66019798-3132-4067-b7b7-4a89aa02e64e - samples
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ABSTRACT:
PROVIDER: EGAD00001008740 | EGA |
REPOSITORIES: EGA
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Project description:Propolis is a resinous honeybee product, rich in polyphenolic compounds and with high economic value. Although extensive studies regarding the chemical composition of different propolis extracts have been carried out, the propolis proteome remained unknown. The present study aimed at characterizing the proteome of two geographically-distinct propolis originating from Belgium and Iran. Propolis extracts were analysed by SDS-PAGE followed by MALDI-TOFand LC/ESI- mass spectrometry (MS). Our in-depth proteomic analysis led to the identification of honeybee venom and royal jelly proteins, and numerous plant-defense proteins in propolis, extending our understanding on the antimicrobial properties of this complex natural substance. The proteome of both propolis was mainly made up of proteins belonging to the poplar tree. The poplar PR-2 (β-1,3-glucanases) and PR-8 (acidic endochitinases) proteins were found to be the major components of both propolis extracts, while bee venom (Api m 1) and royal jelly allergens (MJRP 1and 2) were only identified in the propolis from Belgium. Overall, our proteome analyses revealed that propolis extracts from Belgium and Iran shared a core protein composition originating from the poplar proteome. The majority of identified proteins are involved in the plant defense against pathogens, some belonging to well-known pathogenesis-related families.
2026-03-26 | PXD039653 | Pride
Project description:RNA-sequencing data: 5 normal thyroid tissues, 14 papillary thyroid carcinomas, 2 lymph node metastases, 19 poorly differentiated thyroid carcinomas and 17 anaplastic thyroid carcinomas;
Targeted DNA-sequencing of the 165 genes included in the “Solid and Haematological tumors†panel (BRIGHTCore, Brussels, Belgium): 2 normal thyroid tissues, 2 poorly differentiated thyroid carcinomas and 7 anaplastic thyroid carcinomas;
2 FASTQ files for each sample (paired).
| EGAD00001011678 | EGA
Project description:For establishing a live-cell biobank of Malignant Pleural Mesothelioma (MPM) samples, cultures of two MPM patients were compared to the original tumor tissue using Affymetrix OncoScan Microarrays for genome-wide CNV and LOH detection.
2018-01-18 | GSE109305 | GEO
Project description:Treatment of malignant pleural mesothelioma (MPM) cells with anti-CD26Ab inhibits tumor progression and phase I clinical application of anti-CD26Ab resulted in prolonged disease stabilization in patients with advanced/refractory MPM. In order to elucidate the molecular mechanism of anti-CD26Ab to inhibit MPM progression, microarray analysis was performed on anti-CD26Ab treated MPM cells.
2018-08-01 | GSE100848 | GEO
Project description:Malignant pleural mesotheliomas (MPMs) often show CDKN2A and NF2 inactivation but other highly recurrent mutations have not been described. To identify additional driver genes, we used an integrated genomic analysis of 53 MPM tumor samples to guide a focused sequencing effort that uncovered somatic inactivating mutations in BAP1 in 23% of MPM. The BAP1 nuclear deubiquitinase is known to target histones (together with ASXL1 as a Polycomb repressor subunit) and the HCF1 transcriptional co-factor, and we show that BAP1 knockdown in MPM cell lines affects E2F and Polycomb target genes. These findings implicate transcriptional deregulation in the pathogenesis of MPM. Genomic DNA was harvested from untreated malignant pleural mesothelioma (MPM) cell lines and used to generate gain/loss profiles for each line using aCGH.
2011-05-19 | E-GEOD-29383 | biostudies-arrayexpress
Project description:MicroRNA expression profiles of malignant pleural mesothelioma (MPM) specimens were analyzed to identify novel microRNA that are potentially involved in the oncogenic transformation of human pleural cells. In addition to several novel MPM-associated microRNAs, we observed that the expression level of microRNA-1 was significantly lower in tumors as compared to normal pleural specimens. Subsequently, pre-mir of microRNA-1 was introduced into MPM cell lines to overexpress this microRNA. Phenotypic changes of these altered cells were assayed. The cellular proliferation rate was significantly inhibited after overexpression of microRNA-1. Early and late apoptosis were measured by Annexin V and TUNEL assays, respectively. Taken together, these data suggested that overexpression of microRNA-1 induced apoptosis in these MPM cell lines, acting as a tumor suppressor. We confirmed our observations by assessing in the transduced MPM cells cell cycle-related genes, pro-apoptotic and anti-apoptotic genes, which all showed coordinated, significant changes characteristic of the apoptotic phenotype. Thus, further investigation and validation of our microRNA database of MPM may elucidate previously unrecognized molecular pathways and/ or mechanisms by identifying novel microRNAs that are involved in malignant transformation. Our study has now found microRNA-1 to be one of these MPM-associated microRNAs, with potential pathogenic and therapeutic significance. MicroRNA microarray transcriptional profiling studies of 25 MPM primary tumors as well 6 normal pleural samples from an unmatched patient cohort as normal comparators were performed.
2013-10-01 | E-GEOD-40345 | biostudies-arrayexpress
Project description:BACKGROUND: Malignant pleural mesothelioma (MPM) is difficult to distinguish from reactive mesothelial proliferations (RMPs). MicroRNAs (miRNAs) are small non-coding RNA-strands (~22 nucleotides) that post-transcriptionally regulate gene-expression. Studies have shown that miRNAs are potential diagnostic markers in other cancers; however, it is uncertain whether miRNAs are useful biomarkers for differentiating MPM from RMP. OBJECTIVE: To identify differentially expressed microRNAs which can aid in the diagnostics of MPM. METHODS: We screened with a quantitative RT-PCR (RT-qPCR)-based platform the expression of 742 miRNAs in formalin-fixed paraffin-embedded (FFPE) preoperative diagnostic biopsies, surgically resected MPM-specimens previously treated with chemotherapy, and corresponding non-neoplastic pleura (NNP) from 5 patients. RESULTS: By comparing the change in microRNA expression in patient-matched tissue samples, we identify 14 miRNAs which exhibit statistically significant deregulation between sample groups. CONCLUSION: Based on this initial screening of miRNA expression, we have identified 14 miRNAs which are potential diagnostic biomarkers and may aid in diffferentiating RMP from MPM. qPCR microRNA expression profiling. MicroRNA expression in surgical tissue samples and presurgery diagnostic biopsies of malignant pleural mesotheliomas was compared to corresponding patient-matched non-neoplastic pleura. Patient-matched diagnostic biopsies from still chemotherapy-naïve patients were included to test for chemotherapy-induced changes in microRNA expression.
2014-01-25 | E-GEOD-54394 | biostudies-arrayexpress
Project description:MicroRNA expression profiles of malignant pleural mesothelioma (MPM) specimens were analyzed to identify novel microRNA that are potentially involved in the oncogenic transformation of human pleural cells. In addition to several novel MPM-associated microRNAs, we observed that the expression level of microRNA-1 was significantly lower in tumors as compared to normal pleural specimens. Subsequently, pre-mir of microRNA-1 was introduced into MPM cell lines to overexpress this microRNA. Phenotypic changes of these altered cells were assayed. The cellular proliferation rate was significantly inhibited after overexpression of microRNA-1. Early and late apoptosis were measured by Annexin V and TUNEL assays, respectively. Taken together, these data suggested that overexpression of microRNA-1 induced apoptosis in these MPM cell lines, acting as a tumor suppressor. We confirmed our observations by assessing in the transduced MPM cells cell cycle-related genes, pro-apoptotic and anti-apoptotic genes, which all showed coordinated, significant changes characteristic of the apoptotic phenotype. Thus, further investigation and validation of our microRNA database of MPM may elucidate previously unrecognized molecular pathways and/ or mechanisms by identifying novel microRNAs that are involved in malignant transformation. Our study has now found microRNA-1 to be one of these MPM-associated microRNAs, with potential pathogenic and therapeutic significance.
2013-10-01 | GSE40345 | GEO
Project description:Malignant pleural mesotheliomas (MPMs) often show CDKN2A and NF2 inactivation but other highly recurrent mutations have not been described. To identify additional driver genes, we used an integrated genomic analysis of 53 MPM tumor samples to guide a focused sequencing effort that uncovered somatic inactivating mutations in BAP1 in 23% of MPM. The BAP1 nuclear deubiquitinase is known to target histones (together with ASXL1 as a Polycomb repressor subunit) and the HCF1 transcriptional co-factor, and we show that BAP1 knockdown in MPM cell lines affects E2F and Polycomb target genes. These findings implicate transcriptional deregulation in the pathogenesis of MPM. DNA from 53 malignant pleural mesothelioma tumors was collected and hybridized to aCGH arrays. Data were analyzed to create gain and loss profiles for each tumor. This submission includes gcNormalized-data.
2011-09-25 | E-GEOD-29902 | biostudies-arrayexpress
Project description:Malignant Pleural Mesothelioma (MPM) is an aggressive cancer that is often diagnosed at an advanced stage and is characterized by a long latency period (20-40 years between initial exposure and diagnosis) and prior exposure to asbestos. Currently accurate diagnosis of MPM is difficult due to the lack of sensitive biomarkers, and despite minor improvements in treatment, median survival rates do not exceed 12 months. Accumulating evidence suggests that aberrant expression of long non-coding RNAs (lncRNAs) play an important functional role in cancer biology. LncRNAs are a class of recently discovered non-protein coding RNAs >200 nucleotides in length with a role in regulating transcription. Here we used NCode long noncoding microarrays to identify differentially expressed lncRNAs potentially involved in MPM pathogenesis. High priority candidate lncRNAs were selected on the basis of statistical (P<0.05) and biological significance (>3-fold difference). Expression levels of 9 candidate lncRNAs were technically validated using RT-qPCR, and biologically validated in three independent test sets: (1) 57 archived MPM tissues obtained from extrapleural pneumonectomy patients, (2) 15 cryopreserved MPM and 3 benign pleura, and (3) an extended panel of 10 MPM cell lines. RT-qPCR analysis demonstrated consistent up-regulation of these lncRNAs in independent datasets. ROC curve analysis showed that two candidates were able to separate benign pleura and MPM with high sensitivity and specificity, and were associated with nodal metastases and survival following induction chemotherapy. These results suggest that lncRNAs have potential to serve as biomarkers in MPM. To identify mRNA and lncRNA biomarkers associated with malignant pleural mesothelioma (MPM), we performed gene expression array analysis on 4 MPM cell lines (H28, MM05, MSTO-211H, H226) compared to the immortalised mesothelial line (MeT-5A). All cell lines were profiled in duplicate. Synthesis of the labelled first strand cDNA was conducted using the Superscript Plus Direct cDNA labeling system with starting material of 10ug total RNA. The labeled dNTP mix was added to the reaction to generate labeled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA was purified using low elution volume spin cartridges included in the purification module. Samples were labelled using Alexa Fluor 555 dyes. Samples were then hybridised to NCode Long Noncoding RNA Microarrays. Slides were scanned using an Agilent Scanner. Genes differentially expressed between Met-5A and the MPM cell lines were identified on the basis of P-value and fold change.
2013-08-22 | E-GEOD-48174 | biostudies-arrayexpress