Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CGvHD vs. non-cGvHD gene expression profiling in peripheral blood

ABSTRACT: We performed peripheral blood gene expression profiling to identify an array of transcriptional biomarkers that discriminate presence of active cGvHD requiring immunosuppression following allogeneic HCT. Peripheral blood mononuclear cells were prepared by Ficoll gradient and cryopreserved from 63 patients (median age 50 yrs; range 19-64) following allogeneic HCT (median 475 days post-HCT) on an IRB approved protocol. Samples were randomly selected into a training set (23 cGvHD and 19 without cGvHD) and test set (12 cGvHD and 9 without cGvHD) and processed on the Aligent whole human genome 44k microarray platform. Bioinformatics programs including AILUN, GeneSpring, SAM, and PAM were used to select a minimum gene-set (FDR <5%) to predict cGvHD in the training set. Patient characteristics in the two groups were collected for confounder/interaction analysis across the following parameters: age, gender, disease histology, disease status at HCT, graft source, conditioning regimen, white blood count (WBC) at sample, and follow-up status including relapse and survival. Type, grade, and activity of acute cGvHD and cGvHD at time of sample and at most recent follow-up were determined by two independent investigators by standard clinical criteria.

ORGANISM(S): Homo sapiens

PROVIDER: GSE23924 | GEO | 2013/07/11

SECONDARY ACCESSION(S): PRJNA130511

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

cGvHD vs. non-cGvHD gene expression profiling in peripheral blood

Project description:We performed peripheral blood gene expression profiling to identify an array of transcriptional biomarkers that discriminate presence of active cGvHD requiring immunosuppression following allogeneic HCT. Peripheral blood mononuclear cells were prepared by Ficoll gradient and cryopreserved from 63 patients (median age 50 yrs; range 19-64) following allogeneic HCT (median 475 days post-HCT) on an IRB approved protocol. Samples were randomly selected into a training set (23 cGvHD and 19 without cGvHD) and test set (12 cGvHD and 9 without cGvHD) and processed on the Aligent whole human genome 44k microarray platform. Bioinformatics programs including AILUN, GeneSpring, SAM, and PAM were used to select a minimum gene-set (FDR <5%) to predict cGvHD in the training set. Patient characteristics in the two groups were collected for confounder/interaction analysis across the following parameters: age, gender, disease histology, disease status at HCT, graft source, conditioning regimen, white blood count (WBC) at sample, and follow-up status including relapse and survival. Type, grade, and activity of acute cGvHD and cGvHD at time of sample and at most recent follow-up were determined by two independent investigators by standard clinical criteria. Three-condition experiment, 35 cGvHD vs. 28 non-cGvHD samples vs. 7 controls (cGvHDnoIS; no immunosuppression drug).

2013-07-11 | E-GEOD-23924 | biostudies-arrayexpress

A Biomarker Panel for Chronic Graft-versus-Host Disease

Project description: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.

2016-05-27 | PXD002762 | Pride

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

Tolerance associated gene expression following allogeneic hematopoietic cell transplantation

2015-05-25 | GSE64300 | GEO

Homo sapiens

Project description:Longitudinal Study of Immune Mediated Disorders after Allogeneic HCT Protocol (Immune Mediated Disorders after Allo-HCT) - cGVHD 6501

| PRJNA378820 | ENA

Longitudinal Study of Immune Mediated Disorders after Allogeneic HCT Protocol (Immune Mediated Disorders after Allo-HCT) - cGVHD 6501

Project description:Longitudinal Study of Immune Mediated Disorders after Allogeneic HCT Protocol (Immune Mediated Disorders after Allo-HCT) - cGVHD 6501

| PRJNA378819 | ENA

Single-cell RNA sequencing analysis of blood B cells from human allogeneic hematopoietic transplant patients

Project description:Single cell analysis of gene expression in blood B cells from allogeneic hematopoietic stem cell transpant (HCT) patients that either developed chronic GVHD, or never developed chronic GVHD.

2023-05-02 | GSE161343 | GEO

Identification of fibrotinflammatory and fibrotic transcriptomic subsets of human sclerotic cutaneous chronic graft-versus-host disease

Project description:Cutaneous sclerotic chronic graft-versus-host disease (cGVHD) is a common and highly morbid complication of allogeneic hematopoietic stem cell transplantation (HSCT). We identified genes that are significantly upregulated in the skin of sclerotic cGVHD patients (n = 17) compared to HSCT patients without sclerotic cGVHD (n = 9) by bulk RNA sequencing. This revealed two transcriptomic groups of affected patients: those with fibrotic and inflammatory/Th1 gene expression, the fibroinflammatory group, and those with predominantly fibrotic/TGF-associated expression, the fibrotic group. This transcriptomic heterogeneity was also associated with histopathologic heterogeneity, with the fibroinflammatory sub-cluster showing more histopathologic features of epidermal cGVHD and inflammation. Further study will help elucidate if these gene expression and histopathologic findings can be used to tailor treatment decisions. Multiple highly induced genes in the skin (SFRP4, SERPINE2, COMP) were also found to be significantly induced in sclerotic cGVHD patient plasma (n = 16) compared to control HSCT patients without sclerotic cGVHD (n = 17), suggesting these TGF and Wnt pathway mediators as candidate blood biomarkers of disease.

2023-11-14 | GSE216645 | GEO

Human CD4+ T-cell transcriptome in early arthritis

Project description:An exploration of the peripheral blood CD4+ T-cell transcriptome of early arthritis clinic attendees, seeking novel diagnostic tools and pathophysiological insights. Ex-vivo CD4+ T-cell RNA was obtained following first early arthritis clinic attendance from 173 patients. Four diagnostic categories were confirmed at median 28 months follow-up. Outcome categories are ACPA- RA (A; n=31), ACPA+ RA (B; n=41), Non-RA Inflammatory arthritis (C; n=56), and Non-RA/Non-Inflammatory arthritis (D; n=45). In order to derive and validate a diagnostic gene signature, samples were split into Training set (where patients could be diagnosed at presentation; n=111) and validation set of undifferentiated arthritis (UA; n=62) patients, in whom diagnosis could only be confirmed after the follow-up period. Arrays were processed in two phases (phases 1 and 2). Phase 1 was split into 4 labelling batches, Phase 2 was split into 2 labelling batches. Batch effects were controlled for using this information using the empirical Bayes approach of Johnson et al. (2007). The supplementary file 'GSE20098_non-normalized.txt' contains non-normalized data for Samples GSM502124-GSM502280 and GSM506251-GSM506266.

2012-03-03 | E-GEOD-20098 | biostudies-arrayexpress

Human herpesvirus 6B (HHV-6B) detection and genome-wide host expression profiles implicate HHV-6B as a pulmonary pathogen after hematopoietic cell transplantation

Project description:Limited understanding of the immunopathogenesis of human herpesvirus 6B (HHV-6B) has prevented its acceptance as a pulmonary pathogen after hematopoietic cell transplantation (HCT). We conducted a prospective multicenter study of patients undergoing bronchoalveolar lavage (BAL) for pneumonia after allogeneic HCT. We tested blood and BAL fluid (BALF) for HHV-6B DNA and mRNA transcripts associated with lytic infection and performed RNA-seq on paired blood. Among 116 participants, HHV-6B DNA was detected in 37% of BALs, 49% of which had HHV-6B mRNA detection. We established an HHV-6B DNA threshold (≥2.3 log10copies/ml in BALF) that was highly predictive of HHV-6B mRNA detection and increased risk for death from respiratory failure (adjusted HR, 2.35; 95% CI, 1.08-5.11). Participants with HHV-6B DNA in BALF exhibited distinct host gene expression signatures, notable for enriched interferon signaling pathways in participants clinically diagnosed with idiopathic pneumonia. These data implicate HHV-6B as a pulmonary pathogen after allogeneic HCT.

2023-12-18 | GSE244210 | GEO

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