A genome-wide CRISPR/Cas9 screen reveals KDM2B as a modifier of protein binding to heparan sulfate
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE163162 | GEO | 2021/01/28
REPOSITORIES: GEO
Similar Datasets
Project description:Heparan sulfate proteoglycans (HSPGs) are expressed on virtually all animal cells and are involved in many important biological processes. Each HSPG consists of a core protein with one or more covalently attached linear heparan sulfate (HS) chains composed of alternating glucosamine and uronic acids that are heterogeneously N- and O-sulfated. The arrangement and orientation of the sulfated sugar residues of HS specify the location of distinct ligand binding sites on the cell surface, and these modifications can vary temporally during development and spatially across tissues. While most of the enzymes involved in HS biosynthesis have been studied extensively, much less information exists regarding the specific mechanisms that give rise to the variable composition and binding properties of HS.
2021-01-28 | GSE145789 | GEO
Project description:Heparan (HS) proteoglycans (HSPGs) are common on the cell surface and mediate many physiological processes. Binding of HSPG ligands is determined by the sulfation code on the heparan sulfate chain and the HS chain can be N-/2-O/6-O- or 3-O-sulfated, generating a heterogenous sulfation pattern. 3-O sulfated HS (3S-HS) have been reported to play a role in several pathological processes such as the coagulation system, viral pathogenesis, or in the binding and internalization of tau in Alzheimer’s disease. Few 3S-HS-specific interactors are known and the role of 3S-HS in health and disease is limited, especially in the central nervous system. Using human CSF as a surrogate for the extracellular compartment of the CNS, we determined the interactome of synthetic heparan sulfate oligosaccharides with defined sulfation patterns. These AE-MS studies significantly expand the proteins that can interact with HS and for which 3O sulfation is required. LRP1 was found as a novel 3S-HS interactor, requiring GlcA-GlcNS6S3S for binding, similar to ATIII. Both interactions were validated via Western blot. Our dataset brings forward new HS and 3S-HS ligands which can be pertinent to unravel molecular mechanisms dependent on 3S-HS in (patho)physiological conditions.
2022-08-09 | PXD034935 | Pride
Project description:Embryonic stem (ES) cells continuously decide whether to maintain pluripotency or differentiate. While exogenous LIF and BMP4 perpetuate a pluripotent state, less is known about factors initiating differentiation. We show that heparan sulfate (HS) proteoglycans are critical co-receptors for signals inducing ES cell differentiation. Genetic targeting of NDST1 and 2, two enzymes required for N-sulfation of proteoglycans, blocked differentiation. This phenotype was rescued by HS presented in trans or by soluble heparin. NaClO3-, which reduces sulfation of proteoglycans, potently blocked differentiation of wild type cells. Mechanistically, N-sulfation was identified to be critical for functional autocrine FGF4 signalling. Micro array analysis identified the pluripotency maintaining transcription factors Nanog, KLF2/4/8, Tbx3 and Tcf3 to be negatively regulated, whereas markers of differentiation such as Gbx2, Dnmt3b, FGF5 and Brachyury were induced by sulfation-dependent-FGFR signalling. We show that several of these genes are heterogeneously expressed in ES cells and targeting of heparan sulfation or FGFR-signalling facilitated a homogenous Nanog/KLF4/Tbx3 positive ES cell state. This finding suggests that the recently discovered heterogeneous state of ES cells is regulated by HS-dependent FGFR signalling. Similarly, culturing blastocysts with NaClO3- eliminated GATA6 positive primitive endoderm progenitors generating a homogenous Nanog positive inner cell mass. Functionally, reduction of sulfation robustly improved de novo ES cell derivation efficiency. We conclude that N-sulfated HS is required for FGF4 signalling to maintain ES cells primed for differentiation in a heterogeneous state. Inhibiting this pathway facilitates a more naïve ground state. Four groups with three biological replicates and a technical duplicate in each
2010-04-09 | E-GEOD-15974 | biostudies-arrayexpress
Project description:Embryonic stem (ES) cells continuously decide whether to maintain pluripotency or differentiate. While exogenous LIF and BMP4 perpetuate a pluripotent state, less is known about factors initiating differentiation. We show that heparan sulfate (HS) proteoglycans are critical co-receptors for signals inducing ES cell differentiation. Genetic targeting of NDST1 and 2, two enzymes required for N-sulfation of proteoglycans, blocked differentiation. This phenotype was rescued by HS presented in trans or by soluble heparin. NaClO3-, which reduces sulfation of proteoglycans, potently blocked differentiation of wild type cells. Mechanistically, N-sulfation was identified to be critical for functional autocrine FGF4 signalling. Micro array analysis identified the pluripotency maintaining transcription factors Nanog, KLF2/4/8, Tbx3 and Tcf3 to be negatively regulated, whereas markers of differentiation such as Gbx2, Dnmt3b, FGF5 and Brachyury were induced by sulfation-dependent-FGFR signalling. We show that several of these genes are heterogeneously expressed in ES cells and targeting of heparan sulfation or FGFR-signalling facilitated a homogenous Nanog/KLF4/Tbx3 positive ES cell state. This finding suggests that the recently discovered heterogeneous state of ES cells is regulated by HS-dependent FGFR signalling. Similarly, culturing blastocysts with NaClO3- eliminated GATA6 positive primitive endoderm progenitors generating a homogenous Nanog positive inner cell mass. Functionally, reduction of sulfation robustly improved de novo ES cell derivation efficiency. We conclude that N-sulfated HS is required for FGF4 signalling to maintain ES cells primed for differentiation in a heterogeneous state. Inhibiting this pathway facilitates a more naïve ground state.
2009-11-13 | GSE15974 | GEO
Project description:Sepsis patients are at increased risk for hospital-acquired pulmonary infections, potentially due to post-septic immunosuppression known as the compensatory anti-inflammatory response syndrome (CARS). CARS has been attributed to leukocyte dysfunction, with an unclear role for endothelial cells. The pulmonary circulation is lined by an endothelial glycocalyx, a heparan sulfate-rich layer essential to pulmonary homeostasis. Heparan sulfate degradation occurs early in sepsis, leading to lung injury. Endothelial synthesis of new heparan sulfates subsequently allows for glycocalyx reconstitution and endothelial recovery. We hypothesized that remodeling of the reconstituted endothelial glycocalyx, mediated by alterations in the endothelial machinery responsible for heparan sulfate synthesis, contributes to CARS. Our experimental animal model of CARS recapitulated post-septic immunosuppression, coincidentally with structural remodeling of endothelial glycocalyx heparan sulfate. We used microarray to identify which heparan sulfate modifying enzyme is responsible for the remodeling of post-septic reconstituted glycocalyx, characterized with enrichment of heparan sulfate disaccharides sulfated at the 6-O position of glucosamine.
2019-04-14 | GSE129775 | GEO
Project description:The general area of research interests of my lab is the glycobiology of HSPGs in cell-cell/cell-matrix interactions and growth factor signalling. Heparan sulfate binding proteins in neural development and differentiation. We used the Glyco-gene Chips to study the gene expression responses of mouse neural cells to heparin-binding growth factors. The experimental systems studied is in vivo (developing mouse brain). The goal is to examine the global responses of neural cells to particular growth factors during differentiation in terms of effects on HS biosynthetic enzymes and proteoglycan core proteins, as well as growth factors and their receptors. Analysis of A) P1 mouse brain wild type for Heparan sulfate 2-O sulfotransferase (HS2ST) and B) heterozygous for Heparan sulfate 2-O sulfotransferase (HS2ST) loss of function mutation.
2010-12-11 | E-GEOD-26010 | biostudies-arrayexpress
Project description:Heparan sulfate (HS) is a linear, sulfated polysaccharide, and expresses abundantly in prostate and PCa tissues. Intriguingly, the HS content and sulfation modifications appear to increase when the prostate becomes malignance, suggesting that HS may critically modulate PCa pathogenesis. We specifically ablated Ext1, the enzyme that initiates HS biosynthesis, in mouse prostate at late development stage. And used microarray to detail the gene expressions affected by Ext1 ablation and identified distinct classes of up-regulated genes during this process.
2013-05-15 | GSE46898 | GEO
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). 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.
2011-09-05 | E-GEOD-31935 | biostudies-arrayexpress
Project description:Heparan sulfate (HS) is a linear, sulfated polysaccharide, and expresses abundantly in prostate and PCa tissues. Intriguingly, the HS content and sulfation modifications appear to increase when the prostate becomes malignance, suggesting that HS may critically modulate PCa pathogenesis. We specifically ablated Ext1, the enzyme that initiates HS biosynthesis, in mouse prostate at late development stage. And used microarray to detail the gene expressions affected by Ext1 ablation and identified distinct classes of up-regulated genes during this process. Prostate tissues were removed from euthanized mice at 5 weeks old for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare gene expression during tumorigenesis among the wildtype, prostate specific knockout of Pten and double knockout of Pten and Ext1 in prostate.
2013-05-15 | E-GEOD-46898 | biostudies-arrayexpress
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.
2011-04-29 | GSE28931 | GEO