To find out microRNA contribute to the development of gallbladder cancer
ABSTRACT: MicroRNAs (miRNAs) play a critical role in the progression of cancer. However, little is known on the miRNAs expression profiles of gallbladder cancer.We performed this microarray to identify miRNAs associated with gallbladder cancer. Overall design: 4 pairs of gallbladder cancer tissues and paired normal gallbladder tissues were collected after colecystectomy.
INSTRUMENT(S): Agilent-046064 Unrestricted_Human_miRNA_V19.0_Microarray (miRNA ID version)
Project description:To further understand the molecular mechanisms in the development of gallbladder cancer, we employed this microarray to identify lncRNAs associated with gallbladder cancer. 9 pairs of gallbladder cancer tissues and paired normal gallbladder tissues were collected after colecystectomy.
Project description:Gallbladder carcinoma (GBC) is a rare cancer entity in Western Europe and the US with an incidence of less than 3/100.000 and a survival rate <10%. Radical surgery is the only potentially curative treatment option but most patients diagnosed with GBC are not resectable. Thus, there is a great need for the development of new treatment options, including targeted therapy for GBC. To dissect the epigenetic regulation during GBC development, we performed global miRNA profiling of 40 GBC and 8 normal gallbladder tissues. MiRNAs that are associated with survival were functionally analysed by cell proliferation and colony formation assays. In addition, we performed whole genome gene expression analysis of cells expressing miRNA mimics or control and performed biochemical assays to dissect miR-145 signalling. The GBC miRNA profiles exhibited large differences compared to normal gallbladder tissues with 49% of miRNAs being differentially expressed (FDR<0.001). In addition, 8 miRNAs were found to be down- and 16 to be up regulated in the GBCs with poor outcome (p<0.05). The most down regulated miRNA was miR-145-5p and the top up regulated miRNA was miR-575. Overexpression of miR-145 led to a significant reduction of cell proliferation and colony formation, whereas, opposite effects were observed for miR-575. Gene expression profiling of cells overexpressing miR-145 revealed activation of the STAT1 signalling pathway by inhibition of PTPRF in cholangiocellular but not hepatocellular carcinoma cells. Thereby, PTPRF directly bound to STAT1 and reduced STAT1 phosphorylation. This study identified pro- and anti-tumorigenic miRNAs in GBC and provides new mechanistic insight in the tumour suppressive function of miR-145 loss leading to active STAT1 signalling. Overall design: To study the expression profiles of miRNAs in gallbladder carcinoma
Project description:Although many protein-coding genes have been identified to be aberrantly expressed in gallbladder cancer, the mechanism that account for the development and progression of gallbladder cancer remains unclear. In recent years, long noncoding RNAs have been shown to play vital roles in mammalian cell biology. In this study, we found that a small number of lncRNAs that are aberrantly expressed. A ten chip study using total RNA recovered five separate gallbladder cancer tissues and five matched adjacent gallbladder normal tissues
Project description:32 pairs of gallbladder cancer tissues and matched normal tissues were sequenced by whole exome seqencing; 51 pairs of gallbladder cancer were processed with targeted gene sequencing.
Project description:Gallbladder carcinoma (GBC) is the most common biliary tract cancer with poor prognosis. Increasing evidences have pointed out that long non-coding RNAs (lncRNAs) play important regulatory roles in cancer biology. The alteration of lncRNAs is associated with many kinds of cancers. However, the contribution of lncRNAs to GBC is still vague. In order to explore the potential lncRNAs involved in GBC, we described lncRNAs profiles in 3 pairs of human GBC tissues and the matched peri-carcinomatous tissues by microarray. Quantitative real-time polymerase chain reaction (qRT-PCR) was used for the validation of the microarray data. To understand potential functions, Gene Ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis and network analysis were employed to figure out significant pathways. With abundant RNA probes, we detected 1,758 lncRNAs and 1,254 mRNAs differentially expressed in the microarray. Compared with PCT (Para-carcinoma tissue), plenty of lncRNAs were significantly up-regulated or down-regulated in GBC. Our data showed that lncRNAs down-regulated in GBC were much more than those up-regulated. Among them, RP11-152P17.2-006 was the most up-regulated, while CTA-941F9.9 was the most down-regulated. The results of qRT-PCR agreed with the data from the microarray. Pathway analysis indicated that 5 pathways were corresponded to differentially expressed transcripts. The data showed that the expression of lncRNAs in GBC was significantly changed, and a series of new lncRNAs associated with GBC were identified. These results suggested that the functions of lncRNAs might be significant in GBC development and progression. Overall design: Two-condition experiment, gallbladder cancer tissues vs. para-carcinoma gallbladder tissues. Biological replicates: 3 control replicates, 3 treated replicates.
Project description:To further understand the molecular mechanisms in the development of glioblastoma cancer, we employed this microarray to identify lncRNAs associated with glioblastoma cancer. Overall design: 4 pairs of glioblastoma cancer tissues and normal glioblastoma tissues were collected after glioma operation.
Project description:We determined the global microRNA expression profiles of primary human gallbladder cells and genetically reprogrammed human gallbladder cells and compared with pancreatic beta cells to ascertain the degree of cellular transdifferentatiation of insulin-producing human gallbladder cells to become beta-like cells. First, we cultured patient-derived gallbladder cells and then we transduced these with beta cell transcription factors to reprogram gallbladder cells to become beta-like cells. We used a pan-islet surface monoclonal antibody to enrich for insulin-producing reprogrammed human gallbladder cells using FACS.
Project description:We determined the global gene expression profiles of primary human gallbladder cells and genetically reprogrammed human gallbladder cells and compared with pancreatic beta cells to ascertain the degree of cellular transdifferentatiation of insulin-producing human gallbladder cells to become beta-like cells. First, we cultured patient-derived gallbladder cells and then we transduced these with beta cell transcription factors to reprogram gallbladder cells to become beta-like cells. We used a pan-islet surface monoclonal antibody to enrich for insulin-producing reprogrammed human gallbladder cells using FACS.
Project description:We carried out an iTRAQ-based quantitative proteomic analysis of gallbladder cancer and adjacent non-tumor tissue to systematically identify differentially expressed proteins in gallbladder cancer. Ten gallbladder adenocarcinoma and ten adjacent non-tumor tissue samples were selected post pathological confirmation for the study. Samples were pooled and In-solution trypsin digestion was carried out. Post digestion, peptides were iTRAQ labeled with 114 and 115 (gallbladder adenocarcinoma) and 116 and 117 (adjacent non-tumor samples). LC-MS/MS analysis of SCX fractions was carried out using a reversed phase analytical C18 column connected to 1200 Series Nanoflow LC interfaced with LTQ-Orbitrap Velos. Data were acquired using Xcalibur 2.1. Proteome Discoverer (v 1.3) suite was used for quantitation and database searches. LC-MS/MS data were searched using Mascot and SEQUEST search algorithms against Human RefSeq 50 supplemented with frequently observed contaminants.
Project description:Poor prognosis in gallbladder cancer is due to late presentation of the disease, lack of reliable biomarkers for early diagnosis and limited targeted therapies. Early diagnostic markers and novel therapeutic targets can significantly improve clinical management of GBC. We carried out quantitative proteomic analysis using a panel of gallbladder cancer cell lines using isobaric tags for relative and absolute quantitation (iTRAQ). We identified 3,655 proteins among which 654 were found to be overexpressed and 387 were downregulated in the invasive cell lines (OCUG-1, NOZ and GB-d1) compared to the non-invasive cell line, TGBC24TKB. Among these, macrophage inhibitory factor (MIF) was observed to be >3-fold overexpressed. MIF is a pleiotropic proinflammatory cytokine that plays a causative role in multiple diseases including cancer. MIF has been reported to play a central role in tumor cell proliferation and invasion in several cancers. Immunohistochemical staining confirmed our findings showing overexpression of MIF in 21 of 29 gallbladder adenocarcinoma cases. A significant decrease in cell viability, colony forming ability and invasive property of the gallbladder cancer cells was observed upon MIF inhibition using MIF siRNA and MIF antagonists. Our findings support the role of MIF in tumor aggressiveness and suggest its potential application as a therapeutic target for gallbladder cancer.