Expression profiling of lncRNA and mRNA in Hepatocellular carcinoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE101728 | GEO | 2019/08/06
REPOSITORIES: GEO
Similar Datasets
Project description:To explore the critical roles of miRNAs playing in the pathogenesis of hepatocellular carcinoma, the Agilent microarray was used to the profiling of miRNA expression in 7 pairs of HCC and matched adjacent tumor-free tissues.
2019-10-15 | GSE108724 | GEO
Project description:To explore the potential involvement of lncRNAs in hepatocellular carcinoma (HCC) oncogenesis, we conducted lncRNA and mRNA profiling in 3 pairs of human HCC and adjacent normal tissue (NT) by microarray. With abundant probes accounting for 33,045 lncRNAs and 30,215 coding transcripts in our microarray, the number of lncRNAs and coding transcripts that could be detected here is 10,149 and 14,944, respectively. From the data, thousands of lncRNAs and mRNAs were found to bedifferentially expressed (Fold Change≥2.0) in HCC tissues compared with NT and identified 624 lncRNAs and 1050 mRNAs were differentially expressed in all three HCC tissues.Bioinformatic analysis (gene ontology, pathway and network analysis) was performed for further study of these differentially expressed mRNAs.By qRT-PCR analysis in nineteen pairs HCC and adjacent normal tissues, we found that eightl ncRNAs were aberrantly expressed in HCC compared with corresponding NT, which is consistent with microarray data. Additionally, change trends of seven lncRNAs were basically identical to their nearby coding genes. In this study, to explore the potential involvement of lncRNAs in hepatocellular carcinoma (HCC) oncogenesis, we conducted lncRNA and mRNA profiling in 3 pairs of human HCC and adjacent normal tissue (NT) by microarray.
2014-02-21 | E-GEOD-55191 | biostudies-arrayexpress
Project description:LncRNA profiling of hepatocellular carcinoma vs. matched noncancerous liver tissue, aimed to analyze the lncRNA expression profile of hepatocellular carcinoma (HCC) and identify prognosis-related lncRNAs.
2023-06-25 | GSE72170 | GEO
Project description:LncRNAs are playing essential roles in epigenetic regulation, mRNA translation, and protein modification. However, the function of SLC7A11-AS1, an antisense lncRNA derived from the solute carrier family 7 member 11 (SLC7A11) gene, remains incompletely known. In this study, we utilized shRNA technology to knock down SLC7A11-AS1 in HepG2 cells, aiming to investigate the role of SLC7A11-AS1 in hepatocellular carcinoma. RNA-seq results revealed that there were 2536 differentially expressed genes upon SLC7A11-AS1 knockdown.
2024-07-17 | GSE244762 | GEO
Project description:The role of TGF-β-induced epithelial-mesenchymal transition (EMT) in cancer cell dissemination is well established, but the involvement of lncRNAs in TGF-β signaling is still unknown. In this study, we observed that the lncRNA-Activated by TGF-β (lncRNA-ATB) was upregulated in hepatocellular carcinoma (HCC) metastases and associated with poor prognosis. lncRNA-ATB upregulated ZEB1 and ZEB2 by competitively binding the miR-200 family and then induced EMT and invasion. In addition, lncRNA-ATB promoted organ colonization of disseminated tumor cells by binding IL11 mRNA, inducing autocrine of IL11 and triggering STAT3 signaling. Globally, lncRNA-ATB promotes the invasion-metastasis cascade. Thus, these findings suggest that lncRNA-ATB, a mediator of TGF-β signaling, could predispose HCC patients to metastases and may serve as a potential target for anti-metastatic therapies. To identify mRNA species bound by lncRNA-ATB, we performed an RIP to pull down endogenous mRNAs associated with the lncRNA-ATB and sequenced the retrieved RNA.
2014-02-08 | E-GEOD-54799 | biostudies-arrayexpress
Project description:To identify the novel tumor suppressors in hepatocellular carcinoma (HCC), we have employed whole genome microarray expression profiling as a discovery platform in HCC and paired normal liver tissues to identify genes which down-regulated in HCC. Among which, INTS6 and its pseudogene, namely INTS6P1, were found to be dramatically down-regulated in HCC. The down-regulated expression of INTS6 and INTS6P1 in HCC was further confirmed by real-time PCR. RNA was extracted from 3 pairs of HCC and normal liver tissue harvested from patients to undergo microarray study.
2015-01-03 | E-GEOD-64631 | biostudies-arrayexpress
Project description:Long noncoding RNAs (lncRNAs) are a class of non-coding RNAs longer than 200 nt that function in endogenous gene regulation and tumorigenesis. Hepatocellular carcinoma (HCC) is a heterogeneous disease with different treatment outcome. It is a challenge to develop a prognostic marker to identify HCC patients who are at greatest risk for recurrence or death. In this study, we try to screen lncRNAs whose expression levels are associated with recurrence or death of HCC patients through an extensive lncRNA profiling study on a cohort of 59 HCC patients. For these experiments, we used RNA extracted from 59 HCC tissues and 20 normal livers. Total RNAs from the 20 normal livers were pooled and used as a reference for all microarray experiments. For each microarray experiment, Cy5-labeled probes derived from the DNase-treated total RNA from each HCC sample was hybridized against Cy3-labeled probes derived from common reference on Arraystar Human LncRNA Microarray (Arraystar, Rockville, USA). LncRNAs whose expression was significantly associated with disease-specific survival and time to recurrence were selected based on microarray data. The univariate Cox proportional hazards model was used to assess the association of lncRNAs with survival. We computed a statistical significance level (P value) for two endpointsM-bM-^@M-^Tthe time to cancer-related death and time to recurrence, based on univariate Cox proportional hazards models in BRB-ArrayTools version 4.2.0.
2012-08-16 | E-GEOD-40144 | biostudies-arrayexpress
Project description:To explore the potential involvement of lncRNAs in hepatocellular carcinoma (HCC) oncogenesis, we conducted lncRNA and mRNA profiling in 3 pairs of human HCC and adjacent normal tissue (NT) by microarray. With abundant probes accounting for 33,045 lncRNAs and 30,215 coding transcripts in our microarray, the number of lncRNAs and coding transcripts that could be detected here is 10,149 and 14,944, respectively. From the data, thousands of lncRNAs and mRNAs were found to bedifferentially expressed (Fold Change≥2.0) in HCC tissues compared with NT and identified 624 lncRNAs and 1050 mRNAs were differentially expressed in all three HCC tissues.Bioinformatic analysis (gene ontology, pathway and network analysis) was performed for further study of these differentially expressed mRNAs.By qRT-PCR analysis in nineteen pairs HCC and adjacent normal tissues, we found that eightl ncRNAs were aberrantly expressed in HCC compared with corresponding NT, which is consistent with microarray data. Additionally, change trends of seven lncRNAs were basically identical to their nearby coding genes.
2014-02-21 | GSE55191 | GEO
Project description:Baicalein, a purified flavonoid compound with defined chemical structure extracted from the dry roots of Scutellaria radix that is a broadly used herb in China, has been proved to possess significant anti-hepatoma activity by inhibiting cell proliferation, invasion, metastasis and inducing apoptosis, autophagy via several cancer-related signaling molecules. In recent years, emerging studies have demonstrated that Chinese medicinal herbs can exert their anti-tumor effects through targeting lncRNAs，such as curcumin, camptothecin, resveratrol，paclitaxel. However, there is still no related report about the effects of baicalein on lncRNA expression profile when it exerts its inhibition on hepatoma tumor growth. To investigate whether the antitumor effect of baicalein is related to its modulation of lncRNA expression in hepatocellular carcinoma (HCC), we profiled the lncRNA expression in HCC cell line Bel-7402 treated with baicalein (0, 40, 80μM) for 24 hours using lncRNA microarray and detected the changes by comparing the lncRNA expression profile of HCC cell line Bel-7402 treated with baicalein (40 and 80 μM) and its DMSO control (0 μM). These findings suggest that modulation of lncRNA expression may be an important mechanism underlying the anti-hepatoma effects of baicalein and lay the groundwork for further investigations. To investigate whether the antitumor effect of baicalein is related to its modulation of lncRNA expression in hepatocellular carcinoma (HCC), we profiled the miRNA expression in HCC cell line Bel-7402 treated with baicalein (0, 40, 80μM) for 24 hours using miRNA microarray and detected the changes by comparing the lncRNA expression profile of HCC cell line Bel-7402 treated with baicalein (40 and 80 μM) and its DMSO control (0 μM). These findings suggest that modulation of lncRNA expression may be an important mechanism underlying the anti-hepatoma effects of baicalein and lay the groundwork for further investigations.
2018-03-01 | GSE95504 | GEO
Project description:Objective: The aim of this study was to reveal the function of the long non-coding RNA (lncRNA) RP11-556E13.1 (RP11) and its clinical significance in hepatocellular carcinoma. Methods: LncRNA and mRNA expression profiling was performed using lncRNA and mRNA microarrays in 5 pairs of HCC and adjacent tissues. 112 paired HCC and adjacent tissue samples were analyzed by semiquantitative real-time polymerase chain reaction (sqRT-PCR) to evaluate the expression of RP11 and its possible associated clinical significance. Smart silencer RNA (siRNA) was used to knockdown the expression of RP11 in HCC cells. After knockdown, the function of RP11 was determined in vitro using some kinds of cell functional experiments in HCC cells including cell proliferation assay, cell apoptosis assay and cell cycle assay. Western blotting (WB) was performed to detect proteins that were presumably associated with these functional changes. An Affymetrix Human HTA2.0 microarray was used to detect differentially expressed genes in HCC cells after RP11 knockdown. GO enrichment and KEGG pathway enrichment analysis were then performed to elucidate the biological roles of these differentially expressed mRNAs.
2022-04-18 | GSE200861 | GEO