Circulating long non-coding RNAs as diagnostic markers of lupus nephritis and 5-year follow-up disease flares

Emerging evidence underscores the pivotal role of long non-coding RNAs (lncRNAs) as epigenetic regulators in the immunopathogenesis of systemic lupus erythematosus (SLE). There is a paucity of comprehensive studies that investigate lncRNA associated with lupus nephritis (LN) and disease flares. Thus, we aimed to identify a specific circulating lncRNA panel with high diagnostic accuracy of LN and predictive power of disease flare incidence.

To investigate the feasibility of early diagnosis of LN and disease flares, we examined lncRNAs present in plasma obtained from patients with SLE (n = 96) and healthy individuals (CNT) (n = 25). Non-coding RNA sequencing analysis was used to determine lncRNA in plasma, and the ability to diagnose renal damage and disease flares in a 5-year follow-up study was estimated by the area under the curve (AUC) and by using multivariate Cox's proportional hazards regression.

From the ncRNA sequencing results, we identified 9,155 circulating lncRNAs and 148 differentially expressed between patients with SLE and CNT. Seven of these lncRNAs (AL139317.5, AC019080.1, LINC02185, LINC00708, AC239868.1, AC087392.4, and LATS2-AS1) presented statistically significant high expression for the discrimination of the LN (AUC ≥ 0.90), along with high specificity and positive predictive values (≥80%). A panel combining the 7-lncRNA gave an AUC that improved the read count of the single lncRNAs (1.000, p < 0.00001). In addition, six of these lncRNAs were associated with disease flares (AUC ≥ 0.64) and the 4-lncRNA panel was an independent predictor of disease flares (odds ratio = 8.71, p = 0.005 with a c statistic of 0.864, p < 0.0001), with high levels being a strong independent predictor of 60-month follow-up flares (hazard ratio 4.75, p = 0.005). Higher plasma 4-lncRNA panel values were also related to shorter time free of lupus flares. Finally, functional pathway analysis revealed that the lncRNA-miRNA-target gene network was linked to various inflammation pathways (MAPK, JAK-STAT, and p53 signaling pathways) in immune dysregulation and tissue damage in SLE (TGF-β signaling) and regulation of actin cytoskeleton (adherens junction and focal adhesion).

We identified, for the first time, a specific lncRNA expression profile associated with renal damage and an increased incidence of 5-year follow-up disease flares in patients with SLE, being excellent predictive biomarkers for disease activity and organ damage.