eccDNAs are apoptotic products with high innate immunostimulatory activity

Abstract

Extrachromosomal circular DNA elements (EccDNAs) have been described in the literature for several decades, and are known for their broad existence across different species 1 , 2 . However, their biogenesis, and functions are largely unknown. By developing a new circular DNA enrichment method, here we purified, and sequenced full-length eccDNAs with Nanopore sequencing. We found that eccDNAs are mapped across the entire genome in a close to random fashion, suggesting a biogenesis mechanism of random ligation of genomic DNA fragments. Consistently, we found that apoptosis inducers can increase eccDNA generation, which is dependent on apoptotic DNA fragmentation followed by ligation by the DNA ligase 3. Importantly, we demonstrated that eccDNAs can function as potent innate immunostimulants in a sequence-independent, but circularity, and cytosolic DNA sensing Sting-dependent fashion. Collectively, our study not only revealed the origin, biogenesis, and immunostimulant function of eccDNAs, but also uncovered their sensing pathway and potential clinical implications in immune response.

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH

“…Given the prevalence of ecDNA in cancer, there is an urgent need for better characterization of unique genetic and epigenetic features of ecDNA in order to understand how it may differ from chromosomal DNA and obtain clues about how it is formed and maintained in tumors. However, isolation and targeted profiling of megabase-sized, clonal ecDNAs is currently challenging due to their large sizes and sequence complexity, in contrast to small kilobase-and subkilobase-sized DNA circles known as extrachromosomal circular DNA elements (eccDNAs) observed also in non-cancer cells and apoptotic byproducts 4,5 .…”

Extrachromosomal Circular DNA (eccDNA): From Chaos to Function

“…Some studies reported that the vast majority of eccDNA originates from repetitive elements ( Motejlek et al, 1993 ; Cohen and Mechali, 2001 ; Moller et al, 2015 ); others suggested that they prefer to reside in some hotspots such as UTRs of genes, GC islands, and transcriptionally activated chromatins ( Shibata et al, 2012 ; Mehanna et al, 2017 ). A recent study supported an even distribution model in drug-induced apoptosis cells ( Wang Y et al, 2021 ). Although the driving force of these patterns is still unknown, it is reasonable to speculate that eccDNA origination may be determined by the mechanisms of eccDNA generation under different cellular conditions ( Figure 3 ).…”

“…It is suspected that drug treatment on cancer cells may induce cell apoptosis with eccDNA generation and subsequent change in the tumor microenvironment dramatically. This work highlighted the potential role of microDNA in drug resistance of cancer cells and shed new light on cancer immunotherapy ( Wang Y et al, 2021 ).…”

“…Several models of the eccDNA biogenesis have been proposed: 1) The chromothripsis model ( Figure 2A ): Chromothripsis is the catastrophic shattering of a chromosome followed by massive genomic rearrangement in a random order, leading to complex genomic structural rearrangements in confined genomic regions. As the “shattering” procedure results in clustered DNA double-strand breaks (DSBs), following by DNA repairing or aberrant DNA replication, and which make it a perfect circumstance to generate eccDNA ( Nazaryan-Petersen et al, 2020 ); in 2021, Wang’s team ( Wang Y et al, 2021 ) reported that apoptosis can promote eccDNA generation in human and mouse cells. It is not surprising; apoptosis, just like chromothripsis, can induce DNA fragmentation and may provide massive DNA fragments for eccDNA formation; 2) Episome model ( Figure 2B ).…”

cir-DNA sequencing revealed the landscape of extrachromosomal circular DNA in articular cartilage and the potential roles in osteoarthritis

“…Extrachromosomal circular DNA (eccDNA) refers to the circular DNA derived from genomic DNA but free of chromosomes. Recent studies have shown that eccDNA is extensively expressed in different tissues and may be involved in varied physiological and pathological processes including immune, inflammation, aging and tumors 6-9 . However, the expression of eccDNA in cartilage tissue and its pathological significance in OA are still unknown.…”