RNA profiling of matched pair samples of primary breast cancer vs. lung and pleura metastasis
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE145752 | GEO | 2020/09/03
REPOSITORIES: GEO
Similar Datasets
Project description:Expression levels of proteins and phosphoproteins, covering major cancer signaling pathways with a special focus on breast cancer biology, were obtained for a series of 164 breast cancer tumor specimens with positive estrogen receptor status. Tumor specimens from patients diagnosed with primary invasive breast carcinoma were collected at the time of surgery between 2005 and 2011 and provided by the NCT Tissue Bank Heidelberg as well as by the Department of Gynecology and Obstetrics / National Center for Tumor Diseases Heidelberg. None of the patients had received neoadjuvant therapy.Tumor specimens were processed within 20 min after surgery. Samples were stored snap frozen at -80M-BM-0C until further use. Only tumor samples with > 70% tumour cells and positive estrogen receptor status (immunoreactive score M-bM-^IM-% 3) as assessed by routine immunohistochemistry were selected for this study (n = 164). Tumor lysates were printed on a series of nitrocellulose coated glass slides and probed with with differnt primary antibodies directed against proteins and phosphoproteins of interest. Primary antibodies were selected to recognize proteins involved in major cancer signaling pathways with a special focus on breast cancer biology.
2014-02-18 | E-GEOD-50861 | biostudies-arrayexpress
Project description:Expression levels of proteins and phosphoproteins, covering major cancer signaling pathways with a special focus on breast cancer biology, were obtained for a series of 109 breast cancer tumor specimens with positive estrogen receptor status. Tumor specimens from patients diagnosed with primary invasive breast carcinoma were collected at the time of surgery between 2008 and 2010 at the Department of Gynecology and Obstetrics / National Center for Tumor Diseases Heidelberg. None of the patients had received neoadjuvant therapy. Institutional Review Board approval was received as ethics vote no. S039/2008 and informed consent was obtained from all patients. Tumor specimens were processed within 20 min after surgery. Samples were stored snap frozen at -80M-BM-0C until further use. Only tumor samples with > 70% tumour cells and positive estrogen receptor status (immunoreactive score M-bM-^IM-% 3) as assessed by routine immunohistochemistry were selected for this study (n = 109). Tumor lysates were printed on a series of nitrocellulose coated glass slides and probed with 128 different primary antibodies directed against proteins and phosphoproteins of interest. Primary antibodies were selected to recognize proteins involved in major cancer signaling pathways with a special focus on breast cancer biology.
2014-02-18 | E-GEOD-47066 | biostudies-arrayexpress
Project description:The serine/threonine kinase mammalian target of rapamycin (mTOR) governs growth, metabolism, and aging in response to insulin and amino acids (aa), and is often activated in metabolic disorders and cancer. Much is known about the regulatory signaling network around mTOR, but surprisingly few direct mTOR substrates have been established to date. To tackle this gap in our knowledge, we took advantage of a combined quantitative phosphoproteomic and interactomic strategy. We analyzed the insulin- and aa-responsive phosphoproteome upon inhibition of the mTOR complex 1 (mTORC1) component raptor, and analyzed in parallel the interactome of endogenous mTOR. By overlaying these two datasets, we identified acinus L as a potential novel mTORC1 target. We confirmed acinus L as a direct mTORC1 substrate by co-immunoprecipitation and MS-enhanced kinase assays. Our study delineates a triple proteomics strategy of combined phosphoproteomics, interactomics, and MS-enhanced kinase assays for the de novo-identification of mTOR network components, and provides a rich source of potential novel mTOR interactors and targets for future investigation.<br><br>Additional contact details:<br><a href="mailto:k.thedieck@umcg.nl">Prof. Dr. Kathrin Thedieck</a><br>Department of Pediatrics, University of Groningen, University Medical Center Groningen (UMCG), 9713 AV Groningen, The Netherlands.<br>Faculty VI - School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany.<br><br>Prof. Dr. Bettina Warscheid<br>Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany.<br>BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.<br>
2015-04-28 | PXD001196 | Pride
Project description:The serine/threonine kinase mammalian target of rapamycin (mTOR) governs growth, metabolism, and aging in response to insulin and amino acids (aa), and is often activated in metabolic disorders and cancer. Much is known about the regulatory signaling network around mTOR, but surprisingly few direct mTOR substrates have been established to date. To tackle this gap in our knowledge, we took advantage of a combined quantitative phosphoproteomic and interactomic strategy. We analyzed the insulin- and aa-responsive phosphoproteome upon inhibition of the mTOR complex 1 (mTORC1) component raptor, and analyzed in parallel the interactome of endogenous mTOR. By overlaying these two datasets, we identified acinus L as a potential novel mTORC1 target. We confirmed acinus L as a direct mTORC1 substrate by co-immunoprecipitation and MS-enhanced kinase assays. Our study delineates a triple proteomics strategy of combined phosphoproteomics, interactomics, and MS-enhanced kinase assays for the de novo-identification of mTOR network components, and provides a rich source of potential novel mTOR interactors and targets for future investigation.<br><br>Additional contact details:<br><a href="mailto:k.thedieck@umcg.nl">Prof. Dr. Kathrin Thedieck</a><br>Department of Pediatrics, University of Groningen, University Medical Center Groningen (UMCG), 9713 AV Groningen, The Netherlands.<br>Faculty VI - School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany.<br><br>Prof. Dr. Bettina Warscheid<br>Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany.<br>BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.<br>
2015-04-28 | PXD001245 | Pride
Project description:The serine/threonine kinase mammalian target of rapamycin (mTOR) governs growth, metabolism, and aging in response to insulin and amino acids (aa), and is often activated in metabolic disorders and cancer. Much is known about the regulatory signaling network around mTOR, but surprisingly few direct mTOR substrates have been established to date. To tackle this gap in our knowledge, we took advantage of a combined quantitative phosphoproteomic and interactomic strategy. We analyzed the insulin- and aa-responsive phosphoproteome upon inhibition of the mTOR complex 1 (mTORC1) component raptor, and analyzed in parallel the interactome of endogenous mTOR. By overlaying these two datasets, we identified acinus L as a potential novel mTORC1 target. We confirmed acinus L as a direct mTORC1 substrate by co-immunoprecipitation and MS-enhanced kinase assays. Our study delineates a triple proteomics strategy of combined phosphoproteomics, interactomics, and MS-enhanced kinase assays for the de novo-identification of mTOR network components, and provides a rich source of potential novel mTOR interactors and targets for future investigation.<br><br>Additional contact details:<br><a href="mailto:k.thedieck@umcg.nl">Prof. Dr. Kathrin Thedieck</a><br>Department of Pediatrics, University of Groningen, University Medical Center Groningen (UMCG), 9713 AV Groningen, The Netherlands.<br>Faculty VI - School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany.<br><br>Prof. Dr. Bettina Warscheid<br>Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany.<br>BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.<br>
2015-04-28 | PXD001244 | Pride
Project description:RNAi of signal transduction components in Drosophila S2 cells We performed RNAi knockdown experiments on 15 different signal transduction components in Drosophila S2 cells and prepared RNA libraries from the poly-adenylated fraction of the RNA. SOLiD sequencing of strand-specific, barcoded transcriptome libraries yielded expression profiles allowing us to extract common pathway signatures and indicated that Cka may function as novel regulator in Ras/MAPK signaling. ArrayExpress Release Date: 2011-07-08 Person Roles: investigator Person Last Name: Boutros Person First Name: Michael Person Email: m.boutros@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ Person Roles: investigator Person Last Name: Sandmann Person First Name: Thomas Person Email: t.sandmann@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ Person Roles: investigator Person Last Name: Horn Person First Name: Thomas Person Email: t.horn@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ Person Roles: submitter Person Last Name: Kerr Person First Name: Grainne Person Email: g.kerr@dkfz.de Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany Person Affiliation: Signaling and Functional Genomics, DKFZ
2011-07-14 | GSE30602 | GEO
Project description:miRNAs are small non-coding RNAs frequently altered in human malignancies. They regulate protein-coding gene expression by mediating mRNA degradation and/or repressing translation via the association with the 3M-bM-^@M-^Y untranslated region (3M-bM-^@M-^Y UTR) of the mRNAs. Aberrant miRNA expression can influence several gene networks and pathways implicated in tumorigenesis and metastasis formation. To reveal miRNAs involved in breast cancer progression we investigated miRNA expression in 77 ductal breast carcinoma biopsies and 17 mammoplasties by microarray analysis. 16 differentially expressed miRNAs were identified comparing patients with or without disease relapse within 72 months from surgery. We have performed a microarray miRNA expression analysis on 77 ductal breast carcinoma biopsies and 17 normal tissues from mammoplastic reductions using the Human Agilent platform (V2). 77 frozen tumor specimens were selected from the Tumor Bank of the Department of Obstetrics and Gynecology, University of Turin. They were obtained from patients who underwent primary surgical treatment between 1988 and 2001 at a median age of 54 years (25-82). Eligibility criteria were the following: diagnosis of invasive breast cancer, all T and N stages, no distant metastasis at diagnosis (M0), complete clinical-pathological data and updated follow up. All patients were treated with radical modified mastectomy or quadrantectomy and axillary dissection plus breast irradiation. As normal breast controls 17 frozen mammoplastic reductions (EPFL, Lausanne) were included in the screening. Appropriate ethical approval was obtained for this study.
2012-12-16 | E-GEOD-26659 | biostudies-arrayexpress
Project description:In this study, we performed high-throughput sequencing to evaluate the gene expression profiles of Human Nasal Epithelial Cells (HNEpC) (C-12620, PromoCell, Heidelberg, Germany) after exposure to acidification for 6 hours.
2023-09-17 | GSE242933 | GEO
Project description:In this study, we performed high-throughput sequencing to evaluate the gene expression profiles of Human Nasal Epithelial Cells (HNEpC) (C-12620, PromoCell, Heidelberg, Germany) after exposure to PM2.5 for 24 hours.
2022-12-06 | GSE220165 | GEO
Project description:In this study, we performed high-throughput sequencing to evaluate the gene expression profiles of Human Nasal Epithelial Cells (HNEpC) (C-12620, PromoCell, Heidelberg, Germany) after exposure to LPS for 6 hours.
2023-09-01 | GSE241554 | GEO