Transcriptome analysis identifies signaling pathways related to meat quality in broiler chickens – the extracellular matrix (ECM) receptor interaction signaling pathway

Background. Inhibin subunit beta B (INHBB) is a protein-coding gene that participated in the synthesis of the transforming growth factor-β (TGF-β) family members. The study is aimed at exploring the clinical significance of INHBB in patients with colorectal cancer (CRC) by bioinformatics analysis. Methods. Real-time PCR and analyses of Oncomine, Gene Expression Omnibus (GEO), and The Cancer Genome Atlas (TCGA) databases were utilized to evaluate the INHBB gene transcription level of colorectal cancer (CRC) tissue. We evaluated the INHBB methylation level and the relationship between expression and methylation levels of CpG islands in CRC tissue. The corresponding clinical data were obtained to further explore the association of INHBB with clinical and survival features. In addition, Gene Set Enrichment Analysis (GSEA) was performed to explore the gene ontology and signaling pathways of INHBB involved. Results. INHBB expression was elevated in CRC tissue. Although the promoter of INHBB was hypermethylated in CRC, methylation did not ultimately correlate with the expression of INHBB. Overexpression of INHBB was significantly and positively associated with invasion depth, distant metastasis, and TNM stage. Cox regression analyses and Kaplan-Meier survival analysis indicated that high expression of INHBB was correlated with worse overall survival (OS) and disease-free survival (DFS). GSEA showed that INHBB was closely correlated with 5 cancer-promoting signaling pathways including the Hedgehog signaling pathway, ECM receptor interaction, TGF-β signaling pathway, focal adhesion, and pathway in cancer. INHBB expression significantly promoted macrophage infiltration and inhibited memory T cell, mast cell, and dendritic cell infiltration. INHBB expression was positively correlated with stromal and immune scores of CRC samples. Conclusion. INHBB might be a potential prognostic biomarker and a novel therapeutic target for CRC.

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Differential Gene Signature and Signaling Pathways in Childhood Burkitt (BL) vs Diffuse Large B-Cell Lymphoma (DLBCL).

Blood ◽

10.1182/blood.v110.11.4142.4142 ◽

2007 ◽

Vol 110 (11) ◽

pp. 4142-4142

Author(s):

Nancy S. Day ◽

Janet Ayello ◽

Ian Waxman ◽

Evan Shereck ◽

Catherine McGuinn ◽

...

Keyword(s):

Protein Kinase ◽

Signaling Pathways ◽

Signaling Pathway ◽

Cell Lines ◽

Expression Profiles ◽

B Cell Lymphoma ◽

Cytokine Receptor ◽

Receptor Interaction ◽

Signal Pathways ◽

Type I

Abstract The prognosis and treatment of both major forms of advanced childhood B-NHL (BL and DLBCL) is similar with short and intensive multi-agent chemotherapy (Cairo/Patte et al., Blood, 2007 and Patte/Cairo et al., Blood, 2007). Despite both BL and DLBCL being germinal center derived, our recent cytogenetic results of BL vs DLBCL in the FAB LMB 96 study have demonstrated significant differences in secondary chromosomal aberrations in BL vs DLBCL and a differential prognosis based on secondary cytogenetic findings (Poirel/Cairo/Patte, Blood, 2003a). Thus, we sought to identify genes that could uniquely differentiate childhood BL vs DLBCL and discover potential genetic mechanisms of differential molecular pathogenesis and to determine the signal pathways that contribute to the genetic disparity between these two histological types of childhood B-NHL. Nine BL (7 patient samples and 2 cell lines, Raji and Ramos) and 3 DLBCL (1 patient sample and 2 cell lines, Pfeiffer and DB) were compared. Total RNA was isolated, reverse transcribed to cDNA biotinylated cRNA and hybridized to Affymetrix U133A_2 as we have previously described (Jiang/Cairo et al., Journal of Immunology, 2004). Data were analyzed using Agilent GeneSpring 7.3. Signal intensities were compared using one way ANOVA and Welch Test for statistical analysis. Two-fold changes between BL and DLBCL were considered as significant (p<0.05). KEGG Pathways were evaluated for the genes identified. There were 120 genes over-expressed and 217 genes under-expressed in BL vs DLBCL. BL expressed significantly higher level of Ki-67 (a measure of lymphoma-cell proliferation) than DLBCL (2.68F). BL also expressed higher level of the pro-apoptotic gene, p53 compared to DLBCL (1.46F). Over-expressed genes in BL vs DLBCL included TNFSF10 (11.87F), RHOQ (3.16F), PIP5K1B (5.22F) among many others. The genes significantly under-expressed in BL vs DLBCL included PIGL (0.45F), Inositol (myo)-1 (or 4)-monophosphatase 1 (IMPA1; 0.28F), cAMP-dependent regulatory type I, alpha protein kinase (PRKAR1A; 0.37F) among many others. TNFSF10 induces apoptosis in transformed and tumor cells and is known to participate in pathways including cytokine-cytokine receptor interaction and induction of apoptosis through DR3 and DR4/5 death receptors. PIP5K1B is involved in the Rho signaling pathway and PIGL catalyzes the second step of glycosylphosphatidylinositol (GPI) biosynthesis. Since activation of IL3R-mediated cAMP-dependent protein kinase leads to increased cell survival, we searched gene expression profiles in BL vs DLBCL that were involved in IL signaling pathways. The genes that were identified to be over-expressed in BL vs DLBCL included IL2RG (2.24F), IL8RB, IL18 receptor accessory protein (IL18RAP), IL18, IL18R1, and IL1R2 (natural log values of 11.11, 22.95, 2.16, 1.73 and 11.84, respectively in BL vs non-detectable values in DLBCL). Taken together, since IL1, IL2, IL8, and IL18 all belong to IL1 super family, these results suggest significant involvement of TNF (TRAIL) and IL1 super family via cytokine-cytokine receptor interaction and activation of the Rho signaling pathway in Burkitt vs DLBCL lymphomagenesis.

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RNA-Seq Analysis Identifies Differentially Expressed Genes in Subcutaneous Adipose Tissue in Qaidaford Cattle, Cattle-Yak, and Angus Cattle

Animals ◽

10.3390/ani9121077 ◽

2019 ◽

Vol 9 (12) ◽

pp. 1077 ◽

Cited By ~ 2

Author(s):

Chengchuang Song ◽

Yongzhen Huang ◽

Zhaoxin Yang ◽

Yulin Ma ◽

Buren Chaogetu ◽

...

Keyword(s):

Adipose Tissue ◽

Meat Quality ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Cell Metabolism ◽

Differentially Expressed ◽

Receptor Interaction ◽

Control Group ◽

Rna Seq ◽

Angus Cattle

In the beef industry, fat tissue is closely related to meat quality. In this study, high-throughput RNA sequencing was utilized for adipose tissue transcriptome analysis between cattle-yak, Qaidamford cattle, and Angus cattle. The screening and identification of differentially expressed genes (DEGs) between different breeds of cattle would facilitate cattle breeding. Compared to Angus cattle adipose tissue, a total of 4167 DEGs were identified in cattle-yak adipose tissue and 3269 DEGs were identified in Qaidamford cattle adipose tissue. Considering cattle-yak as a control group, 154 DEGs were identified in Qaidamford cattle adipose tissue. GO analysis indicated the significant enrichment of some DEGs related to lipid metabolism. The KEGG pathway database was also used to map DEGs and revealed that most annotated genes were involved in ECM-receptor interaction and the PI3K-Akt signal pathway, which are closely related to cell metabolism. Eight selected DEGs related to adipose tissue development or metabolism were verified by RT-qPCR, indicating the reliability of the RNA-seq data. The results of this comparative transcriptome analysis of adipose tissue and screening DEGs suggest several candidates for further investigations of meat quality in different cattle breeds.

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Intestinal mucosa-derived DNA methylation signatures in the penetrating intestinal mucosal lesions of Crohn’s disease

Scientific Reports ◽

10.1038/s41598-021-89087-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yuan Li ◽

Zhiming Wang ◽

Xiuwen Wu ◽

Gefei Wang ◽

Guosheng Gu ◽

...

Keyword(s):

Dna Methylation ◽

Extracellular Matrix ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Disease Activity ◽

Signaling Pathways ◽

Intestinal Mucosa ◽

Receptor Interaction ◽

Positive Regulation ◽

Mucosal Lesions

AbstractThe purpose of this study was to evaluate genome-wide DNA methylation changes in intestinal mucosa tissue of adult patients with Crohn's disease comprehensively. DNA methylation chip was used to analyze abnormal methylation sites among penetrating and non-penetrating intestinal mucosa tissue of Crohn's disease and normal intestinal mucosa tissue of healthy controls. Methylation abnormalities of different locus were verified by pyrosequencing and quantitative polymerase chain reaction. Differential DNA methylation sites were participated in the positive regulation of apoptosis and the positive regulation of IL-8 production and were enriched in signaling pathways related to inflammatory bowel disease and extracellular matrix receptor interaction signaling pathways. Correlation analysis showed that the methylation abnormalities of HLA-DRB1 (r = − 0.62, P < 0.001), MUC1 (r = − 0.45, P = 0.01), YPEL5 (r = − 0.55, P = 0.001) and CBLB (r = − 0.62, P < 0.001) were significantly negatively correlated with their relative expression levels. The degree of methylation abnormality of MUC1 was negatively correlated with the disease activity score of Crohn's disease (r = − 0.50, P = 0.01). Apoptosis, interleukin-8 production and abnormal extracellular matrix might be involved in the mechanism of penetrating intestinal mucosal lesions in Crohn's disease. The degree of abnormal methylation of MUC1 was negatively correlated with the disease activity of Crohn's disease.

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The Role of Formyl Peptide Receptor 1 in Uterine Contraction During Parturition

Frontiers in Pharmacology ◽

10.3389/fphar.2021.696697 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chaolu Chen ◽

Shuaiying Zhu ◽

Long Bai ◽

Meihua Sui ◽

Danqing Chen

Keyword(s):

Inflammatory Response ◽

Signaling Pathway ◽

Transcriptome Analysis ◽

Gene Set Enrichment Analysis ◽

Formyl Peptide Receptor ◽

Receptor Interaction ◽

Hub Genes ◽

Peptide Receptor ◽

Formyl Peptide

Parturition involves the transformation of the quiescent myometrium into a highly excitable and contractile state, a process that is driven by changes in myometrial gene expression. This study aimed to identify myometrial transcriptomic signatures and potential novel hub genes in parturition, which have great significance for understanding the underlying mechanisms of successful parturition and treating labor-associated pathologies such as preterm birth. In our study, comparative transcriptome analysis was carried out on human myometrial tissues collected from women undergoing caesarean section at term in the presence (TL = 8) and absence of labor (TNL = 8). A total of 582 differentially expressed genes (DEGs) between TL and TNL tissues were identified. Gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG) and gene set enrichment analysis (GSEA) revealed that the DEGs were enriched in signal transduction, regulation of signaling receptor activity, inflammatory response, cytokine-cytokine receptor interaction, IL-17 signaling pathway, TNF signaling pathway, among others. Thus, transcriptome analysis of the myometrium during term labor revealed that labor onset was associated with an inflammatory response. Moreover, protein-protein interactions network analysis identified FPR1, CXCL8, CXCL1, BDKRB2, BDKRB1, and CXCL2 as the hub genes associated with onset of labor. Formyl peptide receptor 1 (FPR1) was highly expressed in laboring myometrial tissues, with the activation of FPR1 in vitro experiments resulting in increased myometrial contraction. Our findings demonstrate the novel role of FPR1 as a modulator of myometrial contraction.

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Comparative transcriptome analysis reveals that the extracellular matrix receptor interaction contributes to the venous metastases of hepatocellular carcinoma

Cancer Genetics ◽

10.1016/j.cancergen.2015.06.002 ◽

2015 ◽

Vol 208 (10) ◽

pp. 482-491 ◽

Cited By ~ 27

Author(s):

Hong Zhang ◽

Junyi Ye ◽

Xiaoling Weng ◽

Fatao Liu ◽

Lin He ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Extracellular Matrix ◽

Transcriptome Analysis ◽

Receptor Interaction ◽

Comparative Transcriptome ◽

Comparative Transcriptome Analysis

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Transcriptome Analysis Revealed Ameliorative Effects of Bacillus Based Probiotic on Immunity, Gut Barrier System, and Metabolism of Chicken under an Experimentally Induced Eimeria tenella Infection

Genes ◽

10.3390/genes12040536 ◽

2021 ◽

Vol 12 (4) ◽

pp. 536

Author(s):

Fareed Uddin Memon ◽

Yunqiao Yang ◽

Imdad Hussain Leghari ◽

Feifei Lv ◽

Ahmed M. Soliman ◽

...

Keyword(s):

Signaling Pathway ◽

Transcriptome Analysis ◽

Group Versus ◽

Mapk Signaling ◽

Positive Control ◽

Eimeria Tenella ◽

Mitogen Activated Protein Kinase ◽

Receptor Interaction ◽

Gut Barrier ◽

Barrier Integrity

In this study, we performed transcriptome analysis in the cecum tissues of negative control untreated non-challenged (NC), positive control untreated challenged (PC), and Bacillus subtilis (B. subtilis) fed challenged chickens (BS + ET) in order to examine the underlying potential therapeutic mechanisms of Bacillus based probiotic feeding under an experimental Eimeria tenella (E. tenella) infection. Our results for clinical parameters showed that birds in probiotic diet decreased the bloody diarrhea scores, oocyst shedding, and lesion scores compared to positive control birds. RNA-sequencing (RNA-seq) analysis revealed that in total, 2509 up-regulated and 2465 down-regulated differentially expressed genes (DEGs) were detected in the PC group versus NC group comparison. In the comparison of BS + ET group versus PC group, a total of 784 up-regulated and 493 down-regulated DEGs were found. Among them, several DEGs encoding proteins involved in immunity, gut barrier integrity, homeostasis, and metabolism were up-regulated by the treatment of probiotic. Functional analysis of DEGs also revealed that some gene ontology (GO) terms related with immunity, metabolism and cellular development were significantly affected by the exposure of probiotic. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that the DEGs in the cecum of B. subtilis-fed challenged group were mainly participated in the pathways related with immunity and gut barrier integrity, included mitogen-activated protein kinase (MAPK) signaling pathway, toll-like receptor (TLR) signaling pathway, extracellular matrix (ECM)–receptor interaction, tight junction, and so on. Taken together, these results suggest that Bacillus based probiotic modulate the immunity, maintain gut homeostasis as well as barrier system and improve chicken metabolism during E. tenella infection.

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Transcriptome analysis identifies signaling pathways related to meat quality in broiler chickens – the ECM receptor interaction signaling pathway

10.21203/rs.3.rs-32669/v1 ◽

2020 ◽

Author(s):

Yanting Du ◽

Jishuang San ◽

Gaofeng Wu ◽

Rifeng Xu ◽

Jiancheng Yang ◽

...

Keyword(s):

Meat Quality ◽

Broiler Chickens ◽

Molecular Mechanisms ◽

Chicken Meat ◽

Receptor Interaction ◽

Gene Pools ◽

Lipid Uptake ◽

Rna Seq ◽

Transmembrane Receptors ◽

Total Muscle

Abstract Background Meat quality characteristics, including juiciness, flavor, and tenderness, can be mostly attributed to the total muscle fat content, intramuscular fat (IMF), and the composition of its fatty acids (FAs), which are regulated by the balance between lipid uptake, transport, synthesis, and subsequent metabolism, involving many genes and pathways. However, the detailed molecular mechanisms remain unclear. Results The present study reports the RNA-sequencing (RNA-seq) analysis of chest muscle and leg muscle tissue of the Zhuanghe dagu chicken (ZD chicken) and the Arbor Acres Broiler chicken (AA chicken). We identified certain differentially expressed genes that affect IMF deposition , such as EHHADH , TECRL , NDUFAB1 , PCCB , and HIBCH , which were upregulated in ZD chickens, and GCDH , TPI1 , ABHD13 , PSMC1 , MYST2 , and FBXO11 , which were upregulated in AA chickens. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes indicated that the extracellular matrix (ECM)–receptor interaction pathway is co-enriched in both tissues, and forms a sub-pathway of other enriched pathways. Intriguingly, the ECM–receptor interaction pathway genes are regulated differently in different gene pools. Collagens, which are main ECM constituents, and laminin and integrinβ1 transmembrane receptors were significantly downregulated in both tissues of the AA chicken. Conclusions RNA-seq analysis of two tissues from two breeds of chicken hinted that interactions between transmembrane receptors and ECM components of fat cells affect breed-specific adipogenesis, which would affect quality and flavor of chicken meat. These findings will contribute to improving the quality attributes of chicken meat.

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Transcriptome Analysis Reveals Impaired Fertility and Immunity Under Salinity Exposure in Juvenile Grass Carp

Frontiers in Marine Science ◽

10.3389/fmars.2021.697813 ◽

2021 ◽

Vol 8 ◽

Author(s):

Jingjing Zhang ◽

Zhi Wu ◽

Yujie He ◽

Xinhui Li ◽

Jie Li

Keyword(s):

Signaling Pathway ◽

Transcriptome Analysis ◽

Grass Carp ◽

Enrichment Score ◽

Receptor Interaction ◽

Receptor Signaling ◽

Steroid Biosynthesis ◽

Kegg Pathways ◽

Risk Of Death ◽

Receptor Signaling Pathway

Grass carp (Ctenopharyngodon idellus) is one of the most economically important aquaculture species and is widely cultured in China. However, its wild populations in many rivers are increasingly declining, and seawater intrusion is one of the most important threats to their survival. However, the mechanisms underlying the decline due to salinity pressure are still unknown. Here, we performed a comparative transcriptome analysis of C. idellus larvae in response to salinity exposures; a total of 481 differentially expressed genes (DEGs) were identified. These DEGs were significantly enriched in eight Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, among which steroid biosynthesis was the most important one, with the highest enrichment score. The pathway plays an important role in the development of the testes and ovary. Interestingly, all DEGs in steroid biosynthesis showed a down regulation, indicating that salinity exposure may pose damage to the fertility of C. idellus. Furthermore, three immunity-associated pathways (cytokine–cytokine receptor interaction, Toll-like receptor signaling pathway, and NOD-like receptor signaling pathway) were also significantly enriched, suggesting impaired immunity and a high risk of disease infection under salinity exposure. Overall, damage to both fertility and immunity would decrease the number of offspring and increase the risk of death due to disease infection. Our results provide a potential molecular mechanism underlying the decline of wild C. idellus populations in the Pearl River.

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Transcriptome Analysis in the Head Kidney of Rainbow Trout (Oncorhynchus mykiss) Immunized with a Combined Vaccine of Formalin-Inactivated Aeromonas salmonicida and Vibrio anguillarum

Vaccines ◽

10.3390/vaccines9111234 ◽

2021 ◽

Vol 9 (11) ◽

pp. 1234

Author(s):

Jongwon Lim ◽

Suhee Hong

Keyword(s):

Rainbow Trout ◽

Signaling Pathway ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Vibrio Anguillarum ◽

Enrichment Analysis ◽

Aeromonas Salmonicida ◽

Coagulation Cascade ◽

Receptor Interaction ◽

Combined Vaccine

This study aimed to identify the molecular mechanisms regulated by a combined vaccine against Aeromonas salmonicida and Vibrio anguillarum (O1 serotype). These bacteria cause furunculosis and vibriosis, respectively, and are associated with a high mortality in rainbow trout in Korea. The vaccine upregulated gene expression of TCRα, T-bet, sIgM, and mIgM, markers of an activated adaptive immune response. On days 1, 3, and 5, transcriptome analysis revealed 862 (430 up- and 432 downregulated), 492 (204 up- and 288 downregulated), and 741 (270 up- and 471 downregulated) differentially expressed genes (DEGs), respectively. Gene ontology (GO) enrichment analysis identified 377 (108 MF, 132 CC, 137 BP), 302 (60 MF, 180 CC, 62 BP), and 314 (115 MF, 129 CC, 70 BP) GOs at days 1, 3, and 5, respectively. Kyoto Encyclopedia of Genetic and Genomic enrichment analysis identified eight immune system-related pathways like cytokine-cytokine receptor interaction, NF-kappaB signaling pathway, TNF signaling pathway, NOD-like receptor signaling pathway, cytosolic DNA sensing pathway, cell adhesion molecule, complement and coagulation cascade, and antigen processing and presentation. In the analysis of the protein–protein interaction of immune-related DEGs, a total of 59, 21, and 21 interactional relationships were identified at days 1, 3, and 5, respectively, with TNF having the highest centrality at all three time points.

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