Systemic Lupus Erythematosus Patients with DNASE1L3·Deficiency Have a Distinctive and Specific Genic Circular DNA Profile in Plasma

Abstract

Cell-free (cf) extrachromosomal circular DNA (eccDNA) has a potential clinical application as a biomarker. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with a complex immunological pathogenesis, associated with autoantibody synthesis. A previous study found that SLE patients with deoxyribonuclease 1-like 3 (DNASE1L3) deficiency exhibit changes in the frequency of short and long eccDNA in plasma compared to controls. Here, using the DifCir method for differential analysis of short-read sequenced purified eccDNA data based on the split-read signal of the eccDNA on circulomics data, we show that SLE patients with DNASE1L3 deficiency have a distinctive profile of eccDNA excised by gene regions compared to controls. Moreover, this profile is specific; cf-eccDNA from the top 93 genes is detected in all SLE with DNASE1L3 deficiency samples, and none in the control plasma. The top protein coding gene producing eccDNA-carrying gene fragments is the transcription factor BARX2, which is involved in skeletal muscle morphogenesis and connective tissue development. The top gene ontology terms are ‘positive regulation of torc1 signaling’ and ‘chondrocyte development’. The top Harmonizome terms are ‘lymphopenia’, ‘metabolic syndrome x’, ‘asthma’, ‘cardiovascular system disease‘, ‘leukemia’, and ‘immune system disease’. Here, we show that gene associations of cf-eccDNA can serve as a biomarker in the autoimmune rheumatic diseases.

RAES：a rapid and high-fidelity method for artificial extrachromosomal circular DNA synthesis and its application as a bacterial DNA-free vector for robust microRNA overexpression

“…As its distinct topological structure and enigmatic functions in cells, eccDNA, the "magic" mobile and circular DNA molecule, has attracted increasing research interest in recent years. Although numerous studies suggested its potential role in various physiological and pathological statuses, including tumorigenesis [7,21,26], drug-resistance [16,34], aging [35,36], human reproduction [4,8,9] and immune-response [24,37,38], the detailed molecular role of eccDNA remains to be elucidated. One major hurdle in the area is the lack of a rapid and cost-effective method for eccDNA synthesis.…”

A distinct circular DNA profile intersects with proteome changes in the genotoxic stress-related hSOD1G93A model of ALS

“…Mapping and quantification of produced per gene eccDNAs (PpGCs) was realized as described [ 55 , 56 ]. EccDNA reads were mapped with Circle_Finder [ 38 , 57 ] using as arguments the mm10 built of the mouse genome and a minNonOverlap threshold between two split reads of 10 bp.…”

“…We used our method, DifCir, for differential analysis of sequenced purified eccDNA data based on their split read signal [ 55 , 56 ]. We calculated the mean values of the PpGCs for each group of replicates and selected for differentially produced per gene eccDNAs (DPpGCs), whose absolute difference of the means between the two groups was more than a selection threshold θ DPpGC = onefold change (FC) in log 2 scale.…”

“…Similar to the procedure previously reported in transcriptomics [ 59 ], DNA methylomics [ 60 ] and circulomics [ 55 , 56 ], we implemented a democratic method to search for commonly abundant molecules in different samples. To find the minimum cutoff value of PpGC to be considered as a positive vote, we calculated the empirical PpGC distribution for controls and ALS.…”

Circular and Circulating DNA in IBD: from Pathogenesis to Potential Molecular Therapies

“…These problems make the prediction of eccDNA markers from plasma samples a daunting task. However, the use of DifCir on the circulomics analysis of eccDNAs from Systemic Lupus Erythematosus (SLE) patients with DNASE1L3•deficiency have disclosed a distinctive and specific genic eccDNA profile of these patients [112].…”