HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE191267 | GEO | 2021/12/22
REPOSITORIES: GEO
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Project description:Purpose: To explore the potential integrated molecular network by long non-coding RNA HOXA11-AS in keloid fibroblast Methods: Using primary cultured keloid-derived fibroblasts (sample 0), small interfering RNAs were designed and transfected into two keloid fibroblast samples (samples 1 and 2) to knockdown HOXA11-AS. One nonspecific transfection control (sample 3) and one blank control (sample 4) were used to remove nonspecific overlap from the studied group. The lncRNAs, messenger RNAs (mRNAs), and microRNAs (miRNAs) of five samples were sequenced to identify differentially expressed (DE) profiles in HOXA11-AS-knockdown keloid fibroblasts in samples 1 and 2, which facilitated removal of overlap with the nonspecific controls (samples 3 and 4). Using stepwise bioinformatic analysis, DE lncRNA and mRNAs characterized by close and natural antisense relationship were constructed into an interactive network by bioinformatic analysis. Based on this network, a lncRNA–mRNA–protein interaction network was extended by integration of the human protein–protein interaction (PPI) network. The Page Rank algorithm was used to score each mRNA in the extended LMN network to reveal significant functioning genes. Next, screened genes were validated by real-time PCR and western blot ting. Validated genes were used to construct a competing endogenous network based on DE miRNA profiles. Results: SNED1, NIPAL3, and VTN were detected significantly changed in HOXA11-AS-knockdown keloid fibroblasts. Only NIPAL3 was predicted to be involved in an intergated network for HOXA11-AS via three competing endogenous miRNAs (hsa-miRNA-19a-3p, hsa-miR-141-3p, and hsa-miR-140- 5p). Conclusion: An interactive molecular network of HOXA11-AS–three miRNAs–NIPAL3 was predicted in keloid fibroblasts
2021-12-22 | GSE191265 | GEO
Project description:Purpose: To explore the potential integrated molecular network by long non-coding RNA HOXA11-AS in keloid fibroblast Methods: Using primary cultured keloid-derived fibroblasts (sample 0), small interfering RNAs were designed and transfected into two keloid fibroblast samples (samples 1 and 2) to knockdown HOXA11-AS. One nonspecific transfection control (sample 3) and one blank control (sample 4) were used to remove nonspecific overlap from the studied group. The lncRNAs, messenger RNAs (mRNAs), and microRNAs (miRNAs) of five samples were sequenced to identify differentially expressed (DE) profiles in HOXA11-AS-knockdown keloid fibroblasts in samples 1 and 2, which facilitated removal of overlap with the nonspecific controls (samples 3 and 4). Using stepwise bioinformatic analysis, DE lncRNA and mRNAs characterized by close and natural antisense relationship were constructed into an interactive network by bioinformatic analysis. Based on this network, a lncRNA–mRNA–protein interaction network was extended by integration of the human protein–protein interaction (PPI) network. The Page Rank algorithm was used to score each mRNA in the extended LMN network to reveal significant functioning genes. Next, screened genes were validated by real-time PCR and western blot ting. Validated genes were used to construct a competing endogenous network based on DE miRNA profiles. Results: SNED1, NIPAL3, and VTN were detected significantly changed in HOXA11-AS-knockdown keloid fibroblasts. Only NIPAL3 was predicted to be involved in an intergated network for HOXA11-AS via three competing endogenous miRNAs (hsa-miRNA-19a-3p, hsa-miR-141-3p, and hsa-miR-140- 5p). Conclusion: An interactive molecular network of HOXA11-AS–three miRNAs–NIPAL3 was predicted in keloid fibroblasts
2021-12-22 | GSE191266 | GEO
Project description:HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network
| PRJNA790821 | ENA
Project description:HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [miRNA-Seq]
| PRJNA790834 | ENA
Project description:HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [RNA-Seq]
| PRJNA790825 | ENA
Project description:HspB5/alphaB-crystallin is an ubiquitously expressed member of the small heat shock protein family which help cells to survive cellular stress conditions and are also implicated in neurodegenerative diseases. MicroRNAs are small non-coding RNAs fine-tuning protein expression mainly by inhibiting the translation of target genes. Our earlier finding of an increase in HspB5/alphaB-crystallin protein amount after heat shock in rat hippocampal neurons without a concomitant increase of mRNA prompted us to look for microRNAs as a posttranscriptional regulatory mechanism. Microarray miRNA expression data of rat hippocampal neurons under control and stress conditions in combination with literature search, miRNA binding site prediction and conservation of target sites yielded nine candidate microRNAs. Of these candidates, five (miR-101a-3p, miR-129-2-3p, miR-330-5p, miR-376b-3p, and miR-491-5p) were able to convey a downregulation by binding to the HspB5 3'- or 5'-UTR in a luciferase reporter gene assay while one (miR-140-5p) led to an upregulation. Overexpression of these six microRNAs in C6 glioma cells showed that three of them (miR-101a-3p, miR-140-5p, and miR-376b-3p) regulated endogenous HspB5 protein amount significantly in the same direction as in the reporter gene assay. In addition, overexpression of miR-330-5p and miR-491-5p in C6 cells resulted in regulation of HspB5 in the opposite direction as expected from the luciferase assay. Analysis of miRNA expression in rat hippocampal neurons after cellular stress by qPCR showed that miR-491-5p was not expressed in these cells. In total, we therefore identified four microRNAs, namely miR-101a-3p, miR-140-5p, miR-330-5p, and miR-376b-3p, which can regulate rat HspB5 directly or indirectly.
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Project description:The specific causes of recurrent spontaneous abortion (RSA) remain unknown in 37-79% of affected women. The aim of this study was to explore the expression levels of 6 miRNAs in natural killer (NK) cells from the decidua of patients with unexplained RSA (URSA) and to predict the target genes of 3 miRNAs.Two groups were examined: URSA (n=20) and controls (n=20). Flow cytometry analysis was used to identify NK cells isolated from the decidua. Transcriptional levels of miRNA were monitored using quantitative real-time reverse transcription-polymerase chain reaction. Prediction and analysis of mRNA targets of differentially expressed miRNAs were performed using bioinformatics methods.Five miRNAs [miR-34a (+281%, P<0.001), miR-155 (+396%, P<0.001), miR-141 (+142%, P<0.01), miR-125a (+279%, P<0.001), and miR-125b (+185%, P<0.001)] were up-regulated, while miR-24 was down-regulated (-64%, P<0.01) in the URSA group, compared to the control group. This study identified potential miRNA targets: miR-34a-3p/5p, 585/1718 (targets of miR-34a-3p/targets of miR-34a-5p), miR-141-3p/5p, 2270/629 (targets of miR-141-3p/targets of miR-141-5p), and miR-24, 2320 target genes. A total of 140 pathways related to target genes were identified including PI3K-Akt, focal adhesion, MAPK, Wnt, regulation of the actin cytoskeleton, T cell receptor, TGF-?, and estrogen signaling pathways.This study suggests that miR-34a-3p/5p, miR-141-3p/5p, and miR-24 in decidual NK cells could be associated with URSA. These findings might contribute to the panel of diagnostic and prognostic biomarkers with clinical utility, and facilitate the development of new strategies for targeted therapy against URSA.
| S-EPMC4805134 | biostudies-literature
Project description:Neuropathic pain in spinal cord injury (SCI) is associated with inflammation in both the peripheral and central nervous system (CNS), which may contribute to the initiation and maintenance of persistent pain. An understanding of factors contributing to neuroinflammation may lead to new therapeutic targets for neuropathic pain. Moreover, novel circulating biomarkers of neuropathic pain may facilitate earlier and more effective treatment. MicroRNAs (miRNAs) are short, non-coding single-stranded RNA that have emerged as important biomarkers and molecular mediators in physiological and pathological conditions. Using a genome-wide miRNA screening approach, we studied differential miRNA expression in plasma from 68 healthy, community-dwelling adults with and without SCI enrolled in ongoing clinical studies. We detected 2367 distinct miRNAs. Of these, 383 miRNAs were differentially expressed in acute SCI or chronic SCI versus no SCI and 71 were differentially expressed in chronic neuropathic pain versus no neuropathic pain. We selected homo sapiens (hsa)-miR-19a-3p and hsa-miR-19b-3p for additional analysis based on p-value, fold change, and their known role as regulators of neuropathic pain and neuroinflammation. Both hsa-miR-19a-3p and hsa-miR-19b-3p levels were significantly higher in those with chronic SCI and severe neuropathic pain versus those with chronic SCI and no neuropathic pain. In confirmatory studies, both hsa-miR-19a-3p and hsa-miR-19b-3p have moderate to strong discriminative ability to distinguish between those with and without pain. After adjusting for opioid use, hsa-miR-19b-3p levels were positively associated with pain interference with mood. Because hsa-miR-19 levels have been shown to change in response to exercise, folic acid, and resveratrol, these studies suggest that miRNAs are potential targets of therapeutic interventions.
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Project description:This is a prospective-retrospective study to determine if the expression of the miRNA’s miR-31-3p and miR-31-5p are prognostic of patient outcomes or predictive of the benefit from anti-EGFR therapy in stage III Colon Cancer. The present study will utilize FFPE tumor samples collected from patients enrolled in the PETACC-8 study conducted by the Fédération Francophone de Cancérologie Digestive (FFCD). This phase 3 clinical trial prospectively randomized fully resected stage III colon cancer patients to receive adjuvant treatment with either FOLFOX-4 plus cetuximab or FLOFOX-4 alone.
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Project description:Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. We report that the miR-106b~25cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. To identify the relevant targets of individual miRNAs in the miR-106b~15 cluster and elucidate the molecular mechanisms underlying the proliferative effects of this microRNA cluster, we assessed the global transcriptomic changes by deep-sequencing total neonatal mouse cardiomyocyte RNA after exogeneous transfection with hsa-miR-106b-5p, hsa-miR-93-5p, hsa-miR-25-3p and compared the transcriptomic profiles to cardiomyocytes transfected with cel-miR-67, a control miRNA.
2021-06-25 | GSE178867 | GEO