Metaproteome
Ontology highlight
ABSTRACT:
SUBMITTER: Yu Han
PROVIDER: OEX00020523 | NODE | 2023-05-31
REPOSITORIES: NODE
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Project description:The current project is designed to evaluate the utility of proteomics in identifying pharmacodynamic (PD) biomarkers for biosimilarity assessment. This is an extension of the data submitted in GSE207945 which profiled longitudinal plasma samples from healthy subjects treated with single therapeutic doses/high doses of IFNβ-1a (30 μg) or Pegylated IFNβ-1a (125 μg) or placebo, to identify candidate PD biomarkers for the two biologics (n=248 for IFNβ-1a and N=528 for pegIFNβ-1a). The current project is a continuation study profiling longitudinal plasma samples from healthy subjects treated with an intermediate/lower dose of IFNβ-1a (15 μg) and pegIFNβ-1a (62.5 μg). Here, we reproduced the previous PD biomarker candidate responses at a lower dose, and further characterized their PD response using characteristics such as significant area under the effect curve, dose-response, temporal profile and return to baseline, variability and sensitivity of the biomarker with sensitive doses on the steep portion of the dose-response curve and mechanism of action using all three tested dose groups (high, intermediate and low).
2026-06-23 | GSE300488 | GEO
Project description:Hypoxia regulates fibroblast function by changing intracellular signaling and secretion factors, which influences the states of nearby cells. In this work, we investigated the effects of conditioned medium (CM) from human adult dermal fibroblasts (HDFs) cultured in normoxic and hypoxic conditions on cervical cancer (HeLa) cells. The HeLa cells showed decreased cell viability, in-creased apoptosis, and cell cycle arrest in response to CM from hypoxic-cultured HDFs (H-CM) compared with CM from normoxic-cultured HDFs (N-CM). Among the proteins up-regulated (> 2-fold) in H-CM compared with N-CM, LTBR decreased the viability of HeLa cells. Among the intracellular proteins down-regulated (> 2-fold) in HeLa cells treated with H-CM compared with N-CM, the most enriched biological process GO term and KEGG pathway were protein deubiq-uitination and hsa05166:HTLV-I infection, respectively. In the protein–protein interaction net-work of intracellular proteins with altered expression (> 2-fold), 1 up-regulated (TNF) and 8 down-regulated (ESR1, MCL1, TBP, CD19, LCK, PCNA, CHEK1, and POLA1) hub proteins were defined. Among the down-regulated hub proteins, the most enriched biological process GO term and KEGG pathway were leading strand elongation and hsa05166:HTLV-I infection, respectively. This study reveals that H-CM had enhanced anti-cancer effects on cervical cancer cells compared with N-CM, and it induced intracellular signaling patterns related to those enhanced anti-cancer effects.
2022-03-04 | GSE185979 | GEO
Project description:Hypoxia regulates fibroblast function by changing intracellular signaling and secretion factors, which influences the states of nearby cells. In this work, we investigated the effects of conditioned medium (CM) from human adult dermal fibroblasts (HDFs) cultured in normoxic and hypoxic conditions on cervical cancer (HeLa) cells. The HeLa cells showed decreased cell viability, in-creased apoptosis, and cell cycle arrest in response to CM from hypoxic-cultured HDFs (H-CM) compared with CM from normoxic-cultured HDFs (N-CM). Among the proteins up-regulated (> 2-fold) in H-CM compared with N-CM, LTBR decreased the viability of HeLa cells. Among the intracellular proteins down-regulated (> 2-fold) in HeLa cells treated with H-CM compared with N-CM, the most enriched biological process GO term and KEGG pathway were protein deubiq-uitination and hsa05166:HTLV-I infection, respectively. In the protein–protein interaction net-work of intracellular proteins with altered expression (> 2-fold), 1 up-regulated (TNF) and 8 down-regulated (ESR1, MCL1, TBP, CD19, LCK, PCNA, CHEK1, and POLA1) hub proteins were defined. Among the down-regulated hub proteins, the most enriched biological process GO term and KEGG pathway were leading strand elongation and hsa05166:HTLV-I infection, respectively. This study reveals that H-CM had enhanced anti-cancer effects on cervical cancer cells compared with N-CM, and it induced intracellular signaling patterns related to those enhanced anti-cancer effects.
2022-03-04 | GSE185978 | GEO
Project description:The aging of pancreatic beta-cells may undermine their ability to compensate for insulin resistance, leading to the development of type 2 diabetes (T2D). Aging beta-cells acquire markers of cellular senescence and develop a senescence-associated secretory phenotype (SASP) that can lead to senescence and dysfunction of neighboring cells through paracrine actions, contributing to beta-cell failure. Herein, we defined the beta-cell SASP signature based on unbiased proteomic analysis of conditioned media of cells obtained from human senescent beta-cells. These experiments revealed that the beta-cell SASP is enriched for factors associated with inflammation, cellular stress response, and extracellular matrix remodeling across species.
2021-03-18 | GSE162521 | GEO
Project description:This study employed the NanoString nCounter platform to perform targeted, quantitative molecular profiling of longitudinally collected FFPE tumor samples to elucidate molecular mechanisms underlying resistance to anti–PD-1 therapy. nCounter® Vantage 3D™ Single Nucleotide Variant assay was integrated using a solid tumor panel to screen 104 driver variants across 25 genes frequently mutated in solid tumors. We quantified the expression of 770 cancer-related mRNA transcripts to identify persistently activated oncogenic pathway signatures in non-responders, which were further complemented by quantitative profiling of 27 total and phosphoproteins using antibody–oligonucleotide conjugates for functional validation of pathway activity. To characterize the tumor microenvironment spatially, GeoMx Digital Spatial Profiler analysis was utilized to assess the distribution of 38 proteins across distinct histological regions, revealing an immunosuppressive spatial architecture associated with treatment resistance.
2026-01-31 | GSE318248 | GEO
Project description:In this study, we describe the development and use of an ad hoc protein microarray to study the immune response induced by the three major 4CMenB antigenic components (fHbp, NHBA and NadA) in individual sera from vaccinated infants, adolescents and adults.
2020-08-28 | GSE152785 | GEO
Project description:To compare the cell signaling events between PC-3 cells and MDA-MB-468 cells, we performed a Reverse Phase of Protein Array (RPPA) profiling on 468 and PC-3 Cells that treated with DMSO, AZD5363, MS21 at 1µM for 24hr respectively.
2019-11-27 | GSE141079 | GEO
Project description:Background: Stress cardiomyopathy (SCM) is a unique form of LV dysfunction that more often occurs in women. Patients with SCM have a higher Troponin I/B-type natriuretic peptide ratio than AMI, but little is known about other circulating proteins. The goals of this study were to compare plasma proteins in SCM and AMI to learn about the pathophysiology of SCM and also to identify putative biomarkers of SCM. Methods: Blood was drawn in normal controls (n=6), women with AMI (n=12) or women with acute SCM (n=15). Two-week follow up samples were available in AMI (n=4) and SCM patients (n=11). Relative concentrations of 1310 serum proteins were measured in each of the 48 samples using the SOMAscan aptamer based assay. Women with AMI tended to be younger (57.87 ± 16.0 vs. 65.08 ± 9.11 years, p=0.12) and had a higher peak troponin I (AMI 32.03 ± 29.46 vs. SCM 2.68 ± 2.6 ng/mL, p=0.02). No differentially expressed proteins were detected (absolute log2 fold change>1; q<0.05) between AMI and SCM in the acute or recovery phase. In the normal vs. AMI comparison there was differential expression of 35 proteins. In the normal vs. SCM comparison there were 45 proteins with differential expression. Pathway analysis demonstrated activation of complement, coagulation, and inflammation in both AMI and SCM. Conclusions: The acute phase of SCM is characterized by a severe inflammatory response similar to AMI. Despite recovery of LV function in SCM at two weeks, differences in circulating proteins remain in comparison to normal controls.
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2018-03-07 | GSE98881 | GEO
Project description:Aberrant secretion of cytokines contributes to pathogenesis of leukemia and is considered a prognostic signature for recurrence of AML. We asked whether molecular targeting of TIFA can perturb NF-κB-dependent secretion of leukemic cytokines and attain better therapeutic efficacy. We performed cytokine antibody array to profile cytokines secreted by U937 cells in response to TIFA dominant-negative fragments and cytarabine treatment.
2016-11-21 | GSE87383 | GEO