Molecular characterisation of lupus low disease activity state (LLDAS) and DORIS remission by whole-blood transcriptome-based pathways in a pan-European systemic lupus erythematosus cohort

Abstract

Objectives: To unveil biological milieus underlying low disease activity (LDA) and remission versus active systemic lupus erythematosus (SLE).

Methods: We determined differentially expressed pathways (DEPs) in SLE patients from the PRECISESADS project (NTC02890121) stratified into patients fulfilling and not fulfilling the criteria of (1) Lupus LDA State (LLDAS), (2) Definitions of Remission in SLE remission, and (3) LLDAS exclusive of remission.

Results: We analysed data from 321 patients; 40.8% were in LLDAS, and 17.4% in DORIS remission. After exclusion of patients in remission, 28.3% were in LLDAS. Overall, 604 pathways differed significantly in LLDAS versus non-LLDAS patients with an false-discovery rate-corrected p (q)<0.05 and a robust effect size (dr)≥0.36. Accordingly, 288 pathways differed significantly between DORIS remitters and non-remitters (q<0.05 and dr≥0.36). DEPs yielded distinct molecular clusters characterised by differential serological, musculoskeletal, and renal activity. Analysis of partially overlapping samples showed no DEPs between LLDAS and DORIS remission. Drug repurposing potentiality for treating SLE was unveiled, as were important pathways underlying active SLE whose modulation could aid attainment of LLDAS/remission, including toll-like receptor (TLR) cascades, Bruton tyrosine kinase (BTK) activity, the cytotoxic T lymphocyte antigen 4 (CTLA-4)-related inhibitory signalling, and the nucleotide-binding oligomerization domain leucine-rich repeat-containing protein 3 (NLRP3) inflammasome pathway.

Conclusions: We demonstrated for the first time molecular signalling pathways distinguishing LLDAS/remission from active SLE. LLDAS/remission was associated with reversal of biological processes related to SLE pathogenesis and specific clinical manifestations. DEP clustering by remission better grouped patients compared with LLDAS, substantiating remission as the ultimate treatment goal in SLE; however, the lack of substantial pathway differentiation between the two states justifies LLDAS as an acceptable goal from a biological perspective.

Keywords: Autoimmune Diseases; Autoimmunity; Immune System Diseases; Lupus Erythematosus, Systemic; Outcome Assessment, Health Care.

Figure 1

Volcano plots in SLE patients fulfilling the LLDAS and DORIS remission criteria. Volcano plot of Reactome pathways in (A) patients in LLDAS or (B) patients in DORIS remission. The horizontal dashed line indicates the log-transformed false-discovery rate (FDR)-corrected probability threshold (q=0.05) for the moderated t-test statistic; the vertical dashed lines indicate the moderated robust effect size threshold (|dr|=0.36). Pathways not differing significantly yet with a sufficient effect size are highlighted in yellow, whereas significantly differing pathways with an insufficient effect size for both conditions are highlighted in red. Significantly differing pathways with a sufficient effect size for both conditions are highlighted in green. DORIS, definitions of remission in systemic lupus erythematosus; LLDAS, lupus low disease activity state; SLE, systemic lupus erythematosus.

Figure 2

Clusters of individualised Reactome pathways. Individualised Reactome pathways after clustering of selected features associated with (A) LLDAS or (B) DORIS remission. The bars to the right illustrate the distribution of relevant clinical features across clusters. Cluster 1, LLDAS/DORIS remission-enriched cluster; cluster 2, mixed cluster; cluster 3, non-LLDAS/DORIS remission cluster; DORIS, definitions of remission in systemic lupus erythematosus; LLDAS, lupus low disease activity state.

Figure 3

Immune system Reactome pathways according to biological clusters and main functions. Distribution of individualised immune system Reactome pathways in clusters (A) by LLDAS and (B) by DORIS remission. The coloured bars represent manual annotation according to the main functions of each pathway cluster, with pink denoting pathways with inhibitory functions on the immune system, red denoting inflammasome/inflammatory pathways enriched in cytokines, grey denoting toll-like receptor (TLR) and related functions, blue denoting type I interferon (IFN) pathways, and purple denoting antigen processing and B-cell pathways. DORIS, definitions of remission in systemic lupus erythematosus; LLDAS, lupus low disease activity state.

Figure 4

Druggable toll-like receptor (TLR) cascades. Drug–pathway interactions within TLR cascades associated with definitions of remission in systemic lupus erythematosus (DORIS) remission (from: https://idg.reactome.org, with modifications); only selected parts of pathways are shown, and irrelevant pathways or parts of pathways are omitted. The complete pathways are detailed in online supplemental figure S2. Panel A depicts TLR 7/8 and TLR9 pathways; pathway–drug interactions with TLR7 and TLR9 are highlighted with red squares (the number of related drugs is indicated) and demonstrated in panels B and C. Parts of the MyD88:MAL(TIRAP) cascade initiated on the plasma membrane belonging to the druggable TLR cascades are detailed in panel D; this cascade constitutes the terminal effector of TLR2, TLR5, and TLR10 pathways. Within this pathway, Bruton tyrosine kinase (BTK) is a key druggable component, whose inhibitors are shown in panel E.