Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Canis lupus familiaris
PROVIDER: GSE135183 | GEO | 2019/08/01
REPOSITORIES: GEO
Similar Datasets
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
Project description:Cancer-associated stroma (CAS) and matched normal stroma (NS) samples from 13 cases of canine mammary adenoma
2020-04-06 | GSE135454 | GEO
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
Project description:Spontaneous canine simple mammary carcinomas (mCA) are often viewed as models of human mCA. Cancer-associated stroma (CAS) is central for initiation and progression of human cancer, and is likely to play a key role in canine tumours as well. However, canine CAS lacks characterisation and it remains unclear how canine and human CAS compare. Formalin-fixed paraffin embedded (FFPE) tissue constitutes a valuable resource of patient material, but chemical crosslinking has largely precluded its analysis by next-generation RNA sequencing (RNAseq). We have recently established a protocol to isolate CAS and normal stroma from archival FFPE tumours using laser-capture microdissection followed by RNAseq. Using this approach, we have analysed stroma from 15 canine mCA. Our data reveal strong reprogramming of canine CAS. We demonstrate a high-grade molecular homology between canine and human CAS, and show that enrichment of upregulated canine CAS genes strongly correlates with the enrichment of an independently derived human stromal signature in the TCGA breast tumour dataset. Relationships between different gene signatures observed in human breast cancer are largely maintained in the canine model, suggesting a close interspecies similarity in the network of cancer signalling circuitries. Finally, we establish the prognostic potential of the canine CAS signature in human samples, emphasising the relevance of studying canine CAS as a model of the human disease. In conclusion, we provide a proof-of-principle to analyse specific subsections of FFPE tissue by RNAseq, and compare stromal gene expression between human and canine mCA to reveal molecular drivers in CAS supporting tumour growth and malignancy.
| S-EPMC6737962 | biostudies-literature
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
Project description:Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma
| PRJNA557680 | ENA
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
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
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