Shared and Distinctive Transcriptomic and Proteomic Pathways in Adult and Juvenile Dermatomyositis

Abstract

Objective: Transcript and protein expression were interrogated to examine gene locus and pathway regulation in the peripheral blood of active adult dermatomyositis (DM) and juvenile DM patients receiving immunosuppressive therapies.

Methods: Expression data from 14 DM and 12 juvenile DM patients were compared to matched healthy controls. Regulatory effects at the transcript and protein level were analyzed by multi-enrichment analysis for assessment of affected pathways within DM and juvenile DM.

Results: Expression of 1,124 gene loci were significantly altered at the transcript or protein levels across DM or juvenile DM, with 70 genes shared. A subset of interferon-stimulated genes was elevated, including CXCL10, ISG15, OAS1, CLEC4A, and STAT1. Innate immune markers specific to neutrophil granules and neutrophil extracellular traps were up-regulated in both DM and juvenile DM, including BPI, CTSG, ELANE, LTF, MPO, and MMP8. Pathway analysis revealed up-regulation of PI3K/AKT, ERK, and p38 MAPK signaling, whose central components were broadly up-regulated in DM, while peripheral upstream and downstream components were differentially regulated in both DM and juvenile DM. Up-regulated components shared by DM and juvenile DM included cytokine:receptor pairs LGALS9:HAVCR2, LTF/NAMPT/S100A8/HSPA1A:TLR4, CSF2:CSF2RA, EPO:EPOR, FGF2/FGF8:FGFR, several Bcl-2 components, and numerous glycolytic enzymes. Pathways unique to DM included sirtuin signaling, aryl hydrocarbon receptor signaling, protein ubiquitination, and granzyme B signaling.

Conclusion: The combination of proteomics and transcript expression by multi-enrichment analysis broadened the identification of up- and down-regulated pathways among active DM and juvenile DM patients. These pathways, particularly those which feed into PI3K/AKT and MAPK signaling and neutrophil degranulation, may be potential therapeutic targets.

Figure 1. Adult dermatomyositis multi-enrichment of transcript and protein pathways.

Pathway clusters (large nodes A, B, C, D) are connected to regulated gene loci (small nodes). Nodes are red for transcript, yellow for protein, red/yellow for both with altered regulation. Heatmaps show patient (column) expression fold change versus healthy controls for each gene locus (row), with black box indicating significant changes. Heatmap column groups are grouped red for transcript, yellow for protein data. Heatmap rows are grouped red for transcript, yellow for protein, red-yellow for both with altered regulation. Heatmap cells are colored by direction: blue for down-regulation, red for up-regulation, white for no change, and grey for no protein data available for the corresponding gene. Abbreviations: DM, dermatomyositis; tx, transcript

Figure 2. Juvenile dermatomyositis multi-enrichment of transcript and protein pathways.

Pathway clusters (large nodes E, F, G, H) are connected to gene loci with altered regulation (small nodes). Node and heatmap colors assigned as in Figure 1, using purple for transcript and blue for protein data. Heatmap cells are colored by direction: blue for down-regulation, red for up-regulation, white for no change, and grey for no protein data available for the corresponding gene. Abbreviations: JDM, juvenile dermatomyositis; tx, transcript

Figure 3. Adult and juvenile dermatomyositis multi-enrichment of transcript and protein pathways.

Pathway clusters (large nodes I, J, K, L) are connected to gene loci with altered regulation (small nodes). Node and heatmap colors assigned as in Figures 1 and 2, using red for adult DM transcript, yellow for adult DM protein, purple for JDM transcript, and blue for JDM protein data. Heatmap cells are colored by direction: blue for down-regulation, red for up-regulation, white for no change, and grey for no protein data available for the corresponding gene. Abbreviations: dermatomyositis, DM; JDM, juvenile dermatomyositis; tx, transcript

Figure 4

Schematic of gene and protein regulation changes in dermatomyositis (DM) and juvenile dermatomyositis (JDM) peripheral blood, in context of multiple affected pathways. Gene loci are colored red for up-regulation, blue for down-regulation, and white for no change in expression. A solid outline indicates gene loci altered in DM, dashed outline indicates gene loci altered in JDM, and both solid and dashed outlines indicate changes in DM and JDM. Some genes are grouped into labeled boxes by pathway component. An arrow indicates a direct signaling effect, and a red flat cap indicates inhibition.