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A modular analysis framework for the discovery of biomarkers of Systemic Lupus Erythematosus

ABSTRACT: Transcriptional modules were used as a basis for the selection of biomarkers and the development of a multivariate transcriptional indicator of disease progression in patients with systemic lupus erythematosus.

ORGANISM(S): Homo sapiens

PROVIDER: GSE11909 | GEO | 2008/08/11

SECONDARY ACCESSION(S): PRJNA109109

REPOSITORIES: GEO

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A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus

Project description:The analysis of patient blood transcriptional profiles offers a means to investigate the immunological mechanisms relevant to human diseases on a genome-wide scale. In addition, such studies provide a basis for the discovery of clinically relevant biomarker signatures. We designed a strategy for microarray analysis that is based on the identification of transcriptional modules formed by genes coordinately expressed in multiple disease data sets. Mapping changes in gene expression at the module level generated disease-specific transcriptional fingerprints that provide a stable framework for the visualization and functional interpretation of microarray data. These transcriptional modules were used as a basis for the selection of biomarkers and the development of a multivariate transcriptional indicator of disease progression in patients with systemic lupus erythematosus. Thus, this work describes the implementation and application of a methodology designed to support systems-scale analysis of the human immune system in translational research settings. This SuperSeries is composed of the SubSeries listed below.

2008-08-11 | GSE11907 | GEO

Spatial transcriptomics of Cutaneous and Systemic Lupus Erythematosus skin

Project description:We performed spatial transcriptomics on a case series of different clinical subtypes of cutaneous lupus erythematosus including acute cutaneous lupus erythematosus (malar rash, systemic lupus erythematosus). Our goals were to (1) determine which differentially expressed genes (DEGs) could be attributed to specific cell populations in specific locations within the tissue, (2) determine if spatial transcriptomics could better distinguish between CLE clinical subtypes than bulk RNA approaches and (3) examine potential cell-cell communication pathways within the skin lesions.

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Systemic Lupus Erythematosus patient blood with controls

Project description:The experiment consists of 31 Systemic Lupus Erythematosus patient blood samples and 29 healthy donor blood samples.

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Transcription profiling of human systemic lupus erythematosus patients to develop a transcriptional indicator of disease progression

Project description:Transcriptional modules were used as a basis for the selection of biomarkers and the development of a multivariate transcriptional indicator of disease progression in patients with systemic lupus erythematosus. Experiment Overall Design: The proposed biomarker-selection strategy relies on modules for reducing highly dimensional microarray data sets in a stepwise manner. Starting from the full set of 28 modules, only those for which a set minimum proportion of transcripts are significantly changed between the study groups are selected (e.g., minimum proportion of differentially expressed transcripts at p < 0.05 = 15% overexpressed or underexpressed transcripts; in the example given, 11 SLE modules meet this criterion). This eliminates from the selection pool the modules registering fewer consistent changes that could be attributed to noise. Transcriptional vectors were derived for the entire cohort of 22 untreated pediatric SLE patients with the use of this set of 11 SLE modules. Patient profiles were also generated for an independent set of 31 children with SLE treated with steroids and/or cytotoxic drugs and/or hydroxychloroquine. A nonparametric method for analyzing multivariate ordinal data was used to score the patients. Lupus disease flares can lead to irreversible worsening of the patient's status. We tested the relevance of this multivariate transcriptional score for longitudinal monitoring of the disease activity in a cohort of 20 pediatric SLE patients (two to four time points/patient, intervals between each time point varied from one month to 18 months). Half of the patients had been included in our cross-sectional analysis before they were enrolled in this longitudinal study. Parallel trends were observed between multivariate transcriptional scores and a clinical severity score. The positive association was verified statistically with the use of a linear-regression model. Experiment Overall Design:

2008-10-01 | E-GEOD-11909 | biostudies-arrayexpress

DNA methylation in systemic lupus erythematosus patients

Project description:To screen specific DNA methylation markers in systemic lupus erythematosus (SLE) patient's blood DNA, whole-blood DNAs from 6 female SLE patients and 6 female controls were analyzed by methylation microarray.

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Human peripheral blood cells: systemic lupus erythematosus vs healthy individual.

Project description:Gene expression profiling of peripheral blood cells from patients with systemic lupus erythematosus (SLE) vs healthy individual (HI).

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High-Density Lipoproteins - small RNA Signatures in Systemic Erythematosus Lupus.

Project description:Study of high-density lipoproteins using 6 human plasma samples. The study sought to find small RNA signatures in systemic erythematosus lupus.

2018-10-27 | GSE121865 | GEO

Human peripheral blood cells: systemic lupus erythematosus vs healthy individual.

Project description:Gene expression profiling of peripheral blood cells from patients with systemic lupus erythematosus (SLE) vs healthy individual (HI). Peripheral blood was obtained from patients with SLE (n=21) and HI (n=45). Blood samples from 45 HI are used as control.

2010-10-01 | E-GEOD-20864 | biostudies-arrayexpress

lncRNA profiling in moDCs of systemic lupus erythematosus

Project description:Recent studies have shown that alterations in the function of dendritic cells (DCs) are involved in the pathogenesis of systemic lupus erythematosus (SLE). However, the role of DCs participating in SLE remains unclear. We profiled the lncRNAs of LPS-stimulated moDCs in SLE patients compared with healthy controls.

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microRNA profilling in dendritic cells of systemic lupus erythematosus

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2017-02-09 | GSE79240 | GEO

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