Background DNA microarray-based gene expression abnormalities in peripheral blood from patients with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) have been widely investigated.1) However, while single nucleotide-level information of the transcriptome has been expected to provide greater understanding of pathogenesis, no results have yet been reported.
Objectives To identify novel transcriptome-wide gene expression abnormalities in peripheral blood in SLE and RA.
Methods Peripheral blood samples were collected from 12 subjects (3 SLE patients, 3 RA patients, 6 healthy controls). Total RNA was purified from the samples and a cDNA library was prepared. Using a high-throughput sequencer (Illumina IIx), base sequence data were collected by pair end sequencing. These datasets were analyzed by several bioinformatics methods.
Results Total number of read pairs was around 50 million in all samples. Average depth was about 30 coverages, which was sufficient for whole transcriptome analysis. Transcript mapped on the human genome (UCSC hg19) was compared with UCSC RefGene information and read coverages in all exon and samples were calculated. In gene expression analysis, 9 genes were significantly up-regulated in SLE samples compared to those from HC and RA. For example, SDC1, known as a type I transmembrane heparan sulfate proteoglycan which is highly expressed on plasma cells and plasmacytoid dendritic cells, was over transcribed in SLE. Moreover, comprehensive single nucleotide level variant analysis identified novel multiple isoforms (SLE: 125, RA: 79) characterized by SLE and RA.
Conclusions Reading of single nucleotide-level gene expression information with a high-throughput sequencer revealed unique abnormalities in the transcriptome. Our strategy, including in-house code, was able to identify unique variants transcriptome-wide. Combination methods of high-throughput sequencing and bioinformatics will prove powerful in the detection of transcriptome abnormalities observed in autoimmune diseases.
Higgs BW et.al. Ann Rheum Dis. 2011;70:2029-2036
Disclosure of Interest : None declared