Ena-DATASET-MSKCC-01-03-2017-18:58:54:915-35 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001003200 | EGA |
REPOSITORIES: EGA
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Project description:Files from whole exome sequencing of matched normals and multiple tumors from 7 melanoma patients. The tumors include primary tumors and distant metastases.
| EGAD00001006410 | EGA
Project description:Exercise prevents cancer incidence and recurrence, yet the underlying mechanism remains mostly unknown. Here we report that exercise induces a metabolic reprogramming of internal organs, increasing their nutrient demand, thus protecting them against metastatic colonization by limiting nutrient availability to the tumor, which we termed exercise induced metabolic-shield. Proteomic and ex-vivo metabolic-capacity analyses of mice internal organs revealed that exercise induces catabolic processes, glucose uptake, mitochondrial activity, and GLUT expression. Proteomic analysis of routinely active subjects' plasma demonstrated increased carbohydrate utilization following exercise. Further, epidemiological data of a 20-year follow-up of a large human cohort of cancer free participants, revealed that exercise prior to cancer initiation has a modest impact on cancer incidence in low metastatic stages, but significantly reduced the likelihood of highly metastatic cancer as compared to inactive participants. We utilized two exercise protocols, wherein the mice were subjected to exercise either both pre- and post- melanoma injection or only pre-injection. We found that exercise prior to cancer injection significantly protects against metastases in distant organs, regardless of the three melanoma metastases models we used. Mechanistically, ex-vivo inhibition of the mTOR pathway, via rapamycin treatment, reversed the protection from the exercise induced metabolic-shield. Under limited glucose conditions, active stroma consumed significantly more glucose, at the expense of the tumor, as reflected in histology analyses of mice melanoma metastases. Our data suggests that cancers’ metabolic plasticity and the exercise-induced metabolic reprogramming of the stroma are clashing, raising the opportunity to block metastases by challenging cancers’ metabolic needs.
2023-03-11 | PXD035648 | Pride
Project description:Exercise prevents cancer incidence and recurrence, yet the underlying mechanism remains mostly unknown. Here we report that exercise induces a metabolic reprogramming of internal organs, increasing their nutrient demand, thus protecting them against metastatic colonization by limiting nutrient availability to the tumor, which we termed exercise induced metabolic-shield. Proteomic and ex-vivo metabolic-capacity analyses of mice internal organs revealed that exercise induces catabolic processes, glucose uptake, mitochondrial activity, and GLUT expression. Proteomic analysis of routinely active subjects' plasma demonstrated increased carbohydrate utilization following exercise. Further, epidemiological data of a 20-year follow-up of a large human cohort of cancer free participants, revealed that exercise prior to cancer initiation has a modest impact on cancer incidence in low metastatic stages, but significantly reduced the likelihood of highly metastatic cancer as compared to inactive participants. We utilized two exercise protocols, wherein the mice were subjected to exercise either both pre- and post- melanoma injection or only pre-injection. We found that exercise prior to cancer injection significantly protects against metastases in distant organs, regardless of the three melanoma metastases models we used. Mechanistically, ex-vivo inhibition of the mTOR pathway, via rapamycin treatment, reversed the protection from the exercise induced metabolic-shield. Under limited glucose conditions, active stroma consumed significantly more glucose, at the expense of the tumor, as reflected in histology analyses of mice melanoma metastases. Our data suggests that cancers’ metabolic plasticity and the exercise-induced metabolic reprogramming of the stroma are clashing, raising the opportunity to block metastases by challenging cancers’ metabolic needs.
2023-03-11 | PXD035630 | Pride
Project description:The ability to predict metastatic potential is of clinical and biological importance. Numerous metastasis/relapse predictors exist for breast cancer patients; however, what is less well established is whether predicting metastasis to specific organs sites is feasible. In this study we sought to determine: 1) the degree to which gene signatures vary across tumors and their metastases, 2) if genomic intrinsic subtypes associate with particular organs of relapse, and 3) if other genomic signatures can predict spread to specific organs. Using a gene expression microarray data set of >1000 breast tumors and metastases, we observed that >90% of 298 gene signatures were similarly expressed between matched pairs of breast tumors and metastases; those most altered were reflective of cell types including fibroblasts and immune cells. Significant associations were identified between tumor subtypes and organ of first relapse. Among these, HER2-enriched tumors were significantly associated with liver, and Basal-like and Claudin-low tumors with brain and lung. Correspondingly, previously published brain and lung metastasis signatures, along with embryonic stem cell and tumor initiating cell signatures, were also associated with Basal-like and Claudin-low subtypes. These signatures strongly correlated with low Differentiation Scores (DS) and, to a lesser extent, high proliferation. Interestingly, within Basal-like and Claudin-low tumors, low DS further predicted for brain and lung metastases. In total, intrinsic subtype and DS provide clinically useful information that identifies the distant organ sites that should be most closely monitored for signs of disease recurrence. 414 samples profiled on Agilent microarrays.
2011-06-20 | E-GEOD-26338 | biostudies-arrayexpress
Project description:Results When compared with each other, primary tumors and regional metastases showed statistically indistinguishable gene expression patterns. Supervised analyses comparing patients with distant metastases versus primary tumors or regional metastases showed that the distant metastases were distinct and distinguished by the lack of expression of fibroblast/mesenchymal genes, and by the high expression of a 13-gene profile (that is, the âvascular endothelial growth factor (VEGF) profileâ) that included VEGF, ANGPTL4, ADM and the monocarboxylic acid transporter SLC16A3. At least 8 out of 13 of these genes contained HIF1α binding sites, many are known to be HIF1α-regulated, and expression of the VEGF profile correlated with HIF1α IHC positivity. The VEGF profile also showed prognostic significance on tests of sets of patients with breast and lung cancer and glioblastomas, and was an independent predictor of outcomes in primary breast cancers when tested in models that contained other prognostic gene expression profiles and clinical variables. Conclusions These data identify a compact in vivo hypoxia signature that tends to be present in distant metastasis samples, and which portends a poor outcome in multiple tumor types. Microarrays and immunohistochemistry were used to analyze primary breast tumors, regional (lymph node) metastases, and distant metastases in order to identify biological features associated with distant metastases.
2009-03-31 | E-GEOD-3521 | biostudies-arrayexpress
Project description:The ability to predict metastatic potential is of clinical and biological importance. Numerous metastasis/relapse predictors exist for breast cancer patients; however, what is less well established is whether predicting metastasis to specific organs sites is feasible. In this study we sought to determine: 1) the degree to which gene signatures vary across tumors and their metastases, 2) if genomic intrinsic subtypes associate with particular organs of relapse, and 3) if other genomic signatures can predict spread to specific organs. Using a gene expression microarray data set of >1000 breast tumors and metastases, we observed that >90% of 298 gene signatures were similarly expressed between matched pairs of breast tumors and metastases; those most altered were reflective of cell types including fibroblasts and immune cells. Significant associations were identified between tumor subtypes and organ of first relapse. Among these, HER2-enriched tumors were significantly associated with liver, and Basal-like and Claudin-low tumors with brain and lung. Correspondingly, previously published brain and lung metastasis signatures, along with embryonic stem cell and tumor initiating cell signatures, were also associated with Basal-like and Claudin-low subtypes. These signatures strongly correlated with low Differentiation Scores (DS) and, to a lesser extent, high proliferation. Interestingly, within Basal-like and Claudin-low tumors, low DS further predicted for brain and lung metastases. In total, intrinsic subtype and DS provide clinically useful information that identifies the distant organ sites that should be most closely monitored for signs of disease recurrence.
2011-06-20 | GSE26338 | GEO
Project description:Study of primary renal cancers as well as metastases derived from renal cancers in various distant organs.
| EGAS00001001176 | EGA
Project description:Next Generation Sequencing was applied to investigate the heterogeneity between tumors and distant metastases in different models of Breast Cancer cell lines and primary-derived xenografts. Global transcriptional profiling of the primary tumor and matched distant metastases (lung, liver, spleen) as well as circulating tumor cells (CTCs) allowed to identify glucocorticoid signalling as a mediator of metastasis.
2019-03-14 | GSE124817 | GEO
Project description:The development of metastases is a complex multi-step process manifested by diverse patterns, involving single or multiple organs and different time-courses of distant recurrences. The aim of this study was to characterise molecular patterns associated with patterns of organ-specific metastatic spread observed in the clinic from FFPE embedded breast carcinomas and lymph node metastases. This study includes patients with four patterns of first metastatic sites: bone only (with no visceral metastases within 6 months of first metastasis); to viscera only (with no bone metastasis within 6 months of first metastasis); to bone and visceral organs within a 6 month period; and no recorded distant metastasis. The study population was composed of 5,061 patients diagnosed with invasive primary breast cancer without distant metastasis at the time of diagnosis between 1975 and 2005 from Guyâs Hospital. From the study population, an incidence-based case-control design was used to include patients from each of the metastatic groups and a control series randomly matched to cases according to having no reported metastasis up to the calendar date of metastasis. The aim of this expression profiling study was to characterise any molecular patterns that may be associated with the organ-specific metastatic spread observed in the clinic from FFPE embedded breast carcinomas and lymph node metastases.
2017-12-01 | E-MTAB-4003 | biostudies-arrayexpress
Project description:We aimed to understand the transcriptome patterns of organ-derived cancer cell isolates from MMTV-PyMT mice. Tissues from primary tumors and organs harboring distal metastases were harvested from cancer bearing female mice. Although metastatic progression from primary tumors to lung tissue is well studied in the MMTV-PyMT model, metastases to other distal organs and the significance of intratumor heterogeneity across metastases from distal organs remain unclear. To gain insight, we established an array of metastatic cell lines harvested from the MMTV-PyMT breast cancer mouse model. Sequencing at bulk and single-cell level were performed and used to examine the effects of cell heterogeneity on metastases and organ tropism
2021-04-01 | GSE165393 | GEO