Identification of Circulating lncRNA Expression Profiles in Patients with Atrial Fibrillation

Purpose. To investigate the expression profiles of long noncoding RNAs (lncRNAs) in patients with atrial fibrillation (AF). Methods. The peripheral blood monocytes of a total of 20 patients with AF and 20 healthy subjects were collected for gene chip technology to detect differentially expressed lncRNAs from 2017.01 to 2017.08. Reverse transcription polymerase chain reaction (RT-PCR) was applied for further verification. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to identify the functions of differentially expressed genes and related pathways. Results. There were 19 lncRNAs differentially expressed ( FC ≥ 2 , P < 0.05 ), of which 6 were upregulated and 13 were downregulated. Two of three upregulated lncRNAs ( P = 0.014 and 0.006 for HNRNPU-AS1 and LINC00861, respectively) and two of three downregulated lncRNAs ( P = 0.028 and 0.032 for RP11-443B7.3 and CTD-2616J11.14, respectively) were randomly confirmed by RT-PCR and showed a significantly different expression with the RNA-seq results. GO analysis showed that differentially expressed genes enriched in differentially expressed transcripts in biological process were mainly involved in metabolic process, catabolic process, and biosynthetic process. Differentially expressed transcripts in cellular component were mainly involved in nuclear lumen, organelle lumen, and cytoplasm. Differentially expressed transcripts in molecular function were mainly involved in protein binding, RNA binding, and molecular function. KEGG enrichment pathway analysis showed that some of the enrichment pathways associated with differentially expressed lncRNAs include calcium signaling pathway, NF-kappa B signaling pathway, cytokine-cytokine receptor interaction, and Toll-like receptor signaling pathway. HNRNPU-AS1 was the highest positive correlated lncRNA in the networks. Conclusions. The expression of lncRNA in peripheral blood of AF patients is different from that of normal people. The physiological functions of these differentially expressed lncRNAs may be related to the pathogenesis of AF, which provide experimental basis and new therapeutic target for prognosis and treatment of patients with AF. HNRNPU-AS1 may play an important role in the pathophysiology and mechanisms of AF.

Download Full-text

Expression profile of circulating lncRNAs in patients with atrial fibrillation

10.21203/rs.2.15759/v1 ◽

2019 ◽

Author(s):

Zhong-bao Ruan ◽

Bing-di Gongben ◽

Ge-cai Chen ◽

Li Zhu

Keyword(s):

Atrial Fibrillation ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Peripheral Blood ◽

Rna Binding ◽

Differentially Expressed ◽

Receptor Interaction ◽

Molecular Function ◽

Rt Pcr ◽

Chip Technology

Abstract Background: Atrial fibrillation (AF) is one of the most common cardiac arrhythmias. However, the exact pathophysiology and mechanisms about AF remains unclear. Accumulating studies have demonstrated that long non-coding RNAs (lncRNAs) play a vital role in the regulation of almost all biological processes. However, relationships between AF and lncRNAs are still unknown. Methods: The peripheral blood monocytes of a total of 20 patients with AF and 20 healthy subjects were collected for gene chip technology to detect differentially expressed lncRNAs. Reverse transcription polymerase chain reaction (RT-PCR) was applied for further verification. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to identify the functions of differentially expressed genes and related pathways. Results: There were 19 lncRNAs differentially expressed (FC ≥ 2, p <0.05), of which 6 were up-regulated and 13 were down-regulated. Two of three upregulated lncRNAs (P=0.014 and 0.006 for HNRNPU-AS1and LINC00861, respectively) and two of three downregulated lncRNAs (P=0.028 and 0.032 for RP11-443B7.3 and CTD-2616J11.14, respectively) were randomly confirmed by RT‐PCR. And showed a significantly different expression with the RNA-seq results. GO analysis showed that differentially expressed genes enriched in differentially expressed transcripts in biological process were mainly involved in metabolic process, catabolic process and biosynthetic process. Differentially expressed transcripts in cellular component were mainly involved in nuclear lumen, organelle lumen and cytoplasm et al. Differentially expressed transcripts in molecular function were mainly involved in protein binding, RNA binding and molecular function et al. KEGG enrichment pathway analysis showed that some of the enrichment pathways associated with differentially expressed lncRNAs include Calcium signaling pathway, NF-kappa B signaling pathway, cytokine-cytokine receptor interaction and Toll-like receptor signaling pathway, etc. HNRNPU-AS1 was the highest positive correlated lncRNA in the networks. Conclusions: The expression of lncRNA in peripheral blood of AF patients is different from that of normal people. The physiological functions of these differentially expressed lncRNAs may be related to the pathogenesis of AF, which provide experimental basis and new therapeutic target for prognosis and treatment of patients with AF. HNRNPU-AS1 may play a important role in the pathophysiology and mechanisms of AF.

Download Full-text

Expression profile analysis of Differentially Expressed Genes in Human Coronary Artery Endothelial Cells Induced by Serum from Kawasaki Disease: A preliminary study

10.21203/rs.3.rs-54163/v1 ◽

2020 ◽

Author(s):

Xue Fan ◽

Meng Li ◽

Min Xiao ◽

Cong Liu ◽

Mingguo Xu

Keyword(s):

Endothelial Cells ◽

Coronary Artery ◽

Kawasaki Disease ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

Receptor Interaction ◽

Healthy Children ◽

Rna Seq ◽

Human Coronary Artery

Abstract Background: Kawasaki disease (KD) leads to coronary artery damage and the etiology of KD is unknown. The present study was designed to explore the differentially expressed genes (DEGs) in KD serum-induced human coronary artery endothelial cells (HCAECs) by RNA-sequence (RNA-seq). Methods: HCAECs were stimulated with serum (15% (v/v)), which were collected from 20 healthy children and 20 KD patients, for 24 hours. DEGs were then detected and analyzed by RNA-seq and bioinformatics analysis. Results: The expression of SMAD1, SMAD6, CD34, CXCL1, PITX2, and APLN was validated by qPCR. 102 genes, 59 up-regulated and 43 down-regulated genes, were significantly differentially expressed in KD groups. GO enrichment analysis showed that DEGs were enriched in cellular response to cytokines, cytokine-mediated signaling pathway, and regulation of immune cells migration and chemotaxis. KEGG signaling pathway analysis showed that DEGs were mainly involved in cytokine−cytokine receptor interaction, chemokine signaling pathway, and TGF−β signaling pathway. Besides, the mRNA expression levels of SMAD1, SMAD6, CD34, CXCL1, and APLN in the KD group were signiﬁcantly up-regulated compared with the normal group, whilePITX2 was significantly down-regulated. Conclusion: 102 DEGs in KD serum-induced HCAECs were identified, and six new targets were proposed as potential indicators of KD.

Download Full-text

Comparative transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine–cytokine receptor interaction pathway related to health status

Genome ◽

10.1139/gen-2017-0074 ◽

2017 ◽

Vol 60 (12) ◽

pp. 1021-1028 ◽

Cited By ~ 2

Author(s):

M.H. Ye ◽

H. Bao ◽

Y. Meng ◽

L.L. Guan ◽

P. Stothard ◽

...

Keyword(s):

Health Status ◽

Differentially Expressed Genes ◽

Peripheral Blood ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Cytokine Receptor ◽

Functional Enrichment ◽

Differentially Expressed ◽

Receptor Interaction ◽

Marker Genes

While some research has looked into the host genetic response in pigs challenged with specific viruses or bacteria, few studies have explored the expression changes of transcripts in the peripheral blood of sick pigs that may be infected with multiple pathogens on farms. In this study, the architecture of the peripheral blood transcriptome of 64 Duroc sired commercial pigs, including 18 healthy animals at entry to a growing facility (set as a control) and 23 pairs of samples from healthy and sick pen mates, was generated using RNA-Seq technology. In total, 246 differentially expressed genes were identified to be specific to the sick animals. Functional enrichment analysis for those genes revealed that the over-represented gene ontology terms for the biological processes category were exclusively immune activity related. The cytokine–cytokine receptor interaction pathway was significantly enriched. Nine functional genes from this pathway encoding members (as well as their receptors) of the interleukins, chemokines, tumor necrosis factors, colony stimulating factors, activins, and interferons exhibited significant transcriptional alteration in sick animals. Our results suggest a subset of novel marker genes that may be useful candidate genes in the evaluation and prediction of health status in pigs under commercial production conditions.

Download Full-text

Differential Analysis of Expressed Genes in Diabetic Nephropathy Based on Bioinformatics Technology

10.21203/rs.3.rs-770285/v1 ◽

2021 ◽

Author(s):

Yu Liu ◽

Jundong Wang ◽

wencheng Chi ◽

Jing Xie ◽

LaiKuan Teh ◽

...

Keyword(s):

Gene Expression ◽

Diabetic Nephropathy ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Biological Effects ◽

Cytokine Receptor ◽

Differentially Expressed ◽

Receptor Interaction ◽

Differential Analysis ◽

Core Genes

Abstract Objective: Bioinformatics technology was used in this study to analyze the expression data of patients with diabetic nephropathy (DN) and normal subjects from the microarray. The purpose of this study was to screen the differentially expressed genes in DN and to explore the pathogenesis and potential therapeutic targets of DN. Methods: The data of gene expression in the gse142153 gene chip was downloaded from the gene expression database (GEO). The up-regulated and down-regulated expressed genes were analyzed by R language. The core genes of differentially expressed genes were analyzed by string database, Cytoscape software and its plug-in. The differentially expressed genes were analyzed by gene ontology and Kyoto Encyclopedia of genes and genomes. Results: A total of 112 differentially expressed genes were screened, including 50 down-regulated genes and 62 up-regulated genes. There are 10 up-regulated core genes including CXCL8, MMP9, IL1B, IL6, IL10, CXCL2, CCL20, ATF3, CXCL3, F3. Their biological effects are mainly concentrated in the IL-17 signaling pathway, rheumatoid arthritis, viral protein interaction with cytokine and cytokine receptor, Amoebiasis, TNF signaling pathway, Legionellosis, Cytokine-cytokine receptor interaction, Lipid, and atherosclerosis, Malaria, NOD-like receptor signaling pathway, etc. Conclusion: Analysis of differentially expressed genes and core genes enhanced the understanding of the pathogenesis of DN and provided a potential train of thought for the treatment of DN.

Download Full-text

Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes

PeerJ ◽

10.7717/peerj.7752 ◽

2019 ◽

Vol 7 ◽

pp. e7752 ◽

Cited By ~ 6

Author(s):

Ana O. Quintana-Escobar ◽

Geovanny I. Nic-Can ◽

Rosa María Galaz Avalos ◽

Víctor M. Loyola-Vargas ◽

Elsa Gongora-Castillo

Keyword(s):

Somatic Embryogenesis ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Expression Profiles ◽

Coffea Canephora ◽

Differentially Expressed ◽

Auxin Signaling ◽

Quantitative Expression ◽

Sequencing Technologies ◽

Auxin Signaling Pathway

Background Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Methods Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. Results A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. Discussion The results of this study allow a better understanding of the genes involved in the auxin signaling pathway as well as their expression profiles during the SE process.

Download Full-text

Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites

Journal of Translational Medicine ◽

10.1186/s12967-020-02696-z ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Lin Zhang ◽

Ming Fan ◽

Francesco Napolitano ◽

Xin Gao ◽

Ying Xu ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Cancer Progression ◽

Expression Profiles ◽

Treatment Strategies ◽

Target Organ ◽

Differentially Expressed ◽

Primary Breast Tumor ◽

Receptor Interaction ◽

Molecular Characteristics ◽

Organ Specific

Abstract Background Metastasis is the most devastating stage of cancer progression and often shows a preference for specific organs. Methods To reveal the mechanisms underlying organ-specific metastasis, we systematically analyzed gene expression profiles for three common metastasis sites across all available primary origins. A rank-based method was used to detect differentially expressed genes between metastatic tumor tissues and corresponding control tissues. For each metastasis site, the common differentially expressed genes across all primary origins were identified as organ-specific metastasis genes. Results Pathways enriched by these genes reveal an interplay between the molecular characteristics of the cancer cells and those of the target organ. Specifically, the neuroactive ligand-receptor interaction pathway and HIF-1 signaling pathway were found to have prominent roles in adapting to the target organ environment in brain and liver metastases, respectively. Finally, the identified organ-specific metastasis genes and pathways were validated using a primary breast tumor dataset. Survival and cluster analysis showed that organ-specific metastasis genes and pathways tended to be expressed uniquely by a subgroup of patients having metastasis to the target organ, and were associated with the clinical outcome. Conclusions Elucidating the genes and pathways underlying organ-specific metastasis may help to identify drug targets and develop treatment strategies to benefit patients.

Download Full-text

Identification of Differentially Expressed Genes and Signaling Pathways Related to Ovarian Endometriosis by Integrated Bioinformatics Analysis

10.21203/rs.3.rs-80648/v1 ◽

2020 ◽

Author(s):

Kainan Lin ◽

Zhenyan Pan ◽

Renke He ◽

Hanchu Wang ◽

Kai Zhou ◽

...

Keyword(s):

Mrna Expression ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Kegg Pathway ◽

Expression Profiles ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Go Analysis ◽

Pathway Enrichment

Abstract Purpose: Endometriosis was a common gynecological disease, however, the specific mechanism and the key molecules of endometriosis remained uncertain. This study aimed to single out key genes associated with poor prognosis, and further uncover underlying mechanisms.Methods: Data regarding mRNA expression profiles used in this study were retrieved from the Gene Expression Omnibus (GEO) database, a total of three mRNA expression profiles were included for subsequent analysis (GSE31515, GSE58178 and GSE120103). Then, we conducted Gene Ontology analysis (GO analysis), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and protein-protein interaction (PPI) analysis by the software R.Results: A total of 304 differentially expressed genes (DEGs) between endometriosis tissues and normal endometrium tissues were identified in integrated analysis, including 185 up-regulated genes and 119 down-regulated genes. GO analysis reveals that the DEGs of endometriosis were closely associated with molecular origin of bacteria. KEGG pathway enrichment analysis indicates that the DEGs were mainly involved in AGE-RAGE signaling pathway in diabetic complications. In addition, PPI of these DEGs was visualized by Cytoscape platform with utilization of Search Tool for the Retrieval of Interacting Genes (STRING). PPI analysis identifies 10 potential DEGs-related protein targets, including CCND1, IL6, CCL2, COL1A2, PTGS2, VCAM1, COL3A1, ELN, SERPINE1, HSP90B1. Conclusion: In conclusion, the present study reveals that bacterial contamination, defect of female reproductive system development, retrograde menstruation and the AGE-RAGE signaling pathway may be involved in the development of endometriosis In addition, these identified DEGs may be of clinical significance for the diagnosis and treatment of the endometriosis.

Download Full-text

Comparative analysis of the transcriptional responses of five Leishmania species to trivalent antimony

Parasites & Vectors ◽

10.1186/s13071-021-04915-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Julián Medina ◽

Lissa Cruz-Saavedra ◽

Luz Helena Patiño ◽

Marina Muñoz ◽

Juan David Ramírez

Keyword(s):

Comparative Analysis ◽

Differentially Expressed Genes ◽

Metabolic Pathways ◽

Rna Binding ◽

De Novo ◽

Expression Profiles ◽

Differentially Expressed ◽

Orthologous Genes ◽

Transcriptional Responses ◽

Species Specific

Abstract Background Leishmaniasis is a neglected tropical disease caused by several species of Leishmania. The resistance phenotype of these parasites depends on the characteristics of each species, which contributes to increased therapeutic failures. Understanding the mechanism used by the parasite to survive under treatment pressure in order to identify potential common and specific therapeutic targets is essential for the control of leishmaniasis. The aim of this study was to investigate the expression profiles and potential shared and specific resistance markers of the main Leishmania species of medical importance [subgenus L. (Leishmania): L. donovani, L. infantum and L. amazonensis; subgenus L. (Viannia): L. panamensis and L. braziliensis)] resistant and sensitive to trivalent stibogluconate (SbIII). Methods We conducted comparative analysis of the transcriptomic profiles (only coding sequences) of lines with experimentally induced resistance to SbIII from biological replicates of five Leishmania species available in the databases of four articles based on ortholog attribution. Simultaneously, we carried out functional analysis of ontology and reconstruction of metabolic pathways of the resulting differentially expressed genes (DEGs). Results Resistant lines for each species had differential responses in metabolic processes, compound binding, and membrane components concerning their sensitive counterpart. One hundred and thirty-nine metabolic pathways were found, with the three main pathways comprising cysteine and methionine metabolism, glycolysis, and the ribosome. Differentially expressed orthologous genes assigned to species-specific responses predominated, with 899 self-genes. No differentially expressed genes were found in common among the five species. Two common upregulated orthologous genes were found among four species (L. donovani, L. braziliensis, L. amazonensis, and L. panamensis) related to an RNA-binding protein and the NAD(P)H cytochrome-B5-oxidoreductase complex, associated with transcriptional control and de novo synthesis of linoleic acid, critical mechanisms in resistance to antimonials. Conclusion Herein, we identified potential species-specific genes related to resistance to SbIII. Therefore, we suggest that future studies consider a treatment scheme that is species-specific. Despite the limitations of our study, this is the first approach toward unraveling the pan-genus genetic mechanisms of resistance in leishmaniasis. Graphical Abstract

Download Full-text

Gene Expression in CLL Cells Associated with Lymphadenopathy and Chromosome 11q23 Deletion.

Blood ◽

10.1182/blood.v104.11.971.971 ◽

2004 ◽

Vol 104 (11) ◽

pp. 971-971

Author(s):

John D. Dickinson ◽

Avadhut Joshi ◽

Jamie Gilmore ◽

Philip J. Bierman ◽

Sanger Warren ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Cell Signaling ◽

Differentially Expressed Genes ◽

Peripheral Blood ◽

Expression Profiles ◽

Differentially Expressed ◽

Mediastinal Lymphadenopathy ◽

Fibroblast Growth Factor 21 ◽

Mutational Status

Abstract Previously we have demonstrated that peripheral blood samples with B-cell Chronic Lymphocytic Leukemia (CLL) have different gene expression profiles associated with chromosome aberrations detected by fluorescence in situ hybridization (FISH). In particular, the vast majority of differentially expressed genes were related to the presence of the 11q23 deletion. The 11q23 deletion has previously been shown to be correlated with shortened over-all survival and extensive/bulky lymphadenopathy. In this study we sought to identify genes whose expression may play role in the progression of CLL in patients that carry the 11q23 deletion. Gene expression from 10,700 human gene specific 50-mer oligos (MWG Biotech, Ebersberg, Germany) was compared between two groups of peripheral blood CLL samples. The first group consisted of CLL patients with the 11q23 deletion detected by FISH as well as with the presence of abdominal/mediastinal lymphadenopathy. The second group consisted of CLL patients without the 11q23 deletion and without the presence of known abdominal/mediastinal lymphadenopathy. The non-11q deletion group included CLL patients with the 13q14 deletion, trisomy 12, 17p13 deletion, as well as several without any detectable abnormality. Immunoglobulin heavy chain variable region (IgVH) mutational status was compared in CLL samples in both groups to ensure that resulting expression differences were not the result of this known prognostic marker. Median of ratios was compared between the two groups. Eighty-eight (87) genes had a p-value < 0.01. Gene function was classified at the European Molecular Biology Laboratory (EMBL) Bioinformatic Harvester website. Twenty of these differentially expressed genes were cell cycle/cell signaling related genes that were over-expressed in the 11q23 deletion group. Examples include: activating transcription factor 4, rho-associated coiled-coil containing protein kinase 2, fibroblast growth factor 21 precursor, signal transducing adaptor molecule 1, mad2-like 1, interferon receptor 1, pim-2 oncogene, and zw10 interactor. In comparison, using the same peripheral blood CLL samples, 78 genes were differentially expressed (p < 0.01) between those samples that had a mutated IgVH versus those that had an unmutated IgVH. Therefore, the presence of both the 11q23 deletion and bulky abdominal/mediastinal lymphadenopathy significantly alters the gene expression profile of peripheral blood CLL cells, particularly genes related to the cell cycle and cell signaling related processes. Biological roles of some of these genes may help further elucidate the basis of the clinical behavior of CLL patients

Download Full-text

Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes

BioMed Research International ◽

10.1155/2019/8340573 ◽

2019 ◽

Vol 2019 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Zhaoyan Li ◽

Lei Zhong ◽

Zhenwu Du ◽

Gaoyang Chen ◽

Jing Shang ◽

...

Keyword(s):

Signaling Pathway ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Receptor Interaction ◽

Hub Genes ◽

Expression Levels ◽

Network Analyses ◽

Synovial Membranes

Background. Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods. The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p<0.05 and gene count >2 were set as the cut-off point. Moreover, protein-protein interaction (PPI) network construction was applied for exploring the hub genes in osteoarthritis. The expression levels of the top ten hub genes in knee osteoarthritis synovial membranes and controls were detected by quantitative real-time PCR system. Results. A total of 229 DEGs were identified in osteoarthritis synovial membranes compared with normal synovial membranes, including 145 upregulated and 84 downregulated differentially expressed genes. The KEGG pathway analysis results showed that up-DEGs were enriched in proteoglycans in cytokine-cytokine receptor interaction, chemokine signaling pathway, rheumatoid arthritis, and TNF signaling pathway, whereas down-DEGs were enriched in the PPAR signaling pathway and AMPK signaling pathway. The qRT-PCR results showed that the expression levels of ADIPOQ, IL6, and CXCR1 in the synovium of osteoarthritis were significantly increased (p <0.05).

Download Full-text