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Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional analysis of whole blood in patients with auto-inflammatory disorders

ABSTRACT: HOIL1 deficient disease is a new early onset fatal autosomal recessive human disorder charaterized by chronic auto-inflammation, recurrent invasive bacterial infections and progressive muscular amylopectinosis. We studied the transcriptional profiles of whole blood from one HOIL dificient patient and other auto-inflammatory patients, including CINCA, Muckle-Wells syndrome and MVK deficiency. Whole blood was collected in Tempus tubes from 41 healthy children and patients with CINCA (2), MWS (5), MVK deficiency (2) and HOIL deficiency (1) diseases. RNA was extracted and globin reduced. Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips.

ORGANISM(S): Homo sapiens

SUBMITTER: Zhaohui Xu

PROVIDER: E-GEOD-40561 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional analysis of whole blood in patients with auto-inflammatory disorders

Project description:HOIL1 deficient disease is a new early onset fatal autosomal recessive human disorder charaterized by chronic auto-inflammation, recurrent invasive bacterial infections and progressive muscular amylopectinosis. We studied the transcriptional profiles of whole blood from one HOIL dificient patient and other auto-inflammatory patients, including CINCA, Muckle-Wells syndrome and MVK deficiency.

2012-10-28 | GSE40561 | GEO

Transcriptome analysis in primary fibroblasts from HOIL-1-deficient patients upon TNF-α or IL-1β stimulation

Project description:HOIL-1 deficient disease is a new early onset fatal autosomal recessive human disorder charaterized by chronic auto-inflammation, recurrent invasive bacterial infections and progressive muscular amylopectinosis. We studied the effect of TNF-α and IL-1β on transcriptional changes of primary fibroblasts from HOIL-1-, MYD88- and NEMO-deficient patients. Primary fibroblasts were obtained from HOIL-1, MYD88- and NEMO-deficient patients and healthy donors and stimulated with TNF-α or IL-1β for 2 and 6 hours. RNA were extracted and globin reduced. Labeled cRNA were hybridized to Illumina Human HT-12 Beadchips.

2012-10-28 | E-GEOD-40560 | biostudies-arrayexpress

Transcriptome analysis in peripheral blood mononuclear cells (PBMC) from HOIL-1-deficient patients upon TNF-α or IL-1β stimulation

Project description:HOIL-1 deficient disease is a new early onset fatal autosomal recessive human disorder charaterized by chronic auto-inflammation, recurrent invasive bacterial infections and progressive muscular amylopectinosis. We studied the effect of TNF-α and IL-1β on transcriptional changes of PBMCs from HOIL-1- and MYD88-deficient patients. PBMCs were obtained from HOIL-1 and MYD88-deficient patients and healthy donors and stimulated with TNF-α or IL-1β for 2 and 6 hours. RNA were extracted. Labeled cRNA were hybridized to Illumina Human HT-12 V4 Beadchips.

2012-10-28 | E-GEOD-40838 | biostudies-arrayexpress

Transcriptional analysis of whole blood, primary fibroblasts, and PBMCs upon TNF-alpha or IL-1beta stimulation from HOIL-1-deficient patients

Project description:This SuperSeries is composed of the following subset Series: GSE40560: Transcriptome analysis in primary fibroblasts from HOIL-1-deficient patients upon TNF-alpha or IL-1beta stimulation GSE40561: Transcriptional analysis of whole blood in patients with auto-inflammatory disorders GSE40838: Transcriptome analysis in peripheral blood mononuclear cells (PBMC) from HOIL-1-deficient patients upon TNF-alpha or IL-1beta stimulation Refer to individual Series

2012-10-28 | E-GEOD-40752 | biostudies-arrayexpress

Transcriptome analysis in peripheral blood mononuclear cells (PBMC) from HOIL-1-deficient patients upon TNF-α or IL-1β stimulation

2012-10-28 | GSE40838 | GEO

Transcriptome analysis in primary fibroblasts from HOIL-1-deficient patients upon TNF-α or IL-1β stimulation

2012-10-28 | GSE40560 | GEO

A composite immune signature parallels disease progression across T1D subjects (RNA-Seq Cohort 0 WB)

Project description:Technical replicate testing was performed to determine the measurement precision of each analyte. Peripheral blood samples were collected in tempus tubes from a healthy control subject with no family history of autoimmunity (n=1) and from subjects with Type 1 diabetes (n=4). Total RNA was isolated independently from 3 replicate aliquots of the same tempus samples and then globin-reduced. RNAseq libraries were prepared from the globin-reduced RNA.

2020-02-03 | GSE131526 | GEO

Whole blood transcriptional profiles of patients with active tuberculosis (TB) and other inflammatory and infectious diseases

Project description:Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis (M. tuberculosis), is a major cause of morbidity and mortality worldwide and efforts to control TB are hampered by difficulties with diagnosis, prevention and treatment. Most people infected with M. tuberculosis remain asymptomatic, termed latent TB, with a 10% lifetime risk of developing active TB disease, but current tests cannot identify which individuals will develop disease. The immune response to M. tuberculosis is complex and incompletely characterized, hindering development of new diagnostics, therapies and vaccines. The goals of this study include: 1. Identify a transcript signature for active TB in intermediate and high burden settings, correlating with radiological extent of disease and reverting to that of healthy controls following treatment; 2. Identify a specific transcript signature that discriminated active TB from other inflammatory and infectious diseases; 3. Classify TB signature using modular and pathway analysis tools. Three milliliters of whole blood was collected in Tempus tubes from 12 pediatric streptococcus, 40 pediatric staphylococcus, 31 still’s disease, 82 pediatric systemic lupus erythematosus (SLE) and 28 adult SLE patients. RNA was extracted and globin reduced. Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips. Healthy controls were included to match patients’ demographic data. Genespring software was used to analyze active TB transcript signatures, comparing with healthy controls and other inflammatory and infectious diseases.

2010-08-11 | E-GEOD-22098 | biostudies-arrayexpress

In vitro response of fibroblasts isolated from patients with RBCK1 deficiency

Project description:Loss-of-expression and loss-of-function mutations in HOIL1 (RBCK1) results in disruption of the linear ubiquitination assembly complex (LUBAC). Impairment of LUBAC results in impaired NF-kB activation in response to TNF and IL-1b in fibroblastic cells, but also display enhanced pro-inflammatory responses to TNF and IL-1b in leukocytes. Autosomal recessive complete human HOIL-1/RBCK1 deficiency is a new disorder with unbalanced cellular responses to pro-inflammatory cytokines, resulting in the paradoxical association of auto-inflammation and pyogenic bacterial disease, as well as the surprising development of muscular amylopectinosis. The genome-wide gene expression analysis showed that human HOIL-1 deficiency results in impaired NF-B activation in response to TNF- and IL-1 in fibroblastic cells.

2014-10-01 | GSE31064 | GEO

Transcriptional profiling of peripheral blood - comparison of results obtained from samples stored in two RNA stabilizing reagents

Project description:RNA stabilizing reagents have been developed to ensure that transcription profiles of whole blood samples reflect the physiological state at the time of the blood drawn. Ability to preserve and maintain the in vivo gene expression status ex vivo is essential for gene expression profiling and biomarker discovery from clinical sample material. We compared transcriptional profiles obtained from samples collected using two established peripheral blood RNA collection systems, TEMPUS™ and PAXgene™. We demonstrated that TEMPUS™ and PAXgene™ systems can be used in combination with RiboAmp® mRNA amplification without a need for a separate globin reduction step. However, use of samples collected through different blood collection methods in the same experiment should be avoided.

2012-11-05 | GSE29487 | GEO

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