Receptor Interaction Pathway Research Articles

Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods.

The molecular mechanism of the occurrence and development of papillary thyroid carcinoma (PTC) has been widely explored, but has not been completely elucidated. The present study aimed to identify and analyze genes associated with PTC by bioinformatics methods. Two independent datasets were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between PTC tissues and matched non-cancerous tissues were identified using GEO2R tool. The common DEGs in the two datasets were screened out by VennDiagram package, and analyzed by the following tools: KOBAS, Database for Annotation, Visualization, and Integrated Discovery (DAVID), Search tool for the retrieval of interacting genes/proteins (STRING), UALCAN and Gene expression profiling interactive analysis (GEPIA). A total of 513 common DEGs, including 259 common up-regulated and 254 common down-regulated genes in PTC, were screened out. These common up-regulated and down-regulated DEGs were most significantly enriched in cytokine–cytokine receptor interaction and metabolic pathways, respectively. Protein–protein interactions (PPI) network analysis showed that the up-regulated genes: FN1, SDC4, NMU, LPAR5 and the down-regulated genes: BCL2 and CXCL12 were key genes. Survival analysis indicated that the high expression of FN1 and NMU genes significantly decreased disease-free survival of patients with thyroid carcinoma. In conclusion, the genes and pathways identified in the current study will not only contribute to elucidating the pathogenesis of PTC, but also provide prognostic markers and therapeutic targets for PTC.

Identification of SERPINE1, PLAU and ACTA1 as biomarkers of head and neck squamous cell carcinoma based on integrated bioinformatics analysis

BackgroundHead and neck squamous cell carcinoma (HNSCC) is the six leading cancer by incidence worldwide. The 5-year survival rate of HNSCC patients remains less than 65% due to lack of symptoms in the early stage. Hence, biomarkers which can improve detection of HNSCC should improve clinical outcome.MethodsGene expression profiles (GSE6631, GSE58911) and the Cancer Genome Atlas (TCGA) HNSCC data were used for integrated bioinformatics analysis; the differentially expressed genes (DEGs) were then subjected to functional and pathway enrichment analysis, protein–protein interaction (PPI) network construction. Subsequently, module analysis of the PPI network was performed and overall survival (OS) analysis of hub genes in subnetwork was studied. Finally, immunohistochemistry was used to verify the selected markers.ResultsA total of 52 up-regulated and 80 down-regulated DEGs were identified, which were mainly associated with ECM–receptor interaction and focal adhesion signaling pathways. Importantly, a set of prognostic signatures including SERPINE1, PLAU and ACTA1 were screened from DEGs, which could predict OS in HNSCC patients from TCGA cohort. Experiment of clinical samples further successfully validated that these three signature genes were aberrantly expressed in the oral epithelial dysplasia and HNSCC, and correlated with aggressiveness of HNSCC patients.ConclusionsSERPINE1, PLAU and ACTA1 played important roles in regulating the initiation and progression of HNSCC, and could be identified as key biomarkers for precise diagnosis and prognosis of HNSCC, which will provide potential targets for clinical therapies.

Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO)

BackgroundChronic periodontitis (CP) is a multifactorial inflammatory disease. For the diagnosis of CP, it is necessary to investigate molecular biomarkers and the biological pathway of CP. Although analysis of mRNA expression profiling with microarray is useful to elucidate pathological mechanisms of multifactorial diseases, it is expensive. Therefore, we utilized pooled microarray gene expression data on the basis of data sharing to reduce hybridization costs and compensate for insufficient mRNA sampling. The aim of the present study was to identify molecular biomarker candidates and biological pathways of CP using pooled datasets in the Gene Expression Omnibus (GEO) database.MethodsThree pooled transcriptomic datasets (GSE10334, GSE16134, and GSE23586) of gingival tissue with CP in the GEO database were analyzed for differentially expressed genes (DEGs) using GEO2R, functional analysis and biological pathways with the Database of Annotation Visualization and Integrated Discovery database, Protein-Protein Interaction (PPI) network and hub gene with the Search Tool for the Retrieval of Interaction Genes database, and biomarker candidates for diagnosis and prognosis and upstream regulators of dominant biomarker candidates with the Ingenuity Pathway Analysis database.ResultsWe shared pooled microarray datasets in the GEO database. One hundred and twenty-three common DEGs were found in gingival tissue with CP, including 81 upregulated genes and 42 downregulated genes. Upregulated genes in Gene Ontology were significantly enriched in immune responses, and those in the Kyoto Encyclopedia of Genes and Genomes pathway were significantly enriched in the cytokine-cytokine receptor interaction pathway, cell adhesion molecules, and hematopoietic cell lineage. From the PPI network, the 12 nodes with the highest degree were screened as hub genes. Additionally, six biomarker candidates for CP diagnosis and prognosis were screened.ConclusionsWe identified several potential biomarkers for CP diagnosis and prognosis (e.g., CSF3, CXCL12, IL1B, MS4A1, PECAM1, and TAGLN) and upstream regulators of biomarker candidates for CP diagnosis (TNF and TGF2). We also confirmed key genes of CP pathogenesis such as CD19, IL8, CD79A, FCGR3B, SELL, CSF3, IL1B, FCGR2B, CXCL12, C3, CD53, and IL10RA. To our knowledge, this is the first report to reveal associations of CD53, CD79A, MS4A1, PECAM1, and TAGLN with CP.

Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome.

ObjectiveVaricose veins are a common problem worldwide and can cause significant impairments in health-related quality of life, but the etiology and pathogenesis remain not well defined. This study aims to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.MethodsWe harvested great saphenous veins (GSV) from patients who underwent coronary artery bypass grafting (CABG) and varicose veins from conventional stripping surgery. RNA-Sequencing (RNA-Seq) technique was used to obtain the complete transcriptomic data of both GSVs from CABG patients and varicose veins. Weighted Gene Co-expression network analysis (WGCNA) and further analyses were then carried out with the aim to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.ResultsFrom January 2015 to December 2016, 7 GSVs from CABG patients and 13 varicose veins were obtained. WGCNA identified 4 modules. In the brown module, gene ontology (GO) analysis showed that the biological processes were focused on response to stimulus, immune response and inflammatory response, etc. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that the biological processes were focused on cytokine-cytokine receptor interaction and TNF signaling pathway, etc. In the gray module, GO analysis showed that the biological processes were skeletal myofibril assembly related. The immunohistochemistry staining showed that the expression of ASC, Caspase-1 and NLRP3 were increased in GSVs from CABG patients compared with varicose veins. Histopathological analysis showed that in the varicose veins group, the thickness of vascular wall, tunica intima, tunica media and collagen/smooth muscle ratio were significantly increased, and that the elastic fiber/internal elastic lamina ratio was decreased.ConclusionThis study shows that there are clear differences in transcriptomic information between varicose veins and GSVs from CABG patients. Some inflammatory RNAs are down-regulated in varicose veins compared with GSVs from CABG patients. Skeletal myofibril assembly pathway may play a crucial role in the pathogenesis of varicose veins. Characterization of these RNAs may provide new targets for understanding varicose veins diagnosis, progression, and treatment.

Transcriptome analysis of the spleen provides insight into the immunoregulation of Mastacembelus armatus under Aeromonas veronii infection

Mastacembelus armatus, also known as the zigzag eel, is an economically important species of freshwater fish that is very popular with consumers as a high-grade table fish in China. Recently, the wild population of this fish has declined gradually due to overfishing and various types of ecological imbalance. Meanwhile, the aquaculture of this spiny eel has flourished in southern China. To understand the immune response of zigzag eel to Aeromonas veronii, we carried out transcriptome sequencing of zigzag eel spleens after artificial bacterial infection. After assembly, 110,328 unigenes were obtained with 44.42% GC content. A total of 27,098 unigenes were successfully annotated by four public protein databases, namely, Nr, UniProt, KEGG and KOG. Differential expression analysis revealed the existence of 1278 significantly differentially expressed unigenes at 24 h post infection, with 767 unigenes upregulated and 511 unigenes downregulated. After GO and KEGG enrichment analyses, many immune-related GO categories and pathways were significantly enriched. The typical significantly enriched pathways included toll-like receptor signaling pathway, cytokine-cytokine receptor interaction and TNF signaling pathway. In addition, 40,027 microsatellites (SSRs) and 52,716 candidate single nucleotide polymorphisms (SNPs) were identified from the infection and control transcriptome libraries. Overall, this transcriptomic analysis provided valuable information for studying the immune response of zigzag eels against bacterial infection.

Long-term and high dose dexamethasone injection decreases the expression of Immunoglobulin Heavy (Light) Chain Variable Region Genes (IGH(L)Vs) in the mouse spleen

Glucocorticoid hormones have been widely used in clinical practice as potent anti-inflammatory and immunosuppressive agents. However, the underlying mechanisms of how they work remain unaddressed. Here, we used RNA-set to profile spleen gene expression in adult mice after consistent intraperitoneal injection of dexamethasone. We identified 13565 genes in control (injected with 0.9% NaCl) and 13702 genes in dexamethasone-injected group, 12920 genes were expressed in both, but 645 genes were identified only in control and 782 genes were identified only in the dexamethasone group. In the dexamethasone-injected group 101 and 67 genes were down-and up-regulated, respectively. Among these, 129 were coding genes, 19 were identified as non-coding genes or pseudogenes, and the remaining 20 were TEC (to be experimentally confirmed) genes. Gene ontology (GO) and KEGG pathway analysis revealed that the cytokine-cytokine receptor interaction pathway was highly enriched in these differentially expressed genes, and that a majority of the 129 identified coding genes were involved in immune system and cell adhesion-associated processes. Moreover, systemic lupus erythematosus, renin-angiotensin system, fat digestion and absorption, and glycerolipid metabolism pathways were significantly affected in the dexamethasone-treatment group. No obvious signaling pathway was enriched in the control group. Additionally, 20 immunoglobulin heavy or light chain variable region genes (IGH(L)Vs) were down regulated in the dexamethasone-injected group. IGH(L)Vs encode the variable region of immunoglobulin heavy chain and determine the diversity and specificity of antibodies. We were unable to determine the function of the 19 non-coding genes with differential expression following dexamethasone treatment. Our findings indicate that the expression of IGH(L)Vs and non-coding genes play an important role in the anti-inflammatory and immunosuppressive effects of dexamethasone and could be developed as potential agents in clinical practice.

Profiling analysis of long non-coding RNA and mRNA in parathyroid carcinoma.

Parathyroid carcinoma (PCa) is a rare endocrine neoplasia that typically has unfavourable outcomes. The contribution of long non-coding RNAs (lncRNAs) to the development of malignant and benign parathyroid tumours remains largely unknown. In this study, we explored transcriptomic profiling of lncRNA and mRNA expression in 6 PCa, 6 parathyroid adenoma (PAd) and 4 normal parathyroid (PaN) tissues. In total, 2641 lncRNA transcripts and 2165 mRNA transcripts were differentially expressed between PCa and PAd. Enrichment analysis demonstrated that dysregulated transcripts were involved mainly in the extracellular matrix (ECM)-receptor interaction and energy metabolism pathways. Bioinformatics analysis suggested that ATF3, ID1, FOXM1, EZH2 and MITF may be crucial to parathyroid carcinogenesis. Series test of cluster analysis segregated differentially expressed lncRNAs and mRNAs into several expression profile models, among which the 'plateau' profile representing components specific to parathyroid carcinogenesis was selected to build a co-expression network. Seven lncRNAs and three mRNAs were selected for quantitative RT-PCR validation in 16 PCa, 41 PAd and 4 PaN samples. Receiver-operator characteristic curves analysis showed that lncRNA PVT1 and GLIS2-AS1 yielded the area under the curve values of 0.871 and 0.860, respectively. Higher hybridization signals were observed in PCa for PVT1 and PAd for GLIS2-AS1. In conclusion, the current evidence indicates that PAd and PCa partially share common signalling molecules and pathways, but have independent transcriptional events. Differentially expressed lncRNAs and mRNAs have intricate interactions and are involved in parathyroid tumourigenesis. The lncRNA PVT1 and GLIS2-AS1 may be new potential markers for the diagnosis of PCa.

Protein Network Analysis of the Serum and Their Functional Implication in Patients Subjected to Traumatic Brain Injury.

Traumatic brain injury (TBI) often leads to severe neurobehavioral impairment, but the underlying molecular mechanism remains to be elucidated. Here, we collected the sera from 23 patients (aged from 19 to 81 years old, third day after TBI as TBI-third group) subjected to TBI from The First Hospital of Kunming City, and the sera from 22 healthy donors (aged from 18 to 81 years old and as control group). Then, three samples from TBI-third group and three samples from control group were subjected to the protein microarray detection, and bioinformatics analysis. Then, enzyme-linked immunosorbent assay (ELISA) was used to verify significantly altered protein levels. Results showed that, when compared with the control group, all significantly differentially expressed proteins [DEPs, P < 0.05, FDR < 0.05, fold change (FC) > 2] contained 172 molecules in the TBI-third group, in which 65 proteins were upregulated, while 107 proteins were downregulated. The biological processes of these DEPs, mostly happened in the extracellular region and the extracellular region parts, are mainly involved in the regulation of cellular process, signaling and signal transduction, cell communication, response to stimuli, the immune system process and multicellular organismal development. Moreover, the essential molecular functions of them are cytokine activity, growth factor activity and morphogen activity. Additionally, the most significant pathways are enriched in cytokine–cytokine receptor interaction and PI3K-Akt signaling pathways among downregulated proteins, and pathways in cancer and cytokine–cytokine receptor interaction among upregulated proteins. Of these, we focused on the NGF, NT-3, IGF-2, HGF, NPY, CRP, MMP-9, and ICAM-2 with a high number of interactors in Protein–Protein Interaction (PPI) Network indicated by bioinformatics report. Furthermore, using ELISA test, we confirmed that all increase in the levels of NGF, NT-3, IGF-2, HGF, NPY, CRP, MMP-9, and ICAM-2 in the serum from TBI patients. Together, we determined the screened protein expressional profiles in serum for TBI patients, in which the cross-network between inflammatory factors and growth factors may play a crucial role in TBI damage and repair. Our findings could contribute to indication for the diagnosis and treatment of TBI in future translational medicine and clinical practice.

RNA deep sequencing reveals novel transcripts and pathways involved in the unsaturated fatty acid metabolism in chicken

Fatty acids in chicken meat especially the unsaturated fatty acids (UFA) contribute in the nutritional value, meat quality, and human health. A deeper knowledge in the genomics of fatty acids (FA) is important as it identifies effective markers to be used in marker-assisted breeding in chickens for higher UFA leading to the economic benefits in chicken production industry. Therefore, this study aimed to investigate trancriptome profilling in the liver tissues collected from chicken with divergent UFA contents in the breast muscle tissues using RNA deep-sequencing. Liver tissues from chicken with higher (n = 3) and lower (n = 3) UFA were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample ranged from 24.30 to 29.97 million. Approximately 367 genes were differentially regulated with the significance level of p-adjusted value <0.05. Among them, 187 genes were up-regulated and 180 were down-regulated (P < 0.01, FC > 1.5) in higher UFA group. Differentially regulated genes in high UFA liver samples were enriched in metabolic processes such as heme binding, sodium channel activity, and iron ion binding. Pathway analysis identified the metabolic pathways, ECM receptor interaction, focal adhesion, peroxisome, Wnt signaling and TGF-Beta signaling pathways which may play important roles in UFA metabolism. Differential gene expression analysis identified candidate genes in the ATP synthesis, apovitellenin, cytochrome P450, hydroxysteroid, solute carrier and stearoyl-CoA desaturase family. These differentially expressed genes and pathways may lead to UFA variation and could be used as genetic marker for UFA traits in chickens. However, further validation is required to confirm the effect of these genes in the UFA-related molecules metabolism in other chicken populations.

Regulatory Effect of Bacillus subtilis on Cytokines of Dendritic Cells in Grass Carp (Ctenopharyngodon Idella).

Bacillus subtilis is a common group of probiotics that have been widely used in the feed industry as they can increase host resistance to pathogens and balance the immune response. However, the regulatory mechanism of Bacillus subtilis on the host immune system remains unclear in teleosts. In this study, we isolated and enriched dendritic cells from white blood cells (WBCs), and then stimulated them with Bacillus subtilis. Morphological features, specific biological functions, and authorized functional molecular markers were used in the identification of dendritic cells. Subsequently, we collected stimulated cells at 0, 4, and 18 h, and then constructed and sequenced the transcriptomic libraries. A transcriptome analysis showed that 2557 genes were up-regulated and 1708 were down-regulated at 4 h compared with the control group (|Fold Change| ≥ 4), and 1131 genes were up-regulated and 1769 were down-regulated between the cells collected at 18 h and 4 h (|Fold Change| ≥ 4). Gene Ontology (GO) annotations suggested many differentially expressed genes (DEGs) (p < 0.05 and |Fold Change| ≥ 4) were involved in immune-related biological functions including immune system progress, cytokine receptor binding, and cytokine binding. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the cytokine–cytokine receptor interaction pathways were significantly enriched at both time points (p < 0.05), which may play a key role in the response to stimulation. Furthermore, mRNA expression level examination of several pro-inflammatory cytokines and anti-inflammatory cytokines genes by quantitative real-time polymerase chain reaction (qRT-PCR) indicated that their expressions can be significantly increased in Bacillus subtili, which suggest that Bacillus subtilis can balance immune response and tolerance. This study provides dendritic cell (DC)-specific transcriptome data in grass carp by Bacillus subtilis stimulation, allowing us to illustrate the molecular mechanism of the DC-mediated immune response triggered by probiotics in grass carp.

M30 - NEXT-GENERATION RNA SEQUENCING OF POST-MORTEM ANTERIOR CINGULATE AND DORSOLATERAL PREFRONTAL CORTICES TO IDENTIFY DIFFERENTIALLY EXPRESSED GENES IN PATHOLOGY-VERIFIED LEWY BODY DEMENTIA

Background Lewy Body Dementias (LBD) include Dementia with Lewy Bodies (DLB) and Parkinson's Disease Dementia (PDD). DLB is the second most common neurodegenerative dementia, and it is associated with increased mortality, earlier nursing home admissions, higher risk of falls, poorer quality-of-life, more health resource utilisation, higher costs, and more caregivers’ burden than Alzheimer's disease. There are no disease-modifying treatments for LBD, and reliable cost-effective biomarkers that can aid early diagnosis of LBD remain elusive. Identifying Differentially Expressed Genes (DEG) in LBD brains can reveal underlying functionally disrupted molecular pathways, and it may lead to novel biomarkers and potential RNA drugs for LBD. However, relevant studies investigating transcriptomics of LBD remain sparse. Methods We studied anterior cingulate and dorsolateral prefrontal cortices of post-mortem pathology-verified brains from the following three groups, (i) DLB (n=7), (ii) PDD (n=7), and (iii) non-demented older people (n=6). Total RNA was extracted, and their quality was assessed by Agilent 2100 Bioanalyzer (N=40). Next-generation RNA-sequencing (RNA-seq) (75 bp; paired-end; minimum 30 million clean reads/ sample) was completed using Illumina HiSeq-4000. After appropriate quality control, reads were aligned to the human genome by HISAT2. Aligned reads were counted by featureCounts, and DEG were identified by edgeR 3.18.1 with Benjamini-Hochberg false discovery correction (5%). Functional analyses of identified DEGs were performed using Ingenuity Pathway Analysis. Subgroup analyses were performed between LBD with and without pathogenic GBA (Glucosidase, Beta Acid) mutations. Results We have identified specific significantly upregulated and downregulated DEGs in LBD, while comparing with non-demented older people. Downregulated DEGs in LBD include Oxytocin Receptor (OXTR), Myeloperoxidase (MPO), Selectin E (SELE), Cathepsin G (CTSG), and Somatostatin (SST), and upregulated DEGs in LBD include X-Inactive Specific Transcript (XIST), Polypeptide N-acetyl galactosaminyl transferase 6 (GALNT6), and mitochondrial Proline dehydrogenase (PRODH). DEGs in LBD are significantly enriched for prion diseases, cytokine-cytokine receptor interaction, phagosome, and glycerophospholipid metabolism pathways. We have also identified the DEGs that significantly differ between DLB and PDD, and the transcriptomic differences between the two cortical regions. Discussion Although this has been an explorative study, this is the hitherto largest RNA-seq study investigating the transcriptomics of pathology-verified LBD brains. In addition to enhancing our understanding of LBD neurobiology at molecular level, this study has identified specific RNA targets that may be novel biomarkers and therapeutic targets for DLB and PDD. Further replication experiments, and more bioinformatic analyses of our data are on-going. We are currently investigating serum exosomal RNA cargo of people with LBD for evaluating the peripheral biomarker potential of identified DEGs. Translational relevance and therapeutic potential of identified DEGs will be evaluated by in-vitro experiments.

The screening of pivotal gene expression signatures and biomarkers in renal carcinoma.

Renal cell carcinoma (RCC) is one of the most common malignancies in the urinary system, among which the proportion of clear cell RCC (ccRCC) is over 80%. This study aims to explore potential signaling pathways and key biomarkers that drive RCC progression. The RCC GEO Datasets GSE15641 was featured to screen differentially expressed genes (DEGs). The pathway enrichment and functional annotation of differentially expressed genes were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO). We screened Hub genes from DEGs using protein-protein interaction (PPI) networks and Cytoscape software. The survival and diagnostic analysis of these hub genes was performed to evaluate their potential prognostic and diagnostic value for ccRCC. In GSE15641 dataset, 598 DEGs were captured according to screening criteria (406 up-regulated genes and 192 down-regulated genes). Meanwhile, 15 hub genes were screened out from DEGs using PPI and Cytoscape. Kaplan Meier and ROC curve analysis identified three potential prognostic and diagnostic biomarkers (TGFB1, TIMP1 and VIM) for ccRCC from 15 hub genes. Gene set enrichment analysis (GSEA) revealed that these three dysregulated genes are mainly enriched in primary immunodeficiency, ECM receptor interaction, cytokine receptor interaction and natural killer cell-mediated cytotoxicity pathway. In summary, our findings discovered pivotal gene expression signatures and signaling pathways in the progression of ccRCC. TGFB1, TIMP1 and VIM might contribute to the progression of ccRCC, which could have potential as biomarkers or therapeutic targets for ccRCC.

Integrated Transcriptome Analysis of microRNA and mRNA in Mouse Skin Derived Precursors (SKPs) and SKP Derived Fibroblast (SFBs) by RNA-Seq.

Background: Skin-derived precursors (SKPs) display the characteristics of self-renewal and multilineage differentiation.Objective: The study aimed to explore the molecular mechanisms of mouse SKPs differentiation into SKP-derived fibroblasts (SFBs).Methods: We compared the microRNA (miRNA) profile in mouse SKPs and SFBs by RNA sequenc-ing. Real-time quantitative reverse transcription PCR (qRT-PCR) was performed to validate the miRNA expression. The integrated analysis of miRNA and mRNA expression data was performed to explore the potential crosstalk of miRNA-mRNA in SKP differentiation.Results: 207 differentially expressed miRNAs and 835 miRNA target genes in the gene list of integrated mRNA expression profiling were identified. Gene Ontology (GO) enrichment analysis revealed that cell differentiation and cell proliferation process were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the target genes were significantly most enriched in the cytokine-cytokine receptor interaction, cancer pathways and axon guidance signaling pathway. The most upregulated and downregulated target genes were involved in the Wnt, Notch, cytokine-cytokine receptor interaction, TGF-β, p53 and apoptotic signaling pathway. The miRNA-mRNA regulatory net-works and 507 miRNA-mRNA pairs were constructed. Seven miRNAs (miR-486-3p, miR-504-5p, miR-149-3p, miR-31-5p, miR-484, miR-328-5p and miR-22-5p) and their target genes Wnt4, Dlx2, Se-ma4f, Kit, Kitl, Inpp5d, Igfbp3, Prdm16, Sfn, Irf6 and Clu were identified as miRNA-mRNA crosstalk pairs.Conclusion: These genes and signaling pathways might control SKPs proliferation and SKPs differen-tiation into SFBs during the process of SKPs differentiation, which might promote the application of SKPs in the clinical treatment of skin-related diseases by regulating SKPs proliferation and SKPs differ-entiation.

Far-infrared radiation stimulates platelet-derived growth factor mediated skeletal muscle cell migration through extracellular matrix-integrin signaling.

Despite increased evidence of bio-activity following far-infrared (FIR) radiation, susceptibility of cell signaling to FIR radiation-induced homeostasis is poorly understood. To observe the effects of FIR radiation, FIR-radiated materials-coated fabric was put on experimental rats or applied to L6 cells, and microarray analysis, quantitative real-time polymerase chain reaction, and wound healing assays were performed. Microarray analysis revealed that messenger RNA expressions of rat muscle were stimulated by FIR radiation in a dose-dependent manner in amount of 10% and 30% materials-coated. In 30% group, 1,473 differentially expressed genes were identified (fold change [FC] > 1.5), and 218 genes were significantly regulated (FC > 1.5 and p < 0.05). Microarray analysis showed that extracellular matrix (ECM)-receptor interaction, focal adhesion, and cell migration-related pathways were significantly stimulated in rat muscle. ECM and platelet-derived growth factor (PDGF)-mediated cell migration-related genes were increased. And, results showed that the relative gene expression of actin beta was increased. FIR radiation also stimulated actin subunit and actin-related genes. We observed that wound healing was certainly promoted by FIR radiation over 48 h in L6 cells. Therefore, we suggest that FIR radiation can penetrate the body and stimulate PDGF-mediated cell migration through ECM-integrin signaling in rats.

Combining data from TCGA and GEO databases and reverse transcription quantitative PCR validation to identify gene prognostic markers in lung cancer.

BackgroundThe aim of this study was to predict and explore the possible mechanism and clinical value of genetic markers in the development of lung cancer with a combined database to screen the prognostic genes of lung cancer.Materials and methodsCommon differential genes in two gene expression chips (GSE3268 and GSE10072 datasets) were investigated by collecting and calculating from Gene Expression Omnibus and The Cancer Genome Atlas databases using R language. Five markers of gene composition (ribonucleotide reductase regulatory subunit M2 [RRM2], trophoblast glycoprotein [TPBG], transmembrane protease serine 4[TMPRFF4], chloride intracellular channel 3 [CLIC3], and WNT inhibitory factor-1 [WIF1]) were found by the stepwise Cox regression function when we further screened combinations of gene models, which were more meaningful for prognosis. By analyzing the correlation between gene markers and clinicopathological parameters of lung cancer and its effect on prognosis, the TPBG gene was selected to analyze differential expression, its possible pathways and functions were predicted using gene set enrichment analysis (GSEA), and its protein interaction network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database; then, quantitative PCR and the Oncomine database were used to verify the expression differences of TPBG in lung cancer cells and tissues.ResultsThe expression levels of five genetic markers were correlated with survival prognosis, and the total survival time of the patients with high expression of the genetic markers was shorter than those with low expression (P<0.001). GSEA showed that these high-expression samples enriched the gene sets of cell adhesion, cytokine receptor interaction pathway, extracellular matrix receptor pathway, adhesion pathway, skeleton protein regulation, cancer pathway and TGF-β pathway.ConclusionThe high expression of five gene constituent markers is a poor prognostic factor in lung cancer and may serve as an effective biomarker for predicting metastasis and prognosis of patients with lung cancer.

Gene expression profile of PM014 of immortalized mouse lung epithelial cells in response to the effect of PM014 on radiation-induced fibrosis

Radiotherapy is a major method for cancer treatment, but it frequently causes various side effects such as radiation-induced pneumonia and pulmonary fibrosis. Drugs to treat these side effects are urgently needed in the clinic, since there is no clearly defined medication for treating these symptoms. Previous studies demonstrated that the herbal formula, PM014, is effective for radiation-induced lung injury and fibrosis in mice. In this study, we investigated gene expression profiles to understand the mechanism of action behind the effects of PM014 on radiation induced damage in immortalized lung epithelial cells, MLE12. We performed QuantSeq 3′ mRNA-Seq analysis on the mRNA from radiation treated MLE-12 cells in the presence and absence of PM014. Transcriptome analysis found that 217 genes were significantly affected by PM014. Among them (217 genes, > twofold, p value < 0.05, 4 normalize), 77 genes were found to be upregulated, and 140 genes were downregulated in response to PM014 treatment in a dose dependent manner. Using the Kyoto Encyclopedia of Genes and Genomes analysis, we found that genes involved in cytokine–cytokine receptor interaction pathways were the most strongly affected by PM014. Based on these data, we selected 20 genes, and performed real-time PCR. Expression of 11 genes, including IL-18, IL-12a, Tnfrsf9, IL-17, CCR5, Blnk, Irf8, Nrros, TGF-β, Relt, and Cxcl2 was increased after irradiation, while PM014 treatment showed the reversed expression pattern of these genes. Therefore, PM014 may be useful for the treatment of radiation induced lung injury by modulating genes involved in cytokine–cytokine receptor interaction pathway.

Transcriptome profile in bursa of Fabricius reveals potential mode for stress-influenced immune function in chicken stress model

BackgroundThe molecular mechanisms underlying stress-influenced immune function of chicken (Gallus Gallus) are not clear. The stress models can be established effectively by feeding chickens corticosterone (CORT) hormone. The bursa of Fabricius is a unique central immune organ of birds. RNA-Seq technology was used to investigate differences in the expression profiles of immune-related genes and associated pathways in the bursa of Fabricius to clarify molecular mechanisms. The aim of this study was to broaden the understanding of the stress-influenced immune function in chickens.ResultsDifferentially expressed genes (DEGs) in the bursa of Fabricius between experimental group (basal diet with added CORT 30 mg/kg; C_B group) and control group (basal diet; B_B group) were identified by using RNA-seq technology. In total, we found 1434 significant DEGs (SDEGs), which included 199 upregulated and 1235 downregulated genes in the C_B group compared with the B_B group. The immune system process GO term was the top significantly GO term, including MYD88, TLR4, IL15, VEGFA gene and so on. The cytokine-cytokine receptor interaction pathway and the Toll-like receptor signaling pathway were the key pathways affected by stress. The protein-protein interaction (PPI) analysis of the SDEGs showed that VEGFA, MyD88 and IL15 were hub genes and module analysis showed that MYD88, TLR4 and VEGFA play important roles in response to stress.ConclusionThis study showed that the VEGFA and ILs (such as IL15) via the cytokine-cytokine receptor interaction pathway, MYD88 and TLR4 via the Toll-like receptor signaling pathway may play important roles in the regulation of immune function under stress condition with CORT administration. The results of this study provide a reference for further studies of the molecular mechanisms of stress-influenced immune function.

Whole genome MBD-seq and RRBS analyses reveal that hypermethylation of gastrointestinal hormone receptors is associated with gastric carcinogenesis

DNA methylation is a regulatory mechanism in epigenetics that is frequently altered during human carcinogenesis. To detect critical methylation events associated with gastric cancer (GC), we compared three DNA methylomes from gastric mucosa (GM), intestinal metaplasia (IM), and gastric tumor (GT) cells that were microscopically dissected from an intestinal-type early gastric cancer (EGC) using methylated DNA binding domain sequencing (MBD-seq) and reduced representation bisulfite sequencing (RRBS) analysis. In this study, we focused on differentially methylated promoters (DMPs) that could be directly associated with gene expression. We detected 2,761 and 677 DMPs between the GT and GM by MBD-seq and RRBS, respectively, and for a total of 3,035 DMPs. Then, 514 (17%) of all DMPs were detected in the IM genome, which is a precancer of GC, supporting that some DMPs might represent an early event in gastric carcinogenesis. A pathway analysis of all DMPs demonstrated that 59 G protein-coupled receptor (GPCR) genes linked to the hypermethylated DMPs were significantly enriched in a neuroactive ligand–receptor interaction pathway. Furthermore, among the 59 GPCRs, six GI hormone receptor genes (NPY1R, PPYR1, PTGDR, PTGER2, PTGER3, and SSTR2) that play an inhibitory role in the secretion of gastrin or gastric acid were selected and validated as potential biomarkers for the diagnosis or prognosis of GC patients in two cohorts. These data suggest that the loss of function of gastrointestinal (GI) hormone receptors by promoter methylation may lead to gastric carcinogenesis because gastrin and gastric acid have been known to play a role in cell differentiation and carcinogenesis in the GI tract.

The Overexpression of CD80 and ISG15 Are Associated with the Progression and Metastasis of Breast Cancer by a Meta-Analysis Integrating Three Microarray Datasets.

Breast cancer is a common cancer and could result in a substantial mortality. The study aimed to screen gene signatures associated with the development and metastasis of breast cancer and explore their regulation mechanisms. Three datasets of GSE10797, GSE8977 and GSE3744 were downloaded from GEO (Gene Expression Omnibus) database, containing 55 breast cancer samples and 27 normal samples. After data preprocessing using limma software and RMA (robust multi-array average) algorithm, DEGs (differentially expressed genes) between breast tumor and normal tissues in three individual experiments were identified using MADAM package. Function and pathway enrichment analyses were performed for the DEGs. Transcription factors and TAGs (tumor associated genes) among the DEGs were recognized and the PPI (protein-protein-interaction) network for the DEGs was constructed using Cytoscape software. The mRNA expression was analyzed via real-time quantitative PCR and protein expression was measured by western blotting. Totally, 100 DEGs were identified, including 33 up-regulated genes and 67 down-regulated genes. Among them, up-regulated DEGs such as CD80 was enriched in toll-like receptor (TLR) interaction pathway and the TAG, ISG15 was related to RIG-I-like receptor signaling pathway, while CXCL10 was involved in both of the two pathways. Whereas, the down-regulated DEG, CXCL12 was significantly associated with axon guidance pathway. Additionally, these DEGs were also pivotal nodes in the PPI network with high degrees. Besides, CXCL10 and CD80 were both interacted with IFNG. The mRNA expression of ISG15 was obviously enhanced in human breast cancer cells MCF-7, while no significant difference of CXCL10 mRNA level was found between MCF10A and MCF-7 cells. Moreover, the proteins expression levels of CD80 and ISG15 were significantly increased in MCF-7, MDA-MB-468 and MDA-MB-231 breast cancer cells than in normal MCF10A cells. CD80 might be responsible for the breast cancer's progression and metastasis via regulating innate immune system. In addition, ISG15 is identified as a crucial gene signature associated with breast cancer development and metastasis via RIG-I-like receptor signaling pathway.

Transcriptome analysis identifies activated signaling pathways and regulated ABC transporters and solute carriers after hyperosmotic stress in renal MDCK I cells

Hyperosmolality is found under physiological conditions in the kidneys, whereas hyperosmolality in other tissues may be associated with pathological conditions. In such tissues an association between inflammation and hyperosmolality has been suggested. During hyperosmotic stress, an important phenomenon is upregulation of solute carriers (SLCs). We hypothesize that hyperosmolality affects the expression of many SLCs as well as ABC transporters. Through RNA-sequencing and topological pathway analysis, the cell cycle, the cytokine-cytokine receptor interaction pathway, and the chemokine-signaling pathway were significantly activated in MDCK I cells after hyperosmotic treatment (Δ200 mOsm) with raffinose or NaCl. 9065, 8052 and 5018 genes were significantly regulated by raffinose, NaCl or urea supplementation (500 mOsm), respectively, compared to control (300 mOsm). Cytokines, that have not previously been associated with hyperosmolality, were identified. We further provide an overview of transport proteins that could be of relevance in tissues exposed to hyperosmolality. Especially Slc5a8 was found highly up-regulated.