scholarly journals Analysis of differences in the transcriptomic profiles of eutopic and ectopic endometriums in women with ovarian endometriosis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11045
Author(s):  
Xiao Feng ◽  
Lingbin Qi ◽  
Xiaoyu Xu ◽  
Yun Feng ◽  
Xiaoming Gong ◽  
...  
Keyword(s):  
Malignant Transformation ◽  
Expression Patterns ◽  
Embryo Implantation ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Gene Module ◽  
Ovarian Endometriosis ◽  
Endometrial Cells ◽  
Go Enrichment ◽  
And Migration

Background Endometriosis is a common gynecological disease among women in their reproductive years. Although much effort has been made, the pathogenesis of this disease and the detailed differences between eutopic endometrial cells and ectopic endometrial cells are still unclear. Methods In this study, eutopic and ectopic endometrial cells were collected from patients with and without endometriosis and RNA sequencing was performed. The gene expression patterns and differentially expressed genes (DEGs) in eutopic and ectopic endometrial cells, as well as control endometrial cells, were analyzed using a weighted gene co-expression network analysis (WGCNA) and the DESeq2 package. The functions of significant genes were detected using Gene ontology (GO) enrichment analysis, and qRT-PCR validation was performed. Results The results indicated that eight gene modules were found among these three groups. They also indicated that the gene module, which is highly related to eutopic endometrial cells, was mainly enriched in cell adhesion, embryo implantation, etc., while the gene module related to ectopic endometrial cells was mainly enriched in cell migration, etc. The results of differential expression analysis were generally consistent with the WGCNA results through identified significant DEGs between different groups. These DEGs may play an important role in the occurrence of endometriosis, including the infertility associated gene ARNTL and PIWIL2, tissue remodeling gene MMP11, cell survival and migration gene FLT1, inflammatory response gene GNLY, the tumor suppressor genes PLCD1, etc. Further analysis suggested the function of adhesion is stronger in ectopic endometrial cells than in eutopic endometrial cells, while the ectopic endometrium may have a higher potential risk of malignant transformation than eutopic endometrium. Conclusions Overall, these data provide a reference for understanding the pathogenesis of endometriosis and its relationship with malignant transformation.

scholarly journals Exosomal Aβ-Binding Proteins Identified by “In Silico” Analysis Represent Putative Blood-Derived Biomarker Candidates for Alzheimer´s Disease

2021 ◽  
Vol 22 (8) ◽  
pp. 3933
Author(s):  
Tânia Soares Martins ◽  
Rui Marçalo ◽  
Maria Ferreira ◽  
Margarida Vaz ◽  
Raquel M. Silva ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Expression Patterns ◽  
In Silico Analysis ◽  
Enrichment Analysis ◽  
Disease Diagnosis ◽  
Easy Access ◽  
Altered Expression ◽  
Disease Biomarkers ◽  
Go Enrichment

The potential of exosomes as biomarker resources for diagnostics and even for therapeutics has intensified research in the field, including in the context of Alzheimer´s disease (AD). The search for disease biomarkers in peripheral biofluids is advancing mainly due to the easy access it offers. In the study presented here, emphasis was given to the bioinformatic identification of putative exosomal candidates for AD. The exosomal proteomes of cerebrospinal fluid (CSF), serum and plasma, were obtained from three databases (ExoCarta, EVpedia and Vesiclepedia), and complemented with additional exosomal proteins already associated with AD but not found in the databases. The final biofluids’ proteomes were submitted to gene ontology (GO) enrichment analysis and the exosomal Aβ-binding proteins that can constitute putative candidates were identified. Among these candidates, gelsolin, a protein known to be involved in inhibiting Abeta fibril formation, was identified, and it was tested in human samples. The levels of this Aβ-binding protein, with anti-amyloidogenic properties, were assessed in serum-derived exosomes isolated from controls and individuals with dementia, including AD cases, and revealed altered expression patterns. Identification of potential peripheral biomarker candidates for AD may be useful, not only for early disease diagnosis but also in drug trials and to monitor disease progression, allowing for a timely therapeutic intervention, which will positively impact the patient’s quality of life.

scholarly journals Evaluation of FGFR1 as a diagnostic biomarker for ovarian cancer using TCGA and GEO datasets

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10817
Author(s):  
Huiting Xiao ◽  
Kun Wang ◽  
Dan Li ◽  
Ke Wang ◽  
Min Yu
Keyword(s):  
Ovarian Cancer ◽  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Clinical Information ◽  
Residual Tumor ◽  
Diagnostic Value ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Diagnostic Biomarker

Background Malignant ovarian cancer is associated with the highest mortality of all gynecological tumors. Designing therapeutic targets that are specific to OC tissue is important for optimizing OC therapies. This study aims to identify different expression patterns of genes related to FGFR1 and the usefulness of FGFR1 as diagnostic biomarker for OC. Methods We collected data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. In the TCGA cohort we analyzed clinical information according to patient characteristics, including age, stage, grade, longest dimension of the tumor and the presence of a residual tumor. GEO data served as a validation set. We obtained data on differentially expressed genes (DEGs) from the two microarray datasets. We then used gene set enrichment analysis (GSEA) to analyze the DEG data in order to identify enriched pathways related to FGFR1. Results Differential expression analysis revealed that FGFR1 was significantly downregulated in OC specimens. 303 patients were included in the TCGA cohort. The GEO dataset confirmed these findings using information on 75 Asian patients. The GSE105437 and GSE12470 database highlighted the significant diagnostic value of FGFR1 in identifying OC (AUC = 1, p = 0.0009 and AUC = 0.8256, p = 0.0015 respectively). Conclusions Our study examined existing TCGA and GEO datasets for novel factors associated with OC and identified FGFR1 as a potential diagnostic factor. Further investigation is warranted to characterize the role played by FGFR1 in OC.

scholarly journals 225.Expression of chemokines and their receptors at the human maternal - embryonic interface

2004 ◽  
Vol 16 (9) ◽  
pp. 225 ◽  
Author(s):  
N. J. Hannan ◽  
R. L. Jones ◽  
L. A. Salamonsen
Keyword(s):  
Cell Lines ◽  
Expression Patterns ◽  
Embryo Implantation ◽  
Receptor Expression ◽  
Trophoblast Invasion ◽  
Epithelial Cell Line ◽  
Embryonic Cells ◽  
Trophoblast Cells ◽  
Endometrial Cells ◽  
Decidual Cells

Human embryo implantation is a complex process involving attachment of the developing blastocyst to the receptive endometrial epithelium, and subsequent trophoblast invasion through decidua. This is regulated by crosstalk between the maternal and embryonic cells, however little is known about the factors involved in enabling and directing trophoblast invasion. Chemokines are cytokines that regulate leukocyte chemotaxis via stimulation of adhesion molecules and cell migration. We have previously shown that two chemokines, fractalkine and MCP-3, are produced by endometrial epithelial and decidual cells, maximally around the time of implantation and early pregnancy (1, 2). We hypothesized that endometrially derived fractalkine and MCP-3 are important for the attachment/invasion of fetal trophoblast cells during implantation. To investigate this, expression of fractalkine, MCP-3 and their receptors (CX3CR1, CCR1, CCR2, CCR3 and CCR5) were assessed in cell types present at the maternal-embryonic interface. RNA, extracted from three trophoblast cell lines (JEG-3 and two trophoblast-choriocarcinoma hybrids), a human epithelial cell line (HES), primary endometrial epithelial cells, mid-secretory endometrium and placental tissue, was subjected to RT-PCR for the chemokines and receptors. Both chemokines were produced by endometrial and placental cells. Chemokine receptor expression was more variable, CX3CR1, CCR1, 2 and 3 were expressed by one or more of the trophoblast cells lines while CX3CR1, CCR1, 2 and 5 were expressed by endometrial cells. Marked differences in expression patterns in the different cell lines highlight the importance of studies to select those cell lines of most physiological relevance: in this case, one that most closely resembles early invasive trophoblasts. These data confirm that chemokines are produced by maternal and embryonic cells during implantation and the strong expression of their receptors on trophoblast cells supports a role for chemokines in embryo implantation. Further, these studies have characterized a number of trophoblast cells for future trophoblast migration and attachment assays. (1) Hannan, N., et al. JCEM (in press). (2) Jones, R., et al. JCEM (in press).

scholarly journals Transcriptome Analysis Reveals Genes of Flooding-Tolerant and Flooding-Sensitive Rapeseeds Differentially Respond to Flooding at the Germination Stage

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 693
Author(s):  
Jijun Li ◽  
Sidra Iqbal ◽  
Yuting Zhang ◽  
Yahui Chen ◽  
Zengdong Tan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Flooding Stress ◽  
Go Enrichment ◽  
The Common ◽  
Go Enrichment Analysis ◽  
Insight Into ◽  
Germination Stage

Flooding results in significant crop yield losses due to exposure of plants to hypoxic stress. Various studies have reported the effect of flooding stress at seedling establishment or later stages. However, the molecular mechanism prevailing at the germination stage under flooding stress remains enigmatic. The present study highlights the comparative transcriptome analysis in two rapeseed lines, i.e., flooding-tolerant (Santana) and -sensitive (23651) lines under control and 6-h flooding treatments at the germination stage. A total of 1840 up-regulated and 1301 down-regulated genes were shared by both lines in response to flooding. There were 4410 differentially expressed genes (DEGs) with increased expression and 4271 DEGs with reduced expression shared in both control and flooding conditions. Gene ontology (GO) enrichment analysis revealed that “transcription regulation”, “structural constituent of cell wall”, “reactive oxygen species metabolic”, “peroxidase”, oxidoreductase”, and “antioxidant activity” were the common processes in rapeseed flooding response. In addition, the processes such as “hormone-mediated signaling pathway”, “response to organic substance response”, “motor activity”, and “microtubule-based process” are likely to confer rapeseed flooding resistance. Mclust analysis clustered DEGs into nine modules; genes in each module shared similar expression patterns and many of these genes overlapped with the top 20 DEGs in some groups. This work provides a comprehensive insight into gene responses and the regulatory network in rapeseed flooding stress and provides guidelines for probing the underlying molecular mechanisms in flooding resistance.

scholarly journals RegEnrich gene regulator enrichment analysis reveals a key role of the ETS transcription factor family in interferon signaling

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Weiyang Tao ◽  
Timothy R. D. J. Radstake ◽  
Aridaman Pandit
Keyword(s):  
Network Inference ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Cell Types ◽  
Analysis Data ◽  
R Package ◽  
Gene Regulatory Network Inference ◽  
Go Enrichment ◽  
Different Cell Types

AbstractChanges in a few key transcriptional regulators can lead to different biological states. Extracting the key gene regulators governing a biological state allows us to gain mechanistic insights. Most current tools perform pathway/GO enrichment analysis to identify key genes and regulators but tend to overlook the gene/protein regulatory interactions. Here we present RegEnrich, an open-source Bioconductor R package, which combines differential expression analysis, data-driven gene regulatory network inference, enrichment analysis, and gene regulator ranking to identify key regulators using gene/protein expression profiling data. By benchmarking using multiple gene expression datasets of gene silencing studies, we found that RegEnrich using the GSEA method to rank the regulators performed the best. Further, RegEnrich was applied to 21 publicly available datasets on in vitro interferon-stimulation of different cell types. Collectively, RegEnrich can accurately identify key gene regulators from the cells under different biological states, which can be valuable in mechanistically studying cell differentiation, cell response to drug stimulation, disease development, and ultimately drug development.

Identification of Core Genes Related with Trophinin-Associated Protein (TROAP) Expression in Liver Cancer

2020 ◽  
Author(s):  
Bai Ji ◽  
Hongqiao Cai ◽  
Yan Jiao ◽  
Yahui Liu
Keyword(s):  
Liver Cancer ◽  
Malignant Tumors ◽  
Enrichment Analysis ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Go Enrichment ◽  
And Migration ◽  
High Degree ◽  
Core Genes

Abstract Background: Liver cancer is one of the malignant tumors with the highest incidence in the world. Trophinin-associated protein (TROAP) was related with prognosis in liver cancer. However, the core genes associated with TROAP have not been identified yet. Methods: In this study, we performed in vitro cell experiments and bioinformatics analysis including screening of differentially expressed genes (DEGs), gene ontology (GO) enrichment analysis, and Kyoto Encyclopedia of Gene and Genome (KEGG) enrichment analysis. Hub genes with high degree of connectivity was picked out by establishing protein-protein interaction (PPI) network. Results: Our in vitro cell experiments suggested that down regulation of TROAP inhibited the proliferation and migration of liver cancer cells. A total of 20530 genes were analyzed and 953 differential expressed genes including 529 up-regulated DEGs and 424 down-regulated DEGs were detected. 10 hub genes with higher degree of connectivity including BUB1B, TOP2A, KIF23, UBE2C, KIF15, CDC20, PLK1, HJURP, BUB1, and DLGAP5 were selected. Conclusions: Our study may provide some evidence for the future genomic individualized treatment of liver cancer.

Steroid regulation of secreted phosphoprotein 1 (SPP1) expression in ovine endometrium

2021 ◽  
Vol 33 (4) ◽  
pp. 257
Author(s):  
Tina D. Tremaine ◽  
Ali A. Fouladi-Nashta
Keyword(s):  
Stromal Cells ◽  
Luteal Phase ◽  
Expression Patterns ◽  
Embryo Implantation ◽  
Primary Source ◽  
Ovarian Steroids ◽  
Endometrial Cells ◽  
Paracrine Signalling ◽  
Steroid Regulation ◽  
Secreted Phosphoprotein 1

Secreted phosphoprotein 1 (SPP1) is an extracellular matrix glycoprotein that is highly expressed at the maternal–fetal interface and is a critical mediator of embryo implantation. The objectives of this study were to examine the spatial and temporal cyclical expression patterns and steroid regulation of SPP1 mRNA and protein in ovine endometrium, which may be further indicative of their functionality in embryo implantation. Uterine tissue was obtained following hysterectomy from ovariectomised ewes treated with ovarian steroids. In parallel, invitro culture of endometrial cells was used to investigate the effects of ovarian steroids on SPP1 expression in endometrial and luminal epithelial (LE) cells. A significant sustained mid-luteal phase increase in SPP1 mRNA in intercaruncular regions of the endometrium was observed, indicating that glandular epithelium is likely to be the primary source of SPP1 production. This increase in SPP1 was induced by progesterone treatment and was shown at the protein level by immunohistochemistry analysis. Similarly, treatment of stromal cells with 10ng mL−1 progesterone or in combination with 1ng mL−1 oestradiol significantly increased SPP1 expression (P<0.05). Collectively, expression levels of SPP1 are cycle-dependent and peak in the progesterone-dominant luteal phase. They are dependent on the interaction of uterine LE and stromal cells and may involve paracrine signalling by progesterone receptor-positive stromal cells.

scholarly journals The Key Gene Expression Patterns and Prognostic Factors in Malignant Transformation from Enchondroma to Chondrosarcoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Junqing Wu ◽  
Yue Huang ◽  
Chengxuan Yu ◽  
Xia Li ◽  
Limengmeng Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Malignant Transformation ◽  
Epithelial Mesenchymal Transition ◽  
Expression Patterns ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Gene Interaction Network ◽  
Mesenchymal Transition ◽  
Cell Immunity

Enchondroma (EC) is a common benign bone tumor. It has the risk of malignant transformation to Chondrosarcoma (CS). However, the underlying mechanism is unclear. The gene expression profile of EC and CS was obtained from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using GEO2R. We conducted the enrichment analysis and constructed the gene interaction network using the DEGs. We found that the epithelial-mesenchymal transition (EMT) and the VEGFA-VEGF2R signaling pathway were more active in CS. The CD8+ T cell immunity was enhanced in CS I. We believed that four genes (MFAP2, GOLM1, STMN1, and HN1) were poor predictors of prognosis, while two genes (CAB39L and GAB2) indicated a good prognosis. We have revealed the mechanism in the tumor progression and identified the key genes that predicted the prognosis. This study provided new ideas for the diagnosis and treatment of EC and CS.

scholarly journals LncRNA LINC00857 strengthens the malignancy behaviors of pancreatic adenocarcinoma cells by serving as a competing endogenous RNA for miR-340-5p to upregulate TGFA expression

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247817
Author(s):  
Tingfu Li ◽  
Hongbo Zhao ◽  
Hua Zhou ◽  
Tingting Geng
Keyword(s):  
Pancreatic Adenocarcinoma ◽  
Transforming Growth Factor ◽  
Enrichment Analysis ◽  
Inhibitory Effect ◽  
Pancreatic Disease ◽  
Luciferase Assay ◽  
Invasion And Migration ◽  
Mrna Targets ◽  
Go Enrichment ◽  
And Migration

Background Pancreatic adenocarcinoma (PAAD) is a pancreatic disease with a high mortality rate in the world. This present research intends to identify the function of lncRNA LINC00857/miR-340-5p/Transforming growth factor alpha (TGFA) in the progression of PAAD. Methods Bioinformatics analysis was used to explore the differentially expressed lncRNA/miRNA/mRNA and analyze the relationship between lncRNA/miRNA/mRNA expression and prognosis of PAAD by enquiring TCGA, GEO and GTEX. KEGG pathway analysis and GO enrichment analysis were implemented to annotate the crucial genes regulated by LINC00857. The biological behaviors of PAAD cells were detected by CCK-8, colony formation and transwell assays. Interactive associations between LINC00857 and miR-340-5p, as well as miR-340-5p and TGFA were analyzed by dual luciferase assay. Results By enquiring TCGA database, we got that LINC00857 was highly expressed in patients with PAAD and positively associated with worse prognosis in PAAD patients. Moreover, LINC00857 upregulation promoted the proliferation and clone formation abilities of PAAD cells. Afterwards, the downstream miRNA and mRNA targets of LINC00857 were picked up to construct a ceRNA network. Further study revealed that TGFA expression was positively regulated by LINC00857 and negatively regulated by miR-340-5p. Besides that, the inhibitory effect of miR-340-5p on PAAD cells growth and movement can be blocked by LINC00857 upregulation. While, the malignant behavior of PAAD cells induced by TGFA overexpression can be eliminated by LINC00857 knockdown. Conclusions Upregulation of LINC00857 improved growth, invasion and migration abilities of PAAD cells by modulation of miR-340-5p/TGFA, affording potential targets and biomarkers for the clinical diagnosis and treatment.

378: 14-3-3 Expression Patterns in the Human Kidney: From Fetal Development to the Adult State to Malignant Transformation

2005 ◽  
Vol 173 (4S) ◽  
pp. 103-103
Author(s):  
Adam G. Baseman ◽  
Andrew J. Kirsch ◽  
Fray F. Marshall ◽  
Haiyen E. Zhau ◽  
Leland W.K. Chung ◽  
...  
Keyword(s):  
Malignant Transformation ◽  
Fetal Development ◽  
Expression Patterns ◽  
Human Kidney
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