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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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To detect the heparan sulfate proteoglycans (HSGP) core proteins that are expressed in these cell lines, so that candidates for the Sulf-2 substrate can be identified

ABSTRACT: We are requesting a gene microarray analysis for 10 cell lines that are pertinent to human non-small lung cancer. A main focus of ours has been the role that Sulf-2 plays in non-small cell lung cancer (NSCLC). Sulf-2 is an extracellular sulfatase that acts on internal glucosamine-6-sulfates within heparan sulfate chains. Sulf-2 can activate Wnt signaling, as well as modulate other signaling pathways. Our recent work (Oncogene 29:635, 2010) has shown that Sulf-2 is required for the malignant phenotype of five human NSCLC cell lines (increased migration, increased growth, growth in soft agar, and tumorigenecity in nude mice). Because Sulf-2 acts on HSPGs to regulate signaling, we are interesting in the HSGP core proteins that are expressed in these cell lines, so that candidates for the Sulf-2 substrate can be identified. In addition we would like to define the expression of heparan sulfate 6-O-sulfatransferase (3 genes) to see whether these genes are upregulated in cells that depend on Sulf-2 for their malignant phenotype. Finally, gene profiling will define which Wnt ligands and Wnt receptors (Frizzled''s) are expressed in the cells. We are asking for gene profiling on the 5 Sulf-2 expressing NSCLC lines previously studied (H292, H460, P-ST, B-ST, and Calu-6), 3 Sulf-2 negative NSCLC lines (H1299, H1703, H1975) and two normal bronchial epithelial cell populations (B-C, P-C). All of the cells are human in origin. There are a total of 10 cell types. With 3 repicates for each, the request is for 30 arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Steven Head

PROVIDER: E-GEOD-31935 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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To detect the heparan sulfate proteoglycans (HSGP) core proteins that are expressed in these cell lines, so that candidates for the Sulf-2 substrate can be identified

Project description:We are requesting a gene microarray analysis for 10 cell lines that are pertinent to human non-small lung cancer. A main focus of ours has been the role that Sulf-2 plays in non-small cell lung cancer (NSCLC). Sulf-2 is an extracellular sulfatase that acts on internal glucosamine-6-sulfates within heparan sulfate chains. Sulf-2 can activate Wnt signaling, as well as modulate other signaling pathways. Our recent work (Oncogene 29:635, 2010) has shown that Sulf-2 is required for the malignant phenotype of five human NSCLC cell lines (increased migration, increased growth, growth in soft agar, and tumorigenecity in nude mice).

2011-09-06 | GSE31935 | GEO

Examine differential expression of sulf-1 and sulf-2, enzymes involved in heparan sulfate biosynthesis

Project description:Our specific aim is to examine differential expression of sulf-1 and sulf-2, enzymes involved in heparan sulfate biosynthesis, as well as Wnt ligands and Wnt signaling mediators during corneal wound healing using a mouse corneal scratch model. The specific structural features of heparan sulfate underlie its role in modulating cellular responses to growth factors such as the Wnts. Heparan sulfate 6-O-endosulfatases (sulf-1 and sulf-2) remove 6-O sulfate group from trisulfated disaccharides present on heparan sulfate chains. Our preliminary results suggest that sulf-1 is upregulated at the protein level in the epithelial cells of wounded mouse corneas, as compared to the undamaged contralateral eye. Modulation of heparan sulfate proteoglycan expression and/or structural modifications of its chains might be an important aspect of the regulation of epithelial cell migration and proliferation during wound healing. RNA preparations from four different conditions, were sent to Microarray Core (E). Gene expression was examined in triplicates at 2 time points (8 and 24 hrs post-wounding: 6 arrays), using the contralateral eye as a control at one time point as a control (3 arrays). To account for a systemic response (i.e. bilateral inflammation) to the corneal wounding, corneas of non-wounded mice (3 arrays) were used. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.

2011-04-29 | E-GEOD-28931 | biostudies-arrayexpress

Effect of Continuous Suppression of Heparan Sulfate during Flow on Arterial Endothelial Function

Project description:The arterial endothelium’s response to its flow environment is critical to vascular homeostasis. The endothelial glycocalyx has been shown to play a major role in mechanotransduction, but the extent to which the components of the glycocalyx affect the overall function of the endothelium remains unclear. The objective of this study was to further elucidate the role of heparan sulfate as a mechanosensor on the surface of the arterial endothelium, by (1) expanding the variety of shear waveforms investigated, (2) continuously suppressing heparan sulfate expression rather than using a pre-flow batch treatment, and (3) performing microarray analysis on post-flow samples. Porcine aortic endothelial cells were exposed to non-reversing, reversing, and oscillatory shear waveforms for 24 hours with or without continuous heparan sulfate suppression with heparinase. All shear waveforms significantly increased the amount of heparan sulfate on the surface of the endothelium. Suppression of heparan sulfate to less than 25% of control levels did not inhibit shear-induced cell alignment or nitric oxide production, or alter gene expression, for any of the shear waveforms investigated. We infer that heparan sulfate on the surface of porcine aortic endothelial cells is not the primary mechanosensor for many shear-responsive endothelial cell functions in this species. Porcine aortic endothelial cells were exposed to 3 different shear waveforms for 24 hours with or without the addition of 300 mU/ml heparinase III to the flow media. The shear waveforms inculded Non-reversing (15 ± 15 dyne/cm2, 1 Hz), Steady (15 dyne/cm2), or Oscillatory (0 ± 15 dyne/cm2, 1 Hz) shear. Four replicates of each condition were performed for a total of 24 experiments. Each experimental sample was hybridized to an oligonucleotide array along with a standard reference sample (static cells).

2011-07-21 | E-GEOD-30843 | biostudies-arrayexpress

Heparan sulfate modifications of betaglycan promote TIMP3-dependent ectodomain shedding to fine-tune TGF-β signaling.

Project description:Betaglycan/type III TGF-β receptor (TGFBR3) is an established co-receptor for the TGF-β superfamily with direct binding demonstrated for TGF-β 1-3 and inhibin A. Betaglycan can be membrane-bound or have its ectodomain cleaved/ shed to produce soluble-betaglycan that has been demonstrated to sequester ligands. Extracellular domain of betaglycan is modified with glycosaminoglycan chains at Ser residues S534 and S545, to which heparan sulfate and chondroitin sulfate chains are covalently attached. To delineate the contribution of the heparan and chondroitin sulfate modifications on betaglycan on its shedding and thereby on TGF-β signaling in ovarian cancer biology, we used mutants of betaglycan with alterations to the different glycosaminoglycan modifications. We made the unexpected discovery that the heparan sulfate modifications are essential for maximum ectodomain shedding of betaglycan, which is further essential for the ability of betaglycan to suppress TGF-β signaling and the tumor cells responses to exogenous TGF-β ligand. Using unbiased transcriptomics, we identified TIMP3 as a key regulator of betaglycan shedding and thereby TGF-β signaling. Taken together, these studies are the first to demonstrate a critical link between the well-known modifications on betaglycan and TGF-β signaling responses.

2024-02-21 | GSE237403 | GEO

Heparan sulfate in skin wounds

2008-04-01 | GSE7435 | GEO

B3GALT6 Promotes Dormant Breast Cancer Cell Survival and Recurrence by Enabling Heparan Sulfate-Mediated FGF Signaling

Project description:Breast cancer mortality results from incurable recurrent tumors, putatively seeded by dormant, therapy-refractory residual tumor cells (RTCs). Understanding the mechanisms enabling RTC survival is therefore essential for improving patient outcomes. We derived a dormancy-associated RTC signature that mirrors the transcriptional response to neoadjuvant chemotherapy in patients and is enriched for extracellular matrix-related pathways. In vivo CRISPR-Cas9 screening of dormancy-associated candidate genes identified the galactosyltransferase B3GALT6 as a functional regulator of RTC fitness. B3GALT6 is required for the linkage of glycosaminoglycans (GAGs) to proteins to generate proteoglycans and its germline loss-of-function causes skeletal dysplasias. We determined that B3GALT6-mediated biosynthesis of heparan sulfate GAGs predicts poor patient outcomes, promotes tumor recurrence by enhancing dormant RTC survival in multiple contexts, and does so via a B3GALT6-heparan sulfate/HS6ST1-heparan 6-O-sulfation/FGF1-FGFR2 signaling axis. These findings implicate B3GALT6 in cancer and suggest targeting of FGFR2 signaling as a novel approach to eradicate dormant RTCs, thereby preventing recurrence.

2024-01-01 | GSE241252 | GEO

To examine the expression of Sulf1 and Sulf2, as well as other glycan-related genes, in human Idiopathic pulmonary fibrosis (IPF) lungs compared to normal lung samples

Project description:Microarray analysis to examine glycan-related gene expression in idiopathic pulmonary fibrosis Heparan sulfate 6-O-endosulfatases (Sulf1 and Sulf2) remove 6-O sulfate groups from heparan sulfate intra-chain sites on the cell surface and in the extracellular matrix, and modulate the functions of many growth factors and morphogens including FGF, Wnt and TGF-beta. Works from our laboratory have shown that TGF-beta 1 induces Sulf1 and Sulf2 expression in a cell-type specific manner in the lung, specifically Sulf1 in lung fibroblasts and Sulf2 in type II alveolar epithelial cells. Interestingly TGF-beta 1-induced Sulf1 and Sulf2 in turn modulate TGF-beta 1 function in culture. The aim of this study is to examine the expression of Sulf1 and Sulf2 as well as other glycan-related genes (heparan biosynthetic enzymes, TGF-beta, FGF and Wnt signaling pathway components) in human idiopathic pulmonary fibrosis (IPF) lungs compared to normal lung samples. We will examine gene expression in triplicate samples from RNA of total lung homogenates from IPF and control (normal) lungs

2011-09-05 | E-GEOD-31934 | biostudies-arrayexpress

Heparan sulfate in skin wounds

Project description:Standardized skin wounds were established surgically on mice and allowed to heal during a 15-day period. Expression of genes related to heparan sulfate biosynthesis was studied in wound bed and edges during the healing process. Total RNA was isolated from wound edge (regenerating skin) and wound bed at 2, 6 and 15 days post wounding, as well as from intact control skin. Three animals were used for each time point.

2010-05-22 | E-GEOD-7435 | biostudies-arrayexpress

Structure of the human heparan sulfate polymerase complex EXT1-EXT2

Project description:Heparan sulfates are complex polysaccharides that mediate the interaction with a broad range of protein ligands at the cell surface. A key step in heparan sulfate biosynthesis is catalyzed by the bi-functional glycosyltransferases EXT1 and EXT2, which generate the glycan backbone consisting of repeating Nacetylglucosamine and glucuronic acid units. The molecular mechanism of heparan sulfate chain polymerization remains, however, unknown. Human EXT1 and EXT2, lacking the N-terminal transmembrane helix, were co-expressed as a secreted complex using human embryonic kidney cells (FreeStyle 293-F). We purified 0.5 mg of the complex from 900 mL suspension culture using two immobilized metal affinity chromatography steps and an interspersed protease treatment to cleave off the alkaline phosphatase fusion protein serving as a secretion signal. Mass spectrometry-based proteomic analysis confirmed the quality of the sample with EXT1 and EXT2 found to be the most abundant proteins, and being present in comparable amounts.

2022-12-09 | PXD034871 | Pride