Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA196616 | ENA |
REPOSITORIES: ENA
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Project description:Therapeutic neo-vasculogenesis in vivo can be achieved by the co-transplantation of human endothelial colony-forming progenitor cells (ECFCs) with mesenchymal stem/progenitor cells (MSPCs).The underlying mechanism is not completely understood thus hampering the development of novel stem cell therapies.We hypothesized that proteomic profiling could be used to retrieve the in vivo signaling signature during the initial phase of human neo-vasculogenesis. ECFCs and MSPCs were therefore either transplanted alone or co-transplanted subcutaneously into immune deficient mice. Early cell signaling, occurring within the first 24 hours in vivo, was analyzed using antibody microarray proteomic profiling.Vessel formation and persistence were verified in parallel transplants for up to 24 weeks. Proteomic analysis revealed significant alteration of regulatory components including caspases, calcium/calmodulin-dependent protein kinase, DNA protein kinase,human ErbB2 receptor-tyrosine kinase as well as mitogen-activated protein kinases.Therapeutic candidate caspase-4 was selected from array results for targeting vascular network formation in vitro as well as modulating therapeutic vasculogenesis in vivo. As a proof-of-principle, caspase-4 and general caspase-blocking led to diminished endothelial network formation in vitro and significantly decreased vasculogenesis in vivo. Proteomic profiling ex vivo thus unraveled a signaling signature which can be targeted to modulate neo-vasculogenesis in vivo.
2013-04-09 | GSE45896 | GEO
Project description:The CD4+ regulatory T (Treg) cell lineage comprises thymus-derived (t)Treg cells and peripherally induced (p)Treg cells. As a model for Treg cells, studies employ TGF-β-induced (i)Treg cells generated from CD4+ conventional T (Tconv) cells in vitro. Here, we describe the relationship of iTreg cells to tTreg and Tconv cells. Proteomic analysis revealed that iTreg, tTreg and Tconv cell populations each have a unique protein expression pattern. iTreg cells had very limited overlap in protein expression with tTreg cells, regardless of cell activation status and instead shared signaling and metabolic proteins with Tconv cells. tTreg cells had a uniquely modest response to CD3/CD28-mediated stimulation. As a benchmark, we used a previously defined proteomic signature that sets ex vivo naïve and effector phenotype Treg cells apart from Tconv cells and includes unique Treg cell properties (Cuadrado et al., Immunity, 2018). This Treg cell core signature was largely absent in iTreg cells. We also used a proteomic signature that distinguishes ex vivo effector Treg cells from Tconv cells and naïve Treg cells. This effector Treg cell signature was partially present in iTreg cells. In conclusion, iTreg cells are distinct from tTreg cells and share limited features with ex vivo Treg cells at the proteomic level.
2022-11-28 | PXD038302 | Pride
Project description:Hematopoietic stem cells (HSCs) in the fetal liver mature from pre-HSCs that originate in the major arteries of the embryo. To generate HSCs from other cell sources it will be necessary to reproduce the maturation of HSCs from pre-HSCs ex vivo. We refined the markers used to purify pre-HSCs and HSCs matured ex vivo, and compared the transcriptomes of pre-HSCs, ex vivo matured HSCs, and fetal liver HSCs. We found that maturation of pre-HSCs into HSCs in vivo or ex vivo is accompanied by the downregulation of genes involved in embryonic development and vasculogenesis, and upregulation of genes involved in hematopoietic organ development, lymphoid development, and immune responses. Ex vivo matured HSCs more closely resemble fetal liver HSCs than pre-HSCs, but are not their molecular equivalents. We show that functional ex vivo-matured and fetal liver HSCs increase the expression of programmed death ligand 1 (PD-L1). PD-L1 does not mark all pre-HSCs, but cell surface PD-L1 was present on functional HSCs after ex vivo culture. PD-L1 signaling, however, is not required for engraftment of embryonic HSCs. Hence, up-regulation of PD-L1 is a correlate of, but not a requirement for HSC maturation.
2017-12-26 | GSE104689 | GEO
Project description:Background. Dendritic cell (DC)-based neoantigen vaccination holds potential as a safe and effective adjuvant therapy for patients with early-stage, resectable NSCLC. DCs have the unique ability to elicit robust antitumoral T-cell responses, while neoantigens are ideal targets to elicit high-affinity T cell responses with excellent tumor specificity. Here, we present the results of a phase I clinical trial in which a novel DC vaccine targeting neoantigens was evaluated in six patients with early stage, resected NSCLC. Methods. Autologous monocyte-derived DCs loaded with neoantigens (Neo-mDCs) were manufactured according to a 4-day protocol. Neo-mDCs were injected intravenously following an intrapatient dose escalation scheme. Primary endpoint of the trial was safety. Secondary endpoints were feasibility, immunogenicity, and relapse-free survival. Results. Vaccine manufacturing was feasible in 6 of 10 patients. Toxicity was limited to grade 1-2 adverse events. Systemic T cell responses were observed in 5 out of 6 vaccinated patients and were dominated by CD8+ T cells, which could be detected ex vivo at high frequencies >1.5 years after the last dose. Furthermore, single cell analysis indicated that the CD8+ T cell responsive population was polyclonal and exhibited the near entire spectrum of T cell differentiation states, including a naïve-like state associated with long lasting memory, but excluding exhausted cell states. Three of six vaccinated patients experienced disease relapse.Conclusion. Neo-mDC vaccination is safe, feasible and induces polyclonal populations of neoantigen-specific T-cell responses containing long lasting memory and effector cells in early-stage NSCLC patients, suggesting clinical potential.
2024-03-18 | GSE240361 | GEO
Project description:Ascites or solid tumour samples from patients with ovarian cancer were collected and grown in culture as ex vivo models of purified tumour cells. RNA-seq was performed on these models to establish gene expression profiles, which allow identification of genes that are differentially expressed between patients with differing tumour intrinsic properties. These samples have been interrogated for the presence of a gene expression signature indicative of sensitivity to an inhibitor of poly(ADP-ribose) glycohydrolase (PARG). These samples are processed in the same manner as previous studies: “E-MTAB-7223 - RNA-seq of human ex vivo ovarian cancer models with matched stromal cells” and “E-MTAB-10801 - RNA-seq of human ex vivo ovarian cancer models with matched stromal cells - part II” with no stromal counterparts included in this current sequencing batch.
2021-10-10 | E-MTAB-11000 | biostudies-arrayexpress
Project description:Background. Dendritic cell (DC)-based neoantigen vaccination holds potential as a safe and effective adjuvant therapy for patients with early-stage, resectable NSCLC, a tumor type typically characterized by high mutational loads. DCs have the unique ability to elicit robust antitumoral T-cell responses, while neoantigens are ideal targets to elicit high-affinity T cell responses with exquisite tumor specificity. Here, we present the results of a phase I clinical trial in which a novel DC vaccine targeting neoantigens was evaluated in six patients with early stage, resected NSCLC. Methods. Tumor samples were subjected to a comprehensive neoantigen identification approach encompassing genomics, transcriptomics and immunopeptidomics. Patients underwent leukapheresis for the manufacturing of monocyte-derived DCs loaded with neoantigens (Neo-mDCs) according to a four-day protocol. Neo-mDCs were injected intravenously following an intrapatient dose escalation scheme. Primary endpoint of the trial was safety. Secondary endpoints were feasibility, immunogenicity, and relapse-free survival. As a quality control, dendritic cells transfected with the mRNA-encoded neoantigen were analyzed by shotgun proteomics to validate expression of the mRNA-encoded neoantigen. Results. The vaccine was demonstrated to be feasible and safe. T cell responses were observed in 5 of 6 vaccinated patients and were dominated by CD8+ T cells, which could be detected ex vivo at high frequencies >1.5 years after the last dose. Furthermore, single cell analysis indicated that the CD8+ T cell responsive population was polyclonal and exhibited the near entire spectrum of T cell differentiation states, including a naïve-like state associated with long lasting memory. Additionally, mRNA-encoded neoantigen were detected by shotgun proteomics in four patients out of the six patients that were tested.
2024-03-17 | PXD044799 | Pride
Project description:Identification of a stable molecular signature in breast tumor endothelial cells that persists ex vivo
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Project description:This study provides a comprehensive multi-omics analysis of the human host response during acute leptospirosis. We performed integrated transcriptomic and proteomic profiling of peripheral blood mononuclear cells (PBMCs) from clinically confirmed leptospirosis patients and healthy controls. Our analysis reveals widespread dysregulation of host pathways, including potent activation of TNF-alpha/NF-kappaB signaling, interferon responses, and inflammatory and immunometabolic pathways. We identified a conserved core host response signature, validated key immune mediators in an ex vivo whole-blood infection model, and pinpointed a multi-protein signature associated with the disease. This dataset offers a valuable resource for understanding the molecular mechanisms of host-pathogen interactions in leptospirosis and identifies potential biomarkers and therapeutic targets.
2026-05-13 | PXD070502 | Pride
Project description:Gene expression signature of ex vivo expanded TILs for 14 day
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Project description:The identification of genes driving organ development is central to understanding which signaling pathways drive the pathogenesis of various diseases including cancer. This dataset depicts the proteomic changes observed in C57BL/6J mice expressing wild-type or 3SA-phospho mutant versions of the Bcl-2-associated death promoter, BAD. This data shows that BAD regulates postnatal mammary gland morphogenesis in puberty. Three conserved serine residues on BAD are co-ordinately phosphorylated to regulate its activity. Non-phosphorylated BAD mutant delayed pubertal ductal elongation. This defect was specific to the epithelial compartment as transplant and ex vivo organoid assays of mutant epithelium recapitulated decreased tubule migration. Proteomic signature between BAD+/+ and phosphomutant BAD-3SA mammary glands identified differences in actin-binding and focal adhesion components. Mechanistically, non-phosphorylated BAD impedes protein translation, specifically in protrusions, through aberrant hypophosphorylated 4E-BP1. These findings reveal a critical enhancement of localized translation for efficient pubertal-mammary-gland morphogenesis and identifies BAD as a novel regulator of this process.
2021-03-29 | PXD014347 | Pride