Ontology highlight
ABSTRACT:
PROVIDER: PRJNA576344 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10242800_1.fastq.gz | Fastqsanger.gz | |||
| SRR10242800_2.fastq.gz | Fastqsanger.gz | |||
| SRR10242801_1.fastq.gz | Fastqsanger.gz | |||
| SRR10242801_2.fastq.gz | Fastqsanger.gz | |||
| SRR10242802_1.fastq.gz | Fastqsanger.gz |
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Project description:Canine mast cell tumour proliferation depends to a large extent on the activity of KIT, a tyrosine kinase receptor. Inhibitors of the KIT tyrosine kinase have recently been introduced and successfully applied as a therapeutic agent for this tumour type. However, little is known on the downstream target genes of this signalling pathway and molecular changes after inhibition. Transcriptome analysis of the canine mast cell tumour cell line C2 treated for up to 72 hours with the tyrosine kinase inhibitor masitinib identified significant changes in the expression levels of approximately 3500 genes representing 16% of the canine genome. Approximately 40% of these genes had increased mRNA expression levels including genes associated with the pro-proliferative pathways of B- and T-cell receptors, chemokine receptors, steroid hormone receptors and EPO-, RAS and MAP kinase signalling. Proteome analysis of C2 cells treated for 72 hours identified 24 proteins with changed expression levels, most of which being involved in gene transcription, e.g. EIA3, EIA4, TARDBP, protein folding, e.g. HSP90, UCHL3, PDIA3 and protection from oxidative stress, GSTT3, SELENBP1. Transcriptome and proteome analysis of neoplastic canine mast cells treated with masitinib confirmed the strong important and complex role of KIT in these cells. Approximately 16% of the total canine genome and thus the majority of the active genes were significantly transcriptionally regulated. Most of these changes were associated with reduced proliferation and metabolism of treated cells. Interestingly, several pro-proliferative pathways were up-regulated which may represent attempts of masitinib treated cells to activate alternative pro-proliferative pathways. These pathways may contain hypothetical targets for a combination therapy with masitinib to further improve its therapeutic effect. The present study aimed at identifying the transcriptional and translational responses of neoplastic canine mast cells to the tyrosine kinase inhibitor masitinib. To this end, C2 cells, a cell line with a tandem duplication in the juxtamembrane unit and thus constitutively activated KIT, were treated with masitinib and changes in the global mRNA and protein expression levels were characterized.
2012-07-24 | E-GEOD-32657 | biostudies-arrayexpress
Project description:Canine mast cell tumour proliferation depends to a large extent on the activity of KIT, a tyrosine kinase receptor. Inhibitors of the KIT tyrosine kinase have recently been introduced and successfully applied as a therapeutic agent for this tumour type. However, little is known on the downstream target genes of this signalling pathway and molecular changes after inhibition. Transcriptome analysis of the canine mast cell tumour cell line C2 treated for up to 72 hours with the tyrosine kinase inhibitor masitinib identified significant changes in the expression levels of approximately 3500 genes representing 16% of the canine genome. Approximately 40% of these genes had increased mRNA expression levels including genes associated with the pro-proliferative pathways of B- and T-cell receptors, chemokine receptors, steroid hormone receptors and EPO-, RAS and MAP kinase signalling. Proteome analysis of C2 cells treated for 72 hours identified 24 proteins with changed expression levels, most of which being involved in gene transcription, e.g. EIA3, EIA4, TARDBP, protein folding, e.g. HSP90, UCHL3, PDIA3 and protection from oxidative stress, GSTT3, SELENBP1. Transcriptome and proteome analysis of neoplastic canine mast cells treated with masitinib confirmed the strong important and complex role of KIT in these cells. Approximately 16% of the total canine genome and thus the majority of the active genes were significantly transcriptionally regulated. Most of these changes were associated with reduced proliferation and metabolism of treated cells. Interestingly, several pro-proliferative pathways were up-regulated which may represent attempts of masitinib treated cells to activate alternative pro-proliferative pathways. These pathways may contain hypothetical targets for a combination therapy with masitinib to further improve its therapeutic effect.
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Project description:In the present study, canine mast cell tumor (MCT) transcriptome was characterized in order to identify a set of candidate genes potentially useful for MCT classification and prognosis prediction. Fifty-one canine MCT biopsies were enrolled in the study. Isolated and purified total RNAs were individually hybridized to the Agilent Canine V2 4x44k DNA microarray. The comparison of reference differentiated and undifferentiated MCT transcriptome revealed a total of 597 differentially expressed genes (450 up-regulated and 147 down-regulated). The functional analysis of this set of genes provided evidence that they were mainly involved in cell cycle, DNA replication, p53 signaling pathway, nucleotide excision repair and pyrimidine metabolism. Class prediction analysis identified 13 transcripts providing the greatest accuracy of class prediction and divided samples into two categories (differentiated and undifferentiated MCTs). The molecular classification here used was prognostically significant, as the groups were directly correlated with survival time (p = 0.0026). In this study, we analyzed the gene expression profiles of 51 mast cell tumour samples using Agilent Canine V2 4x44k (G2519F, Design ID 021193) DNA microarray platform (60 arrays, 8 replicates) based on single-colour detection (Cyanine-3 only). Microarrays are scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides are scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal left, after all the FE processing steps have been completed, is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
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Project description:We performed whole-exome sequencing of tumour bulks from opposite side of the neoplasm (A/B). From each we selected a panel of sub-clonal mutations and profiled multiple single tumour glands from the same neoplasm using high depth targeted re-sequencing. The aim was to infer tumour evolutionary dynamics and reconstruct the timeline of progression
2014-12-22 | E-MTAB-2247 | biostudies-arrayexpress
Project description:in the present study we investigate polarized canine macrophages using transcriptome sequencing, a larger panel of flow cytometry markers, and antimicrobial functional assays. Transcriptome analysis of primary canine monocyte-derived macrophages revealed unique, previously unreported signatures for polarized M1 and M2 macrophages.
2022-09-30 | GSE207661 | GEO
Project description:In this study the global expression profiles of primary cutaneous mast cell tumours that metastasised were compared with those of primary tumours that did not metastasise. The objective was to identify genes involved in mast cell tumour metastatic progression that may represent targets for therapeutic intervention and biomarkers for prediction of tumour metastasis.
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