Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma
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ABSTRACT:
ORGANISM(S): Canis lupus familiaris
PROVIDER: GSE135183 | GEO | 2019/08/01
REPOSITORIES: GEO
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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:[original title] Metastatic Canine Mammary Carcinomas can be Identified by a Gene Expression Profile that partly Overlaps with Human Breast Cancer Profiles. Introduction: Similar to human breast cancer mammary tumors of the female dog are commonly associated with a fatal outcome due to the development of distant metastases. However, the molecular defects leading to metastasis are largely unknown and the value of canine mammary carcinoma as a model for human breast cancer is unclear. In this study, we analyzed the gene expression signatures associated with mammary tumor metastasis and asked for parallels with the human equivalent. Methods: Messenger RNA expression profiles of twenty-seven lymph node metastasis positive or negative canine mammary carcinomas were established by microarray analysis. Differentially expressed genes were functionally characterized and associated with molecular pathways. The findings were also correlated with published data on human breast cancer. Results: Metastatic canine mammary carcinomas had 1,011 significantly differentially expressed genes when compared to non-metastatic carcinomas. Metastatic carcinomas had a significant up-regulation of genes associated with cell cycle regulation, matrix modulation, protein folding and proteasomal degradation whereas cell differentiation genes, growth factor pathway genes and regulators of actin organization were significantly down-regulated. Interestingly, 265 of the 1,011 differentially expressed canine genes are also related to human breast cancer and, vice versa, parts of a human prognostic gene signature were identified in the expression profiles of the metastatic canine tumors. Conclusions: Metastatic canine mammary carcinomas can be discriminated from non-metastatic carcinomas by their gene expression profiles. More than one third of the differentially expressed genes are also described of relevance for human breast cancer. Many of the differentially expressed genes are linked to functions and pathways which appear to be relevant for the induction and maintenance of metastatic progression and may represent new therapeutic targets. Furthermore, dogs are in some aspects suitable as a translational model for human breast tumors in order to identify prognostic molecular signatures and potential therapeutic targets.
2010-12-01 | GSE20718 | GEO
Project description:Molecular mechanisms of the canine mammary malignancy. RNA isolated from canine mammary tumours of the 3rd grade of malignancy was pooled and hybrydized on the same microarray as RNA isolated from canine mammary tumours of the 1st grade of malignancy. Based on the results the "malignancy portrait" was assessed.
2013-10-01 | GSE44033 | GEO
Project description:Molecular mechanisms of the canine mammary malignancy. RNA isolated from canine mammary tumours of the 3rd grade of malignancy was pooled and hybrydized on the same microarray as RNA isolated from canine mammary tumours of the 1st grade of malignancy. Based on the results the "malignancy portrait" was assessed. Dye-swap experiment, gene expression in the most malignant canine mammary tumours (the 3rd grade of malignancy) was compared to the less malignant tumours (1st grade of malignancy).
2013-10-01 | E-GEOD-44033 | biostudies-arrayexpress
Project description:[original title] Metastatic Canine Mammary Carcinomas can be Identified by a Gene Expression Profile that partly Overlaps with Human Breast Cancer Profiles. Introduction: Similar to human breast cancer mammary tumors of the female dog are commonly associated with a fatal outcome due to the development of distant metastases. However, the molecular defects leading to metastasis are largely unknown and the value of canine mammary carcinoma as a model for human breast cancer is unclear. In this study, we analyzed the gene expression signatures associated with mammary tumor metastasis and asked for parallels with the human equivalent. Methods: Messenger RNA expression profiles of twenty-seven lymph node metastasis positive or negative canine mammary carcinomas were established by microarray analysis. Differentially expressed genes were functionally characterized and associated with molecular pathways. The findings were also correlated with published data on human breast cancer. Results: Metastatic canine mammary carcinomas had 1,011 significantly differentially expressed genes when compared to non-metastatic carcinomas. Metastatic carcinomas had a significant up-regulation of genes associated with cell cycle regulation, matrix modulation, protein folding and proteasomal degradation whereas cell differentiation genes, growth factor pathway genes and regulators of actin organization were significantly down-regulated. Interestingly, 265 of the 1,011 differentially expressed canine genes are also related to human breast cancer and, vice versa, parts of a human prognostic gene signature were identified in the expression profiles of the metastatic canine tumors. Conclusions: Metastatic canine mammary carcinomas can be discriminated from non-metastatic carcinomas by their gene expression profiles. More than one third of the differentially expressed genes are also described of relevance for human breast cancer. Many of the differentially expressed genes are linked to functions and pathways which appear to be relevant for the induction and maintenance of metastatic progression and may represent new therapeutic targets. Furthermore, dogs are in some aspects suitable as a translational model for human breast tumors in order to identify prognostic molecular signatures and potential therapeutic targets. Thirteen simple mammary carcinomas with invasive growth and lymph node metastases at the time of tumor resection and 14 simple carcinomas without lymph node metastases were included in the study. None of the patients had radiographically detectable pulmonary metastases at the time of tumor resection. Distant metastases as the cause of death were determined postoperatively by radiographic detection of metastases or necropsy. Selection criteria for carcinomas without lymph node metastases included an invasive growth, a negative lymph node status, a histological grade III and a minimal tumor diameter above the average of the lymph node positive tumors (> 2.42 cm). All animals with non-metastatic carcinomas had a survival rate of over 24 months except animal no. 22 (2627) which developed radiographic detectable lung metastases 8 months after surgery. Tumor and lymph node histologies were evaluated independently by two board-certified pathologists, following the criteria of the WHO classification of canine mammary tumors and the Nottingham grading system. All 27 tumors were simple carcinomas and characterized by an invasive, mostly solid growth pattern, marked cellular pleomorphism, anisokaryosis and 3 or more mitotic figures per high power field.
2010-12-01 | E-GEOD-20718 | biostudies-arrayexpress
Project description:Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma
| PRJNA557680 | ENA
Project description:We explored the expression profile of circRNAs in canine mammary tumours using high-throughput sequencing technology. In our study, we analysed the expression profiles of 3 pairs of canine mammary tumours and their adjacent normal tissues. The total RNA was extracted, and a RNA library was constructed. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses revealed that these genes were mainly concentrated in 14 biological pathways. We selected 11 validated circRNAs and further confirmed the existence of these circRNAs by qRT-PCR. The circRNA-miRNA network diagram was constructed by using Cytoscape software. We found a total of 14851 circRNAs and 106 differentially expressed circRNAs in canine mammary tumours and their adjacent normal tissues (fold change ≥ 2, P ≤ 0.05). There were 64 upregulated circRNAs and 42 downregulated circRNAs. The main GO functions were the regulation of the regulated secretory pathway, the regulation of neurotransmitter secretion and the positive regulation of phagocytosis. Most of these pathways were related to the cGMP-PKG (cyclic guanosine monophosphate) signalling pathway, the cAMP (cyclic adenosine monophosphate) signalling pathway and the OXYTOCIN signalling pathway. CircRNAs have the function of adsorbing miRNA, similar to a sponge, and we further constructed the interaction network of circRNAs and miRNAs. The screened source genes closely related to canine mammary tumours included RYR2, PDE4D, ROCK2, CREB3L2 and UBA3. The screened circRNAs related to canine mammary tumours included chr27:26618544-26687235-, chr26:8194880-8201833+, and chr17:7960861-7967766-.In conclusion, our study uncovered circRNA expression profiles in canine mammary tumours. Moreover, some circRNAs may be used as potential biomarkers for screening dogs with high-risk canine mammary tumours.
2019-09-23 | GSE137825 | GEO