Cell-free DNA profiles of dermatomyositis and its potential role in discriminating phenotypes

Abstract

Background: Cell-free DNA (cfDNA) functions in the early-detection and monitoring of autoimmune diseases including systemic lupus erythematosus and rheumatoid arthritis. However, investigations into cfDNA profiles in dermatomyositis and their potential clinical implications remain scarce.

Objectives: To explore the overall landscape of cfDNA profiles in dermatomyositis and investigate potential roles in discriminating subtypes.

Methods: Following informed consent, 24 treatment-naïve patients diagnosed with dermatomyositis and 16 healthy controls were enrolled. We examined cfDNA concentrations, fragment distribution patterns, 5'-end motif frequencies and genetic variation profiles in all participants and studied potential correlation with laboratory parameters. Moreover, intergroup differences of cfDNA profiles among patients and potential correlation between extracellular DNases levels and cfDNA were investigated.

Results: Compared to healthy controls, dermatomyositis patients exhibited elevated cfDNA concentrations, with significantly longer cfDNA fragments, primarily centered around 180-360 bp; nonetheless, no correlation was witnessed between lab parameters and cfDNA levels. The A-end predominated the 5'-end motif, whereas the C-end was underrepresented, contrasting with the patterns observed in healthy controls. In addition, genetic variations in several genes, including PDE4DIP and BRCA2, were commonly detected in cfDNA from dermatomyositis patients. Notably, end-motif profiles and cfDNA fragment length exhibited variations between anti-transcription intermediary factor 1-gamma positive patients with and without malignancies. However, owing to limited sample size, we failed to draw conclusions regarding extracellular DNase levels.

Conclusions: This study presents the first comprehensive depiction of cfDNA profiles in patients with dermatomyositis. Furthermore, cfDNA features exhibit variability across some sub-phenotypes and may serve as discriminatory indices. Finally, potential involvement of extracellular DNases in cfDNA profiles in dermatomyositis shall be further investigated.

Keywords: 5’ end-motif; cell-free DNA; dermatomyositis; fragmentation; genetic variance.

Figure 1

Schematic algorithm of the study.

Figure 2

Plasma cfDNA levels, correlation with ANA and cfDNA fragment length distribution profiles in dermatomyositis. Plasma levels of cfDNA were significantly elevated in patients with dermatomyositis compared to healthy controls, but no intergroup variances were found among the subgroups (A, B). ANA dilution showed no notable differences among subgroups and no clear trend was observed between ANA titers and cfDNA levels (C, D). cfDNA fragments assigned to 180~360bp predominate in nearly all patients (E); the intergroup variance was displayed as regards different cfDNA fragment length (F). *P < 0.05. ns, not significant.

Figure 3

End-motif profiles of cfDNA. Heatmap of the top 30 four-mer end motifs across patient subgroups (A). A-end predominates in all patients, while proportion of C-end is far lower in TWT subgroup compared to TOT subgroup (B, C). The intergroup variances as regards 2-mer end-motifs (D). *P < 0.05, **P < 0.01. ns, not significant.

Figure 4

Results of high throughput cfDNA sequencing. Circos plot represents the chromosome, sequencing coverage, and the variance density from TOT, OM and TWT subgroup, respectively, from the outermost layer to the innermost (A). Genetic variances for all enrolled patients (B), TWT subgroup (C) and TOW subgroup (D). Levels of genetic variances number and variant allele frequency of each subgroup (E, F). Association between variant allele frequency and cfDNA levels (G). ns, not significant.