ScGR-seq: simulatenous profiling of glycomic and transcriptomic in single cell [scRNA-Seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE218310 | GEO | 2024/01/04
REPOSITORIES: GEO
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Project description:Single-cell sequencing has emerged as an indispensable technology to dissect the cellular heterogeneity, but never been applied to integrated analysis of glycans and RNA. Using oligonucleotide-labeled lectins, we developed a sequencing-based method to jointly analyze the glycome and the transcriptome in single cells. Using the developed method, we analyzed the relationship between the two modalities of human induced pluripotent stem cells during the differentiation into neural progenitor cells.
2021-07-27 | GSE151642 | GEO
Project description:Dysregulation of glyco-gene expression in cancer can lead to aberrant glycans and glycoconjugates, which in turn can promote tumorigenesis. Cervical cancer display augmentation of aberrant sialylated glycans and increase of glyco-genes, which encoded enzymes participate in the sialylation pathways. Besides sialiltranferases, other glyco-genes, analyzed individually are reported as altered in cervical cancer. Here we show a comprehensive analysis of glyco-gene expression in cervical cancer to obtain a wide scenery of global changes in glycosylation pathways. First, we compared glyco-gene expression between normal tissue and cervical cancer. Second, we analyzed the glycogene expression in subtypes of cc to obtain hallmarks of glyco-gene expression in each case. Our results indicate that in cervical cancer the GPI-anchored biosynthesis is increased in cc while the synthesis of chondroitin and dermatan sulfate are decreased. Moreover, data show that adenocarcinoma displayed a homogenous glyco-gene expression pattern, where chondroitin /dermatan sulfate and heparan sulfate glycogenes are decreased, while keratan sulfate genes are increased. Dysregulation of glyco-gene expression in cancer can lead to aberrant glycans and glycoconjugates, which in turn can promote tumorigenesis. Cervical cancer display augmentation of aberrant sialylated glycans and increase of glyco-genes, which encoded enzymes participate in the sialylation pathways. Besides sialiltranferases, other glyco-genes, analyzed individually are reported as altered in cervical cancer. Here we show a comprehensive analysis of glyco-gene expression in cervical cancer to obtain a wide scenery of global changes in glycosylation pathways. First, we compared glyco-gene expression between normal tissue and cervical cancer. Second, we analyzed the glycogene expression in subtypes of cc to obtain hallmarks of glyco-gene expression in each case. Our results indicate that in cervical cancer the GPI-anchored biosynthesis is increased in cc while the synthesis of chondroitin and dermatan sulfate are decreased. Moreover, data show that adenocarcinoma displayed a homogenous glyco-gene expression pattern, where chondroitin /dermatan sulfate and heparan sulfate glycogenes are decreased, while keratan sulfate genes are increased.
2020-10-24 | GSE159976 | GEO
Project description:While altered protein glycosylation is regarded a trait of oral squamous cell carcinoma (OSCC), its heterogeneous glycoproteome and dynamics with disease progression remain unmapped. Employing an integrated multi-omics approach comprising unbiased and quantitative glycomics and glycoproteomics on resected OSCC tissues, we firstly profiled the N-glycome that overall displayed uniform expression in OSCC patients with (N+, n = 19) and without (N0, n = 12) lymph node metastasis, suggesting relatively stable N-glycosylation during metastasis. Notably, glycoproteomics and advanced correlation analysis uncovered altered site-specific N-glycosylation and associations with clinicopathological features. Importantly, targeted analyses of the multi-omics data unveiled two N-glycans and three N-glycopeptides that were closely associated with patient survival. This study provides novel insight into the complex OSCC tissue N-glycoproteome forming an important resource to further explore the underpinning disease mechanisms and uncover new prognostic glyco-markers for OSCC.
2023-06-08 | PXD037134 | Pride
Project description:The vertebrate ectoderm gives rise to a variety of cell lineages, including neural, neural crest, placodal and non-neural cell fates. How cell fates are specified at the neural plate border (the region surrounding the neural plate) is not fully understood. We therefore carried out 10x scRNAseq of the chick epiblast to investigate cell fate specification at the neural plate border. Embryos were dissected and pooled according to stage. The tissue was then dissociated and FAC sorted to remove dead cells and remaining doublets before cells were stored in MeOH. Due to the time required to dissect embryos, multiple rounds of collections were carried out, with collections from the same stage pooled prior to 10x sequencing. Libraries were sequenced using an Illumina HiSeq 4000 at the Francis Crick Institute, London. This collection was a follow up to E-MTAB-10408.
2023-08-25 | E-MTAB-11444 | biostudies-arrayexpress
Project description:Glycans are key to host-pathogen interactions, whereby recognition by the host and immunomodulation by the pathogen can be mediated by carbohydrate binding proteins, such as lectins of the innate immune system, and their glycoconjugate ligands. Previous studies have shown that excretory-secretory products of the porcine nematode parasite Trichuris suis exert immunomodulatory effects in a glycan-dependent manner. To better understand the mechanisms of these interactions, we prepared N-glycans from T. suis and both analyzed their structures and used them to generate a natural glycan microarray. With this array we explored the interactions of glycans with C-type lectins, C-reactive protein and sera from T. suis infected pigs. Glycans containing LacdiNAc and phosphorylcholine-modified glycans were associated with the highest binding by most of these proteins. In-depth analysis revealed not only fucosylated LacdiNAc motifs with and without phosphorylcholine moieties, but phosphorylcholine-modified mannose and N-acetylhexosaminesubstituted fucose residues, in the context of maximally tetraantennary N-glycan scaffolds. Furthermore, O-glycans also contained fucosylated motifs. In summary, the glycans of T. suis are recognized by both the innate and adaptive immune systems, and also exhibit species-specific features distinguishing its glycome from those of other nematodes.Glycans are key to host-pathogen interactions, whereby recognition by the host and immunomodulation by the pathogen can be mediated by carbohydrate binding proteins, such as lectins of the innate immune system, and their glycoconjugate ligands. Previous studies have shown that excretory-secretory products of the porcine nematode parasite Trichuris suis exert immunomodulatory effects in a glycan-dependent manner. To better understand the mechanisms of these interactions, we prepared N-glycans from T. suis and both analyzed their structures and used them to generate a natural glycan microarray. With this array we explored the interactions of glycans with C-type lectins, C-reactive protein and sera from T. suis infected pigs. Glycans containing LacdiNAc and phosphorylcholine-modified glycans were associated with the highest binding by most of these proteins. In-depth analysis revealed not only fucosylated LacdiNAc motifs with and without phosphorylcholine moieties, but phosphorylcholine-modified mannose and N-acetylhexosaminesubstituted fucose residues, in the context of maximally tetraantennary N-glycan scaffolds. Furthermore, O-glycans also contained fucosylated motifs. In summary, the glycans of T. suis are recognized by both the innate and adaptive immune systems, and also exhibit species-specific features distinguishing its glycome from those of other nematodes.
2024-01-11 | PXD045512 | Pride
Project description:When either Panc-1 or MiaPaCa-2 were plated as a discrete clump of cells in the middle of a plate, two morphologically distinct populations could be created. The cells on the periphery of the cell cluster migrated away from the region of high cell density and took on a classical mesenchymal phenotype with spindle like projections and loss of cell to cell adhesion. Cells that remained in the highly populated center showed greater intercellular adhesion and were more rounded in appearance. This model was included to provide information about whether glyco-gene expression changes observed in models of the epithelial to mesenchymal transition also are involved in migration.
2010-04-29 | GSE21566 | GEO
Project description:Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods: Nodal injected explants (injected with 10pg ndr2 mRNA) constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000075) according to the manufacturer’s protocol for 10000 cells recovery. For single-cell multiomics, zebrafish embryos at 6 hpf were harvested. Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, 4 rxns PN-1000285) according to the manufacturer’s protocol for 10000 cells recovery. Results: A total of 10,614 single-cell transcriptomes and 4,335 multiomics were collected after stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm, which drives a differential expression of those key regulators, such as gsc and ripply1 in these two cell lineages, and further regulates mesendoderm cell fate separation.
2023-01-28 | GSE223636 | GEO
Project description:When either Panc-1 or MiaPaCa-2 were plated as a discrete clump of cells in the middle of a plate, two morphologically distinct populations could be created. The cells on the periphery of the cell cluster migrated away from the region of high cell density and took on a classical mesenchymal phenotype with spindle like projections and loss of cell to cell adhesion. Cells that remained in the highly populated center showed greater intercellular adhesion and were more rounded in appearance. This model was included to provide information about whether glyco-gene expression changes observed in models of the epithelial to mesenchymal transition also are involved in migration. Radial Migration Assay comparing two populations (Migrating vs. Non Migrating) in two pancreatic cancer cell lines (Panc-1 and MiaPaCa-2)
2010-05-27 | E-GEOD-21566 | biostudies-arrayexpress
Project description:The asialoglycoprotein receptor (ASGPR) and the mannose receptor 1 (MRC1) are C-type lectins that identify and remove glycoproteins from circulation. ASGPR recognizes terminal galactose and N-acetylgalactosamine, whereas MRC1 recognizes terminal mannose, fucose, and N-acetylglucosamine. The effects of ASGPR and MRC1 deficiency on the N-glycosylation of individual circulating proteins have been studied. However, the impact on the homeostasis of the major plasma glycoproteins is debated and their glycosylation has not been mapped with high molecular resolution in this context. Therefore, we evaluated the total plasma N-glycome and plasma proteome of ASGR1 and MRC1 deficient mice.
2023-10-24 | PXD042269 | Pride
Project description:The majority of cell surface and secreted proteins are modified by glycans and this glycosylation process plays an important role in the development of multicellular organisms. These glycan modifications enable communication between cells and the extracellular matrix via interactions with specific glycan-binding lectins and the regulation of receptor-mediated signalling. Glycosylation plays an important role in myogenesis and the development of muscle tissue but our molecular understanding of the precise glycans, catalytic enzymes and lectins involved remain only partially understood. Here, we quantified dynamic remodeling of the membrane-associated proteome during in vitro myogenesis. We observed wide-spread changes in the abundance of several receptors and important enzymes regulating glycosylation. Quantification of released N-linked glycans via glycomic analysis confirmed remodeling of the glycome with a switch in sialic acid linkages, and changes in di-galactosylation and paucimannosylation. Quantitative glycoproteomic analysis with stable isotope labelling, enrichment of glycopeptides and analysis via multiple fragmentation approaches identified precise glycoproteins containing these regulated glycans including integrins and growth factor receptors. Myogenesis was also associated with the regulation of several lectins including the up-regulation of Galectin-1 (LGALS1). CRISPR/Cas9-mediated deletion of Lgals1 inhibited differentiation and myotube formation suggesting an early defect in the myogenic program. We also observed similar changes in N-glycosylation and the up-regulation of LGALS1 during postnatal skeletal muscle development in mice. Finally, treatment of new-born mice with recombinant adeno-associated viruses to express LGALS1 in the musculature resulted in enhanced muscle mass. Our data will be a valuable resource to further understand the role of glycosylation and lectins on myogenesis and may aid in the development of intervention strategies aimed at promoting healthy muscle.
2022-02-15 | PXD019372 | Pride