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Genome-wide analysis of differentially expressed profiles of miRNAs, mRNAs, lncRNAs and circRNAs in F. nucleatum infection

ABSTRACT: F. nucleatum is an opportunistic pathogen that usually colonize in oral cavity, thereby closely associated with the development of periodontitis.However, the immune regulation mechanism of F. nucleatum to macrophage’s function in disease progress has not been clearly elucidated.Long non-coding RNA (lncRNA) and circular RNA (circRNA) were discovered to play an important role in regulating occurrence and progression of many diseases and identified as effective biomarkers for diagnosis and prognosis of several diseases. In the present study, the expression profiles of mRNA, lncRNA and circRNA associated with F. nucleatum infection were investigated for the first time. The results revealed that the expressions of 375 mRNAs, 64 lncRNAs, and 180 circRNAs were altered during F. nucleatum infection. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis showed that the target genes were mainly involved in the MAPK signaling pathway, Toll-like receptor signaling pathway, NF-kappa B signaling pathway and apoptosis. Conclusions: The present study firstly provides the expression profiles of mRNAs, lncRNAs and circRNAs during F. nucleatum infection, and describes a novel perspective on the potential roles of lncRNAs and circRNAs underlying the pathogenesis mechanism of F. nucleatum infection.

ORGANISM(S): Homo sapiens

PROVIDER: GSE190606 | GEO | 2021/12/13

REPOSITORIES: GEO

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Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in aorta samples of F. nucleatum-infected mice

Project description:Periodontitis is an independent risk factor for atherosclerosis, and F. nucleatum is one of the periodontal pathogens. Several studies have confirmed that non-coding RNAs could affect all aspects of AS disease progression, including lipid metabolism, foam cell formation, cell necrosis, etc. However, no studies have explored whether F. nucleatum could affect AS disease progression by regulating non-coding RNAs. In this study, we intend to acquire mRNAs, lncRNAs and circRNAs expression profiles of aorta samples of AS mice from the F. nucleatum group and the Control group by next-generation sequencing(NGS) and perform bioinformatics analysis. Results revealed that 465 mRNA expression were up-regulated and 382 mRNA expression were down-regulated significantly. Some lncRNAs and circRNAs could suppress the binding of miRNA with target genes in post-transcriptional regulation. By integrating with DE-miRNAs-DEGs pairs and screening the common miRNAs, and mRNAs, lncRNAs, circRNAs that have targeted and negatively correlated relationship with the common miRNAs, lncRNA-miRNA-mRNA (including 34 DE-miRNAs, 42 DE-lncRNAs, and 111 DE-mRNAs) and circRNA-miRNA-mRNA (including 19 DE-miRNAs, 49 DE-circRNAs, and 87 DE-mRNAs) regulatory co-expression networks were constructed. GO enrichment analysis was performed on the differentially expressed mRNAs, which were found to be related to molecular functions, biological processes and cellular components such as protein binding, nucleus, postsynaptic dense zone, protein phosphorylation. KEGG analysis showed that they were related to ErbB signaling pathway, neurotrophic factor signaling pathway, glucagon signaling pathway and apoptosis signaling pathway. This suggested that F. nucleatum could promote the development of atherosclerosis through non-coding RNAs network regulation.

2023-02-22 | GSE225589 | GEO

LncRNA and circRNA expression profiles of Aβ25-35-induced AD mice hippocampus treated with Tripterygium Glycoside

Project description:Tripterygium glycosides (TG) was reported to have effect of ameliorating Alzheimer's disease (AD). However, the mechanism is not clear. We aimed to investigate the lncRNAs and circRNAs expression profiles of AD treated with TG by using microarray. LncRNAs, mRNA and circRNA in 3 AD mice and 3 AD+TG mice hippocampal were detected by microarray. The most differentially expressed lncRNAs, mRNA and circRNA in AD+TG group were screened. The differentially expressed lncRNAs and circRNAs were analyzed for GO enrichment and KEGG pathway. Co-expression analysis of lncRNAs and mRNA was performed by calculating correlation coefficients. Protein-protein interaction (PPI) network analysis was performed on mRNAs using STRING. LncRNA-target-TFs network were analyzed by Network software. CircRNA-mirNA network were conducted by Cytoscape software. A total of differentially expressed 661 lncRNAs, 64 circRNAs and 503 mRNAs were detected in AD mice treated with TG. The Pou4f1, Egr2, Mag, and Nr4a1 were the hub genes in the PPI network. The KEGG results showed the mRNAs that co-expressed with lncRNAs were enriched in TNF, PI3K-Akt, and Wnt signaling pathway. lncRNA-target-TFs network analysis indicated the TFs including Cebpa, Zic2, and Rxra were the most likely to regulate the detected lncRNAs. The circRNA-miRNA interaction network indicated 275 miRNAs may bind to the 64 circRNAs. In conclusion, the findings supplied a novel perspective for AD pathogenesis. And the detected lncRNAs, mRNAs, and circRNAs might be novel therapeutics targets for AD.

2022-05-30 | GSE204817 | GEO

Transcriptome-wide N6-methyladenosine modification profiling of long non-coding RNAs and circular RNA during growth of Marek’s disease virus in vitro

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2021-04-28 | GSE166240 | GEO

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in Cryptosporidium baileyi infection

Project description:Background: Cryptosporidium baileyi is the most common Cryptosporidium species in birds. However, effective prevention measures and treatment for C. baileyi infection were less understood. Long non-coding RNA (lncRNA) and circular RNA (circRNA) were discovered to play an important role in regulating occurrence and progression of many diseases and identified as effective biomarkers for diagnosis and prognosis of several diseases. In the present study, the expression profiles of mRNA, lncRNA and circRNA associated with C. baileyi infection were investigated for the first time. Results: The tracheal tissues of experimental (C. baileyi infection) and control chickens were collected for deep RNA sequencing, and 545,479,934 clean reads were obtained. Of them, 1376 novel lncRNAs were identified, including 1161 long intergenic non-coding RNAs (lincRNAs) and 215 anti-sense lncRNAs. 124 lncRNAs were found to be significantly differentially expressed between experimental and control groups. Additionally, 14,698 mRNAs and 9085 circRNAs were identified, and significantly different expressions were observed for 1317 mRNAs and 104 circRNAs between two groups. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of their targets and background genes suggested that these dysregulated genes would be involved in the interaction between host and C. baileyi. Conclusions: The present study firstly provides the expression profiles of mRNAs, lncRNAs and circRNAs during C. baileyi infection, and describes a novel perspective on the potential roles of lncRNAs and circRNAs underlying the pathogenesis mechanism of Cryptosporidium infection.

2018-04-28 | GSE108147 | GEO

circRNA, lncRNA and mRNA profiles of umbilical cord blood exosomes from preterm newborns showing bronchopulmonary

Project description:Purpose: The purpose of this study was to detect the expression profiles of circRNAs, lncRNAs and mRNAs in umbilical cord blood (UCB) exosomes from BPD infants. Methods:Microarray analysis was performed to compare the RNA profiles of UCB-derived exosomes from preterm newborn with and without BPD. Then, circRNA/lncRNA-miRNA-mRNA co-expression networks were built to determine their associations with BPD.Results:A total of 317 circRNAs, 104 lncRNAs, 135 mRNAs showed significant differential expression in UCB-derived exosomes from BPD preterm infants compared with the NBPD group. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted for examining differentially expressed exosomal circRNAs, lncRNAs and mRNAs. Our results showed the GO terms and KEGG pathways mostly involving differentially expressed exosomal RNAs were closely associated with endothelial or epithelial cell development. In addition, two networks were identified, including circRNA-circ_0086018/miR-762/MEN1 and lncRNA-BASP1-AS1/miR-20a-5p/DNAJC22 networks, which may take part in BPD.

2022-08-31 | GSE190215 | GEO

Comprehensive analysis of differentially expressed lncRNA, circRNA and mRNA and their ceRNA networks in mice with severe acute pancreatitis

Project description:Severe acute pancreatitis (SAP) is an acute digestive system disease with high morbidity mortality and hospitalization rate worldwide, due to various causes and unknown pathogenesis. In recent years, a large number of studies have confirmed that non-coding RNAs (ncRNAs) play an important role in many cellular processes and disease occurrence. However, the underlying mechanisms based on the function of ncRNAs, including long noncoding RNA (lncRNA) and circular RNA (circRNA), in SAP remain unclear. In this study, we performed high-throughput sequencing on the pancreatic tissues of 3 normal mice and 3 SAP mice for the first time to describe and analyze the expression profiles of ncRNAs, including lncRNA and circRNA. Our results identified that 49 lncRNAs, 56 circRNAs and 1194 mRNAs were differentially expressed in the SAP group, compared with the control group. Furthermore, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed lncRNAs and circRNAs, and found that the functions of the parental genes are enriched in the calcium-regulated signaling pathway, NF-κB signaling pathway, autophagy and protein digestion and absorption processes, which are closely related to the central events in pathogenesis of SAP. We also constructed lncRNA/circRNA-miRNA-mRNA networks to further explore their underlying mechanism and possible relationships in SAP. We found that in the competitive endogenous RNA (ceRNA) networks, differentially expressed lncRNAs and circRNAs are mainly involved in the apoptosis pathway and calcium signal transduction pathway. In conclusion, we found that lncRNAs and circRNAs play an important role in the pathogenesis of SAP, which may provide new insights in further exploring the pathogenesis of SAP and seek new targets for SAP.

2021-02-16 | GSE161945 | GEO

Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [miRNA-seq]

Project description:Pulmonary fibrosis is a kind of interstitial lung disease with architectural remodeling of tissues and excessive matrix deposition. Apart from mRNA, microRNA, long non-coding RNA (lncRNA) and circular RNA (circRNA) could also play important roles in the regulatory processes of occurrence and progression of pulmonary fibrosis. In the present study, whole transcriptome sequencing analysis was applied to investigate the expression profiles of mRNAs, lncRNAs, circRNAs and miRNAs. After comparing bleomycin-induced pulmonary fibrosis model lung samples and controls, 286 lncRNAs, 192 mRNAs, 605 circRNAs, and 32 miRNAs were found to be differentially expressed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the potential functions of these DE mRNAs and ncRNAs. Various related GO-BP terms such as “inflammatory response”, “positive regulation of interleukin-2 biosynthetic process”, “Regulation of actin cytoskeleton”, “Notch signaling pathway”, “negative regulation of cellular response to vascular endothelial growth factor stimulus”, and KEGG signal pathways such as “Wnt signaling pathway”, “TNF signaling pathway”, “MAPK signaling pathway”, “Regulation of actin cytoskeleton” were enriched implying potential roles in regulatory process. In addition, two co-expression networks (lncRNA-miRNA-mRNA, circRNA-miRNA-mRNA) were also constructed to understand the internal regulating relationships of these mRNAs and ncRNAs. Our study provides a systematic perspective on the potential functions of these DE mRNAs and ncRNAs during PF process, and could help pave the way for effective therapeutics for this devastating and complex disease.

2020-08-21 | GSE153294 | GEO

Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [ncRNA-seq]

2020-08-21 | GSE153278 | GEO

Identification of exosomal mRNA, lncRNA and circRNA signatures in an osteoarthritis synovial fluid-exosomal study

Project description:Aims Osteoarthritis (OA) is a common degenerative disease that is pathologically characterized by destruction of the joint matrix and reduction of articular chondrocytes, resulting in joint deformity and motor dysfunction. However, the molecular mechanisms governing this pathology have not been fully elucidated to date. Methods In this study, we determined the expression levels of lncRNAs, circRNAs, and mRNAs extracted from synovial exosomes of OA and control patients. A network of circRNA/lncRNA–miRNA–mRNA interactions was established using MiRanda and TargetScan software to explore OA pathogenesis. The exosomal lncRNA, circRNA and mRNA expression profiles of the OA and control groups were analysed using LC human competing endogenous RNA (ceRNA) microarrays. The differentially expressed genes were identified to determine their potential roles in the pathogenesis of OA by bioinformatic analysis. Results Compared with the control group, 11 mRNAs, 52 lncRNAs, and 30 circRNAs were upregulated, while 41 mRNAs, 144 lncRNAs, and 68 circRNAs were downregulated in osteoarthritis synovial exosomes. The final ceRNA network of lncRNAs and circRNAs exhibited a complex interaction between ncRNA and mRNA related to OA pathological mechanisms. An intersection analysis of the ceRNA network showed that 22 miRNAs, 45 lncRNAs, and 34 circRNAs in the PI3K/Akt and autophagy pathways correlated with 7 enriched mRNAs and may play important roles in OA pathological mechanisms. Conclusion Our work analysed mRNA/lncRNA/circRNA expression and displayed the ceRNA network of lncRNAs and circRNAs to profile the pathogenesis of OA in synovial exosomes. The results of this study may help to elucidate the pathogenesis of OA and may provide important references for further research attempting to identify more effective targets for the diagnosis and therapy of OA.

2021-10-02 | GSE185059 | GEO

An integrative mRNA and ncRNA analysis of human carotid atherosclerosis

Project description:Atherosclerosis (AS) is the underlying pathological process of severe cardiovascular or cerebrovascular diseases, whereas the molecular and cellular complexity of AS remains poorly elucidated. We here compared the expression of mRNA, lncRNA, circRNA in peripheral white blood cells (PWBCs) from carotid atherosclerotic plaque (CAP)-positive patients and CAP-negative controls through mRNA, lncRNA, and circRNA microarrays. A total of 552 mRNAs, 1,296 lncRNAs and 667 circRNAs were altered in the pathogenesis of AS.

2023-12-30 | GSE152777 | GEO

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