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Reverse phase protein array based protein profiling of breast cancer specimens

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE47066 | GEO | 2014/02/18

SECONDARY ACCESSION(S): PRJNA203402

REPOSITORIES: GEO

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Reverse phase protein array based protein profiling of breast cancer specimens

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

Reverse phase protein array based protein profiling of breast cancer specimens (2)

2014-02-18 | GSE50861 | GEO

Reverse phase protein array based protein profiling of breast cancer specimens (2)

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

Reverse phase protein arrays (RPPAs)

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-09-30 | GSE70776 | GEO

Macro-porous Reversed Phase Separation of Proteins Combined with Reversed Phase Separation of Phosphopeptides and Tandem Mass Spectrometry for Profiling the Phosphoproteome of MDA-MB-231 cells

Project description:A new method of combining macro-porous reversed phase (mRP) protein fractionation with reversed phase liquid chromatography (RPLC) peptide separation tandem mass spectrometry (MS/MS) is reported for profiling the phosphoproteome of a complex sample. In this method, an mRP-C18 column was used to fractionate the proteins from a whole cell lysate of a breast cancer cell line, MDA-MB-231, into 38 fractions. Each fraction was subjected to tryptic digestion, sequential phosphopeptide enrichment by immobilized metal ion affinity chromatography (IMAC) and titanium dioxide (TiO2), followed by capillary RPLC-MS/MS analysis. For comparison, the conventional method of using strong cation exchange (SCX)-RPLC separation of peptides combined with MS/MS was also used for analyzing the phosphoproteome. Replicate experiments by the mRP-RPLC method identified 1585 distinct phosphoproteins with 4519 phosphopeptides, compared to 1585 phosphoproteins with 4297 phosphopeptides by SCX-RPLC, with a total of 1947 phosphoproteins and 6278 phosphopeptides identified from the combined results. While the two methods have similar ability in the identification of the phosphoproteome, they produce complementary information. The phosphoproteins identified in this study, including 67 novel phosphorylation sites from 56 breast cancer related proteins, can serve as the entry point for future validation with biological implications in breast cancer.

2014-07-24 | PXD000948 | Pride

Reverse phase protein arrays (RPPAs) (in vitro)

Project description:Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve antibody slide. All the data points were normalized for protein loading and transformed to a linear value. Linear values were transformed to Log2 value and then median‐centered for hierarchical cluster analysis.

2015-09-30 | GSE70773 | GEO

Reverse phase protein arrays (RPPAs) (in vivo)

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High-throughput Phosphorylation Screening and Validation through Ti(IV)-Nanopolymer Functionalized Reverse Phase PhosphoProtein Array

Project description:Protein phosphorylation is one of the most important and widespread molecular regulatory mechanisms that controls almost all aspects of cellular functions in animals and plants. Here, we introduce a novel chemically functionalized Reverse Phase PhosphoProtein Array (RP3A) to capture and measure phosphoproteomes. RP3A uses polyamidoamine (PAMAM) dendrimer immobilized with Ti(IV) ions to functionalize nitrocellulose membrane, facilitating specific chelation of phosphoproteins from complex protein samples on the array. Globular, water-soluble Ti(IV)-dendrimer allows the RP3A surface highly accessible by phosphoproteins multi-dimensionally and the captured phosphoproteins were subsequently detected using the same validated antibodies as in regular reverse-phase protein arrays. The novel chemical strategy demonstrated superior specificity (1:10,000), high sensitivity (fg level), and good quantitative nature (R2 =0.99) for measuring phosphoproteins. We further applied quantitative phosphoproteomics followed by RP3A to validate the phosphorylation status of a panel of phosphoproteins in response to environmental stresses in Arabidopsis.

2019-11-12 | PXD010208 | Pride

The C10orf10 protein profiling of breast cancer specimens based on a tissue array

Project description:Expression levels of C10orf10 protein were obtained for a series of 100 breast cancer tumor specimens.

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Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [circRNA-Seq breast cancer]

Project description:By using circRNA-seq, we report tumor special circRNA from breast cancer tissues and normal tissues.

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