Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human healthy subjects, patients with Crohns Disease, and patients with Ulcerative Colitis to compare PBMCs in inflammatory bowel disease

ABSTRACT: Comparison of PBMC transcriptional profiles in healthy subjects, patients with Crohn's Disease, and patients with Ulcerative Colitis

ORGANISM(S): Homo sapiens

DISEASE(S): normal

SUBMITTER: Michael Burczynski

PROVIDER: E-GEOD-3365 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells.

Burczynski Michael E ME Peterson Ron L RL Twine Natalie C NC Zuberek Krystyna A KA Brodeur Brendan J BJ Casciotti Lori L Maganti Vasu V Reddy Padma S PS Strahs Andrew A Immermann Fred F Spinelli Walter W Schwertschlag Ulrich U Slager Anna M AM Cotreau Monette M MM Dorner Andrew J AJ

The Journal of molecular diagnostics : JMD 20060201 1

Ulcerative colitis (UC) and Crohn's disease (CD) are common inflammatory bowel diseases producing intestinal inflammation and tissue damage. Although emerging evidence suggests these diseases are distinct, approximately 10% of patients remain classified as indeterminate inflammatory bowel disease even after invasive colonoscopy intended for diagnosis. A molecular diagnostic assay using a clinically accessible tissue would greatly assist in the classification of these diseases. In the present stu ...[more]

PMID: 16436634

Similar Datasets

DNA methylation in Crohns' disease and ulcerative colitis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2012-12-19 | E-GEOD-32149 | biostudies-arrayexpress

DNA methylation in peripheral blood from individuals with Crohns' disease or ulcerative colitis and normal controls

Project description:Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal peripheral blood samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in peripheral blood samples. Samples came from 17 Crohn's disease affected, 11 ulcerative colitis affected, and 20 normal individuals. Within these samples were three twin sets discordant for Crohn's disease and three twin sets discordant for ulcerative colitis. Bisulfite converted DNA from the 48 samples were hybridized to the Illumina Infinium HumanMethylation450 BeadChip v1.1

2012-04-04 | E-GEOD-32148 | biostudies-arrayexpress

Human-derived PBMCs were stimulated by different groups to kill tumor cells.After 48 hours, PBMCs were taken out, and the enrichment of activated proteins of relevant lymphocytes and the regulation of pathways were examined by proteomics.

Project description:In this study, proteomics was used to explore the activation of lymphocytes and related pathways in PBMCs of different stimulation groups. In our study, proteomics analysis showed that the immune cells in PBMCs activated by stimulation group exhibit improved functions related to white blood cell activation, proliferation and cytotoxicity during biological processes. At the same time, KEGG pathway analysis showed that the signaling pathways’ key proteins for leukocyte transendothelial migration, Th1/Th2 cell differentiation, JAK-STAT (involved in many important biological processes such as cell proliferation, differentiation, apoptosis and immune regulation), DNA replication and Th17 cell differentiation were up-regulated; whereas the key proteins of necroptosis pathways in immune cells were down-regulated.

2023-07-20 | PXD026739 | Pride

Combined Tissue-Fluid Proteomics to Unravel Phenotypic Variability in Amyotrophic Lateral Sclerosis

Project description:The lack of biomarkers for early diagnosis, clinical stratification and to monitor treatment response has hampered the development of new therapies for amyotrophic lateral sclerosis (ALS), a clinically heterogeneous neurodegenerative disorder with a variable site of disease initiation and rate of progression. To identify new biomarkers and therapeutic targets, two separate proteomic workflows were applied to study the immunological response and the plasma/brain proteome in phenotypic variants of ALS. Conventional multiplex (TMT) proteomic analysis of peripheral blood mononuclear cells (PBMCs) was performed alongside a recently introduced method to profile neuronal-derived proteins in plasma using brain tissue-enhanced isobaric tagging (TMTcalibrator). The combined proteomic analysis allowed the detection of regulated proteins linked to ALS pathogenesis (RNA-binding protein FUS, superoxide dismutase Cu-Zn and neurofilaments light polypeptide) alongside newly identified candidate biomarkers (myosin-9, fructose-bisphosphate aldolase and plectin). In line with the proteomic results, orthogonal immunodetection showed changes in neurofilaments and ApoE in bulbar versus limb onset fast progressing ALS. Functional analysis of significantly regulated features showed enrichment of pathways involved in regulation of the immune response, Rho family GTPases, semaphorin and integrin signalling. Our cross-phenotype investigation of PBMCs and plasma/brain proteins provides a more sensitive biomarker exploratory platform than conventional case-control studies in a single matrix. The reported regulated proteins may represent novel biomarker candidates and potentially druggable targets.

2020-07-30 | PXD020493 | Pride

Human lung CD8+ T cells compared with paired non-naive peripheral blood CD8+ T cells

Project description:It is unknown whether human lung T cells recirculate or belong to a distinct tissue-specific population. This issue is important for understanding their role in protection against viral infection and their contribution to pathophysiology of lung diseases such as chronic obstructive pulmonary disease. By comparing transcriptional profiles of blood and lung CD8+ T cells, we aimed to reveal specific traits of lung CD8+ T cells. A total of 12 samples was analyzed: 10 patient samples (including 1 technical replicate) and 2 reference samples (including 1 technical replicate). Per patient (in total 3 patients), 3 paired samples were analyzed. These samples were non-naive peripheral blood CD8+ T cells (CD45R0+CD3+CD8+ T cells), memory-type lung CD8+ T cells (CD45R0+CD27+CD3+CD8+ T cells) and effector-type lung CD8+ T cells (CD45R0+CD27-CD3+CD8+ T cells). The reference population consisted of a mix of naive peripheral blood CD8+ T cells from 5 healthy donors.

2011-06-20 | E-GEOD-30027 | biostudies-arrayexpress

Clinical and molecular characteristics indicate mitochondrial dysfunction in Charcot-Marie-Tooth families with the AARS1 Arg326Trp mutation

Project description:Introduction Aminoacyl tRNA-synthetases are ubiquitously expressed enzymes that attach amino acids to their cognate tRNA molecule. Mutations in several of the aminoacyl tRNA-syntheases are described to cause peripheral neuropathy, i.e. AARS1, GARS1, HARS1, YARS1 and WARS1. The Alanyl-tRNA Synthetase (AARS) is encoded by the AARS1. Bi-allelic mutations have been described responsible for epileptic encephalopathy with persistent myelination defect, while mutation in a single allele cause Charcot-Marie-Tooth disease type 2 (CMT2). Do date it is uncertain how a single AARS1 mutation cause tissue specific neuropathy. Methods The AARS1 was sequenced by next-generation sequencing in probands. Family members were examined by Sanger sequencing. Blood samples from affected and healthy controls were used for quantitative RNA analysis, biochemical analysis of alanine, and proteomics. Results Three Norwegian CMT2 families carried the same novel heterozygous AARS1 variant (NM_001605.2:c.976C>T p.(Arg326Trp)). The three families consisted of in total 17 genetically examined family members, of which 11 individuals carried the AARS1 variant and six unaffected individuals did not carry the variant. All individuals carrying the AARS1 variant presented with a mild to moderately severe CMT2 phenotype with adult onset, except a man age 91 years (reported by his son). Label-free quantitative proteomic analysis of four affected individuals pointed towards an effect on the immune system, comprising proteins known to represent components of systemic response to chronic injury and inflammation. Interestingly, a wide-spread impact on mitochondrial dysfunction was identified. Specifically, the oxidative phosphorylation complexes I, IV and V were highly downregulated. Conclusion Three Norwegian CMT2 families with an AARS1 variant, suggests mitochondrial dysfunction in AARS1 neuropathy.

2022-10-14 | PXD023842 | Pride

DNA microarray analysis of PBMCs from BehÃ§etâs disease (BD) patients

Project description:To examine if gene expression profiles of many BehÃ§etâs disease (BD) patients are commonly abnormal compared to those of healthy volunteers, we performed a genome-wide complementary DNA microarray analysis using an Agilent Hu44K array; RNA samples were isolated from the PBMCs of 41 individual BD patients (32 females and 9 males) and 17 normal volunteers. A total of 41 two color arrays were performed and each individual array included a target sample and a control sample.

2016-01-21 | E-GEOD-70403 | biostudies-arrayexpress

Integrated proteome and malonylome analyses reveal the potential meaning of TLN1 and ACTB in end-stage renal disease

Project description:Purpose: End-stage renal disease (ESRD) is a condition that is characterized by the loss of kidney function. ESRD patients suffer from various endothelial dysfunctions, inflammation, and immune system defects. Lysine malonylation (Kmal) is a recently discovered post-translational modification (PTM). Although Kmal has the ability to regulate a wide range of biological processes in various organisms, its specific role in ESRD is limited. Experimental design: In this study, the affinity enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques have been used to create the first global proteome and malonyl proteome (malonylome) profiles of peripheral blood mononuclear cells (PBMCs) from twenty patients with ESRD and eighty-one controls. Results: On analysis, 793 differentially expressed proteins (DEPs) and 12 differentially malonylated proteins (DMPs) with 16 Kmal sites were identified. The Rap1 signaling pathway and platelet activation pathway were found to be important in the development of chronic kidney disease (CKD), as were DMPs TLN1 and ACTB, as well as one malonylated site. One conserved Kmal motif was also discovered. Conclusion: These findings provided the first report on the Kmal profile in ESRD, which could be useful in understanding the potential role of lysine malonylation modification in the development of ESRD.

2023-10-24 | PXD035147 | Pride

Proteins bound to BTBD7_hsa_circ_0000563 in coronary artery disease

Project description:We aimed to clarify the possible functional role of hsa_circ_0000563 in coronary artery disease. Therefore, the ChIRP-MS was conducted to explore the interaction between BTBD7_hsa_circ_0000563 and proteins on a genomic scale in human peripheral blood mononuclear cell (PBMC). This project is the raw files of the proteins bound to hsa_circ_0000563 found by ChIRP-MS in PBMC.

2023-03-11 | PXD033196 | Pride

Comprehensive transcriptome analysis of synovium and peripheral blood reveals major disease heterogeneity early in the RA disease process prior to therapeutic intervention

Project description:We report the first comparative analysis between histology, RNA-seq of synovium and matched peripheral blood, and clinico-radiological parameters in early rheumatoid arthritis (RA). Using a novel modular approach, we describe underlying pathways associated with three pre-dominant RA pathotypes. Myeloid was associated with macrophages, lymphoid with B and plasma cells, and fibroid with minimal inflammatory cell infiltration. Synovium RNA-seq was better correlated with the pathotypes than blood RNA-seq, but peripheral blood signatures, including type I interferon, were detected as associated with particular myeloid or lymphoid pathotypes. This study describes the molecular heterogeneity of RA and provides major new insights into the cross compartmental molecular pathways that underlie RA.

2020-04-09 | E-MTAB-6141 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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