LRRFIP2 modulates the response to hypoxia during embryonic cardiogenesis

Oxygen is crucial for appropriate embryonic and fetal development, including cardiogenesis. The heart is the first organ formed in the embryo and is required to provide oxygen and nutrients to all cells in the body. Embryonic cardiogenesis is a complex process finely regulated and prone to congenital malformations. It takes place in a hypoxic environment that activates the HIF-1a; signaling pathway which mediates cellular and systemic adaptations to low oxygen levels. Since inhibition or overactivation of the HIF-1a; signaling pathway in the myocardium lead to severe cardiac malformations and embryonic lethality, it is important that the cellular response to hypoxia be precisely regulated. While many gene regulatory networks involved in embryonic cardiogenesis have been characterized in detail, the modulation of the response of cardiomyocytes (CM) to hypoxia has remained less studied. We identified LRRFIP2 as a new negative cofactor of HIF-1a;. Indeed, we have shown that the absence of Lrrfip2 expression in a mouse KI model led to an enhance of many HIF-1a; target genes including Igfbp3, Bnip3 and Ndufa4l2 in embryonic CM during development. As results, the absence of Lrrfip2 led to the inhibition of the PI3K/Akt survival pathway, growth defects, mitochondrial dysfunction and to a precocious maturation of the embryonic CMs. Altogether, these defects led to the formation of a smaller heart unable to provide sufficient oxygen to the embryo and finally to a severe hypoxia and a precocious lethality.

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Identification of transcription factors MYC and C/EBPβ mediated regulatory networks in heart failure based on GEO dataset

10.21203/rs.2.16967/v2 ◽

2020 ◽

Author(s):

Haiwei Wang ◽

Xinrui Wang ◽

Liangpu Xu ◽

Hua Cao

Keyword(s):

Heart Failure ◽

Transcription Factors ◽

Signaling Pathways ◽

Signaling Pathway ◽

Insulin Signaling ◽

Regulatory Networks ◽

Target Genes ◽

Transcriptional Profiling ◽

Insulin Signaling Pathway ◽

Failing Heart

Abstract Background: Heart failure is one of leading cause of death worldwide. However, the transcriptional profiling of heart failure is unclear. Moreover, the signaling pathways and transcription factors involving the heart failure development also are largely unknown. Using published Gene Expression Omnibus (GEO) datasets, in the present study, we aim to comprehensively analyze the differentially expressed genes in failing heart tissues, and identified the critical signaling pathways and transcription factors involving heart failure development. Methods: The transcriptional profiling of heart failure was identified from previously published gene expression datasets deposited in GSE5406, GSE16499 and GSE68316. The enriched signaling pathways and transcription factors were analyzed using DAVID website and gene set enrichment analysis (GSEA) assay. The transcriptional networks were created by Cytoscape. Results: Compared with the normal heart tissues, 90 genes were particularly differentially expressed in failing heart tissues, and those genes were associated with multiple metabolism signaling pathways and insulin signaling pathway. Metabolism and insulin signaling pathway were both inactivated in failing heart tissues. Transcription factors MYC and C/EBPβ were both negatively associated with the expression profiling of failing heart tissues in GSEA assay. Moreover, compared with normal heart tissues, MYC and C/EBPβ were down regulated in failing heart tissues. Furthermore, MYC and C/EBPβ mediated downstream target genes were also decreased in failing heart tissues. MYC and C/EBPβ were positively correlated with each other. At last, we constructed MYC and C/EBPβ mediated regulatory networks in failing heart tissues, and identified the MYC and C/EBPβ target genes which had been reported involving the heart failure developmental progress. Conclusions: Our results suggested that metabolism pathways and insulin signaling pathway, transcription factors MYC and C/EBPβ played critical roles in heart failure developmental progress.

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miR-20b-5p attenuates hypoxia-induced apoptosis in cardiomyocytes via the HIF-1α/NF-κB pathway

Acta Biochimica et Biophysica Sinica ◽

10.1093/abbs/gmaa056 ◽

2020 ◽

Vol 52 (9) ◽

pp. 927-934 ◽

Cited By ~ 1

Author(s):

Zhongquan Zhou ◽

Songwen Chen ◽

Zhiming Tian ◽

Shibing Deng ◽

Xuying Yi ◽

...

Keyword(s):

Flow Cytometry ◽

Signaling Pathway ◽

Cell Apoptosis ◽

Target Genes ◽

Annexin V ◽

Pcr Analysis ◽

H9c2 Cell ◽

H9c2 Cells ◽

Flow Cytometry Analysis ◽

Low Oxygen

Abstract Chronic hypoxia is a common inducer of end-stage cardiovascular disease. In cells under hypoxia, the hypoxia-inducible factor-1 (HIF-1) plays a vital role in regulating downstream target genes. However, the mechanism of hypoxia in cardiomyocytes is still unclear. In this study, we aimed to identify novel downstream epigenetic targets of HIF-1α in cardiomyocytes under hypoxia. H9c2 cells were exposed to hypoxia condition, and quantitative real-time PCR analysis was performed to evaluate the expression of miR-20b-5p. The results indicated that the expression of miR-20b-5p was down-regulated in H9c2 cells under low oxygen condition. Meanwhile, HIF-1α overexpression further down-regulated the miR-20b-5p expression in H9c2 cells transfected with HIF-1α plasmids. In addition, Annexin-V-FITC/PI flow cytometry analysis suggested that overexpression of miR-20b-5p attenuated cell apoptosis under hypoxia condition in H9c2 cells. Western blot analysis showed that the hypoxia apparently increased Bax and cleaved-caspase-3, but decreased Bcl-2 expression in H9c2 cells, indicating that hypoxia-induced NF-κB signaling pathway activation is mediated by miR-20b-5p. Hypoxia-induced H9c2 cell apoptosis was reduced after HIF-1α knockdown as shown by the flow cytometry analysis. In conclusion, we identified that miR-20b-5p plays an important role in mediating cardiomyocytes apoptosis under hypoxia, which is mediated by the HIF-1/NF-κB signaling pathway.

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Identification of transcription factors MYC and C/EBPβ mediated regulatory networks in heart failure

10.21203/rs.2.16967/v1 ◽

2019 ◽

Author(s):

Haiwei Wang ◽

Xinrui Wang ◽

Liangpu Xu ◽

Hua Cao

Keyword(s):

Heart Failure ◽

Transcription Factor ◽

Transcription Factors ◽

Signaling Pathway ◽

Insulin Signaling ◽

Regulatory Networks ◽

Target Genes ◽

Transcriptional Profiling ◽

Normal Heart ◽

Developmental Progress

Abstract Background: Heart failure is one of leading cause of death worldwide. However, the transcriptional profiling of heart failure is unclear. Moreover, the signaling pathways and transcription factors involving the heart failure developmental progress also are largely unclear.Methods: The transcriptional profiling of heart failure was identified from integrated gene expression datasets. The enriched pathways and transcription factors were analyzed using DAVID and GSEA assay. The transcriptional networks were created by Cytoscape.Results: Compared with the normal heart tissues, we found 90 genes were particularly differentially expressed in heart failing tissues, and those genes were associated with multiple metabolism pathways and insulin signaling pathway. Metabolism and insulin signaling pathway were both inactivated in heart failing tissues. Transcription factors MYC and C/EBPβ were both negatively associated with the expression profiling of heart failing tissues in GSEA assay. Moreover, compared with normal heart tissues, MYC and C/EBPβ were down regulated in heart failing tissues. Furthermore, MYC and C/EBPβ mediated downstream target genes were decreased in heart failing tissues. MYC and C/EBPβ were positively correlated with each other. At last, we constructed the transcription factor MYC and C/EBPβ mediated regulatory networks in heart failing tissues, and identified the MYC and C/EBPβ target genes which had been reported involving the failure developmental progress by literature research. Conclusions: Our results suggested that transcription factor MYC and C/EBPβ played critical roles in heart failure developmental progress. And new heart failure treatments may be developed by targeting MYC and C/EBPβ.

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Hypoxic Regulation of Gene Transcription and Chromatin: Cause and Effect

International Journal of Molecular Sciences ◽

10.3390/ijms21218320 ◽

2020 ◽

Vol 21 (21) ◽

pp. 8320

Author(s):

Jessica D. Kindrick ◽

David R. Mole

Keyword(s):

Transcriptional Activation ◽

Cellular Response ◽

Target Genes ◽

Hypoxia Inducible Factor ◽

Transcriptional Response ◽

Epigenetic Landscape ◽

Low Oxygen ◽

Epigenetic Modifiers ◽

Oxygen Sensitive ◽

Cell Type Specific

Cellular responses to low oxygen (hypoxia) are fundamental to normal physiology and to the pathology of many common diseases. Hypoxia-inducible factor (HIF) is central to this by enhancing the transcriptional activity of many hundreds of genes. The cellular response to HIF is cell-type-specific and is largely governed by the pre-existing epigenetic landscape. Prior to activation, HIF-binding sites and the promoters of HIF-target genes are already accessible, in contact with each other through chromatin looping and display markers of activity. However, hypoxia also modulates the epigenetic environment, both in parallel to and as a consequence of HIF activation. This occurs through a combination of oxygen-sensitive changes in enzyme activity, transcriptional activation of epigenetic modifiers, and localized recruitment to chromatin by HIF and activated RNApol2. These hypoxic changes in the chromatin environment may both contribute to and occur as a consequence of transcriptional regulation. Nevertheless, they have the capacity to both modulate and extend the transcriptional response to hypoxia.

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Hypoxic microenvironment shapes HIV-1 replication and latency

Communications Biology ◽

10.1038/s42003-020-1103-1 ◽

2020 ◽

Vol 3 (1) ◽

Cited By ~ 2

Author(s):

Xiaodong Zhuang ◽

Isabela Pedroza-Pacheco ◽

Isabel Nawroth ◽

Anna E. Kliszczak ◽

Andrea Magri ◽

...

Keyword(s):

Cellular Response ◽

Lymphoid Tissues ◽

Low Oxygen ◽

Hiv Replication ◽

Hypoxic Environment ◽

Key Factor ◽

Direct Binding ◽

Latent Hiv ◽

Hiv 1

AbstractViral replication is defined by the cellular microenvironment and one key factor is local oxygen tension, where hypoxia inducible factors (HIFs) regulate the cellular response to oxygen. Human immunodeficiency virus (HIV) infected cells within secondary lymphoid tissues exist in a low-oxygen or hypoxic environment in vivo. However, the majority of studies on HIV replication and latency are performed under laboratory conditions where HIFs are inactive. We show a role for HIF-2α in restricting HIV transcription via direct binding to the viral promoter. Hypoxia reduced tumor necrosis factor or histone deacetylase inhibitor, Romidepsin, mediated reactivation of HIV and inhibiting HIF signaling-pathways reversed this phenotype. Our data support a model where the low-oxygen environment of the lymph node may suppress HIV replication and promote latency. We identify a mechanism that may contribute to the limited efficacy of latency reversing agents in reactivating HIV and suggest new strategies to control latent HIV-1.

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Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

Frontiers in Immunology ◽

10.3389/fimmu.2020.618687 ◽

2021 ◽

Vol 11 ◽

Author(s):

Min Cao ◽

Xu Yan ◽

Baofeng Su ◽

Ning Yang ◽

Qiang Fu ◽

...

Keyword(s):

Signaling Pathways ◽

Signaling Pathway ◽

Regulatory Networks ◽

Target Genes ◽

Differentially Expressed ◽

Edwardsiella Tarda ◽

Circular Rnas ◽

Integrated Analysis ◽

Apoptosis Pathway ◽

Sebastes Schlegelii

Sebastes schlegelii, an important aquaculture species, has been widely cultured in East Asian countries. With the increase in the cultivation scale, various diseases have become major threats to the industry. Evidence has shown that non-coding RNAs (ncRNAs) have remarkable functions in the interactions between pathogens and their hosts. However, little is known about the mechanisms of circular RNAs (circRNAs) and coding RNAs in the process of preventing pathogen infection in the intestine in teleosts. In this study, we aimed to uncover the global landscape of mRNAs, circRNAs, and microRNAs (miRNAs) in response to Edwardsiella tarda infection at different time points (0, 2, 6, 12, and 24 h) and to construct regulatory networks for exploring the immune regulatory mechanism in the intestine of S. schlegelii. In total, 1,794 mRNAs, 87 circRNAs, and 79 miRNAs were differentially expressed. The differentially expressed RNAs were quantitatively validated using qRT-PCR. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most of the differentially expressed mRNA genes and the target genes of ncRNAs were related to immune signaling pathways, such as the NF-κB signal pathway, pathogen recognition receptors related to signaling pathways (Toll-like receptors and Nod-like receptors), and the chemokine signaling pathway. Based on these differentially expressed genes, 624 circRNA-miRNA pairs and 2,694 miRNA-mRNA pairs were predicted using the miRanda software. Integrated analyses generated 25 circRNA-miRNA-mRNA interaction networks. In a novel_circ_0004195/novel-530/IκB interaction network, novel_530 was upregulated, while its two targets, novel_circ_0004195 and IκB, were downregulated after E. tarda infection. In addition, two circRNA-miRNA-mRNA networks related to apoptosis (novel_circ_0003210/novel_152/apoptosis-stimulating of p53 protein 1) and interleukin (novel_circ_0001907/novel_127/interleukin-1 receptor type 2) were also identified in our study. We thus speculated that the downstream NF-κB signaling pathway, p53 signaling pathway, and apoptosis pathway might play vital roles in the immune response in the intestine of S. schlegelii. This study revealed a landscape of RNAs in the intestine of S. schlegelii during E. tarda infection and provided clues for further study on the immune mechanisms and signaling networks based on the circRNA-miRNA-mRNA axis in S. schlegelii.

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An in-depth analysis of the intestinal microbiome & metabolites of rats under high-altitude hypoxic-condition

10.21203/rs.3.rs-22784/v1 ◽

2020 ◽

Author(s):

Sicong Su ◽

Weili Liu ◽

Yu Liang ◽

Zhigang Qiu ◽

Shang Wang ◽

...

Keyword(s):

The Body ◽

Metagenomic Sequencing ◽

Low Oxygen ◽

Targeted Metabolomics ◽

Intestinal Microbes ◽

Oxygen Environment ◽

Intestinal Microorganisms ◽

Hypoxic Environment ◽

Significant Difference ◽

Depth Analysis

Abstract Background Under anoxic conditions, the body will undergo a series of changes to compensate for the low oxygen environment. Changes in gut microbes are an important part of this. Currently, there are relatively few studies on the changes of intestinal microorganisms and metabolites in the low-oxygen environment of plateau. This study employed a non-targeted metabolomics approach coupled with shotgun metagenomic sequencing to analysis the changes of intestinal microorganisms and metabolites in rats under hypoxic environment. Results Significant difference in biodiversity were observed. At the genus level, the relative abundance of Lactobacillus, Alistipes in the hypoxic cohort were significantly increased, while Flavonifractor, Faecalibacterium and Dorea were significantly decreased(P < 0.05). Non-targeted metabolomics analysis showed significant differences in 4 metabolic pathways (pyrimidine metabolism, aminoacyl-tRNA biosynthesis, nicotinate and nicotinamide metabolism, thyroid hormone synthesis) between T group and C group (P < 0.05). Furthermore, correlation analysis of metagenomic and metabolomic data sets showed that there was a certain relative quantitative relationship between some bacterial genera and differential metabolites. Conclusions Our results indicate that a plateau hypoxic environment can significantly alter the composition of intestinal microbes in the host.Compared with the plain control group, the relative increase of some bacteria genera was accompanied by the increase of related metabolites, suggesting that these bacteria genera and metabolites were closely related to the low-oxygen environment in the plateau.It provides a certain foundation for the next research.

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Analysis of deep sequencing Exosome-microRNA expression profile from Chicken Type Ⅱ Pneumocytes derived reveals potential role of gga-miRNA-451 in inflammation

10.21203/rs.2.17460/v1 ◽

2019 ◽

Author(s):

Yabo Zhao ◽

Yali Fu ◽

Mengyun Zou ◽

Yingfei Sun ◽

Xun Yin ◽

...

Keyword(s):

Signaling Pathway ◽

Target Genes ◽

Chicken Embryo Fibroblast ◽

Chronic Respiratory Disease ◽

Mapk Signaling ◽

The Body ◽

Protective Effects ◽

Exosomal Mirnas ◽

Study Results ◽

And Function

Abstract Background: Exosomes are nanosized extracellular vesicles secreted by multiple cells in the body, including those located in the respiratory tract and lungs. They are emerging as important inflammatory mediators and can release their contents, especially microRNAs (miRNAs), to both neighboring and distal cells. Mycoplasma gallisepticum (MG) can target host cell and cause chronic respiratory disease (CRD) in chickens. Although exosomal miRNAs have been demonstrated to produce an important effect on microbial pathogenesis and inflammatory response as crucial regulatory noncoding RNAs, the mechanism by which exosomal miRNAs regulate MG-induced inflammation remains to be elucidated. Methods: the expression of exosome-microRNA derived from MG-infected chicken type Ⅱ pneumocytes (CP-Ⅱ) was screened, and the target genes and function of differentially expressed miRNAs (DEGs) were predicted. To verify the inflammatory functions of exosomal gga-miR-451 via targeting YWHAZ, Western blot, ELISA, and RT-qPCR were used in this study. Results: A total of 722 miRNAs were identified from the two exosomal small RNA (sRNA) libraries, and 279 novel miRNAs were discovered; 30 miRNAs (9 up-regulated and 21 down-regulated) were significantly changed (P＜0.05). Function annotation analysis of DEGs showed that the target miRNAs were significantly enriched in treatment group, such as cell cycle, Toll-like receptor signaling pathway and MAPK signaling pathway, etc. The results have also confirmed that gga-miR-451-absent exosomes derived from MG-infected CP-Ⅱ cells increased inflammatory cytokine production in DF-1 (chicken embryo fibroblast) cells, and Wild Type CP-Ⅱ cells-derived-exosomes displayed protective effects. Conclusion: our work suggests that exosomes from MG-infected CP-Ⅱ cells alter the dynamics of the DF-1 cells, and may contribute to pathology of the MG infection via exosomal gga-miR-451 targeting YWHAZ involving in inflammation. This could potentially be used as a biomarker for diagnostics and treatment.

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Analysis of the transcriptional logic governing differential spatial expression in Hh target genes

10.1101/333260 ◽

2018 ◽

Author(s):

Manuel Cambón ◽

Óscar Sánchez

Keyword(s):

Transcription Factors ◽

Cellular Response ◽

Target Genes ◽

Threshold Model ◽

Theoretical Models ◽

Transcriptional Responses ◽

Cubitus Interruptus ◽

Spatial Expression ◽

Complex Process ◽

Transcription Process

AbstractThis work provides theoretical tools to analyse the transcriptional effects of certain biochemical mechanisms (i.e. affinity and cooperativity) that have been proposed in previous literature to explain the differential spatial expression of Hedgehog target genes involved in Drosophila development. Specifically we have focused on the expression of decapentaplegic and patched. The transcription of these genes is believed to be controlled by opposing gradients of the activator and repressor forms of the transcription factor Cubitus interruptus (Ci). This study is based on a thermodynamic approach, which provides expression rates for these genes. These expression rates are controlled by transcription factors which are competing and cooperating for common binding sites. We have made mathematical representations of the different expression rates which depend on multiple factors and variables. The expressions obtained with the model have been refined to produce simpler equivalent formulae which allow for their mathematical analysis. Thanks to this, we can evaluate the correlation between the different interactions involved in transcription and the biological features observed at tissular level. These mathematical models can be applied to other morphogenes to help understand the complex transcriptional logic of opposing activator and repressor gradients.Author summaryMorphogenic differentiation is a complex process that involves emission, reception and cellular response to different signals. It is well known that the same morphogenic signal can give rise to different cellular transcriptional responses that usually depend, among other factors, on transcription factors. In concordance with the activator threshold model, classically it has been distinguished between high and low threshold target genes in order to explain how cells receiving the same signal can activate different genes. However, in particular cases where the transcription is controlled by two opposing transcription factors, it has been tested that this logic is not valid. This motivates the necessity for describing new theoretical models in order to understand better these cellular responses. By a theoretical analysis we have deduced different versions of transcriptional logic that are significantly determined by how the opposing transcription factors cooperate between them in the transcription process. We have also tested these different scenarios focussing on the Drosophila Hh target genes, and we have reproduced similar conclusions to the ones obtained by other methodologies.

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

Current Genomics ◽

10.2174/1389202919666181012145416 ◽

2019 ◽

Vol 20 (1) ◽

pp. 49-60 ◽

Cited By ~ 2

Author(s):

Rongying Zhou ◽

Yujie Mao ◽

Lidan Xiong ◽

Li Li

Keyword(s):

Mrna Expression ◽

Signaling Pathway ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Target Genes ◽

Gene List ◽

Mouse Skin ◽

Cytokine Receptor ◽

Receptor Interaction ◽

Integrated Analysis

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 sequencing. 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 miRNAmRNA regulatory networks 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, Sema4f, 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 differentiation 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 differentiation.

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