Gene expression in macrophages derived form wild-type and Ndfst1-deficient mice before and after foam cell conversion
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE51009 | GEO | 2014/11/04
SECONDARY ACCESSION(S): PRJNA219513
REPOSITORIES: GEO
Similar Datasets
Project description:In order to examine the role of macrophage heparan sulfate proteoglycans in atherogenesis, we inactivated the biosynthetic gene N-acetylglucosamine N-deacetylase-N-sulfotransferase 1 (Ndst1) in macrophages. In order to determine the impact of altering Ndst1 expression, we crossbred mice bearing a conditional loxP-flanked (M-bM-^@M-^\floxedM-bM-^@M-^]) allele of Ndst1 (Ndst1f/f) to transgenic mice expressing the bacterial Cre recombinase under control of the lysozyme 2 promoter (LysMCre) to drive inactivation of the gene in myeloid cells. We compared the transcriptome of bone marrow derived macrophages from Ndst1f/fLysMCre- and Ndst1f/fLysMCre+ macrophages in basal growth medium and after foam cell conversion using 50M-BM-5g/ml of aggregated LDL (agLDL) to asses the impact of altered macrophage heparan sulfate sulfation on gene expression. Total RNA obtained from bone marrow derived macrophages (BMDM) derived form two wild-type and two Ndfst1-deficient mice before and after foam cell conversion and analyzed in diplicate (n=4 for each conditions; total of 4 conditions)
2014-11-04 | E-GEOD-51009 | 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. 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: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:Schmallenberg virus (SBV) is an insect-transmitted orthobunyavirus that can cause abortions and congenital malformations in the offspring of ruminants. Even though the two viral surface glycoproteins Gn and Gc are involved in host cell entry, the specific cellular receptors of SBV are currently unknown. Using genome-wide CRISPR-Cas9 forward screening, we identified 3′-phosphoadenosine 5′-phosphosulfate (PAPS) transporter 1 (PAPST1) as an essential factor for SBV infection. PAPST1 is a sulfotransferase involved in heparan sulfate proteoglycan synthesis encoded by the solute carrier family 35 member B2 gene (SLC35B2). SBV cell surface attachment and entry were largely reduced upon the knockout of SLC35B2, whereas the reconstitution of SLC35B2 in these cells fully restored their susceptibility to SBV infection. Furthermore, treatment of cells with heparinase diminished infection with SBV, confirming that heparan sulfate plays an important role in cell attachment and entry, although to various degrees, heparan sulfate was also found to be important to initiate infection by two other bunyaviruses, La Crosse virus and Rift Valley fever virus. Thus, PAPST1-triggered synthesis of cell surface heparan sulfate is required for the efficient replication of SBV and other bunyaviruses.
2022-02-03 | GSE196011 | GEO
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
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: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:DNA damage response kinase ATM regulates the genetic program of lymphocytes with phsiologically induced DNA DSBs. In bone marrow-derived macrophages, related kinase DNAPKcs is also responsible for activating DNA damage responses after infection with Listeria monocytogenes. Here we show that both ATM and DNA-PKcs regulate the genetic program of Listeria monocytogenes-infected macrophages. Two independent bone marrow-derived macrophage cultures for each genotype (LysMcre/+ and Scid: Atmc/c: LysMcre/+) were infected with Listeria monocytogenes for 24 hrs at an MOI of 5. RNA was isolated using RNeasy (Qiagen). Gene expression profiling was performed using Illumina MouseRef-8 expression microarrays.
2015-07-03 | E-GEOD-70467 | biostudies-arrayexpress
Project description:Background & Aims: Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer deaths in the United States. Tyrosine sulfation, catalyzed by the tyrosylprotein sulfotransferase 2 (TPST2), is a post-translational modification essential for protein-protein interactions and cellular functions. SLC35B2 is a key transporter that transports the universal sulfate donor 3’-phosphoadenosine 5’-phosphosulfate (PAPS) into the Golgi apparatus where the protein sulfation occurs. The goal of this study is to determine whether and how SLC35B2-TPST2 axis of tyrosine sulfation plays a role in PDAC. Methods: Gene expression was analyzed in PDAC patients and mice. Human PDAC MIA PaCa-2 and PANC-1 cells were used for in vitro studies. TPST2 deficient MIA PaCa-2 cells were generated to assess xenograft tumor growth in vivo. Mouse PDAC cells derived from the KrasLSL-G12D/+;Tp53L/+;Pdx1-Cre (KPC) mice were used to generate Tpst2 KO KPC cells to evaluate tumor growth and metastasis in vivo. Results: High expressions of SLC35B2 and TPST2 were correlated with poor PDAC patient survival. Knockdown of SLC35B2 or TPST2, or pharmacological inhibition of sulfation inhibited PDAC cell proliferation and migration in vitro. TPST2 deficient MIA PaCa-2 cells exhibited inhibited xenograft tumor growth. Orthotopic inoculation of Tpst2 KO KPC cells in mice showed inhibition of primary tumor growth, local invasion, and metastasis. Mechanistically, the integrin ITGB4 was found to be a novel substrate of TPST2. Inhibition of sulfation destabilizes ITGB4 protein, which may have accounted for the suppression of metastasis. Conclusions: Targeting the SLC35B2-TPST2 axis of tyrosine sulfation may represent a novel approach for therapeutic intervention of PDAC.
2023-10-08 | GSE215104 | GEO