

2019 ◽  
Author(s):  
Meili Zheng ◽  
Lei Zhao ◽  
Xinchun Yang
Keyword(s):  
Heart Failure ◽  
Adipose Tissue ◽  
Expression Profile ◽  
Epicardial Adipose Tissue ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Circular Rna ◽  
Circular Rnas ◽  
Artery Disease ◽  
Pathway Analyses

AbstractRecent studies have reported circular RNA (circRNA) expression profiles in various tissue types; specifically, a recent work showed a detailed circRNA expression landscape in the heart. However, circRNA expression profile in human epicardial adipose tissue (EAT) remains undefined. RNA-sequencing was carried out to compare circRNA expression patterns in EAT specimens from coronary artery disease (CAD) cases between the heart failure (HF) and non-HF groups. The top highly expressed EAT circRNAs corresponded to genes involved in cell proliferation and inflammatory response, including KIAA0182, RHOBTB3, HIPK3, UBXN7, PCMTD1, N4BP2L2, CFLAR, EPB41L2, FCHO2, FNDC3B and SPECC1. Among the 141 circRNAs substantially different between the HF and non-HF groups (P<0.05;fold change>2), hsa_circ_0005565 stood out, and was mostly associated with positive regulation of metabolic processes and insulin resistancein GO and KEGG pathway analyses, respectively. These data indicate EAT circRNAs contribute to the pathogenesis of metabolic disorders causing HF.

scholarly journals Comprehensive Analysis of Differentially Expressed Circular RNAs in Patients with Senile Osteoporotic Vertebral Compression Fracture

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Xiaocong Yao ◽  
Minbo Liu ◽  
Fang Jin ◽  
Zhongxin Zhu
Keyword(s):  
Signaling Pathways ◽  
Rna Sequencing ◽  
Regulatory Networks ◽  
Vertebral Compression Fracture ◽  
Expression Profiles ◽  
Compression Fracture ◽  
Osteoporotic Vertebral Compression Fracture ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Pathophysiological Mechanism

Aim. Circular RNAs (circRNAs) have been found to contribute to the regulation of many diseases and are abundantly expressed in various organisms. The present study is aimed at systematically characterizing the circRNA expression profiles in patients with senile osteoporotic vertebral compression fracture (OVCF) and predicting the potential functions of the regulatory networks correlated with these differentially expressed circRNAs. Methods. The circRNA expression profile in patients with senile OVCF was explored by using RNA sequencing. The prediction of the enriched signaling pathways and circRNA-miRNA networks was conducted by bioinformatics analysis. Real-time quantitative PCR was used to validate the selected differentially expressed circRNAs from 20 patients with senile OVCF relative to 20 matched healthy controls. Results. A total of 884 differentially expressed circRNAs were identified, of which 554 were upregulated and 330 were downregulated. The top 15 signaling pathways associated with these differentially expressed circRNAs were predicted. The result of qRT-PCR of the selected circRNAs was consistent with RNA sequencing. Conclusions. CircRNAs are differentially expressed in patients with senile OVCF, which might contribute to the pathophysiological mechanism of senile osteoporosis.

scholarly journals Lethal Dissemination of H5N1 Influenza Virus Is Associated with Dysregulation of Inflammation and Lipoxin Signaling in a Mouse Model of Infection

2010 ◽  
Vol 84 (15) ◽  
pp. 7613-7624 ◽  
Author(s):  
Cristian Cilloniz ◽  
Mary J. Pantin-Jackwood ◽  
Chester Ni ◽  
Alan G. Goodman ◽  
Xinxia Peng ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Inflammatory Response ◽  
Inflammatory Responses ◽  
Synergistic Effects ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Influenza Viruses ◽  
Type I ◽  
Highly Pathogenic ◽  
H5n1 Influenza

ABSTRACT Periodic outbreaks of highly pathogenic avian H5N1 influenza viruses and the current H1N1 pandemic highlight the need for a more detailed understanding of influenza virus pathogenesis. To investigate the host transcriptional response induced by pathogenic influenza viruses, we used a functional-genomics approach to compare gene expression profiles in lungs from 129S6/SvEv mice infected with either the fully reconstructed H1N1 1918 pandemic virus (1918) or the highly pathogenic avian H5N1 virus Vietnam/1203/04 (VN/1203). Although the viruses reached similar titers in the lung and caused lethal infections, the mean time of death was 6 days for VN/1203-infected animals and 9 days for mice infected with the 1918 virus. VN/1203-infected animals also exhibited an earlier and more potent inflammatory response. This response included induction of genes encoding components of the inflammasome. VN/1203 was also able to disseminate to multiple organs, including the brain, which correlated with changes in the expression of genes associated with hematological functions and lipoxin biogenesis and signaling. Both viruses elicited expression of type I interferon (IFN)-regulated genes in wild-type mice and to a lesser extent in mice lacking the type I IFN receptor, suggesting alternative or redundant pathways for IFN signaling. Our findings suggest that VN/1203 is more pathogenic in mice as a consequence of several factors, including the early and sustained induction of the inflammatory response, the additive or synergistic effects of upregulated components of the immune response, and inhibition of lipoxin-mediated anti-inflammatory responses, which correlated with the ability of VN/1203 to disseminate to extrapulmonary organs.

scholarly journals Transcriptomic Analysis of circRNAs in the Peripheral Blood of Nonarteritic Anterior Ischemic Optic Neuropathy

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Jinshan Suo ◽  
Xinling Xu ◽  
Haoyan Xu ◽  
Naifang Hou ◽  
Jiaming Zhang ◽  
...  
Keyword(s):  
Expression Profile ◽  
Optic Neuropathy ◽  
Peripheral Blood ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Interaction Network ◽  
Original Data ◽  
Anterior Ischemic Optic Neuropathy ◽  
Circular Rnas ◽  
Ischemic Optic Neuropathy

The aim of the study is to explore the expression profile variation of circular RNAs (circRNAs) in the peripheral blood of subjects with nonarteritic anterior ischemic optic neuropathy (NAION) and without NAION, to analyze the differential expression results, and to predict the role of circRNAs in disease development, providing novel ideas and methods for treatment and diagnosis. High-throughput sequencing to explore the expression profiles of RNAs in the peripheral blood of 6 NAION patients and 5 healthy controls was applied. Quality control obtained the advanced data from the original data by ticking out the unqualified data. Then, cluster analysis, volcano plot, coexpression network, and protein-protein interaction network (PPI) were performed. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were used to analyze the whole expressed genes. Lastly, the quantitative real-time Polymerase Chain Reaction (qRT-PCR) was used to verify those significantly differentially expressed circRNAs and do some bioinformatics analysis and prediction in 12 NAION patients and 12 controls. There were significant differences in the expression of 49 circRNAs in the peripheral blood of NAION patients, in which there were 24 upregulations and 25 downregulations (variation folds > 2 and P < 0.05 ), and it was confirmed that hsa_circ_0005583, hsa_circ_0003922, hsa_circ_0002021, and hsa_circ_0000462 were significantly downregulated (variation folds > 2 and P < 0.05 ), especially hsa_circ_0005583 which was the most significantly changed one ( P < 0.001 ), and are related to processes such as neurodegeneration, oxidative stress, immunity, and metabolism. The expression profile of circRNAs in the peripheral blood of NAION patients is significantly changed, enriching our understanding of the disease.

scholarly journals Circular RNA expression profile of lung squamous cell carcinoma: identification of potential biomarkers and therapeutic targets

2020 ◽  
Vol 40 (4) ◽  
Author(s):  
Yawei Wang ◽  
Haiyan Zhang ◽  
Jian Wang ◽  
Bei Li ◽  
Xiuwen Wang
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Expression Profile ◽  
Squamous Cell ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Lung Squamous Cell Carcinoma ◽  
Circular Rnas ◽  
Diagnostic Biomarkers ◽  
Diagnostic Potential

Abstract Emerging evidences indicated that exosomal circular RNAs (circRNAs) could serve as diagnostic biomarkers for cancers. However, the expression profiles and clinical significance of circRNAs in lung squamous cell carcinoma (LUSC) remain largely unknown. Herein, we analyzed circRNAs expression profile in six pairs of plasma exosome samples of LUSC patients using high-throughput sequencing. A total of 252 differentially expressed exosomal circRNAs were identified, including 133 up-regulated circRNAs and 119 down-regulated circRNAs. Subsequently, the circRNAs–miRNAs–mRNAs interaction network was built to investigate potential function of circRNAs. Three up-regulated circRNAs (hsa_circ_0014235, hsa_circ_0025580 and hsa_circ_0026403) were implied to participate in cancer-related pathways. QRT-PCR experiment confirmed the up-regulation of hsa_circ_0014235 and hsa_circ_0025580. Finally, clinical studies indicated that hsa_circ_0014235 and hsa_circ_0025580 could serve as novel diagnostic biomarkers for LUSC. Taken together, our study revealed exosomal circRNAs expression profile in LUSC for the first time and showed the important diagnostic potential for circRNAs in LUSC.

scholarly journals Comprehensive Analyses of circRNA Expression Profiles and Function Prediction in Chicken Cecums After Eimeria tenella Infection

2021 ◽  
Vol 11 ◽  
Author(s):  
Hailiang Yu ◽  
Changhao Mi ◽  
Qi Wang ◽  
Wenbin Zou ◽  
Guojun Dai ◽  
...  
Keyword(s):  
Immune Response ◽  
High Throughput Sequencing ◽  
Inflammatory Responses ◽  
Expression Profiles ◽  
Killer Cell ◽  
Eimeria Tenella ◽  
Differentially Expressed ◽  
Economic Losses ◽  
Circular Rnas ◽  
Poultry Production

Coccidiosis is an important intestinal parasitic disease that causes great economic losses to the global poultry production industry. Circular RNAs (circRNAs) are long non-coding RNAs that play important roles in various infectious diseases and inflammatory responses. However, the expression profiles and functions of circRNAs during Eimeria tenella (E. tenella) infection remain unclear. In this study, high-throughput sequencing was carried out to detect circRNAs in chicken cecal tissues from the control (JC), resistant (JR), and susceptible (JS) groups on day 4.5 postinfection (pi), respectively. A total of 104 circRNAs were differentially expressed, including 47 circRNAs between the JS and JC groups, 38 between the JR and JS groups, and 19 between the JR and JC groups. Functional analyses indicated that these differentially expressed circRNAs were involved in pathways related to E. tenella infection; the adaptive immune response was enriched in the JS vs JC group, the NF-kappa B signaling and natural killer cell-mediated cytotoxicity pathways were enriched in the JS vs JC and JR vs JC groups, while the B cell receptor signaling pathway was enriched in only the JR vs JC group. Moreover, the coexpression network of differentially expressed circRNAs and mRNAs suggested that circRNA2202 and circRNA0759 associated with DTX1 in the JS vs JC group, circRNA4338 associated with VPREB3 and CXCL13L3 in the JR vs JC group, and circRNA2612 associated with IL8L1 and F2RL2 in the JR vs JS group were involved in the immune response upon E. tenella infection. In conclusion, our results provide valuable information on the circRNAs involved in the progression of chicken E. tenella infection and advance our understanding of the circRNA regulatory mechanisms of host resistance and susceptibility to E. tenella infection in chickens.

scholarly journals RNA-sequencing Reveal the Molecular Mechanism of Moxibustion on Neutrophil Gene Expression Profile During Breast Cancer Chemotherapy

2020 ◽  
Author(s):  
Yajie JI ◽  
Xinyue ZHANG ◽  
Siyu LI ◽  
Shanyan SHA ◽  
Weili CHEN ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cell Adhesion ◽  
Rna Sequencing ◽  
Expression Profile ◽  
Expression Profiles ◽  
Regulatory Function ◽  
Rna Seq ◽  
Breast Cancer Chemotherapy ◽  
Before And After

Abstract BackgroundMoxibustion is a Traditional Chinese Medicine (TCM) therapy that can prevent neutropenia after breast cancer (BC) chemotherapy. We aimed to explore the mechanism of moxibustion for treating BC chemotherapy-induced neutropenia (CIN).MethodsFifty patients with BC undergoing chemotherapy and who met the inclusion criteria were randomized into an intervention (IT) group and control (OC) group. After excluding cases, there were 14 cases in the RNA sequencing (RNA-seq) group and 17 cases in the verification group. Neutrophils were extracted from the peripheral blood of the patients in both groups before and after chemotherapy. RNA-seq and bioinformatics analysis were performed in RNA-seq group. The verification group were verified using real time quantity polymerase chain reaction (RT-qPCR).ResultsRNA-seq screened 1092 DEGs before and after chemotherapy in the OC group, and 571 DEGs in the IT group. Compared with the OC group, the IT group had 707 DEGs after chemotherapy. The effect of moxibustion on the patients’ neutrophil gene expression profiles was related to the cell adhesion, adaptive immune response and metabolic pathways, and leukocyte migration, etc. The co-network results showed that TSC22D1 and TGFB1I1 have core regulatory function. GO and KEGG enrichment pathway analysis suggested a close correlation with the TGFβ1/TSC22D1-mediated cell adhesion molecules (CAMs) pathway. RT-qPCR showed that CD177 in the neutrophils was significantly upregulated after chemotherapy compared with that before chemotherapy (P < 0.05) without moxibustion, while TSC22D1 showed a downward trend (P = 0.094). Moxibustion significantly increased the expression of TSC22D1, ANKFY1, and ITGB3 in the neutrophils (P < 0.05) after BC chemotherapy.ConclusionThe mechanism of moxibustion in improving CIN may be related to the regulation of the TSC22D1 expression profile in neutrophil. We present a novel insight into the mechanism of moxibustion treatment of CIN in patients with BC.Trial registrationChinese Clinical Trial Register, ChiCTR-INR-16009557. Registered 23 October 2016, http://www.chictr.org.cn/showproj.aspx?proj=16203.

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