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

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.

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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.

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Pectoral muscle transcriptome analyses reveal high-altitude adaptations in Tibetan chickens

Animal Biology ◽

10.1163/15707563-bja10026 ◽

2020 ◽

Vol 70 (4) ◽

pp. 385-400

Author(s):

Yaodong Hu ◽

Jiayu Su ◽

Liyuan Cheng ◽

Dan Lan ◽

Diyan Li

Keyword(s):

High Altitude ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Pectoral Muscle ◽

Mapk Signaling ◽

Differentially Expressed ◽

Future Research ◽

Protein Coding ◽

Sequencing Technologies ◽

Tibetan Chicken

Abstract The largest muscles in fowl are the pectorals, which provide the power required for birds to fly. Tibetan chickens show specific adaptations to high-altitude conditions, but changes in the muscle transcriptome associated with these adaptations have not been characterized yet. Therefore, in this study, we used next-generation sequencing technologies to generate eight libraries of mRNA sequences for four Tibetan chickens and four Beijing fatty chickens. A comprehensive transcriptome analysis was performed. In the eight samples, 12 333 annotated protein-coding genes were expressed. Among these, 48 differentially expressed genes were found; all of which were upregulated in Tibetan chickens. These differentially expressed genes were mainly involved in kidney morphogenesis, which indicates that hypoxia has an important effect on renal tubule development. Only nine genes were involved in Kyoto Encyclopedia of Genes and Genomes pathways, such as the endocytosis pathway, the MAPK signaling pathway, the calcium signaling pathway and the TGF-beta signaling pathway. The differentially expressed genes identified in this study will be used to facilitate future research into the Tibetan chicken.

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Identification of Circulating lncRNA Expression Profiles in Patients with Atrial Fibrillation

Disease Markers ◽

10.1155/2020/8872142 ◽

2020 ◽

Vol 2020 ◽

pp. 1-8

Author(s):

Zhong-bao Ruan ◽

Fei Wang ◽

Bing-di Gongben ◽

Ge-cai Chen ◽

Li Zhu

Keyword(s):

Atrial Fibrillation ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Peripheral Blood ◽

Rna Binding ◽

Expression Profiles ◽

Differentially Expressed ◽

Receptor Interaction ◽

Molecular Function ◽

Rt Pcr

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.

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Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White pigs

BMC Genomics ◽

10.1186/s12864-020-07361-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Dawei Zhang ◽

Wenjing Wu ◽

Xin Huang ◽

Ke Xu ◽

Cheng Zheng ◽

...

Keyword(s):

Signaling Pathway ◽

Differentially Expressed Genes ◽

Expression Profiles ◽

Subcutaneous Fat ◽

Mapk Signaling ◽

Fat Deposition ◽

Differentially Expressed ◽

Rna Seq ◽

Large White ◽

Pig Breeds

Abstract Background Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of subcutaneous fat tissue is necessary for the rational selection of Chinese domestic pig breeds. In the present study, subcutaneous adipocytes were isolated from Jiaxing Black pigs a Chinese indigenous pig breed with redundant subcutaneous fat deposition and Large White pigs a lean-type pig breed with relatively low subcutaneous fat deposition. The expression profiles of mRNAs and lncRNAs were compared by RNA-seq analysis to identify biomarkers correlated with the differences of subcutaneous fat deposition between the two breeds. Results A total of 1058 differentially expressed genes and 221 differentially expressed lncRNAs were identified in subcutaneous adipocytes between Jiaxing Black and Large White pigs, which included 275 up-regulated mRNAs, 783 down-regulated mRNAs, 118 up-regulated lncRNAs and 103 down-regulated lncRNAs. Gene Ontology and KEGG pathway enrichment analyses revealed that the differentially expressed genes and differentially expressed lncRNAs were mainly involved in the immune response, cell fate determination, PI3K-Akt signaling pathway and MAPK signaling pathway, which are known to be related to adipogenesis and lipid metabolism. The expression levels of differentially expressed genes and differentially expressed lncRNAs according to the RNA-seq data were verified by quantitative PCR, which showed 81.8% consistency. The differences in MAPK pathway activity between Jiaxing Black and Large White pigs was confirmed by western blot analysis, which revealed elevated p38 phosphorylation in Jiaxing Black pigs. Conclusions This study offers a detailed characterization of mRNAs and lncRNAs in fat- and lean-type pig breeds. The activity of the MAPK signaling pathway was found to be associated with subcutaneous adipogenesis. These results provide new targets for further investigation of the molecular mechanisms regulating subcutaneous fat deposition in pigs.

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Berberine ameliorates vascular dysfunction by a global modulation of lncRNA and mRNA expression profiles in hypertensive mouse aortae

PLoS ONE ◽

10.1371/journal.pone.0247621 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0247621

Author(s):

Na Tan ◽

Yi Zhang ◽

Yan Zhang ◽

Li Li ◽

Yi Zong ◽

...

Keyword(s):

Signaling Pathway ◽

Differentially Expressed Genes ◽

Microarray Data ◽

Vascular Function ◽

Expression Profiles ◽

Vascular Endothelial Cell ◽

Differentially Expressed ◽

Therapeutic Effects ◽

Endothelial Cell Function ◽

Qrt Pcr

Objective The current study investigated the mechanism underlying the therapeutic effects of berberine in the vasculature in hypertension. Methods Angiotensin II (Ang II)-loaded osmotic pumps were implanted in C57BL/6J mice with or without berberine administration. Mouse aortae were suspended in myograph for force measurement. Microarray technology were performed to analyze expression profiles of lncRNAs and mRNAs in the aortae. These dysregulated expressions were then validated by qRT-PCR. LncRNA-mRNA co-expression network was constructed to reveal the specific relationships. Results Ang Ⅱ resulted in a significant increase in the blood pressure of mice, which was suppressed by berberine. The impaired endothelium-dependent aortic relaxation was restored in hypertensive mice. Microarray data revealed that 578 lncRNAs and 554 mRNAs were up-regulated, while 320 lncRNAs and 377 mRNAs were down-regulated in the aortae by Ang Ⅱ; both were reversed by berberine treatment. qRT-PCR validation results of differentially expressed genes (14 lncRNAs and 6 mRNAs) were completely consistent with the microarray data. GO analysis showed that these verified differentially expressed genes were significantly enriched in terms of “cellular process”, “biological regulation” and “regulation of biological process”, whilst KEGG analysis identified vascular function-related pathways including cAMP signaling pathway, cGMP-PKG signaling pathway, and calcium signaling pathway etc. Importantly, we observed that lncRNA ENSMUST00000144849, ENSMUST00000155383, and AK041185 were majorly expressed in endothelial cells. Conclusion The present results suggest that the five lncRNAs ENSMUST00000144849, NR_028422, ENSMUST00000155383, AK041185, and uc.335+ might serve critical regulatory roles in hypertensive vasculature by targeting pivotal mRNAs and subsequently affecting vascular function-related pathways. Moreover, these lncRNAs were modulated by berberine, therefore providing the novel potential therapeutic targets of berberine in hypertension. Furthermore, lncRNA ENSMUST00000144849, ENSMUST00000155383, and AK041185 might be involved in the preservation of vascular endothelial cell function.

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Faculty Opinions recommendation of Physcomitrella patens auxin-resistant mutants affect conserved elements of an auxin-signaling pathway.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.5704956.5686057 ◽

2010 ◽

Author(s):

Jiri Friml ◽

Steffen Vanneste

Keyword(s):

Signaling Pathway ◽

Physcomitrella Patens ◽

Auxin Signaling ◽

Auxin Signaling Pathway ◽

Resistant Mutants

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Salidroside promoted osteogenic differentiation of adipose-derived stromal cells through Wnt/β-catenin signaling pathway

Journal of Orthopaedic Surgery and Research ◽

10.1186/s13018-021-02598-w ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Xiao-hua Li ◽

Fu-ling Chen ◽

Hong-lin Shen

Keyword(s):

Western Blot ◽

Osteogenic Differentiation ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Stromal Cells ◽

Differentially Expressed ◽

Calcium Deposition ◽

Western Blot Assay ◽

Adipose Derived Stromal Cells ◽

Interfering Rna

Abstract Background Bone disease causes short-term or long-term physical pain and disability. It is necessary to explore new drug for bone-related disease. This study aimed to explore the role and mechanism of Salidroside in promoting osteogenic differentiation of adipose-derived stromal cells (ADSCs). Methods ADSCs were isolated and treated with different dose of Salidroside. Cell count kit-8 (CCK-8) assay was performed to assess the cell viability of ADSCs. Then, ALP and ARS staining were conducted to assess the early and late osteogenic capacity of ADSCs, respectively. Then, differentially expressed genes were obtained by R software. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the differentially expressed genes were further analyzed. The expression of OCN, COL1A1, RUNX2, WNT3A, and β-catenin were measured by real-time PCR and Western blot analysis. Last, β-catenin was silenced by small interfering RNA. Results Salidroside significantly increased the ADSCs viability at a dose-response manner. Moreover, Salidroside enhanced osteogenic capacity of ADSCs, which are identified by enhanced ALP activity and calcium deposition. A total of 543 differentially expressed genes were identified between normal and Salidroside-treated ADSCs. Among these differentially expressed genes, 345 genes were upregulated and 198 genes were downregulated. Differentially expressed genes enriched in the Wnt/β-catenin signaling pathway. Western blot assay indicated that Salidroside enhanced the WNT3A and β-catenin expression. Silencing β-catenin partially reversed the promotion effects of Salidroside. PCR and Western blot results further confirmed these results. Conclusion Salidroside promoted osteogenic differentiation of ADSCs through Wnt/β-catenin signaling pathway.

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HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽

10.3390/v13020244 ◽

2021 ◽

Vol 13 (2) ◽

pp. 244 ◽

Cited By ~ 1

Author(s):

Antonio Victor Campos Coelho ◽

Rossella Gratton ◽

João Paulo Britto de Melo ◽

José Leandro Andrade-Santos ◽

Rafael Lima Guimarães ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Differentially Expressed Genes ◽

Cd4 T Cells ◽

Expression Profiles ◽

Meta Analysis ◽

Differentially Expressed ◽

Rna Seq ◽

Infected Cells ◽

Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

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The role of ferroptosis in breast cancer patients: a comprehensive analysis

Cell Death Discovery ◽

10.1038/s41420-021-00473-5 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Zeng-Hong Wu ◽

Yun Tang ◽

Hong Yu ◽

Hua-Dong Li

Keyword(s):

Breast Cancer ◽

T Cell ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Function Analysis ◽

Cancer Prognosis ◽

Differentially Expressed ◽

Immune Checkpoints ◽

Cell Functions

AbstractBreast cancer (BC) affects the breast tissue and is the second most common cause of mortalities among women. Ferroptosis is an iron-dependent cell death mode that is characterized by intracellular accumulation of reactive oxygen species (ROS). We constructed a prognostic multigene signature based on ferroptosis-associated differentially expressed genes (DEGs). Moreover, we comprehensively analyzed the role of ferroptosis-associated miRNAs, lncRNAs, and immune responses. A total of 259 ferroptosis-related genes were extracted. KEGG function analysis of these genes revealed that they were mainly enriched in the HIF-1 signaling pathway, NOD-like receptor signaling pathway, central carbon metabolism in cancer, and PPAR signaling pathway. Fifteen differentially expressed genes (ALOX15, ALOX15B, ANO6, BRD4, CISD1, DRD5, FLT3, G6PD, IFNG, NGB, NOS2, PROM2, SLC1A4, SLC38A1, and TP63) were selected as independent prognostic factors for BC patients. Moreover, T cell functions, including the CCR score, immune checkpoint, cytolytic activity, HLA, inflammation promotion, para-inflammation, T cell co-stimulation, T cell co-inhibition, and type II INF responses were significantly different between the low-risk and high-risk groups of the TCGA cohort. Immune checkpoints between the two groups revealed that the expressions of PDCD-1 (PD-1), CTLA4, LAG3, TNFSF4/14, TNFRSF4/8/9/14/18/25, and IDO1/2 among others were significantly different. A total of 1185 ferroptosis-related lncRNAs and 219 ferroptosis-related miRNAs were also included in this study. From the online database, we identified novel ferroptosis-related biomarkers for breast cancer prognosis. The findings of this study provide new insights into the development of new reliable and accurate cancer treatment options.

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