Single-cell glycome and transcriptome profiling uncovers the glycan signature of each cell subpopulation of human iPSC-derived neurons
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PROVIDER: PRJNA1299297 | ENA |
REPOSITORIES: ENA
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Project description:Human induced pluripotent stem cells (iPSC)-derived cells are often heterogeneous, posing challenges for disease modeling and cell therapy. We previously developed single-cell glycan and RNA sequencing (scGR-seq) to analyze the glycome and transcriptome simultaneously. Here, we applied scGR-seq to examine heterogeneous populations of human iPSC-derived neurons. We identified four subpopulations: mature neurons, immature neurons, undifferentiated neural progenitor cells (undiffNPCs), and mesenchymal cells (MCs). Lectin binding patterns indicated high α1,3-fucose expression in undiffNPCs. MCs exhibited strong binding of a poly-LacNAc-recognizing lectin (rLSLN) and high expression of B3GNT2, a poly-LacNAc synthetic enzyme. Pseudotime analysis revealed that a subpopulation of NPCs acquired mesenchymal features and differentiated into MCs. Immunocytochemistry confirmed the specific detection of undiffNPCs and MCs using anti-Lewis X (α1,3-fucosylated glycan) antibodies and rLSLN. Beyond identifying cell heterogeneity, scGR-seq enables the discovery of glycan markers and detection probes for iPSC-derived cells, aiding in their further cell processing and manipulation.
2025-09-05 | GSE304173 | GEO
Project description:The unfolded protein response (UPR), as its name implies, safeguards secretory pathway proteostasis. The most ancient arm of the UPR, the IRE1-activated, XBP1s-mediated transcriptional response, has roles in secretory pathway maturation beyond resolving proteostatic stress. Understanding the consequences of XBP1s’ transcriptional output for cellular processes is critical for elucidating mechanistic connections between XBP1s and development, immunity, and disease. Here, we show that a key functional consequence of XBP1s activation is a cell type-dependent shift in the distribution of N-glycan structures on endogenous membrane and secreted proteomes. XBP1s activity decreases sialylation of tri- and tetra-antennary N-glycans in the HEK293 membrane proteome and secretome, while substantially increasing the population of high mannose N-glycans only in the secretome. Related, but distinctive, signatures in the HEK293 N-glycome are observed when the entire UPR is activated in a stress-dependent manner using thapsigargin. In HeLa cells, stress-independent XBP1s activation increases the population of cell surface high mannose N-glycans and tetra-antennary N-glycans. mRNA profiling experiments suggest that the XBP1s-mediated remodeling of the N-glycome may re-flect a coordinated consequence of transcriptional resculpting of the N-glycan maturation pathway by XBP1s. The discovery of XBP1s-induced N-glycan structural remodeling on a glycome-wide scale suggests that XBP1s is a master regulator of N-glycan maturation. Moreover, because the sugars on cell surface proteins or on those proteins secreted from an XBP1s-activated cell can be molecularly distinct from those of an unactivated cell, these findings reveal a potential new mechanism for translating intracellular stress signaling pathways into al-tered interactions with the extracellular environment.
2018-10-02 | GSE112589 | GEO
Project description:Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3-Myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA-methylation level. Aggressive pGroup3-Myc MBs and favorable pWNT MBs were most similar in cluster hierarchies concerning overall proteome patterns but showed different protein abundances of the vincristine resistance associated multiprotein complex TriC/CCT and of N-glycan turnover associated factors. The N-glycome reflected proteome subtypes and complex-bisecting N-glycans characterized pGroup3-Myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.
2024-04-23 | GSE222478 | GEO
Project description:Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3-Myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA-methylation level. Aggressive pGroup3-Myc MBs and favorable pWNT MBs were most similar in cluster hierarchies concerning overall proteome patterns but showed different protein abundances of the vincristine resistance associated multiprotein complex TriC/CCT and of N-glycan turnover associated factors. The N-glycome reflected proteome subtypes and complex-bisecting N-glycans characterized pGroup3-Myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures
2024-04-23 | GSE243795 | GEO
Project description:Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3-Myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA-methylation level. Aggressive pGroup3-Myc MBs and favorable pWNT MBs were most similar in cluster hierarchies concerning overall proteome patterns but showed different protein abundances of the vincristine resistance associated multiprotein complex TriC/CCT and of N-glycan turnover associated factors. The N-glycome reflected proteome subtypes and complex-bisecting N-glycans characterized pGroup3-Myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.To biologicallyy validate these results we further generated methylome and proteome data for 29 samples.
2024-04-23 | GSE243768 | GEO
Project description:Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically heterogenous. The application of omics technologies – mainly studying nucleic acids – has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans hold the potential to discover clinically relevant phenotypes and targetable pathways. We compile a harmonized proteome dataset of 167 MBs and integrate findings with DNA methylome, transcriptome and N-glycome data. We show six proteome MB subtypes, that can be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis reveals different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favourable pWNT MBs are most similar in cluster hierarchies concerning overall proteome patterns but show different protein abundances of the vincristine resistance-associated multiprotein complex TriC/CCT and of N-glycan turnover-associated factors. The N-glycome reflects proteome subtypes and complex-bisecting N-glycans characterize pGroup3myc tumors. Our results shed light on targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures. This SuperSeries is composed of the SubSeries listed below.
2024-04-22 | GSE243796 | GEO
Project description:NanoSTRING dendritic cell subpopulation
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Project description:We are interested in investigating changes in both the glycome and transcriptome of human embryonic stem cells upon differentiation. We have chosen as a model system to differentiate human ES cells into neural spheres using a published protocol by Zhang, S.C. et al. (2001; Nat Biotech. 19: 1129-33). Based on the information provided by microarray analysis, proteins of interest can be further investigated to associate a particular glycosyltransferase, for example, with production of a specific glycan structure at a particular stage. Techniques such as the use of RNAi for the knock-down or transfection of hESCs to effect the overexpression of the transcript, followed by subsequent analysis of the glycan structures can be employed. Three developmental stages will be investigated: Stage 1: undifferentiated stem cells; Stage 2: differentiation into embryoid bodies; Stage 3: differentiation into neural spheres. In addition to characterizing the cell surface for glycomic “fingerprints” we want to characterize the genomic transcripts associated with the glycome.
2011-09-05 | E-GEOD-31923 | biostudies-arrayexpress
Project description:Mapping of Single Nuclear Transcriptomic Responses Uncovers Plasticity of Subpopulation of Purkinje Neurons Driving Motor Learning
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Project description:B-cell precursor acute lymphoblastic leukemia (pre-B ALL) with mixed-lineage leukemia gene rearrangement (MLL-r) is a poor-prognosis subtype for which additional therapeutic targets are needed. We evaluated the glycomes, transcriptomes and proteomes of the same samples using only about 10^6 cells for each assay. We found that the expression of many genes involved in glycosylation differ between MLL-r cells and normal controls: 61 of the 221 human glycosyltransferases were differentially expressed in MLL-r cells. The leukemia cell glycome and many proteins associated with glycan biosynthesis were also significantly changed compared to normal control precursor B-cells, indicating that the malignant phenotype of these cells could be regulated by such changes.
2021-10-13 | GSE176364 | GEO