Analysis of deregulated microRNAs in malignant mesothelioma
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ABSTRACT:
ORGANISM(S): Mus musculus Rattus norvegicus Homo sapiens
PROVIDER: GSE29707 | GEO | 2012/01/11
SECONDARY ACCESSION(S): PRJNA141075
REPOSITORIES: GEO
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Project description:The expression of human microRNAs in the cellular fraction of human peripheral blood of patients with diagnosed malignant mesotheliomas and asbestos-exposed controls. Altered expression of several miRNAs were observed for patients with diagnosed malignant mesotheliomas in comparison with asebstos-expsoed controls. The study group consists of 23 patients with diagnosed malignant mesothelioma (mean age 66 years, range 34 – 84 years). Patients were not treated with chemotherapy or radiation therapy before sample collection. The histological subtypes were: one sarcomatoid, seven biphasic, and twelve epithelioid cases. In three cases the histological subtype was unknown. The control group consists of 17 asbestos-exposed age-matched volunteers without any diagnosed cancer (mean age 68 years, range 47 – 80 years). Oligonucleotide microarrays were purchased from the Norwegican Microarray Consortium (www.microarray.no). The mirVana miRNA Probe Set v2.0 (Ambion) based on the miRBase Sequence Database v8.0. was used.
2012-01-11 | E-GEOD-29707 | biostudies-arrayexpress
Project description:Malignant mesothelioma is an aggressive cancer that often originates in the pleural and peritoneal mesothelium. Exposure to asbestos is a frequent cause. But studies in rodents showed that certain multiwalled carbon nanotubes (MWCNTs) can induce malignant mesotheliomas. This study aimed to understand molecular pathways leading to the development of malignant mesotheliomas induced by MWCNTs and amosite asbestos in Wistar rats. Using Affymetrix microarrays, we carried out genome-wide transcriptome analysis on malignant peritoneal meosotheliomas induced by MWCNTs and amosite asbestos. The transcriptome of MWCNTs and amosite asbestos-induced mesotheliomas exhibited commonalities, but also differences pertaining to differentially-expressed genes (DEGs), regulated canonical pathways, and molecular functions.
2024-02-01 | GSE233803 | GEO
Project description:Exposure to asbestos is a risk for malignant mesothelioma in humans. We carried out array comparative genomic hybridization (CGH) analysis in a rat model by repeated intraperitoneal injections of three types of asbestos including chrysotile, crocidolite and amosite. We found a common chromosomal deletion mapped to the chromosome 5q32 locus, containing the genes encoding tumour suppressor genes CDKN2A/2B/ARF. Homozygous deletion of CDKN2A/2B/ARF was observed in the majority (92.6%) of the rat MM samples.
2012-08-14 | GSE36577 | GEO
Project description:Malignant pleural mesothelioma (MPM) is a highly lethal, poorly understood neoplasm that is typically associated with asbestos exposure. We performed transcriptional profiling using high-density oligonucleotide microarrays containing approximately 22,000 genes to elucidate potential molecular and pathobiological pathways in MPM using discarded human MPM tumor specimens (n=40), normal lung specimens (n=4), normal pleura specimens (n=5), and MPM and SV40-immortalized mesothelial cell lines (n=5). In global expression analysis using unsupervised clustering techniques, we found two potential subclasses of mesothelioma which correlate loosely with tumor histology. We also identified sets of genes with expression levels that distinguish between multiple tumor subclasses, normal and tumor tissues, and tumors with different morphologies. Microarray gene expression data were confirmed using quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) and protein analysis for three novel candidate oncogenes (NME2, CRI1, and PDGFC) and one candidate tumor suppressor (GSN). Finally, we used bioinformatics tools (i.e. software) to create and explore complex physiological pathways that may be relevant in mesothelioma tumorigenesis, pathobiology, or both. Tissues and cell lines profiled using microarrays. Discarded MPM surgical specimens (n=40), normal pleura specimens (n=5), and normal lung specimens (n=4) were freshly collected (and snap frozen) from patients who underwent surgery at Boston's Brigham and Women's Hospital (BWH) between October 1998 and August 2000. All of these patients underwent extrapleural pneumonectomy with heated intra-pleural cisplatin chemotherapy delivered after the specimens were removed. All normal specimens were obtained from patients who were never diagnosed with MPM. Two human MPM cell lines (MS589 and MS428) were kindly provided by Jonathan A. Fletcher, M.D., Department of Pathology, BWH. The JMN1B MPM cell line19,20 has been described previously. The SV40-immortalized, non-tumorigenic mesothelial cell line (Met-5A)21 and the MPM cell line MSTO-211H22 were purchased from the American Type Culture Collection. Normal tissues were obtained from additional consented patients undergoing treatment for diseases other than MPM. All MPM samples used in these studies contained relatively pure tumor (greater than 50% tumor cells per high power field examined in a section adjacent to the tissue used). The microscopic slides from the patients' resection specimens were reviewed by one of the authors (J.G.), and the diagnosis and histologic subclassification of MPM confirmed in all cases. Linked clinical and pathological data were obtained for all patients who contributed tumor specimens. Specimens and data were rendered anonymous to protect patient confidentiality. Studies utilizing human tissues were approved by and conducted in accordance with the policies of the Institutional Review Board at BWH.
2005-06-01 | GSE2549 | GEO
Project description:Exposure to asbestos is a risk for malignant mesothelioma in humans. We carried out array comparative genomic hybridization (CGH) analysis in a rat model by repeated intraperitoneal injections of three types of asbestos including chrysotile, crocidolite and amosite. We found a common chromosomal deletion mapped to the chromosome 5q32 locus, containing the genes encoding tumour suppressor genes CDKN2A/2B/ARF. Homozygous deletion of CDKN2A/2B/ARF was observed in the majority (92.6%) of the rat MM samples. Carcinogenesis protocol was performed using specific pathogen-free male and female F1 hybrid rats between Fischer344 and Brown-Norway strains. A total of 27 tumor samples were profiled on Agilent 244A aCGH arrays according to manufacturer's instructions for the screening purpose.
2012-08-13 | E-GEOD-36577 | biostudies-arrayexpress
Project description:Malignant mesothelioma (MM) is an asbestos-related malignancy. Discrimination between MM and reactive mesothelial hyperplasia (RM) is often difficult. MM cells have a broad histological spectrum, and consist mainly of epithelioid, sarcomatoid, and biphasic cell types. The prognosis of MM is generally poor, but better prognosis has been reported with the epithelioid type of MM than the non-epithelioid type. We applied a genome-wide analysis to the identification of new markers that may aid in differentiating the epithelioid type of MM from other histological types and from RM cells.
2014-11-22 | GSE52788 | GEO
Project description:Human malignant mesothelioma (MM) is an aggressive tumor strongly associated with asbestos exposure. SM patients generally have poorer prognosis compared to EM patients. To identify potential genes accounting for the differential prognosis between these two subtypes, we compared the microarray gene expression profiles of rat SM and EM tissues induced by intraperitoneal injections of 3 types of asbestos (chrysotile,crocidolite and amosite).
2014-06-04 | GSE48298 | GEO
Project description:Malignant mesothelioma (MM) is an asbestos-related malignancy. Discrimination between MM and reactive mesothelial hyperplasia (RM) is often difficult. MM cells have a broad histological spectrum, and consist mainly of epithelioid, sarcomatoid, and biphasic cell types. The prognosis of MM is generally poor, but better prognosis has been reported with the epithelioid type of MM than the non-epithelioid type. We applied a genome-wide analysis to the identification of new markers that may aid in differentiating the epithelioid type of MM from other histological types and from RM cells. Array-based comparative genomic hybridization analysis was performed on malignant mesothelioma (MM) primary cell cultures, reactive mesothelial hyperplasia (RM) primary cell cultures; early passage of in vitro primary cell cultures to minimize acquisition of additional genomic changes. If available, matched peripheral blood was applied to analysis.
2014-11-22 | E-GEOD-52788 | biostudies-arrayexpress
Project description:Malignant mesothelioma (MM) is an asbestos-related malignancy and largely unresponsive to conventional chemotherapy or radiotherapy. Novel, more effective therapeutic strategies are needed for this fatal disease. We performed microarray analysis of MM using Affymetrix Human U133 Plus 2.0 array. Aberrant expression of the genes participating in semaphorin signaling were detected in malignant mesothelioma cells. All MM cells downregulated the expression of more than one gene for SEMA3B, 3F, and 3G when compared with Met5a, a normal pleura-derived cell line. In 12 of 14 epithelioid MM cells, the expression level of SEMA3A was lower than that in Met5a. An augmented expression of VEGFA was detected in half of the MM cells. The expression ratio of VEGFA/SEMA3A was significantly higher in the epithelioid MMs than in Met5a and the non-epithelioid MMs. Next, gene expression profiling for the polycomb and trithorax group genes revealed that expression of BAP1, the catalytic subunit of the polycomb repressive deubiquitinase complex, and many trithorax group genes was downregulated in MMs compared with the expression of the same genes in Met5a cells. Perturbation of the polycomb–trithorax balance plays a significant role in the pathogenesis of malignant mesothelioma.
2014-12-31 | GSE29370 | GEO
Project description:Malignant mesothelioma (MM) is an asbestos-related malignancy. MM cells have a broad histological spectrum, and consist mainly of epithelioid, sarcomatoid, and biphasic cell types. The prognosis of MM is generally poor. We applied a copy-number analysis to the identification of new fragile genes in regions 3p21 and 16p13.3 in MM.
2016-11-13 | GSE57464 | GEO