Browse
Submit Data
Databases
API
Help

Dataset Information

367 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Biomarker Panel for Chronic Graft-versus-Host Disease

ABSTRACT: Using a quantitative proteomics approach, we compared pooled plasma samples from 35 patients with cGVHD obtained at a median of 103 days post-HCT and 18 patients without cGVHD obtained at matched timepoints to identify biomarkers for cGVHD.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Qing Zhang

LAB HEAD: Sophie Paczesny

PROVIDER: PXD002762 | Pride | 2016-05-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Biomarker Panel for Chronic Graft-Versus-Host Disease.

Yu Jeffrey J Storer Barry E BE Kushekhar Kushi K Abu Zaid Mohammad M Zhang Qing Q Gafken Philip R PR Ogata Yuko Y Martin Paul J PJ Flowers Mary E ME Hansen John A JA Arora Mukta M Cutler Corey C Jagasia Madan M Pidala Joseph J Hamilton Betty K BK Chen George L GL Pusic Iskra I Lee Stephanie J SJ Paczesny Sophie S

Journal of clinical oncology : official journal of the American Society of Clinical Oncology 20160523 22

<h4>Purpose</h4>To identify diagnostic and prognostic markers of chronic graft-versus-host disease (cGVHD), the major cause of morbidity and mortality after allogeneic hematopoietic cell transplantation (HCT).<h4>Patients and methods</h4>Using a quantitative proteomics approach, we compared pooled plasma samples obtained at matched time points after HCT (median, 103 days) from 35 patients with cGVHD and 18 without cGVHD (data are available via ProteomeXchange with identifier PXD002762). Of 105 p ...[more]

PMID: 27217465

Similar Datasets

MicroRNA profiling of HCT-116 versus HCT-116 treated with 5-aza-2'-deoxycytidine processing human colon cancer cell lines

Project description:UCRs expression signature of HCT-116 cell lines versus HCT-116 cell line treated with DNA methylation inhibitor 5-aza-2'-deoxycytidine

2010-03-09 | E-MTAB-196 | biostudies-arrayexpress

Different gene expression profile in acute coronary sindrome (ACS) patients compared to stable angina(SA) patients.

Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes involved in plaque rupture. Human coronary artery endothelial cells (ECs) were stimulated in vitro for 12 hours with plasma obtained from the coronary sinus (CS) and the aorta (Ao) of patients with ACS (n=8), or patients with stable angina (SA, n=4). For each patient, gene expression profile was evaluated by microarray technology in ECs exposed to plasma obtained from CS and compared to that of ECs exposed to plasma sampled from Ao. In patient with ACS we found 684 genes up-regulated and 283 down-regulated was observed as compared to patients with SA. Functional and network analyses of statistically significant gene showed that the up regulated genes were associated to pathways IL17 Signaling. To validate the microarray data the RNAs were used for Real Time PCR experiment. Human coronary artery endothelial cells (ECs) were stimulated in vitro for 12 hours with plasma obtained from the coronary sinus (CS) and the aorta (Ao) of patients with ACS (n=8), or patients with stable angina (SA, n=4). For each patient, gene expression profile was evaluated by microarray technology in ECs exposed to plasma obtained from CS and compared to that of ECs exposed to plasma sampled from Ao.

2014-02-14 | E-GEOD-54977 | biostudies-arrayexpress

HSA-MIR-455-3P CAN BE A PREDICTIVE BIOMARKER OF ANEMIA IN PATIENTS WITH NON-SMALL CELL LUNG CANCER TREATED WITH CARBOPLATIN PLUS PACLITAXEL

Project description:Lung cancer is the leading cause of cancer-related morbidity and mortality worldwide. The initial treatment of lung cancer depends on the definition of the tumor type and its staging. The most common treatment is chemotherapy, and the first-line treatment is a combination of carboplatin and paclitaxel. Although this treatment has good efficacy, there is a high prevalence of adverse reactions, especially hematological reactions. Studies on new biomarkers related to these adverse reactions, such as circulating miRNAs, are very important for optimizing the quality of life of patients. miRNAs have high stability in several biological fluids and they have specific expressions in different tissues or pathologies. Thus, this study aimed to verify the relationship between circulating miRNAs and adverse hematologic reactions caused by treatment with carboplatin and paclitaxel in patients with lung cancer. miRNAs were extracted from samples collected from six patients without anemia and six patients with anemia using the miRNeasy Serum/Plasma Kit (Qiagen, cat no. 217184). After miRNA extraction, microarray analysis was performed. The samples went through processes of marking, insertion in the chips, hybridization for 18 h, washing, and scanning. All procedures were performed using the Affymetrix multi-user platform®, and were in accordance with the user guide of the commercial kit MicroArrayFlashTag™Biotin HSR RNA Labeling Kit Genechip®4.0 (ThermoFisher, Cat No. /ID: 902445,900720,900454).

2023-11-16 | E-MTAB-13518 | biostudies-arrayexpress

Microarray gene expression profiles of peripheral blood mononuclear cells in patients with advanced stage non-small cell lung cancer treated with first line combination chemotherapy

Project description:We have extended our investigation to advanced-stage NSCLC by analyzing gene expression in peripheral blood mononuclear cells (PBMC) from patients with newly-diagnosed NSCLC and histopathology of either AC or SCC. Furthermore, to establish a direct link between gene expression and chemotherapy treatment, PBMC from patients who have received 4 courses of combination chemotherapy with CDDP and GEM were obtained, and the effects of chemotherapy on global gene expression were evaluated using microarray analyses. We analyzed microarray gene expression profiles of peripheral blood mononuclear cells from 30 patients with newly-diagnosed advanced stage NSCLC, and 20 age, sex, and co-morbidity-matched healthy controls (HC). All the cancer patients received a maximum of six courses of chemotherapy with cisplatin and gemcitabine of a 28-day cycle as first line treatment.Furthermore, to establish a direct link between gene expression and chemotherapy treatment, PBMC from patients who have received 4 courses of combination chemotherapy with CDDP and GEM were obtained, and the effects of chemotherapy on global gene expression were evaluated using microarray analyses.

2012-07-31 | E-GEOD-39345 | biostudies-arrayexpress

Evolutionarily conserved effects of Notch signaling drive intestinal graft-versus-host disease in mice and non-human primates

Project description:Notch signaling promotes T-cell pathogenicity and graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (allo-HCT) in mice, with a dominant role for the Delta-like ligand DLL4. To assess if Notch’s effects are evolutionarily conserved and identify key mechanisms, we studied antibody-mediated DLL4 blockade in a non-human primate (NHP) model similar to human allo-HCT. Short-term DLL4 blockade improved post-transplant survival with striking, durable protection from gastrointestinal GVHD, out of proportion to other disease sites. Unlike prior immunosuppressive strategies tested in the NHP GVHD model, anti-DLL4 interfered with a T-cell transcriptional program associated with intestinal infiltration. In cross-species investigations, Notch inhibition decreased surface abundance of the gut-homing integrin α4β7 in conventional T-cells while preserving α4β7 in regulatory T-cells, with findings suggesting increased 1 competition for 4 binding in conventional T-cells. Secondary lymphoid organ fibroblastic reticular cells emerged as the critical cellular source of Delta-like Notch ligands for Notch-mediated up-regulation of α4β7 integrin in T-cells after allo-HCT. Altogether, DLL4/Notch blockade decreased effector T-cell infiltration into the gut, with increased regulatory to conventional T-cell ratios early after allo-HCT. Our results identify a conserved, biologically unique and targetable role of DLL4/Notch signaling in GVHD.

2023-07-14 | GSE228838 | GEO

High fat diet enriched in eicosapentaenoic and docosahexaenoic acids delays the development of fatty liver in mice.

Project description:To investigate the effects of quality of fat in a high fat diet (HFD) over time on hepatic lipid storage and transcriptome in mice. In this dataset, we include the expression data obtained from dissected mouse liver after being fed with Control, HFD-EPA/DHA and HFD-corn oil diet for 8 and 12 weeks. In total, 24 samples were analyzed. Based on hierarchical clustering and scatter plots, one microarray from the HFD-corn oil group at 8 weeks was removed from subsequent analyses. The Piano package was used for Gene Set Enrichment Analysis (GSEA) to identify the total number of genes regulated and the direction of regulation. Gene Ontology (GO) terms were annotated to each probe-set after performing GSEA. The reporter algorithm was used to analyse the functional enrichment level of individual GO term. Heatmaps were generated using the log10p-values to visualize enriched GO biological processes (BPs) terms.

2015-06-30 | E-GEOD-65370 | biostudies-arrayexpress

Tissue-resident PSGL1loCD4+ T cells promote B cell differentiation and chronic graft-versus-host-disease-associated autoimmunity

Project description:We report application of RNA-seqencing to investigate PSGL1hi and PSGL1lo CD4+T cells transcriptional difference in the GVHD target tissues of spleen, liver and lung at day 30 after HCT.

2020-12-31 | GSE157566 | GEO

Microarray gene expression profiles of peripheral blood mononuclear cells in patients with advanced stage non-small cell lung cancer treated with first line combination chemotherapy with or without Rikkunshito treatment

Project description:We have extended our investigation to advanced-stage NSCLC by analyzing gene expression in peripheral blood mononuclear cells (PBMC) from patients with newly-diagnosed NSCLC and histopathology of either AC or SCC. Furthermore, to establish a direct link between gene expression and chemotherapy treatment, PBMC from patients who have received 4 courses of combination chemotherapy with CDDP and GEM, or combination chemotherapy plus Rikkunshito were obtained, and the effects of Rikkunshito during chemotherapy on global gene expression were evaluated using microarray analyses. We analyzed microarray gene expression profiles of peripheral blood mononuclear cells from 17 patients with newly-diagnosed advanced stage NSCLC, and 20 age, sex, and co-morbidity-matched healthy controls (HC). All the cancer patients received a maximum of six courses of chemotherapy with cisplatin and gemcitabine of a 28-day cycle as first line treatment. Furthermore, to establish a direct link between gene expression and Rikkunshito treatment, PBMC from patients who have received 4 courses of combination chemotherapy with CDDP and GEM puls Rikkunshito (9 pateints) or dry powder placebo (8 patients) were obtained, and the effects of chemotherapy on global gene expression were evaluated using microarray analyses.

2014-10-02 | E-GEOD-61926 | biostudies-arrayexpress

Tolerance associated gene expression following allogeneic hematopoietic cell transplantation

Project description:Biologic markers of immune tolerance may facilitate tailoring of immune suppression duration after allogeneic hematopoietic cell transplantation (HCT). In a cross-sectional study, peripheral blood samples were obtained from tolerant (n=15, median 38.5 months post-HCT) and non-tolerant (n=17, median 39.5 post-HCT) HCT recipients and healthy control subjects (n=10) for analysis of immune cell subsets and differential gene expression. There were no significant differences in immune subsets across groups. We identified 281 probe sets unique to the tolerant (TOL) group and 122 for non-tolerant (non-TOL). These were enriched for process networks including NK cell cytotoxicity, antigen presentation, lymphocyte proliferation, and cell cycle and apoptosis. Differential gene expression was enriched for CD56, CD66, and CD14 human lineage-specific gene expression. Differential expression of 20 probe sets between groups was sufficient to develop a classifier with > 90% accuracy, correctly classifying 14/15 TOL cases and 15/17 non-TOL cases. These data suggest that differential gene expression can be utilized to accurately classify tolerant patients following HCT. Prospective investigation of immune tolerance biologic markers is warranted. Samples were collected after allogeneic hematopoietic cell transplantation (HCT) or in healthy control subjects. Peripheral blood samples were obtained from tolerant (n=15, median 38.5 months post-HCT) and non-tolerant (n=17, median 39.5 post-HCT) HCT recipients and healthy control subjects (n=10).

2015-05-25 | E-GEOD-64300 | biostudies-arrayexpress

Tandem Mass Tag (TMT)-coupled LC-MS/MS in OA and RA patients synovial tissues

Project description:All the synovial tissue specimens for TMT relative quantitative proteomics and further experiments were obtained from the patients with RA or OA undergoing surgical joint replacement at the clinical of joint surgery (Xi'an Hong Hui Hospital, Xi'an Jiaotong University, China). The diagnosis of the patients were accorded to the criteria of the American College of Rheumatology (ACR) and European League Against Rheumatism (EULAR) in 2010.a quantitative proteomic profiling of synovial tissue obtained from RA and OA patients was carried out by using TMT labeling followed by high resolution mass spectrometry analysis. We have identified 4822 proteins out of which 510 proteins were found to be differentially expressed by ≥1.2 fold change in the synovial tissue from RA verses OA patients.

2021-12-30 | PXD027703 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data