Background/Purpose: Sjögren’s syndrome (SS) is a common, clinically heterogeneous autoimmune disease characterized by exocrine gland dysfunction that involves both innate and adaptive immune responses. SS etiology is complex, with environmental, genetic, and genomic factors contributing.  Of the many genetic associations reported in complex diseases, >80% map to non-protein coding DNA sequences; however, many reside in regions shown to be transcriptionally active. We used RNA-seq to identify differentially expressed (DE) protein-coding (~3% of the genome) and non-coding transcripts in 57 SS cases and 37 healthy controls.

Methods: RNA samples were isolated from whole blood and prepared for sequencing using the NuGEN Encore kit and sequenced using the Illumina HiSeq 2000. Raw FASTQ files were aligned to the human genome using TOPHAT. DE transcripts were determined using DESeq with a false discovery rate q-value of 0.05 and a fold change of >2.

Results: After the alignment, the reads were summarized for 55,076 transcripts across the human genome annotated by Ensembl. A total of 2614 DE transcripts were identified. Of the protein-coding regions, SRP14 was the most statistically DE locus in the case-control analysis (q=2.03x10E-20, FC=2.32). Two other DE protein-coding transcripts of interest were identified: UQCRB (q=1.94x10E-19, FC=2.86) and ATP5I (q=1.88x10E-18, FC=2.34). Biological functions of these genes are unclear. Among the 408 DE non-protein coding transcripts, we observed DE of a long non-coding RNA (lncRNA) at 2p25.1 (q=3.69x10E-5, FC=2.55). lncRNAs are important regulators of the human genome with diverse functions; however, most have yet to be characterized.  Bioinformatics evaluation in the 2p25.1 region showed transcription factor binding sites and transcription of lncRNA sequences using immunologically relevant cell lines. To formulate functional hypotheses for the lncRNA at 2p25.1, we evaluated co-expression patterns with protein coding sequences and identified T cell activation and development as the most likely pathways influenced. When evaluating the difference in anti-Ro status, we found the FC increased to 2.85 in anti-Ro(+)patients and decreased to FC=2.24 when anti-Ro(-), indicating a possible relationship to antibody status.

Conclusion: In this SS RNA-seq study, we identified multiple candidate loci and, for the first time, DE lncRNA regions in SS. Although the function of the lncRNAs identified in this study are unknown, many others have been described to function as scaffolds, decoys, signals, and guides for various proteins by conferring nucleotide sequence specificity not possible by motifs alone.  Future studies in SS are warranted to elucidate the functional consequences of these lncRNA.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/rna-sequencing-identifies-novel-differentially-expressed-coding-and-non-coding-transcripts-in-sjogrens-syndrome-2/