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RNA-Seq for enrichment and analysis of IRF5 transcript expression in SLE
Rivka C Stone1, Peicheng Du, Di Feng
1Department of Biochemistry & Molecular Biology, New Jersey Medical School, and New Jersey Medical School-University Hospital Cancer Center, UMDNJ, Newark, New Jersey, USA.
Plos One
|January 26, 2013
Summary
Systemic lupus erythematosus (SLE) patients show a unique interferon regulatory factor 5 (IRF5) gene expression profile. This IRF5 transcript signature is linked to specific SLE risk factors and can differentiate patient groups.
Area of Science:
- Immunogenetics
- Molecular Biology
- Rheumatology
Background:
- Polymorphisms in the interferon regulatory factor 5 (IRF5) gene are associated with systemic lupus erythematosus (SLE) risk.
- IRF5 expression and alternative splicing are altered in SLE patients.
- The functional impact of IRF5 alternative splicing in SLE remains unclear.
Purpose of the Study:
- To investigate differences in IRF5 transcript profiles between healthy donors and SLE patients.
- To determine if IRF5-SLE risk haplotypes influence the expressed IRF5 transcript profile.
- To establish an IRF5 transcript signature for SLE patient stratification.
Main Methods:
- Molecular cloning to identify and isolate IRF5 transcript variants from monocytes.
- Next-generation sequencing for in-depth, quantitative analysis of IRF5 transcript expression.
- De novo junction discovery to identify novel alternatively spliced transcripts.
Main Results:
- 14 new differentially spliced IRF5 variants were identified, creating an IRF5 variant transcriptome.
- SLE patients exhibit a distinct IRF5 transcript signature compared to healthy donors.
- An IRF5-SLE risk haplotype was found to define the four most abundant IRF5 transcripts in SLE patients.
- The IRF5 transcript signature allowed for clustering of SLE patients with the H2 risk haplotype.
Conclusions:
- SLE patients possess a unique IRF5 alternative splicing signature.
- IRF5 transcript profiling can serve as a biomarker for SLE.
- Genetic risk factors (IRF5 haplotypes) directly influence the IRF5 transcript profile in SLE.
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