Determine changes of lncRNAs expression in malignant hepatocytes
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE56384 | GEO | 2014/04/01
SECONDARY ACCESSION(S): PRJNA243082
REPOSITORIES: GEO
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Project description:We performed a hybridization-based microarray analysis for lncRNA expression to understand the involvement of lncRNAs in HCC and to investigate differentially expressed lncRNAs in HCC, thereby characterizing their potential roles in tumor growth. The expression profiles of SMMC7721 HepG2 and Huh7 human HCC cell lines and the HL-7702 human immortalized normal hepatocyte cells were performed by the lncRNA microassay. SMMC7721, HepG2 and Huh7 human HCC cell lines were defined as the experimental group and HL-7702 cell line was used as the control.
2014-04-01 | E-GEOD-56384 | 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. 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: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:Small, compact genomes confer a selective advantage to viruses, yet human cytomegalovirus (HCMV) expresses the long non-coding RNAs (lncRNAs) RNA1.2, RNA2.7, RNA4.9, and RNA5.0. These lncRNAs account for majority of the viral transcriptome, but their functions remain largely unknown. Here, we showed that HCMV lncRNAs, except for RNA5.0, are required throughout the entire viral life cycle. Deletion of each lncRNA resulted in a decrease in viral progeny during lytic replication and failing to efficiently establish latent reservoirs and reactivate. Nanopore direct RNA sequencing of native lncRNA molecules revealed that each lncRNA exhibited a dynamic modification landscape, depending on the state of infection. Global analysis of the lncRNA interactome identified 32, 11, and 89 host factors that specifically bind to RNA1.2, RNA2.7, and RNA4.9, respectively. Moreover, 52 proteins commonly bound to the three lncRNAs were identified, including 11 antiviral immunity-related proteins. Our molecular analyses found that three lncRNAs are modified with N⁶-methyladenosine (m6A) and interact with m6A readers in all infection states. In-depth functional analysis revealed that m6A–mediated lncRNA stabilization as the key mechanism by which lncRNAs are maintained at high levels. Our study lays the groundwork for understanding viral lncRNA–mediated regulation of host-virus interaction throughout the HCMV life cycle.
2022-11-14 | PXD034587 | Pride
Project description:The role of TGF-M-NM-2-induced epithelial-mesenchymal transition (EMT) in cancer cell dissemination is well established, but the involvement of lncRNAs in TGF-M-NM-2 signaling is still unknown. In this study, we observed that the lncRNA-Activated by TGF-M-NM-2 (lncRNA-ATB) was upregulated in hepatocellular carcinoma (HCC) metastases and associated with poor prognosis. lncRNA-ATB promotes the invasion-metastasis cascade, which suggest that lncRNA-ATB, a mediator of TGF-M-NM-2 signaling, could predispose HCC patients to metastases and may serve as a potential target for anti-metastatic therapies. SMMC-7721 hepatoma cells were continuously treated with 10 ng/ml of recombinant TGF-M-NM-21 for 21 days. Total RNA recovered from three untreated cells and three treated cells were used to acquire different expression profiles of mRNAs and lncRNAs.
2014-02-08 | E-GEOD-54797 | biostudies-arrayexpress
Project description:Functional studies of long noncoding RNAs (lncRNAs) have long been hindered by a lack of methods to assess their evolution. Here, we present lncHOME (lncRNA Homology Explorer), a computational pipeline that identifies a unique coPARSE-lncRNA class with conserved genomic locations and patterns of RNA binding protein (RBP) binding sites. Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish. Using CRISPR-Cas12a knockout and rescue assays, we found that knocking out many human coPARSE-lncRNAs led to cell proliferation defects that were rescued by predicted zebrafish homologs. Knocking down the coPARSE-lncRNAs in zebrafish embryos caused severe developmental delays that were rescued by human homologs. Moreover, we verified that human, mouse, and zebrafish coPARSE-lncRNA homologs tend to bind similar RBPs with their conserved fuctions relying on specific RBP binding sites. Overall, our study demonstrates a comprehensive approach for studying functional conservation of lncRNAs and implicates numerous lncRNAs in regulating cellular physiology.
2024-01-26 | PXD046452 | Pride
Project description:Liver regeneration has important implications because many therapeutic strategies for the surgical treatment of liver diseases, such as removal of liver tumors and liver transplantation, depend on the ability of the liver to regenerate physically and functionally. Recent studies reported that lncRNAs control cell proliferation in hepatocellular carcinoma (HCC). However, the role of lncRNAs in liver regeneration and the overall mechanisms remain largely unknown. To address this issue, we carried out a genome-wide lncRNA microarray analysis during liver regeneration in mice after 2/3 partial hepatectomy (PH) at various time points. The results revealed differential expression of thousands of lncRNAs during liver regeneration. Six-week-old male wildtype C57Bl/6 mouse liver samples were obtained at 0, 1.5, 12, and 24 hours after 2/3 PH, and three mice were analyzed for each time point. Total RNA was isolated using Trizol.Mouse Stringent LncRNA Array (4 x 44K, ArrayStar, Rockville, MD) were used to monitor the expression level of approximately 14000 lncRNAs identified from the NCBI RefSeq, UCSC, RNAdb2.0, NRED, Fantom3.0 and UCRs. LncRNAs differentially expressed were identified by comparing expression levels during liver regeneration in mice after 2/3 partial hepatectomy (PH) at various time points.
2013-04-24 | E-GEOD-43687 | biostudies-arrayexpress
Project description:Long noncoding RNAs (LncRNAs) are an important class if pervasive genes involved in a variety of biological functions. LncRNAs have been recently implicated as having oncogenic and tumor suppressor roles. To further investigate the function of lncRNA in gastric cancer, we use lncRNA microarray to describe LncRNAs profiles in 6 pairs of human gastric adenocarcinoma and the corresponding adjacent nontumorous tissues. The experimental samples are divided into two groups(normal and tumor) to compare lncRNA expression profiling of those
2013-12-09 | E-GEOD-53137 | biostudies-arrayexpress
Project description:38 paires of tumor tissues and adjacent non-tumor tissues from HCC patients The number of known lncRNAs increased sharply upon the tiling microarrays and RNA-sequencing were applied to identify lncRNAs. However, only about a dozen of lncRNAs have been well characterized and demonstrated to be tightly associated with development and progression of HCC. A major challenge remains to identify functional lncRNAs associated with HCC. Previous reports mainly selected differentially expressed lncRNAs in cancer tissue or cell lines as candidates for further validation and characterizing. Here, based on mRNA and lncRNA gene expression profiles data collected from tumor and adjacent normal tissues of thirty-eight HCC patients, we adapted integrative omics strategy to identify HCC-associated lncRNAs.
2017-06-21 | GSE84005 | GEO
Project description:38 paires of tumor tissues and adjacent non-tumor tissues from HCC patients The number of known lncRNAs increased sharply upon the tiling microarrays and RNA-sequencing were applied to identify lncRNAs. However, only about a dozen of lncRNAs have been well characterized and demonstrated to be tightly associated with development and progression of HCC. A major challenge remains to identify functional lncRNAs associated with HCC. Previous reports mainly selected differentially expressed lncRNAs in cancer tissue or cell lines as candidates for further validation and characterizing. Here, based on mRNA and lncRNA gene expression profiles data collected from tumor and adjacent normal tissues of thirty-eight HCC patients, we adapted integrative omics strategy to identify HCC-associated lncRNAs.
2017-06-21 | GSE84004 | GEO