LNCRNAs and mRNAs in a Gynecological Disease
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE77182 | GEO | 2016/01/26
SECONDARY ACCESSION(S): PRJNA309673
REPOSITORIES: GEO
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Project description:Endometriosis is a common gynecological disease that affects 10-20% of women in child-bearing age. It is defined by the presence of endometrial tissues outside the uterus. The causes remain elusive, but the endometrium of these patients differs profoundly from that of disease-free subjects. During pregnancy, the maternal-fetal interface is built onto decidualized endometrium. We investigated whether this interface is normal when the subjects suffer of endometriosis and showed remarkly properties of eutopic endometrium from endometriosis-affected women to spontaneously develop endometriotic-like lesions within direct contact to non-uterine tissues.
2014-11-10 | GSE57831 | GEO
Project description:Identification of differentially expressed lncRNAs and mRNAs in OLF
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Project description:To determine the expression profile and clinical significance of long non-coding RNAs (lncRNAs) in peripheral blood mononuclear cells (PBMCs) of patients with primary gout and healthy control subjects. Human lncRNA microarrays were used to identify the differentially expressed lncRNAs and mRNAs in primary gout (n=6) and healthy subjects (n=6). Bioinformatics analyses were performed to predict the roles of differently expressed lncRNAs and mRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to validate the results in 64 gout patients, and 32 healthy control subjects (HC). The microarray analysis identified 1479 differentially expressed lncRNAs (879 up-regulated and 600 down-regulated), 862 differentially expressed mRNAs (390 up-regulated and 472 down-regulated) in primary gout (fold change>2, P<0.05), respectively. The bioinformatic analysis indicated that the differentially expressed lncRNAs regulated the abnormally expressed mRNAs, which were involved in the pathogenesis of gout through several different pathways. Significant association was observed between these lncRNAs and the Clinical inflammation indicators and lipid metabolism indicators. Our results provide novel insight into the mechanisms of primary gout, and reveal that ENST00000566457 and NR-026756 could effectively discriminate the gout group and the healthy control groups.
2020-11-03 | GSE160170 | GEO
Project description:Background: Long non-coding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. They are aberrantly expressed in many types of diseases. We want to study the lncRNAs profiles in preeclampsia. Preeclampsia has been observed in patients with molar pregnancy where a fetus is absent demonstrating that the placenta is sufficient to cause the condition. So we analyze the lncRNAs profiles in preeclampsia placentas. In this study, we described the lncRNAs profiles in 6 preeclampsia placentas (T) and 5 matched normal pregnancy placentas (N) tissues by microarray. Methodology/Principal Findings: With abundant and varied probes accounting 33,045 LncRNAs in our microarray, the number of lncRNAs that expressed at a certain level could be detected is 28,443. From the data we found there were 738 lncRNAs that differentially expressed (M-bM-^IM-%1.5 fold-change) among preeclampsia placentas compared with matched controls. Up to 18,063 coding transcripts could be detected in placenta samples through 30,215 coding transcripts probes. Coding-non-coding gene co-expression networks (CNC network) were constructed based on the correlation analysis between the differential expressed lncRNAs and mRNAs. According to the GO-Pathway analysis of differential expressed lncRNAs/mRNAs, we choose three lncRNAs to analyze the relationship between lncRNAs and preeclampsia. LOC391533, LOC284100, CEACAMP8 were evaluated by qPCR in 40 of preeclampsia placentas and 40 of controls. The results showed three lncRNAs were aberrantly expressed in preeclampsia placentas compared with controls. Conclusions/Significance: Our study is the first one to determine genome-wide lncRNAs expression patterns in preeclampsia placenta by microarray. The results displayed that clusters of lncRNAs were aberrantly expressed in preeclampsia placenta compared with controls, which revealed that lncRNAs differentially expressed in preeclampsia placenta may exert a partial or key role in preeclampsia development. Misregulation of LOC391533, LOC284100, CEACAMP8 might be associated with preeclampsia. Taken together, this study may provide potential targets for future treatment of preeclampsia and novel insights into preeclampsia biology. LncRNAs/mRNAs profiles in 6 preeclampsia placentas and 5 matched normal pregnancy placentas tissues by microarray using Arraystar v2.0.
2013-09-12 | E-GEOD-50783 | biostudies-arrayexpress
Project description:Inflammatory bowel disease (IBD) is a complex multi-factorial inflammatory disease with Crohn’s disease (CD) and ulcerative colitis (UC) being the two most common forms. A number of transcriptional profiling studies have provided compelling evidence that describe the role of protein-coding genes and microRNAs in modulating the immune responses in IBD. In the present study, we performed a genome-wide transcriptome profiling of lncRNAs and protein-coding genes in inflamed and non-inflamed colon pinch biopsies from the IBD patients using expression microarrays platform. In this study, we identified widespread dysregulation of lncRNAs and protein-coding genes in both inflamed and non-inflamed CD and UC compared to the healthy controls. In case of inflamed CD and UC (iCD and iUC), we identified 438 and 745 differentially expressed lncRNAs, respectively, while in case of the non-inflamed CD and UC (niCD and niUC), we identified 12 and 19 differentially expressed lncRNAs, respectively. We also observed significant enrichment (p-value < 0.001, Pearson’s Chi-squared test) for 96 differentially expressed lncRNAs and 154 protein-coding genes within the IBD susceptibility loci. Furthermore, we found strong positive expression correlations for the intersecting and cis-neighboring differentially expressed IBD loci-associated lncRNA-protein-coding gene pairs. The functional annotation analysis of differentially expressed genes revealed that they are involved in immune response, pro-inflammatory cytokine activity and MHC protein complex. The lncRNA expression profiling in both inflamed and non-inflamed CD and UC, successfully stratified IBD patients from the healthy controls. Taken together, the identified lncRNA transcriptional signature along with clinically relevant parameters suggests their potential as biomarkers in IBD. A total of 96 biopsy samples (including 6 samples used as technical replicates) extracted from different colonic locations from 45 patients (CD=13, UC=20, Controls=12) were profiled using Agilent Custom 8x60K format lncRNA expression microarray. In Gencode v15 lncRNA microarray design, each lncRNA transcript is targeted by two probes covering 22,001 lncRNA transcripts corresponding to 12,963 lncRNA genes. In addition, each array contains 17,535 randomly-selected protein-coding targets, of which 15,182 (unique 12,787) correspond to protein-coding genes.
2015-04-10 | E-GEOD-67106 | biostudies-arrayexpress
Project description:The identification of the expression patterns of long non‑coding RNAs (lncRNAs) and mRNAs in the kidney under normal and renal ischemia/reperfusion (IR) conditions is essential for understanding the genetic mechanisms underlying the pathogenesis of renal IR injury. Here, we have carried out a genome-wide long non-coding RNA and mRNA microarray analysis in mice kidneys with IR. The data revealed that the expression profiles of lncRNAs and mRNAs in the kidneys differed markedly between the Sham group and IR group, and in total 276 differentially expressed (>2‑fold) lncRNAs (201 upregulated, 75 downregulated) and 267 mRNAs (192 upregulated, 75 downregulated) were identified. qRT-PCR analysis was performed to verify the expression patterns of several lncRNAs and mRNAs.We found a specific and strongly differentially expressed lncRNA, an renal ischemia-reperfusion (IR) injury associated RNA, termed lncRNA-IRAR, which was mainly located in tubular epithelia cells. In vitro and in vivo gain- or loss-of-function studies were performed to investigate the role of lncRNA-IRAR during renal IRI. Moreover, an expression volcano map of the differentially expressed mRNAs showed that UCP1 was the most dramatically downregulated gene, and its role in oxidative stress and apoptosis was assessed both in vitro and in vivo. Genetic deletion of UCP1 was used to investigate the effects of UCP1 on ischemia -indued acute kidney injury in mice.
2019-05-21 | GSE131454 | GEO
Project description:Sustained hepatic inflammation can contribute to cancer initiation and progression via tumor-initiating cell expansion, but underlying mechanisms remains unknown. Expression profiles of lncRNAs/mRNAs were measured in normal, chronic hepatitis, cirrhotic and cancerous livers. We found abundant disease-related lncRNAs/mRNAs deregulated across different stages of inflammation-triggered liver disease and refined a transformation gene signature to distinguish pathological liver tissues. Amongst this signature, a conserved lncRNA DANCR was silenced in normal adult liver, but overexpressed in fetal and cancerous livers. Remarkably, increased DANCR significantly correlates with poor prognosis in multiple-center cohorts and is directly induced by inflammatory pathways including NF-κB and STAT3. DANCR could suppress cell differentiation and drive expansion of tumor-initiating cells, leading to chemoresistance. Moreover, in vitro and in vivo inhibition confirms the significance of DANCR as a therapeutic target when combined with other chemotherapy. We illustrate the role of DANCR relies on the regulation of CTNNB1 in a novel miRNA-blocking manner. Our studies reveal the expression of lncRNAs/mRNAs in normal and pathological livers and suggest the importance of oncofetal lncRNA DANCR in inflammation-induced malignant transformation, offering a potential prognostic marker and a therapeutic target for HCC. In the study, 10 normal livers (NL), 10 chronic inflammatory livers (IL), 10 cirrhotic livers (CL), 13 early HCC (eHCC) and 13 advanced HCC (aHCC) samples were profiled their lncRNA/mRNA expression
2014-01-22 | E-GEOD-54238 | biostudies-arrayexpress
Project description:Chemoresistance is a major cause of poor prognosis of breast cancer.More and more mRNAs and lncRNAs are reported to upregulate chemoresistance in breast cancer.To explore the how mRNAs and lncRNAs involved in chemoresistance of breast cancer,we sceened upregulated mRNAs and lncRNA from parental MCF-7 , chemoresistant MCF-7 cells as well as 4 breast cancer tissue sensitive to chemotherapy and 4 resistant to chemotherapy . Total RNA was extracted using Trizol reagent. Agilent Human lncRNA Microarray V6 (4*180K) was used to analyze the global profiling of human lncRNAs and protein-coding transcripts in these samples. The microarray contains 83,835 lncRNAs and 27,233 coding genes.
2020-02-25 | E-MTAB-8787 | biostudies-arrayexpress
Project description:Endometriosis is a highly prevalent gynecological disease affecting 10% of women of reproductive age worldwide. miRNAs may play a role in endometriosis, though their exact function remains unclear. Here, we identified differentially expressed miRNAs in endometriosis and studied their functional role in the disease. (2) Methods: Endometrial tissue was collected from women with endometriosis (n=15) and non-endometriosis controls (n=17). Dysregulated miRNAs were identified through small RNA-sequencing, and their biological significance was explored by target gene prediction and pathway analysis. Selected miRNAs were examined in paired ectopic endometriomas and eutopic endometrium (n=10) using qRT-PCR. Their roles in cell migration and proliferation were further examined in vitro using functional assays. To identify potential target genes, we performed mRNA sequencing on transfected cells and the endometrioma cohort. (3) Results: We identified 14 dysregulated miRNAs in the eutopic endometrium of women with endometriosis compared to endometrial tissue from women without endometriosis. Pathway analysis indicated enrichment in cell migration and proliferation associated pathways. Further ex-vivo studies of miR-193b-5p and miR-374b-5p showed that both miRNAs were up-regulated in endometriomas. Overexpression of these two miRNAs in vitro inhibited cell migration and mRNA sequencing revealed several migration-related genes that are targeted by these miRNAs. (4) Conclusions: Our study identified two key endometrial miRNAs that may be involved in the pathogenesis of endometriosis by regulating cell migration.
2024-11-08 | GSE279835 | GEO