scholarly journals APOBEC3B and SPAG5, the Target Genes of miR-539, Involved into Imatinib-Resistant of Gastrointestinal Stromal Tumors

2020 ◽  
Author(s):  
Qianqian Zhang ◽  
Haiyun Liu ◽  
Xingmin Li ◽  
Hongxing Wang
Keyword(s):  
T Cells ◽  
Gene Network ◽  
Target Genes ◽  
Mirna Gene ◽  
Mitotic Cell ◽  
Mitotic Cell Cycle ◽  
Qrt Pcr ◽  
Imatinib Resistant ◽  
Gene Modules ◽  
Tgf Β1

Abstract Background: Although imatinib can effectively treat gastrointestinal stromal tumor (GIST), some patients are still resistant to it or cannot tolerate the adverse reactions of the drug. This study aimed to investigate potential miRNAs, mRNA and tumor-infiltrating lymphocytes (TILs) associated with the prognosis of imatinib-resistant GIST.Methods: mRNA, miRNA sequencing data and patient clinic traits of primary (imatinib-naive) and imatinib-resistant GIST were obtained from GEO (Gene Expression Omnibus) database. A systems biology approach combining Weighted co-expression network analysis (WGCNA) and differential expression analysis were utilized to detect the imatinib-resistant-related miRNA and gene modules and construct a miRNA-gene network. Tumor-infiltrating immune cells were analyzed by Estimating the Proportion of Immune and Cancer cells (EPIC) and Tumor-Immune System Interactions (TISIDB). miR-539 was measured by qRT-PCR. SPAG5 and APOBEC3B was measured by qRT-PCR and WB. Transforming growth factor (TGF)-β and interleukin (IL)-10 were assessed with enzyme-linked immunosorbent assay (ELISA). The proportions of CD4+ T cells, CD8+ T cells , NK cells and B cells in tumor-infiltrating lymphocyteswere analyzed via flow cytometry (FCM).Results: Two gene modules (brown and yellow) and one miRNA module were associated with the imatinib-resistant. Two hub genes (APOBEC3B and SPAG5) were associated with the imatinib-resistant. Three hub miRNAs were identified to be related to imatinib-resistant (miR-539, miR-376b and miR-18b). G1/S transition of mitotic cell cycle, G2/M transition of mitotic cell cycle, and cell proliferation were common pathways of the gene modules and miRNA module. apolipoprotein B mRNA editing catalytic polypeptide-like 3B (APOBEC3B) and Sperm-associated antigen 5 (SPAG5), which were both target genes of miR-539 was located at the core of miRNA–gene network. APOBEC3B (rho=0.509, p < 2.2e-16) and SPAG5 (rho=0.468, p < 2.2e-16) was positive correlated with the infiltration levels of activated CD4+ T cells. he proportions of CD4+ T cells, and the mRNA and protein relative expression of APOBEC3B and SPAG5 in imatinib-resistant tumor samples significantly increased as compared with tumor samples in imatinib-naive group. Imatinib-resistant tumor samples exhibited significantly downregulation of miR-539 and TGF-β1. Over-expression of miR-539 sensitized imatinib resistant GIST48 cells and increased the secretion of TGF-β1 by inhibiting APOBEC3B and SPAG5.Conclusion: APOBEC3B and SPAG5, the target genes of miR-539 may play as key factor for imatinib-resistant GIST by increasing the proportion of tumor-infiltrated activated CD4+ T cells via TGF-β1. These findings help to advance the understanding of imatinib-resistant GIST and provide potential therapeutic targets.

scholarly journals Bioinformatics analysis of miRNA and mRNA expression profiles to reveal the key miRNAs and genes in osteoarthritis

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Pei-yan Huang ◽  
Jun-guo Wu ◽  
Jun Gu ◽  
Tie-qi Zhang ◽  
Ling-feng Li ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Expression Profile ◽  
Target Genes ◽  
Glycogen Synthase ◽  
Expression Profiles ◽  
Mirna Gene ◽  
Functional Enrichment ◽  
Joint Disease ◽  
Expression Levels ◽  
Qrt Pcr

Abstract Background Osteoarthritis (OA) is a chronic degenerative joint disease and the most frequent type of arthritis. This study aimed to identify the key miRNAs and genes associated with OA progression. Methods The GSE105027 (microRNA [miRNA/miR] expression profile; 12 OA samples and 12 normal samples) and GSE48556 (messenger RNA [mRNA] expression profile; 106 OA samples and 33 normal samples) datasets were selected from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and miRNAs (DEMs) were analyzed using the limma and ROCR packages in R, respectively. The target genes that negatively correlated with the DEMs were predicted, followed by functional enrichment analysis and construction of the miRNA-gene and miRNA-transcription factor (TF)-gene regulatory networks. Additionally, key miRNAs and genes were screened, and their expression levels were verified by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results A total of 1696 DEGs (739 upregulated and 957 downregulated) and 108 DEMs (56 upregulated and 52 downregulated) were identified in the OA samples. Furthermore, 56 target genes that negatively correlated with the DEMs were predicted and found to be enriched in three functional terms (e.g., positive regulation of intracellular protein transport) and three pathways (e.g., human cytomegalovirus infection). In addition, three key miRNAs (miR-98-5p, miR-7-5p, and miR-182-5p) and six key genes (murine double minute 2, MDM2; glycogen synthase kinase 3-beta, GSK3B; transmembrane P24-trafficking protein 10, TMED10; DDB1 and CUL4-associated factor 12, DCAF12; caspase 3, CASP3; and ring finger protein 44, RNF44) were screened, among which the miR-7-5p → TMED10/DCAF12, miR-98-5p → CASP3/RNF44, and miR-182-5p → GSK3B pairs were observed in the regulatory network. Moreover, the expression levels of TMED10, miR-7-5p, CASP3, miR-98-5p, GSK3B, and miR-182-5p showed a negative correlation with qRT-PCR verification. Conclusion MiR-98-5p, miR-7-5p, miR-182-5p, MDM2, GSK3B, TMED10, DCAF12, CASP3, and RNF44 may play critical roles in OA progression.

scholarly journals Identification and Insilico Analysis of Retinoblastoma Serum microRNA Profile and Gene Targets towards Prediction of Novel Serum Biomarkers

2013 ◽  
Vol 7 ◽  
pp. BBI.S10501 ◽  
Author(s):  
Madhu Beta ◽  
Nalini Venkatesan ◽  
Madavan Vasudevan ◽  
Umashankar Vetrivel ◽  
Vikas Khetan ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Target Genes ◽  
Mirna Gene ◽  
Target Prediction ◽  
Fold Change ◽  
Serum Samples ◽  
Gene Target ◽  
Qrt Pcr ◽  
Serum Microrna ◽  
Oncogenic Mirnas

Retinoblastoma (RB) is a malignant tumor of the retina seen in children, and potential non invasive biomarkers are in need for rapid diagnosis and for prognosticating the therapy. This study was undertaken to identify the differentially expressed miRNAs in the serum of children with RB in comparison with the normal age matched serum, to analyze its concurrence with the existing RB tumor miRNA profile, to identify its novel gene targets specific to RB, and to study the expression of a few of the identified oncogenic miRNAs in the advanced stage primary RB patient's serum sample. MiRNA profiling was performed on 14 pooled serum from children with advanced RB and 14 normal age matched serum samples, wherein 21 miRNAs were found to be upregulated (fold change ≥ +2.0, P ≤ 0.05) and 24 to be downregulated (fold change ≤ –2.0, P ≤ 0.05). Furthermore, intersection of 59 significantly deregulated miRNAs identified from RB tumor profiles with that of miRNAs detected in serum profile revealed that 33 miRNAs had followed a similar deregulation pattern in RB serum. Later we validated a few of the miRNAs (miRNA 17-92) identified by microarray in the RB patient serum samples (n = 20) by using qRT-PCR. Expression of the oncogenic miRNAs, miR-17, miR-18a, and miR-20a by qRT-PCR was significant in the serum samples exploring the potential of serum miRNAs identification as noninvasive diagnosis. Moreover, from miRNA gene target prediction, key regulatory genes of cell proliferation, apoptosis, and positive and negative regulatory networks involved in RB progression were identified in the gene expression profile of RB tumors. Therefore, these identified miRNAs and their corresponding target genes could give insights on potential biomarkers and key events involved in the RB pathway.

scholarly journals An Integrated Bioinformatics Analysis of the Potential Regulatory Effects of miR-21 on T-cell Related Target Genes in Multiple Sclerosis

2021 ◽  
Author(s):  
Mostafa Manian ◽  
Ehsan Sohrabi ◽  
Nahid Eskandari ◽  
Mohammad-Ali Assarehzadegan ◽  
Gordon A. Ferns ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
T Cells ◽  
T Cell ◽  
Differentially Expressed Genes ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Mirna Gene ◽  
Differentially Expressed ◽  
Inflammatory Factors ◽  
Ppi Networks

Background: Overexpression of miR-21 is a characteristic feature of patients with Multiple Sclerosis (MS) and is involved in gene regulation and the expression enhancement of pro-inflammatory factors including IFNγ and TNF-α following stimulation of T-cells via the T Cell Receptor (TCR). In this study, a novel integrated bioinformatics analysis was used to obtain a better understanding of the involvement of miR-21 in the development of MS, its protein biomarker signatures, RNA levels, and drug interactions through existing microarray and RNA-seq datasets of MS.   Methods: In order to obtain data on the Differentially Expressed Genes (DEGs) in patients with MS and normal controls, the GEO2R web tool was used to analyze the Gene Expression Omnibus (GEO) datasets, and then Protein-Protein Interaction (PPI) networks of co-expressed DEGs were designed using STRING. A molecular network of miRNA-genes and drugs based on differentially expressed genes was created for T-cells of MS patients to identify the targets of miR-21, that may act as important regulators and potential biomarkers for early diagnosis, prognosis and, potential therapeutic targets for MS.   Results: It found that seven genes (NRIP1, ARNT, KDM7A, S100A10, AK2, TGFβR2, and IL-6R) are regulated by drugs used in MS and miR-21. Finally, three overlapping genes (S100A10, NRIP1, KDM7A) were identified between miRNA-gene-drug network and nineteen genes as hub genes which can reflect the pathophysiology of MS.    Conclusion: Our findings suggest that miR-21 and MS-related drugs can act synergistically to regulate several genes in the existing datasets, and miR-21 inhibitors have the potential to be used in MS treatment.

scholarly journals Abnormal expression of rno_circRNA_014900 and rno_circRNA_005442 induced by ketamine in the rat hippocampus

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jing Mao ◽  
Tianmei Li ◽  
Di Fan ◽  
Hongli Zhou ◽  
Jianguo Feng ◽  
...  
Keyword(s):  
Target Genes ◽  
Circular Rna ◽  
Fold Change ◽  
Rat Hippocampus ◽  
Antidepressant Effect ◽  
Signal Pathways ◽  
Qrt Pcr ◽  
Abnormal Expression ◽  
Reverse Transcription Pcr ◽  
Pathway Analyses

Abstract Background Recent studies have shown that circular RNA (circRNA) is rich in microRNA (miRNA) binding sites. We have previously demonstrated that the antidepressant effect of ketamine is related to the abnormal expression of various miRNAs in the brain. This study determined the expression profile of circRNAs in the hippocampus of rats treated with ketamine. Methods The aberrantly expressed circRNAs in rat hippocampus after ketamine injection were analyzed by microarray chip, and we further validated these circRNAs by quantitative reverse-transcription PCR (qRT-PCR). The target genes of the different circRNAs were predicted using bioinformatic analyses, and the functions and signal pathways of these target genes were investigated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Results Microarray analysis showed that five circRNAs were aberrantly expressed in rat hippocampus after ketamine injection (fold change > 2.0, p < 0.05). The results from the qRT-PCR showed that one of the circRNAs was significantly increased (rno_circRNA_014900; fold change = 2.37; p = 0.03), while one was significantly reduced (rno_circRNA_005442; fold change = 0.37; p = 0.01). We discovered a significant enrichment in several GO terms and pathways associated with depression. Conclusion Our findings showed the abnormal expression of ketamine-induced hippocampal circRNAs in rats.

scholarly journals CircHYBID regulates hyaluronan metabolism in chondrocytes via hsa-miR-29b-3p/TGF-β1 axis

2021 ◽  
Vol 27 (1) ◽  
Author(s):  
Hong-Xing Liao ◽  
Zhi-Hui Zhang ◽  
Hui-Lin Chen ◽  
Ying-Mei Huang ◽  
Zhan-Liang Liu ◽  
...  
Keyword(s):  
Transforming Growth Factor ◽  
Pathological Examination ◽  
Circular Rnas ◽  
Enzyme Linked Immunosorbent Assay ◽  
Mechanism Analysis ◽  
Gain Of Function ◽  
Qrt Pcr ◽  
Intact Cartilage ◽  
Ha Synthase ◽  
Tgf Β1

Abstract Background Hyaluronan (HA) metabolism by chondrocytes is important for cartilage development and homeostasis. However, information about the function of circular RNAs (circRNAs) in HA metabolism is limited. We therefore profiled the role of the novel HA-related circRNA circHYBID in the progression of osteoarthritis (OA). Methods CircHYBID function in HA metabolism in chondrocytes was investigated using gain-of-function experiments, and circHYBID mechanism was confirmed via bioinformatics analysis and luciferase assays. The expression of circHYBID–hsa-miR-29b-3p–transforming growth factor (TGF)-β1 axis was examined by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. CircHYBID, TGF-β1, and HA levels in cartilage samples were evaluated using qRT-PCR and pathological examination. Enzyme-linked immunosorbent assay was used to assess HA accumulation in chondrocyte supernatant. Results CircHYBID expression was significantly downregulated in damaged cartilage samples compared with that in the corresponding intact cartilage samples. CircHYBID expression was positively correlated with alcian blue score. Interleukin-1β stimulation in chondrocytes downregulated circHYBID expression and decreased HA accumulation. Gain-of-function experiments revealed that circHYBID overexpression in chondrocytes increased HA accumulation by regulating HA synthase 2 and HYBID expression. Further mechanism analysis showed that circHYBID upregulated TGF-β1 expression by sponging hsa-miR-29b-3p. Conclusions Our results describe a novel HA-related circRNA that could promote HA synthesis and accumulation. The circHYBID–hsa-miR-29b-3p–TGF-β1 axis may play a powerful regulatory role in HA metabolism and OA progression. Thus, these findings will provide new perspectives for studies on OA pathogenesis, and circHYBID may serve as a potential target for OA therapy.

scholarly journals miR-373-3p Regulates Invasion and Migration Abilities of Trophoblast Cells via Targeted CD44 and Radixin

2021 ◽  
Vol 22 (12) ◽  
pp. 6260
Author(s):  
Hyun-Jung Lee ◽  
Seung Mook Lim ◽  
Hee Yeon Jang ◽  
Young Ran Kim ◽  
Joon-Seok Hong ◽  
...  
Keyword(s):  
Preterm Labor ◽  
Target Genes ◽  
Gene Array ◽  
Migration And Invasion ◽  
Trophoblast Cells ◽  
Invasion And Migration ◽  
Mirna Array ◽  
Qrt Pcr ◽  
Putative Target ◽  
And Migration

Preterm labor (PTL) is one of the obstetric complications, and is known to be associated with abnormal maternal inflammatory response and intrauterine inflammation and/or infection. However, the expression of specific miRNAs associated with PTL is not clear. In this study, we performed combination analysis of miRNA array and gene array, and then selected one miRNA (miR-373-3p) and its putative target genes (CD44 and RDX) that exhibited large expression differences in term and PTL placentas with or without inflammation. Using qRT-PCR and luciferase assays, we confirmed that miR-373-3p directly targeted CD44 and RDX. Overexpression of miR-373-3p reduced the migration and invasion of trophoblast cells, while inhibition of miR-373-3p restored the migration and invasion abilities of trophoblast cells. Finally, we validated the expression of miR-373-3p and its target genes in clinical patients’ blood. miR-373-3p was increased in PTL patients’ blood, and was the most expressed in PTL patients’ blood with inflammation. In addition, by targeting the miR-373-3p, CD44 and RDX was decreased in PTL patients’ blood, and their expression were the lowest in PTL patients’ blood with inflammation. Taken together, these findings suggest that miR-373-3p and its target genes can be potential biomarkers for diagnosis of PTL.

scholarly journals Microrna-130a Downregulates HCV Replication through an atg5-Dependent Autophagy Pathway

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 338 ◽  
Author(s):  
Xiaoqiong Duan ◽  
Xiao Liu ◽  
Wenting Li ◽  
Jacinta A. Holmes ◽  
Annie J. Kruger ◽  
...  
Keyword(s):  
Immune Responses ◽  
Binding Sites ◽  
Target Gene ◽  
Target Genes ◽  
Pyruvate Metabolism ◽  
Host Immune Responses ◽  
Qrt Pcr ◽  
Antiviral Genes ◽  
Autophagy Pathway ◽  
Host Antiviral Response

We previously identified that miR-130a downregulates HCV replication through two independent pathways: restoration of host immune responses and regulation of pyruvate metabolism. In this study, we further sought to explore host antiviral target genes regulated by miR-130a. We performed a RT² Profiler™ PCR array to identify the host antiviral genes regulated by miR-130a. The putative binding sites between miR-130a and its downregulated genes were predicted by miRanda. miR-130a and predicted target genes were over-expressed or knocked down by siRNA or CRISPR/Cas9 gRNA. Selected gene mRNAs and their proteins, together with HCV replication in JFH1 HCV-infected Huh7.5.1 cells were monitored by qRT-PCR and Western blot. We identified 32 genes that were significantly differentially expressed more than 1.5-fold following miR-130a overexpression, 28 of which were upregulated and 4 downregulated. We found that ATG5, a target gene for miR-130a, significantly upregulated HCV replication and downregulated interferon stimulated gene expression. miR-130a downregulated ATG5 expression and its conjugation complex with ATG12. ATG5 and ATG5-ATG12 complex affected interferon stimulated gene (ISG) such as MX1 and OAS3 expression and subsequently HCV replication. We concluded that miR-130a regulates host antiviral response and HCV replication through targeting ATG5 via the ATG5-dependent autophagy pathway.

TGF-β1-induced regulatory T cells

2015 ◽  
Vol 76 (8) ◽  
pp. 561-564 ◽  
Author(s):  
Eva N. Hadaschik ◽  
Alexander H. Enk
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Tgf Β1
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