Next generation sequencing facilitates quantitative analysis of tissue-specific molecular signatures in lupus mice

Purpose: Next-generation sequencing (NGS) technology was used to map expression profiles of effector (spleen) and key target tissues (kidney and brain) in mouse model of Systemic Lupus Erythematosus (SLE). Methods: Total RNA was extracted from total brain, total kidney and total spleen using Trizol and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Paired-end 37-bp mRNA sequencing was performed on Illumina HiSeq2000 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package. Results: We defined kidney-specific molecular signatures of the murine lupus transcriptome that mirrors nephritis-specific transcriptome alterations in human SLE. Conclusions: By the use of the mouse kidney-specific transcriptome and through training of a large whole-blood RNA-sequencing dataset of SLE patients, we developed and validated an algorithm that predicts patients with active LN from SLE patients without LN and suggest vigilance in the monitoring of these patients and potential enrollment in LN prevention studies. Overall design: New Zealand Black (NZB) female mice were crossed with New Zealand White (NZW) male mice. Female hybrids NZB/W-F1 (n=3 at each time-point) were sacrificed with perfusion with PBS at the pre-puberty stage (1 month), pre-autoimmunity stage (3 months) and nephritic stage (6 months old where proteinuria is more than 200 mg/dl for 3 consecutive days) of the disease. Spleen, kidneys and brain were extracted. Age-matched female C57BL/6 mice (n=3) were used as controls.