Canine subcellular Proteomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): TripleTOF 5600
ORGANISM(S): Canis Familiaris (dog) (canis Lupus Familiaris)
TISSUE(S): Spleen, Endothelial Cell Of Venous Sinus Of Red Pulp Of Spleen
DISEASE(S): Spleen Angiosarcoma
SUBMITTER: 
Anup Shah
LAB HEAD: Associate Professor Michelle Hill
PROVIDER: PXD003847 | Pride | 2022-03-02
REPOSITORIES: Pride
Similar Datasets
Project description:In this study, we present the first comparison of global transcriptional changes taking place in canine lymphoma and human diffuse large B-cell lymphoma (DLBCL), with particular reference to the nuclear factor-kappaB (NF-?B) pathway. Microarray data generated from lymph nodes diagnosed with canine DLBCL and healthy lymph nodes were used for differential expression analysis, co-expression analysis and pathway analysis, and compared with analysis of publicly available microarray data from human healthy and DLBCL lymph nodes. The comparisons between species at gene level were performed by mapping the probesets in canine microarrays to orthologous genes in humans and vice versa. A considerable number of differentially expressed genes between canine lymphoma and healthy lymph node samples were also found differentially expressed between human DLBCL and healthy lymph node samples. Principal component analysis (PCA) using a literature derived 120 NF-?B target gene set mapped to 199 orthologous canine array probesets and 259 human array probesets clearly separated the healthy and cancer samples in both canine and human datasets. The analysis demonstrated that for both human and canine DLBCL there is activation of the NF-?B/p65 canonical pathway rather than the alternative pathway. This has therapeutic implications for the use of specific pathway inhibitors for the treatment of DLBCL for both species and also indicates that naturally occurring canine lymphoma could be used as a model to study therapeutic strategies for human lymphoma. The model was further validated by the identification of molecular signatures that could sub-classify canine DLBCL into activated B-cell-like (ABC) or germinal centre B-cell-like (GCB) types equivalent to human subtypes. Canine DLBCL patients were recruited via the clinical oncology service of the University of Edinburgh Royal (Dick) School of Veterinary Studies (DJA), and the University of Wisconsin-Madison School of Veterinary Medicine (DMV). Lymph node biopsy samples were taken, as part of normal diagnostic procedures, from dogs newly diagnosed with lymphoma (naïve) and samples from dogs that had relapsed following standard of care CHOP chemotherapy. Only dogs with confirmed DLBCL after pathological grading were used in this study. This included standard histopathological grading by two independent pathologists and CD3/PAX5 marker analysis. Normal lymph node samples were obtained from canines that were euthanized for non-lymphoma conditions. Microarray data were generated from 35 canine samples (25 DLBCL and 10 healthy) in total. However, data from 2 canine DLBCL samples did not meet our required quality and were removed from further analysis. Only data from 33 (23 DLBCL and 10 healthy) samples were used for analysis. The generated data were used for differential expression analysis, co-expression analysis and pathway analysis, and compared with analysis of publicly available microarray data (GSE12195) from human healthy and DLBCL lymph nodes. The comparisons between species at gene level were performed by mapping the probesets in canine microarrays to orthologous genes in humans and vice versa.
2013-09-26 | E-GEOD-30881 | biostudies-arrayexpress
Project description:A total of seven mildly diseased canine valves were dissected into grossly diseased and grossly normal areas of tissue (n=7 per group). mRNA was extracted using the qiagen RNeasy minikit and assessed by the agilent 2200 bioanalsyser. all samples passed quality control and transcriptomic analysis was performed by Edinburgh genomics using the Affymetrix GeneChip™ Canine Gene 1.1ST Array. Results were reported as CEL files and then analysed in Affymetrix expression console (version 1.4.1.46) using the canine 1.1ST library files from Affymetrix. Robust Multi-array Average (RMA) was used to perform gene level normalisation and signal level summarisation. Following this, quality control assessment was performed on the data set. This included assessment of hybridisation (spike in) controls, labelling (poly-A) controls and area under the curve (AUC) control, probe cell intensity boxplots, a signal histogram graph and principle component analysis (PCA) plot. Following this assessment, the datasets were exported with annotation as a text file or as a CHT file. Affymetrix transcriptome analysis console (version 3.1.0.5) was used to perform paired one-way analysis of variance (ANOVA).
2019-12-26 | E-MTAB-8622 | biostudies-arrayexpress
Project description:Quiescent canine valvular interstitial cells (n=3) and activated valvular interstitial cells (n=3) were grown in 2% FBS. Quiescent cells were treated with either TGFB1 or vehicle for 3 days and activated cells were treated with SB431542 for 4 days. mRNA was extracted using the qiagen RNeasy minikit and assessed by the agilent 2200 bioanalsyser. all samples passed quality control and transcriptomic analysis was performed by edinburgh genomics using the Affymetrix GeneChip™ Canine Gene 1.1ST Array. Results were reported as CEL files and then analysed in Affymetrix expression console (version 1.4.1.46) using the canine 1.1ST library files from Affymetrix. Robust Multi-array Average (RMA) was used to perform gene level normalisation and signal level summarisation.Following this, quality control assessment was performed on the data set. This included assessment of hybridisation (spike in) controls, labelling (poly-A) controls and area under the curve (AUC) control, probe cell intensity boxplots, a signal histogram graph and principle component analysis (PCA) plot. Following this assessment, the datasets were exported with annotation as a text file or as a CHT file. Affymetrix transcriptome analysis console (version 3.1.0.5) was used to perform paired or unpaired one-way analysis of variance (ANOVA).
2019-06-30 | E-MTAB-8096 | biostudies-arrayexpress
Project description:Whole mitral valves from each Whitney grade of disease; normal (n=6), grade 1 (n=5), grade 2 (n=6), grade 3 (n=6) and grade 4 (n=5). mRNA was extracted using the qiagen RNeasy minikit and assessed by the agilent 2200 bioanalsyser. all samples passed quality control and transcriptomic analysis was performed by edinburgh genomics using the Affymetrix GeneChip™ Canine Gene 1.1ST Array. Results were reported as CEL files and then analysed in Affymetrix expression console (version 1.4.1.46) using the canine 1.1ST library files from Affymetrix. Robust Multi-array Average (RMA) was used to perform gene level normalisation and signal level summarisation.Following this, quality control assessment was performed on the data set. This included assessment of hybridisation (spike in) controls, labelling (poly-A) controls and area under the curve (AUC) control, probe cell intensity boxplots, a signal histogram graph and principle component analysis (PCA) plot. Following this assessment, the datasets were exported with annotation as a text file or as a CHT file. Affymetrix transcriptome analysis console (version 3.1.0.5) was used to perform unpaired one-way analysis of variance (ANOVA).
2019-12-26 | E-MTAB-8618 | biostudies-arrayexpress
Project description:Ligaments are prone to injury and degeneration in humans and animals, however the healing potential of ligament is poor and current treatment options lack effectiveness. Stem cell-based therapies hold potential for treatment of ligament injuries. This study aimed to characterise ligament-derived stem cell (LDSC) and ligament fibroblast populations as well as to identify specific niche components which could be used to promote the survival and function of LDSCs. LDSCs and ligament fibroblasts were isolated from canine cranial cruciate ligament and characterised for clonogenicity, multipotency and marker expression. The extracellular matrix (ECM) composition was characterised using a novel metabolic labelling and mass spectrometry approach. Both cell types demonstrated clonogenicity, with significant differences seen in colony size. Stem cell and tenogenic marker expression was increased in LDSCs compared with ligament fibroblasts, although this was only significant for the MSC marker CD73. Both cell types demonstrated multipotency, however this was more marked in LDSCs. A number of collagens, glycoproteins, proteoglycans and ECM regulators were identified in both the LDSC and ligament fibroblast niche using proteomics, with some differences between cell types, including collagens, decorin and fibronectin. Metabolic labelling of cells demonstrated unique turnover profiles for distinct ECM protein groups, with significant differences in new synthesis seen between cell types for a number of proteins, including collagen, decorin and elastin. In conclusion, different cell populations were observed in canine ligament with differences in niche composition and dynamics seen between the two cell types. These differences could be exploited to aid identification of LDSCs and to promote survival and function of LDSCs for potential therapeutic strategies.
2019-01-28 | PXD008602 | Pride
Project description:We developed a new single cell sequencing method to simultaneously sequence methylome and transcriptome for mouse DRG neurons Integrative analysis of transcription and methylation at single cell level
2016-04-12 | E-GEOD-76483 | biostudies-arrayexpress
Project description:Dogs are highly valued companions and work animals that are susceptible to many life-threatening conditions like canine leishmaniosis (CanL). Plasma-derived extracellular vesicles (EVs), exploited extensively in biomarker discovery, constitute a mostly untapped resource in veterinary sciences. Thus, the definition of proteins associated with plasma EVs recovered from healthy and diseased dogs with a relevant pathogen would be important for biomarker development. For this, we recovered using size-exclusion chromatography (SEC), EVs from 19 healthy and 20 CanL dogs’ plasma and performed proteomic analysis by LC-MS/MS to define their core proteomic composition and search for CanL-associated alterations. EVs-specific markers were identified in all preparations and also non-EVs proteins. Some EVs markers like CD82 were specific to the healthy animals, while others like the Integrin beta 3 were identified in most samples. The EVs-enriched preparations allowed the identification of 529 canine proteins that were identified in both groups, while 465 and 154 were only identified in healthy or CanL samples, respectively. A GO enrichment analysis revealed few CanL-specific terms. Leishmania spp. protein identifications were also found alt-hough with only 1 unique peptide. Ultimately, CanL-associated proteins of interest were identified and a core proteome was revealed that will be available for intra- and inter-species comparisons.
2023-05-10 | PXD039610 | Pride
Project description:Canine idiopathic pulmonary fibrosis (CIPF) is a chronic, progressive, interstitial fibrosing lung disease, manifesting as cough, exercise intolerance and ultimately, dyspnea and respiratory failure. It mainly affects West Highland white terriers (WHWTs), lacks curable treatment and has a poor prognosis. Aspiration of gastroesophageal refluxate may play a role in the development of CIPF. In the first part of this study, we completed label-free quantitative proteomic analysis of bronchoalveolar lavage fluid (BALF) from CIPF and healthy WHWTs. In the second part, we evaluated potential protein markers of reflux aspiration from canine gastric juice and vomitus and evaluated whether these were present in BALF from the two groups.
2022-05-20 | PXD028916 | Pride
Project description:Epithelial-mesenchymal transition (EMT) is a highly conserved morphogenic process defined by the loss of epithelial characteristics and the acquisition of a mesenchymal phenotype. EMT is associated with increased aggressiveness, invasiveness, and metastatic potential in carcinoma cells. To assess the contribution of extracellular vesicles following EMT, we conducted a proteomic analysis of shed microvesicles released from Madin-Darby canine kidney (MDCK) cells, and MDCK cells transformed with oncogenic H-Ras (21D1 cells).
2021-03-18 | PXD022290 | Pride
Project description:The association of host histones with parvoviral DNA is poorly understood. We analyzed the chromatinization and histone acetylation of canine parvovirus DNA during infection by confocal imaging and in situ proximity ligation assay combined with chromatin immunoprecipitation and high-throughput sequencing. We found that at late infection parvovirus replication bodies were rich in histones bearing modifications characteristic of transcriptionally active chromatin, i.e. histone H3 lysine acetylation (H3K27ac). The H3K27ac, in particular, was located in close proximity to the viral DNA-binding protein NS1. Importantly, our results show for the first time that in the chromatinized parvoviral genome, particularly the two viral promoters were rich in H3K27ac. Histone acetyltransferase (HAT) inhibitorefficiently interfered with expression of viral proteins and infection progress. Altogether, our data suggest that acetylation of histones on parvoviral DNA is essential for viral gene expression and completion of viral life cycle. Examination of H3K27 acetylation in CPV infected and non-infected NLFK (Norden laboratory feline kidney) cells. Please note that the result in this study, considering the sequencing, is the fact that the viral genome is chromatinized. Processed data in this case would be the aligned read percentages in control cells (of which 0% aligns to parvoviral genome) and infected cells (of which ~9% only aligns to parvoviral genome and not to the cat genome), which is basically the output of the read aligner software without further processing steps (no peaks or regions were identified for the associated publication). Therefore no processed data was provided, and an exception to GEO processed data requirement was made.
2016-02-11 | E-GEOD-77785 | biostudies-arrayexpress