Identification and functional analysis of circulating extrachromosomal circular DNA in schizophrenia implicate its negative effect on the disorder

Abstract

Abstract Background: Extrachromosomal circular DNA (eccDNA) is a circular DNA molecule derived and free from linear chromosome, its characteristics and potential function in SCZ remain unclear. Methods: Here, we explored the presence of circulating eccDNA in the plasma of chronic SCZ and healthy control using Circle-seq. Then the molecular role of SCZ over-represented eccDNAs was investigated by bioinformatical and experimental analysis. Results: 211 over-represented eccDNAs carrying genic segments (eccGene), including eccTAOK2, eccDNMT3B, eccSIRT5, eccJAG1 and so on, were identified in 10 chronic SCZ patients, whereas only 26 over-represented eccGenes were found in 17 healthy people. Human phenotype ontology enrichment analysis upon the 211 SCZ over-represented eccGenes showed that six of them were enriched significantly in the phenotype of progressive intellectual disability. Functional assays of two artificial eccDNAs carrying TAOK2-intronic sequence showed that they attenuated the TAOK2 mRNA expression in both U-251MG and SH-SY5Y cell lines, which the function was further confirmed by dual-luciferase reporter gene assay. In addition, RNA-seq analysis showed that introduction of the artificial eccTAOK2 in U-251MG cells resulted in dysregulation of immune-related biological processes. Conclusions: These findings delineate the circulating eccDNAs profile of SCZ and highlight the regulatory function of eccTAOK2 and its impact on cellular immune processes, underscoring the eccDNA biology and its potential role as a noninvasive biomarker for diagnosis and monitoring of schizophrenia.