Isoform repertoire of Blood mononuclear cells from SLE patients

Abstract

Abstract Systemic Lupus Erythematosus (SLE) is characterized by numerous immunological alterations, including increased expression of immune activators, such as IFNa, along with alterations in cell composition, such as expansion of plasma cells that produce autoantibodies. Alternative Splicing (AS) is a biological process that regulates post-transcriptional alterations of the RNA. Pathogenic AS events have been associated to several diseases. Furthermore, the description of SLE autoantibodies that target components of the spliceosome such as anti-Sm/RNP, anti-Ro/La, and anti-dsDNA has led us to hypothesize that SLE is associated to abnormal AS events. RNA-seq uses standard Short-Read technologies which involve RNA or cDNA fragmentation for the generation of 150 bp sequencing libraries. Since most mammalian mRNAs are 1–2 kb long, using RNA-seq to identify novel alternatively spliced isoforms is extremely challenging. However, emerging Long-Read sequencing technologies allow full-length mRNA sequencing, de novo transcriptome assembly, and isoform profiling. Our lab has built a computational pipeline that combines Long-Read sequencing with RNA-seq data to identify and quantify novel transcripts in peripheral blood mononuclear cells (PBMCs) from SLE patients compared to healthy controls. From our computational analysis, we have observed that SLE patients display differential exon-inclusion and exclusion events in transcripts coding for immune activating and regulatory proteins, respectively. We conclude that SLE might be associated with pathogenic AS events that might place the immune balance under double jeopardy, through activation of immune activating receptors and inhibition of immune inhibiting receptors.