Cell-Free Genic Extrachromosomal Circular DNA Profiles of DNase Knockouts Associated with Systemic Lupus Erythematosus and Relation with Common Fragile Sites

Daniela Gerovska; Patricia Fernández Moreno; Aitor Zabala; Marcos J Araúzo-Bravo

doi:10.3390/biomedicines12010080

Cell-Free Genic Extrachromosomal Circular DNA Profiles of DNase Knockouts Associated with Systemic Lupus Erythematosus and Relation with Common Fragile Sites

Biomedicines. 2023 Dec 28;12(1):80. doi: 10.3390/biomedicines12010080.

Authors

Daniela Gerovska¹, Patricia Fernández Moreno¹, Aitor Zabala¹, Marcos J Araúzo-Bravo^{1

2

3}

Affiliations

¹ Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain.
² Basque Foundation for Science, IKERBASQUE, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain.
³ Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain.

Abstract

Cell-free extrachromosomal circular DNA (cf-eccDNA) has been proposed as a promising early biomarker for disease diagnosis, progression and drug response. Its established biomarker features are changes in the number and length distribution of cf-eccDNA. Another novel promising biomarker is a set of eccDNA excised from a panel of genes specific to a condition compared to a control. Deficiencies in two endonucleases that specifically target DNA, Dnase1 and Dnase1l3, are associated with systemic lupus erythematosus (SLE). To study the genic eccDNA profiles in the case of their deficiencies, we mapped sequenced eccDNA data from plasma, liver and buffy coat from Dnase1 and Dnase1l3 knockouts (KOs), and wild type controls in mouse. Next, we performed an eccDNA differential analysis between KO and control groups using our DifCir algorithm. We found a specific genic cf-eccDNA fingerprint of the Dnase1l3 group compared to the wild type controls involving 131 genes; 26% of them were associated with human chromosomal fragile sites (CFSs) and with a statistically significant enrichment of CFS-associated genes. We found six genes in common with the genic cf-eccDNA profile of SLE patients with DNASE1L3 deficiency, namely Rorb, Mvb12b, Osbpl10, Fto, Tnik and Arhgap10; all of them were specific and present in all human plasma samples, and none of them were associated with CFSs. A not so distinctive genic cf-eccDNA difference involving only seven genes was observed in the case of the Dnase1 group compared to the wild type. In tissue-liver and buffy coat-we did not detect the same genic eccDNA difference observed in the plasma samples. These results point to a specific role of a set of genic eccDNA in plasma from DNase KOs, as well as a relation with CFS genes, confirming the promise of the genic cf-eccDNA in studying diseases and the need for further research on the relationship between eccDNA and CFSs.

Keywords: DifCir; Dnase1; Dnase1l3; buffy coat; chromosomal fragile site (CFS); differentially produced per gene circle (DPpGC); extrachromosomal circular DNA (eccDNA); genome-wide association study (GWAS); liver; plasma; produced per gene circle (PpGC); systemic lupus erythematosus (SLE).

Grants and funding

This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 899417, Ministerio de Ciencia e Innovación, Spain grant No. PID2020-119715 GB-I00/AEI/10.13039/501100011033, and Instituto de Salud Carlos III, Infrastructure of Precision Medicine associated with Science and Technology (IMPaCT) of the Strategic Action in Health (iDATA-MP).