scholarly journals How do avian embryos resume development following diapause? A new role for TGF-β in regulating pluripotency-related genes

2021 ◽  
Author(s):  
Narayan Pokhrel ◽  
Olga Genin ◽  
Dalit Sela-Donenfeld ◽  
Yuval Cinnamon
Keyword(s):  
Embryonic Stem ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Main Role ◽  
Loss Of Function ◽  
Avian Embryos ◽  
Developmental Program ◽  
Different Temperatures ◽  
Two Temperatures

Avian embryos can halt their development for long periods at low temperature in a process called diapause and successfully resume development when reincubated at maternal body temperature. Successful resumption of development depends on different factors, including temperature. We have recently shown that embryos that enter diapause at 18 °C present a significant reduction in their ability to develop normally when put back into incubation, compared to embryos entering diapause at 12 °C. However, the mechanisms underlying these differences are unknown. To address this question, transcriptome analysis was performed to compare the effect of diapause temperature on gene expression, and to identify pathways involved in the process. Genetic comparison and pathway-enrichment analysis revealed that TGF-β and pluripotency-related pathways are differentially regulated at the two temperatures, with higher expression at 12 °C compared to 18 °C. Investigating the involvement of the TGF-β pathway revealed an essential role for BMP4 in regulating the expression of the transcription factors Nanog and Id2, which are known to regulate pluripotency and self-renewal in embryonic stem cells. BMP4 gain- and loss-of-function experiments in embryos in diapause at different temperatures revealed the main role of BMP4 in enabling the resumption of normal development following diapause. Collectively, these findings identify molecular regulators that facilitate embryos' ability to undergo diapause at different temperatures and resume a normal developmental program.

Abstract 361: Creg1 Interacts With Sec8 to Promote Cell-cell Adhesion During Cardiomyogenesis

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Jie Liu ◽  
Yanmei Qi ◽  
Shu-Chan Hsu ◽  
Siavash Saadat ◽  
Saum Rahimi ◽  
...  
Keyword(s):  
Cell Adhesion ◽  
Es Cells ◽  
Embryonic Stem ◽  
Intercellular Junctions ◽  
Amino Acid Residues ◽  
Loss Of Function ◽  
Wild Type ◽  
Adhesion Sites ◽  
Cell Cell

Cellular repressor of E1A-stimulated genes 1 (CREG1) is a 24 kD glycoprotein essential for early embryonic development. Our immunofluorescence studies revealed that CREG1 is highly expressed at myocyte junctions in both embryonic and adult hearts. To explore it role in cardiomyogenesis, we employed gain- and loss-of-function analyses demonstrating that CREG1 is required for the differentiation of mouse embryonic stem (ES) cell into cohesive myocardium-like structures. Chimeric cultures of wild-type and CREG1 knockout ES cells expressing cardiac-specific reporters showed that the cardiomyogenic effect of CREG1 is cell autonomous. Furthermore, we identified a novel interaction between CREG1 and Sec8 of the exocyst complex, which tethers vesicles to the plasma membrane. Mutations of the amino acid residues D141 and P142 to alanine in CREG1 abolished its binding to Sec8. To address the role of the CREG1-Sec8 interaction in cardiomyogenesis, we rescued CREG1 knockout ES cells with wild-type and Sec8-binding mutant CREG1 and showed that CREG1 binding to Sec8 promotes cardiomyocyte differentiation and cohesion. Mechanistically, CREG1, Sec8 and N-cadherin all localize at cell-cell adhesion sites. CREG1 overexpression enhances the assembly of adherens and gap junctions. By contrast, its knockout inhibits the Sec8-N-cadherin interaction and induces their degradation. Finally, shRNA-mediated knockdown of Sec8 leads to cardiomyogenic defects similar to CREG1 knockout. These results suggest that the CREG1 binding to Sec8 enhances the assembly of intercellular junctions and promotes cardiomyogenesis.

scholarly journals Role of Arabidopsis Splicing factor SF1 in Temperature-Responsive Alternative Splicing of FLM pre-mRNA

2020 ◽  
Vol 11 ◽  
Author(s):  
Keh Chien Lee ◽  
Kyung Sook Chung ◽  
Hee Tae Lee ◽  
Jae-Hyeok Park ◽  
Jeong Hwan Lee ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Flowering Time ◽  
Crop Yields ◽  
Transcript Level ◽  
Splicing Factor ◽  
Loss Of Function ◽  
Temperature Dependent ◽  
Temperature Responsive ◽  
Different Temperatures

Small changes in temperature affect plant ecological and physiological factors that impact agricultural production. Hence, understanding how temperature affects flowering is crucial for decreasing the effects of climate change on crop yields. Recent reports have shown that FLM-β, the major spliced isoform of FLOWERING LOCUS M (FLM)—a flowering time gene, contributes to temperature-responsive flowering in Arabidopsis thaliana. However, the molecular mechanism linking pre-mRNA processing and temperature-responsive flowering is not well understood. Genetic and molecular analyses identified the role of an Arabidopsis splicing factor SF1 homolog, AtSF1, in regulating temperature-responsive flowering. The loss-of-function AtSF1 mutant shows temperature insensitivity at different temperatures and very low levels of FLM-β transcript, but a significantly increased transcript level of the alternative splicing (AS) isoform, FLM-δ. An RNA immunoprecipitation (RIP) assay revealed that AtSF1 is responsible for ambient temperature-dependent AS of FLM pre-mRNA, resulting in the temperature-dependent production of functional FLM-β transcripts. Moreover, alterations in other splicing factors such as ABA HYPERSENSITIVE1/CBP80 (ABH1/CBP80) and STABILIZED1 (STA1) did not impact the FLM-β/FLM-δ ratio at different temperatures. Taken together, our data suggest that a temperature-dependent interaction between AtSF1 and FLM pre-mRNA controls flowering time in response to temperature fluctuations.

scholarly journals MicroRNA expression profiling in myopia: a meta-analysis and systematic review

2021 ◽  
Author(s):  
Nan Hong ◽  
Bo Jiang ◽  
Lei Gu ◽  
Si-Yi Chen ◽  
Jian-Ping Tong
Keyword(s):  
Expression Profiling ◽  
Protein Modification ◽  
Meta Analysis ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Ocular Tissue ◽  
Receptor Interaction ◽  
Pathway Enrichment Analysis ◽  
Vote Counting

Background: Myopia (nearsightedness) is currently the most common human eye disorder worldwide. In the recent years, several studies have addressed the role of microRNAs (miRNAs) in the pathogenesis of myopia. Objectives: The aim of this study was to perform a meta-analysis on the miRNA expression profiling studies in myopia to identify commonly dysregulated miRNAs in myopic tissues. Method: Seven independent studies were included in the meta-analysis. A vote-counting strategy were employed as the meta-analysis method. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Ontology (GO) functional enrichment analysis were performed to identify the pathways most strongly affected by the dysregulated mouse miRNAs. Results: According to the vote-counting method, eighteen miRNAs were reported in at least two studies with the consistent direction, of which 13 miRNAs were commonly up-regulated in myopic samples compared with control samples and five miRNAs were commonly down-regulated. Subgroup analyses divided and compared the differentially expressed miRNAs according to species (human and animal) and ocular tissue types. The KEGG analysis showed that the dysregulated mouse miRNAs were most enriched in extracellular matrix (ECM)-receptor interaction signal pathway. The most enriched GO processes regulated by the dysregulated mouse miRNAs was cellular protein modification process. Conclusions. Our meta-analysis recommends several miRNAs may provide some clues of the potential biomarkers in myopia. Further mechanistic studies are warranted to elucidate the biological role of the dysregulated miRNAs in the development of myopia.

scholarly journals TET2 Inhibits Differentiation of Embryonic Stem Cells but Does Not Overcome Methylation-Induced Gene Silencing

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Louis Norman ◽  
Paul Tarrant ◽  
Timothy Chevassut
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Genomic Dna ◽  
Es Cells ◽  
Embryonic Stem ◽  
Gene Promoters ◽  
Loss Of Function ◽  
Promoter Sequences ◽  
Maintenance Methylation

TET2 is a methylcytosine dioxygenase that is frequently mutated in myeloid malignancies, notably myelodysplasia and acute myeloid leukemia. TET2 catalyses the conversion of 5′-methylcytosine to 5′-hydroxymethylcytosine within DNA and has been implicated in the process of genomic demethylation. However, the mechanism by which TET2 loss of function results in hematopoietic dysplasia and leukemogenesis is poorly understood. Here, we show that TET2 is expressed in undifferentiated embryonic stem cells and that its knockdown results in reduction of 5′-hydroxymethylcytosine in genomic DNA. We also present DNA methylation data from bone marrow samples obtained from patients with TET2-mutated myelodysplasia. Based on these findings, we sought to identify the role of TET2 in regulating pluripotency and differentiation. We show that overexpression of TET2 in a stably integrated transgene leads to increased alkaline phosphatase expression in differentiating ES cells and impaired differentiation in methylcellulose culture. We speculate that this effect is due to TET2-mediated expression of stem cell genes in ES cells via hydroxylation of 5′-methylcytosines at key promoter sequences within genomic DNA. This leads to relative hypomethylation of gene promoters as 5′-hydroxymethylcytosine is not a substrate for DNMT1-mediated maintenance methylation. We sought to test this hypothesis by cotransfecting the TET2 gene with methylated reporter genes. The results of these experiments are presented.

scholarly journals Multi-omics analysis of m6A modification-related patterns based on m6A regulators and tumor microenvironment infiltration in lung adenocarcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xincheng Wu ◽  
Zhengping Bai
Keyword(s):  
Tumor Microenvironment ◽  
Lung Adenocarcinoma ◽  
Cytotoxic T Lymphocyte ◽  
Principal Component ◽  
Enrichment Analysis ◽  
Comprehensive Analysis ◽  
Survival Advantage ◽  
Pathway Enrichment Analysis ◽  
Mutation Burden

AbstractEpigenetic modifications, especially N6-methyladenosine (m6A) modification, play a key role in tumor microenvironment (TME) infiltration. However, the regulatory role of m6A modification in the TME of lung adenocarcinoma (LUAD) remains unclear. A total of 2506 patients with LUAD were included in the analysis and divided into different groups according to distinct m6A modification-related patterns based on 23 m6A regulators. A comprehensive analysis was performed to explore TME infiltration in different m6A modification-related patterns. Principal component analysis was performed to obtain the m6Ascore and to quantify m6A modification-related patterns in different individuals. Three distinct m6A modification-related patterns were identified by 23 m6A regulators. The pathway enrichment analysis showed that m6Acluster-A was associated with immune activation; m6Acluster-B was associated with carcinogenic activation; m6Acluster-C was prominently related to substance metabolism. M6Acluster-A was remarkably rich in TME-infiltrating immune cells and patients with this pattern showed a survival advantage. The m6Ascore could predict TME infiltration, tumor mutation burden (TMB), the effect of tumor immunotherapy, and the prognosis of patients in LUAD. High m6Ascore was characterized by increased TME infiltration, reduced TMB, and survival advantage. Patients with a high m6Ascore exhibited significantly improved clinical response to anti-cytotoxic T lymphocyte antigen-4 (anti-CTLA4) immunotherapy. This study explored the regulatory mechanisms of TME infiltration in LUAD. The comprehensive analysis of m6A modification-related patterns may contribute to the development of individualized immunotherapy and the improvement of the overall effectiveness of immunotherapy for LUAD patients.

scholarly journals CYPB upregulates and promotes cell proliferation in endometrial carcinoma

2020 ◽  
Author(s):  
Jing Liu ◽  
Ying Zuo ◽  
Gui-Mei Qu ◽  
Xiao Song ◽  
Zhong-Hui Liu ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Endometrial Cancer ◽  
Enrichment Analysis ◽  
Human Cell Line ◽  
Pathway Enrichment Analysis ◽  
Endometrial Tumor ◽  
Novel Target ◽  
Cancer Tissues ◽  
Cell Gene

Abstract BACKGROUND The molecular pathogenesis of endometrial cancer is not yet completely understood, preventing the development of successful therapies. Here, we determine the effect of CYPB on the growth of endometrial cancer. METHODS In this study, we examined the expression of CYPB in endometrial cancer tissues using immunohistochemistry. CYPB silencing in the human cell line HEC-1-B was used to evaluate the role of CYPB in the malignant phenotype of endometrial tumor cells, while CCK-8 and colony formation assays were performed to assess its effect on tumor cell proliferation. Furthermore, microarray analysis was carried out to compare the global mRNA expression profile between the normal and CYPB-knockdown cell. Gene ontology and KEGG pathway enrichment analysis were performed to determine the potential function of different expressed genes related to CYPB. RESULTS We found that CYPB was upregulated in endometrial cancer, while cells with suppressed expression of CYPB exhibited markedly reduced migration. We identified 1536 differentially expressed genes (onefold change, p< 0.05), among which 652 genes were upregulated and 884 genes were downregulated, and most of them were enriched in cell cycle, glycosphingolipid biosynthesis, adherens junctions, and metabolism pathways. CONCLUSIONS The results of our study suggest that CYPB may serve as a novel regulator of endometrial cell proliferation, thus representing a novel target for gene-targeted endometrial therapy.

SHMT2 is Associated with Tumor Purity, CD8+ T Immune Cells Infiltration, and a Novel Therapeutic Target in Four Different Human Cancers

2022 ◽  
Vol 22 ◽  
Author(s):  
Muhammad Usman ◽  
Yasir Hameed ◽  
Mukhtiar Ahmad ◽  
Muhammad Junaid Iqbal ◽  
Aghna Maryam ◽  
...  
Keyword(s):  
Immune Cells ◽  
Promoter Methylation ◽  
In Silico ◽  
Human Cancer ◽  
Enrichment Analysis ◽  
Genetic Alterations ◽  
Pathway Enrichment Analysis ◽  
Human Cancers ◽  
Tumor Purity

Aims: This study was launched to identify the SHMT2 associated Human Cancer subtypes. Background: Cancer is the 2nd leading cause of death worldwide. Previous reports revealed the limited involvement of SHMT2 in human cancer. In the current study, we comprehensively analyzed the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. Objective:: We aim to comprehensively analyze the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. Earlier, limited knowledge exists in the medical literature regarding the involvement of Serine Hydroxymethyltransferase 2 (SHMT2) in human cancer. Methods: In the current study, we comprehensively analyzed the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. Pan-cancer transcriptional expression profiling of SHMT2 was done using UALCAN while further validation was performed using GENT2. For translational profiling of SHMT2, we utilized Human Protein Atlas (HPA) platform. Promoter methylation, genetic alteration, and copy number variations (CNVs) profiles were analyzed through MEXPRESS and cBioPortal. Survival analysis was carried out through Kaplan–Meier (KM) plotter platform. Pathway enrichment analysis of SHMT2 was performed using DAVID, while the gene-drug network was drawn through CTD and Cytoscape. Furthermore, in the tumor microenvironment, a correlation between tumor purity, CD8+ T immune cells infiltration, and SHMT2 expression was accessed using TIMER. Results: SHMT2 was found overexpressed in 24 different subtypes of human cancers and its overexpression was significantly associated with the reduced Overall survival (OS) and Relapse-free survival durations of Breast cancer (BRCA), Kidney renal papillary cell carcinoma (KIRP), Liver hepatocellular carcinoma (LIHC), and Lung adenocarcinoma (LUAD) patients. This implies that SHMT2 plays a significant role in the development and progression of these cancers. We further noticed that SHMT2 was also up-regulated in BRCA, KIRP, LIHC, and LUAD patients of different clinicopathological features. Pathways enrichment analysis revealed the involvement of SHMT2 enriched genes in five diverse pathways. Furthermore, we also explored some interesting correlations between SHMT2 expression and promoter methylation, genetic alterations, CNVs, tumor purity, and CD8+ T immune cell infiltrates. Conclusion: Our results suggested that overexpressed SHMT2 is correlated with the reduced OS and RFS of the BRCA, KIRP, LIHC, and LUAD patients and can be a potential diagnostic and prognostic biomarker for these cancers.

scholarly journals LncRNA Mrhl orchestrates differentiation programs in mouse embryonic stem cells through chromatin mediated regulation

2019 ◽  
Author(s):  
Debosree Pal ◽  
C V Neha ◽  
Utsa Bhaduri ◽  
Zenia ◽  
Subbulakshmi Chidambaram ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Cell Fate ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Loss Of Function ◽  
Genome Wide ◽  
Development And Differentiation ◽  
Lineage Specific Genes

AbstractLong non-coding RNAs (lncRNAs) have been well-established to act as regulators and mediators of development and cell fate specification programs. LncRNA Mrhl (meiotic recombination hotspot locus) has been shown to act in a negative feedback loop with WNT signaling to regulate male germ cell meiotic commitment. In our current study, we have addressed the role of Mrhl in development and differentiation using mouse embryonic stem cells (mESCs) as our model system of study. We found Mrhl to be a nuclear-localized, chromatin-bound lncRNA with moderately stable expression in mESCs. Transcriptome analyses and loss-of-function phenotype studies revealed dysregulation of developmental processes and lineage-specific genes along with aberrance in specification of early lineages during differentiation of mESCs. Genome-wide chromatin occupancy studies suggest regulation of chromatin architecture at key target loci through triplex formation. Our studies thus reveal a role for lncRNA Mrhl in regulating differentiation programs in mESCs in the context of appropriate cues through chromatin-mediated responses.

scholarly journals CYPB upregulates and promotes cell proliferation in endometrial carcinoma

2020 ◽  
Author(s):  
Jing Liu ◽  
Ying Zuo ◽  
Gui-Mei Qu ◽  
Xiao Song ◽  
Zhong-Hui Liu ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Endometrial Cancer ◽  
Enrichment Analysis ◽  
Human Cell Line ◽  
Pathway Enrichment Analysis ◽  
Endometrial Tumor ◽  
Novel Target ◽  
Cancer Tissues ◽  
Cell Gene

Abstract BACKGROUND The molecular pathogenesis of endometrial cancer is not yet completely understood, preventing the development of successful therapies. Here, we determine the effect of CYPB on the growth of endometrial cancer. METHODS In this study, we examined the expression of CYPB in endometrial cancer tissues using immunohistochemistry. CYPB silencing in the human cell line HEC-1-B was used to evaluate the role of CYPB in the malignant phenotype of endometrial tumor cells, while CCK-8 and colony formation assays were performed to assess its effect on tumor cell proliferation. Furthermore, microarray analysis was carried out to compare the global mRNA expression profile between the normal and CYPB-knockdown cell. Gene ontology and KEGG pathway enrichment analysis were performed to determine the potential function of different expressed genes related to CYPB. RESULTS We found that CYPB was upregulated in endometrial cancer, while cells with suppressed expression of CYPB exhibited markedly reduced migration. We identified 1536 differentially expressed genes (onefold change, p< 0.05), among which 652 genes were upregulated and 884 genes were downregulated, and most of them were enriched in cell cycle, glycosphingolipid biosynthesis, adherens junctions, and metabolism pathways. CONCLUSIONS The results of our study suggest that CYPB may serve as a novel regulator of endometrial cell proliferation, thus representing a novel target for gene-targeted endometrial therapy.

scholarly journals MicroRNA Expression in Cutaneous Lupus: A New Window to Understand Its Pathogenesis

2019 ◽  
Vol 2019 ◽  
pp. 1-26 ◽  
Author(s):  
Silvia Méndez-Flores ◽  
Janette Furuzawa-Carballeda ◽  
Gabriela Hernández-Molina ◽  
Gustavo Ramírez-Martinez ◽  
Nora E. Regino-Zamarripa ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Cross Sectional Study ◽  
Pathway Enrichment Analysis ◽  
Regulatory Cells ◽  
Circulating Mirnas ◽  
Cross Sectional ◽  
Healthy Donors ◽  
Cycle Regulation ◽  
Cutaneous Lupus

Background. The role of miRNAs in the pathogenesis of cutaneous lupus has not been studied. Objective. It was to assess the levels of a selected panel of circulating miRNAs that could be involved in the regulation of the immune response, inflammation, and fibrosis in cutaneous lupus. Methods. It was a cross-sectional study. We included 22 patients with subacute (SCLE) and 20 with discoid (DLE) lesions, and 19 healthy donors (HD). qRT-PCR for miRNA analysis, flow cytometry in peripheral blood, and skin immunohistochemistry were performed to determine the distribution of CD4 T cells and regulatory cells and their correlation with circulating miRNAs. Results. miR-150, miR-1246, miR-21, miR-23b, and miR-146 levels were downregulated in SCLE vs. HD. miR-150, miR-1246, and miR-21 levels were downregulated in DLE vs. HD. Peripheral CD4+/CD25-/IL-4+ cells and CD4+/CD25hi/Foxp3+ were negatively associated with miR-23b, and CD4+/CD25-/IFN-γ+ with miR-1246 in SCLE, whereas CD123+/CD196+/IDO+ cells were positively associated with miR-150 in DLE. In the tissue, CD4+/IL-4+ and CD20+/IL-10+ cells were positively associated with miR-21 and CD4+/IFN-γ+ with miR-31 in SCLE, whereas CD4+/IL-4+ cells were positively associated with miR-150, and CD20+/IL-10+ cells with miR-1246 and miR-146a in DLE. In the SCLE, lower miR-150 levels were correlated with higher CLASI scores. The KEGG pathway enrichment analysis revealed that cell cycle regulation pathways, p53, TGF-β, thyroid hormone, and cancer signaling pathways were shared between miR-21, miR-31, miR-23b, miR-146a, miR-1246, and miR-150. Conclusions. A downregulation of miR-150, miR-1246, and miR-21 in both CLE varieties vs. HD was determined.

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