Background/Purpose – Sjšgren’s syndrome (SS) is a chronic autoimmune disease of unknown etiology that targets salivary and lacrimal glands and may be accompanied bymultiorgan systemic manifestations. To further the understanding of immunopathology associated with SS and identify potential therapeutic targets, we examined the transcriptomeof salivary glands in a mouse models of Sjogren’s syndrome through disease progression.

Methods – We isolated RNA from salivary glands of interleukin-14 alpha-transgenic mouse, a model of SS, at 3 different disease stages: pre-autoimmune, autoimmune and malignant. RNA samples were prepared for sequencing using the Illumina TruSeq RNA prep kit. Sequencing was performed using the Illumina HiSeq 2500. The pass filter reads were mapped to the genome (NCBI/build 37.2 ) using TopHat (version 2.0.4). Probable transcripts were assembled using Cufflinks (version 2.0.2), and differential expressed transcripts were determined using DESeq. Fold change (FC) calculations were obtained using the log2(FPKM) ratio, where FPKM is the fragments per kilobase of exon model per million mapped fragments.

Results – Salivary glands RNAs demonstrated disease-stage specificity. For example, when we compared autoimmune to pre-autoimmune stages, there were 26 DE genes (10 down-regulated, 16 up-regulated) that demonstrated a 2.46 fold change or greater. We found 22 DE genes (3 down-regulated, 19 up-regulated) that showed a 2.4 fold of greater difference when we compared malignant vs pre-autoimmune. Ingenuity pathway analysis demonstrated that the DE genes are associated with cancer, development disorders, hereditary disorder, ophthalmic disease, organismal injury and abnormalities, and reproductive system disease (e.g. GSK3A, KRT12, KRT34, KRT36, KRTAP9-4, NEUROD6, OAS2, PRDM5, RHPN2, TPCN1). Sixteen DE genes, including type I IFN response genes OAS2, were common to the autoimmune to pre-autoimmune and the malignant to pre-autoimmune comparisons. Further evidence that the 16 DE genes, which expression are up-regulated associated disease severity, i.e. gene expression level in malignant is higher than in autoimmune; and in autoimmune higher than in pre-autoimmune.

Conclusion – The sensitivity and dynamic range of RNAseq allow a detailed view of salivary glands transcriptome.  Multiple RNA transcripts show disease-state specificity, suggesting that they may be directly involved in pathogenesis.  These finding are expected to lead to new insights into SS pathogenesis and biologic processes leading to SS-associated malignancy.