Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigating stromal reprogramming in canine mammary adenoma using next-generation RNA sequencing of FFPE subsections

ABSTRACT: Cancer-associated stroma (CAS) and matched normal stroma (NS) samples from 13 cases of canine mammary adenoma

ORGANISM(S): Canis lupus familiaris

PROVIDER: GSE135454 | GEO | 2020/04/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma

Project description:Cancer-associated stroma (CAS) and matched normal stroma (NS) samples from 15 cases of canine mammary carcinoma (mCA).

2019-08-01 | GSE135183 | GEO

Proteomic profiling of stromal reprogramming in canine simple mammary carcinomas using laser-capture microdissected FFPE tissue

Project description:Cancer-associated stroma (CAS) profoundly influences development and progression of tumours including mammary carcinoma (mCA). Spontaneous canine simple mCA represent relevant models of human mCA, notably also with respect to CAS reprogramming. While transcriptomic changes in CAS of mCA are well described, it remains unclear to what extent these differences translate to the protein level. Therefore, we sought to gain insight into the proteomic changes in CAS and compare them with transcriptomic changes in the same tissue. To this end, we analysed CAS and matched normal stroma isolated by laser-capture microdissection (LCM) by LC-MS/MS in a cohort of 14 Formalin-fixed paraffin embedded (FFPE) canine mCAs that we had previously characterized using LCM-RNAseq. Our results reveal clear differences in protein abundance between CAS and normal stroma, which are characterised by changes in the extracellular matrix, the cytoskeleton, and cytokines such as TNF. While the proteomics-based analysis of LCM-FFPE tissue detects fewer targets than RNAseq, the protein and RNA levels show a decent degree of correlation, especially for the most deregulated targets. Moreover, the results from both approaches reveal a comparable picture with regards to pathway activation. Finally, we validate transcriptomic upregulation of LTBP2, IGFBP2, COL6A5, POSTN, FN1, COL4A1, COL12A1, PLOD2, COL4A2, and IGFBP7 in CAS on the protein level and demonstrate their adverse prognostic value for human breast cancer. Given the relevance of canine mCA as model for the human disease, our analysis substantiates these targets as disease-promoting stromal components with implications for breast cancer in both humans and dogs.

2021-03-30 | PXD023023 | Pride

Stromal expression profiling reveals immune-driven adaption to malignancy in canine melanoma subtypes

Project description:Canine mucosal melanoma (CMM) is the most common oral malignancy in dogs and exhibits significantly higher aggressiveness than its cutaneous counterpart (CCM), yet the reasons for this disparity remain unclear. The influence of cancer-associated stroma (CAS) on tumour progression is well-recognized, but a detailed understanding of CAS in canine melanoma is missing. To comprehensively assess stromal reprogramming in canine melanoma, we analysed CAS from 21 CMM, 14 CCM and normal stroma from 10 skin and 9 oral mucosa samples by laser-capture microdissection followed by RNA sequencing. Results were assessed in relation to subtypes, prognostic factors including mitotic count (MC), ulceration, necrosis, pigmentation, and immune cell infiltration (CD3, CD20 and CD68), scored using immunohistochemistry. While stromal reprogramming was evident in both subtypes, it was significantly more pronounced in CMM. Furthermore, MC strongly correlated with stromal gene expression in both subtypes, suggesting CAS reprogramming to depend on tumour malignancy. Comparison of subtypes revealed specific downregulation of key regulators of leukocyte activation and proliferation in mucosal CAS, supporting a role for impaired immune control in CMM aggressiveness. CMM presented with significantly more CD20 infiltrated (excluded or hot) cases than CCM. In CMM, CD20 infiltration was significantly associated with MC, with excluded cases displaying highest MC. Finally, we identify an immune-suppressive stromal signature in a subset of CMM that influences tumour aggressiveness and predicts overall survival in human melanoma patients. Together, these findings provide a solid foundation for understanding the role of CAS in canine melanoma, with relevance for the human disease.

2024-05-31 | GSE266234 | GEO

Investigating stromal reprogramming in canine mammary adenoma using next-generation RNA sequencing of FFPE subsections

Project description:Investigating stromal reprogramming in canine mammary adenoma using next-generation RNA sequencing of FFPE subsections

| PRJNA558957 | ENA

Transcriptomic profiling of canine decidualization and effects evoked by antigestagens on decidualized canine uterine stromal cells

Project description:Maternal-stroma derived decidual cells are the single population in the canine placenta expressing the nuclear progesterone (P4) receptor (PGR), rendering them crucial for the maintenance of canine pregnancy. Indeed, decreased circulating P4 levels or blockage of PGR function with antigestagens (e.g., aglepristone), culminates in the termination of canine pregnancy. As an in vitro model for canine decidualization, dog uterine stromal (DUS; Graubner et al., 2017) cells can be decidualized in vitro with cAMP. The antigestagens aglepristone and mifepristone ablate the expression of decidualization markers in DUS cells (e.g., PGR, PRLR, IGF1 or PTGES). In order to study the mechanisms involved in feto-maternal communication during pregnancy and induction of parturition, the goal of the present work was to assess transcriptional changes mediated by decidualization and antigestagens-induced effects in decidualized DUS cells. Decidualization led to the upregulation of 1841 differentially expressed genes (DEGs, P < 0.01, FDR < 0.01) involved in cellular proliferation and adhesion, mesenchymal-epithelial transition, extracellular matrix organization, and vaso- and immunomodulation. The 1475 DEGs downregulated after decidualization were mostly associated with apoptosis and cell migration. In decidualized DUS cells, aglepristone modulated 1400 DEGs and mifepristone 1558 DEGs. Interestingly, only around half of the identified DEGs were modulated uniquely by one of the antigestagens. In both situations, however, PGR-blockage was associated with an inversion of decidualization-induced effects. Comparison between antigestagens-mediated effects and transcriptional changes in the canine placenta at term allowed the identification of 191 DEGs associated with cell proliferation and adhesion, vascularization and immune activity. These findings emphasize the importance of P4/PGR signaling for decidual cells function.

2022-12-28 | GSE213788 | GEO

Gene expression in canine adipose stromal vascular fraction

Project description:Microarray studies were performed to identify expression patterns by cryopreserved adipose stromal vascular fraction (SVF) preparations that were prepared by three different veterinary stem cell companies from the same source of canine adipose tissue.

2014-03-05 | GSE55351 | GEO

Whole genome DASL analysis of tumour epithelial and stromal compartments during breast cancer progression

Project description:Analysis of gene expression changes in tumour epithelium (DCIS and invasive breast cancer) and stroma both immediately surrounding the lesions and more distantly. Total RNA obtained from Formalin Fixed Paraffin Embedded archival material and the individual compartments (stroma and epithelium) compared independently across the samples. Sample abbreviation key: BC = breast cancer DCIS = ductal carcinoma in situ IDC = invasive ductal carcinoma RM = remote metastasis S = stroma NS = near stroma.

2012-05-10 | E-GEOD-35019 | biostudies-arrayexpress

Canine

Project description:Canine

| PRJNA687522 | ENA

Characterization of canine mesenchymal stromal cell lines (MSC)

Project description:The bone marrow microenvironment is a complex mixture of cells that function in concert to regulate hematopoiesis. Cellular components include fixed nonhematopoietic stromal elements (MSC) as well as monocytes and resident macrophages, which are derived from the hematopoietic stem cells. Clinical studies have shown healing effects, direct or indirect, from the injection of MSC int Keywords: Cell type comparison Canine bone marrow stromal cells were immortalized by transduction with a replication-defective recombinant retrovirus containing the human papilloma virus E6/E7 genes (pLXSN-16 E6E7), as described for human stromal cell lines in Roecklein and Torok-Storb (Blood 85:997-1005, 1995). Transduced clones were selected with 50 ug/ml G418 and resistant clones were isolated, grown to confluency and characterized for morphology, cytokine production and cell surface molecule expression. These cells are intended for clinical research in the canine transplantation model, as a complement for existing human stromal cell lines, for mitigation of graft-versus-host disease and radiation effects.

2008-05-01 | E-GEOD-11310 | biostudies-arrayexpress

Proteomic profiling of canine fibrosarcomas and adjacent unaffected peritumoral tissue using laser-capture microdissected FFPE tissue

Project description:Proteomic profiling of canine fibrosarcomas and adjacent unaffected peritumoral tissue using laser-capture microdissected FFPE tissue

2023-03-11 | PXD029338 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data