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O-GlcNAc proteome of invasive ductal breast carcinomas

ABSTRACT: O-GlcNAc proteins in LNM and non-LNM breast tumors of IDCs were identified by using the strategy of chemo-enzymatic labeling in combination with click chemistry and LC-MS/MS.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Kuan Jiang

PROVIDER: MSV000080753 | MassIVE | Wed Mar 29 06:30:00 BST 2017

SECONDARY ACCESSION(S): PXD002208

REPOSITORIES: MassIVE

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Proteomic analysis of O-GlcNAcylated proteins in invasive ductal breast carcinomas with and without lymph node metastasis.

Jiang Kuan K Gao Yang Y Hou Weiwei W Tian Fang F Ying Wantao W Li Ling L Bai Bingyang B Hou Gang G Wang Peng George PG Zhang Lianwen L

Amino acids 20150915 2

The potential role of protein O-GlcNAcylation in cancer has been studied extensively, and the spread of cancer cells to regional lymph nodes is the first step in the dissemination of breast cancer. However, the correlation between O-GlcNAcylation and lymphatic metastasis in breast cancer remains elusive. In this study, we demonstrated that the overall O-GlcNAcylation as well as O-GlcNAc transferase (OGT) tends to decrease in response to the augmentation of lymph node metastasis (LNM) in invasive ...[more]

PMID: 26374642

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O-GlcNAc proteome of invasive ductal breast carcinomas

Project description:O-GlcNAc proteins in LNM and non-LNM breast tumors of IDCs were identified by using the strategy of chemo-enzymatic labeling in combination with click chemistry and LC-MS/MS.

2015-09-22 | PXD002208 | Pride

Proteome-wide purification of O-GlcNAc proteins

Project description:Global O-GlcNAc profiling: proteome-wide purification and identification of O-GlcNAc proteins using GlcNAz metabolic labeling in combination with Click chemistry and label-free LC-MS/MS-based quantification. OGA inhibition: same workflow as 'Global O-GlcNAc profiling'; inhibition of O-GlcNAcase by a small molecule inhibitor. O-GlcNAc sites: identification of O-GlcNAc sites by metabolic labeling/Click chemistry followed by beta elimination Bioinformatics workflow of Global O-GlcNAc profiling and OGA inhibition experiments: Raw mass spectrometry files have been processed using Progenesis LC-MS (4.0) and exported as Mascot generic format for subsequent Mascot (2.3) database search. Mascot search results were processed using Mascot Percolator and the results have been imported back into Progenesis as well as imported to Scaffold (3.5.1). The Progenesis peptide quantification report has been exported as Excel file. Bioinformatics workflow of O-GlcNAc site identification: Raw mass spectrometry files have been processed using Mascot Distiller 2.3 and searched with Mascot. Mascot search results were processed using the Mascot Percolator and imported into Scaffold (3.5.1). After manual validation, peptide and protein identifications (Scaffold file) were imported into Scaffold PTM 2.0 for the estimation of site localization probabilities.

2013-01-10 | PXD000061 | Pride

Invasive lobular and ductal carcinomas of the breast

Project description:This set of experiments includes 38 IDCs, 21 ILCs, 2 lymphnode metastases, and 3 normal breast samples. It is designed to compare gene expression profiles of IDCs and ILCs. Total RNAs from all samples were isolated using TRIzol, amplified using optimized T7 linear amplification protocol, and labeled with Cy5. Stratagen Universal Human Reference RNA was amplified the same way and labeled with Cy3. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2006-01-06 | GSE3971 | GEO

Invasive lobular and ductal carcinomas of the breast

2006-01-05 | E-GEOD-3971 | biostudies-arrayexpress

Identification of enriched O-GlcNAc proteins in hypertrophic and normal mouse hearts

Project description:Bottom up proteomics of O-GlcNAc antibody enriched proteins from mouse heart tissue (hypertrophic vs. normal). O-GlcNAc proteins were labeled with a click chemistry kit with the tetramethylrhodamine (TAMRA) tag, then the labeled proteins were enriched with TAMRA antibody for proteomics experiments.

2021-12-06 | MSV000088525 | MassIVE

Genome-wide maps of GlcNAc bound proteins and Pho ChIP-seq in Drosophila S2 cells and pupae.

Project description:We developed a strategy to map GlcNAc modified proteins based on a chemical chromatin precipitation strategy. Drosophila S2 cells, as well as wild type (wt) and sxc null pupae, were fed with 100 uM Ac4GalNAz and the resulting DNA was cross-linked, sonicated, and purified. DNA strands cross-linked to GlcNAz proteins were isolated by congugating with alkyn-biotin by Staudinger ligation followed by streptavidin purification. The resulting DNA was constructed into libraries for sequencing. To asses the robustness of our strategy, we compared GalNAz ChIP-seq results in S2 cells with two other GlcNAc ChIP-seq strategies, using a mutant β-1,4-galactosyltransferase (GalT) and the lecting wheat germ agglutinin (WGA). Briefly, GalT was incubated with cross-linked, sonicated and purified DNA along with UDP-GalNAz. Ligation to biotin with click chemistry followed by streptavidin purification resulted in library ready material. For WGA and Pho ChIP-seq, cross-linked and purified DNA was incubated with pho antibody or WGA resin and purified followed by library preperation.

2017-07-18 | GSE84502 | GEO

Genome-wide maps of O-GlcNAc proteins in human breast cancer cells by next generation sequencing

Project description:We applied the chemical reporter-based metabolic labeling method to acquire O-GlcNAc modified proteins chromatin loci. Human breast cancer cell line MCF-7, as well as the genotoxic stress (Adriamycin) adapted cells MCF-7/ADR, were fed with 1 mM GalNAz. Metabolic labeled O-GlcNAz chromatin were crosslinked, sonicated and enriched by bioorthogonal chemistry. Then, the genomic DNA fragments bounded by O-GlcNAc mark were de-crosslinked, and constructed into libraries following by next-generation sequencing (Chemoselective O-GlcNAc chromatin sequencing, COGC-seq). To verify the robustness of this chemical reporter-based metabolic labeling method, we compared the results in MCF-7 and MCF-7/ADR cells with classical lectin succinylated wheat germ agglutinin (sWGA) ChIP-seq strategy. We also analyzed gene expression MCF-7 and MCF-7/ADR cells by RNA-seq.

2020-06-01 | GSE141698 | GEO

Chemoproteomic profiling of O-GlcNAcylated proteins and identification of O-GlcNAc transferases in rice

Project description:O-linked β-N-acetylglucosaminylation (O-GlcNAcylation) is a ubiquitous posttranslational modiﬁcation occurring in both animals and plants. Thousands of proteins along with their O-GlcNAcylation sites have been identified in various animal systems, yet the O-GlcNAcylated proteomes in plants remain poorly understood. Here, we report a large-scale profiling of protein O-GlcNAcylation in a site-specific manner in rice. We first established the metabolic glycan labeling strategy (MGL) with N-azidoacetylgalactosamine (GalNAz) in rice seedlings, which enabled incorporation of azides as a bioorthogonal handle into O-GlcNAc. By conjugation of the azide-incorporated O-GlcNAc with alkyne-biotin containing a cleavable linker via click chemistry, O-GlcNAcylated proteins were selectively enriched for mass spectrometry (MS) analysis. A total of 1,591 unambiguous O-GlcNAcylation sites distributed on 709 O-GlcNAcylated proteins were identified. Additionally, 102 O-GlcNAcylated proteins were identified with their O-GlcNAcylation sites located within a serine/threonine-enriched peptide, causing ambiguous site assignment. The identified O-GlcNAcylated proteins are involved in multiple biological processes such as transcription, translation and plant hormone signaling. Furthermore, we discovered two O-GlcNAc transferases (OsOGTs) in rice. By expressing OsOGTs in Escherichia coli and Nicotiana benthamiana leaves, we confirmed their OGT enzymatic activities and used them to validate the identified rice O-GlcNAcylated proteins. Our dataset provides a valuable resource for studying O-GlcNAc biology in rice, and the MGL method should facilitate the identification of O-GlcNAcylated proteins in various plants.

2023-05-10 | PXD036527 | Pride

Transcription profiling by array of human stromal cells from breast invasive ductal carcinomas

Project description: Not available

| S-ECPF-GEOD-8977 | biostudies-other

Identification of enriched O-GlcNAc proteins in hypertrophic mouse hearts

Project description:We used C57/Bl6 mice subjected to sham or transverse aortic constriction (TAC) to create pressure-overload hypertrophy (POH). From the hearts, we stabilized and labelled the O-GlcNAc moiety with tetramethylrhodamine azide (TAMRA) before enriching by TAMRA immunoprecipitation (files with "TAMRAIP"). Global proteomics were performed on the non-enriched matching samples (files with "GlobalDigest"). Sham sample IDs: 529, 545, 547, 551, 552. TAC sample IDs: 524, 528, 562, 563, 564. O-GlcNAc proteins were labeled with a click chemistry kit with TAMRA tag (ThermoFisher Scientific), then the labeled proteins were enriched with TAMRA antibody for proteomics experiments. Data was searched against the UniProt mouse database using PEAKS Studio for label free quantitation. Protein abundances were log2 transformed, normalized to median, and missing values imputed using Perseus.

2022-02-07 | MSV000088797 | MassIVE

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