Identification and Characterization of Extrachromosomal Circular DNA in Human Placentas With Fetal Growth Restriction

Abstract

Many studies have confirmed that extrachromosomal circular DNAs (eccDNAs/ecDNAs) exist in tumor and normal cells independently of the chromosome and are essential for oncogene plasticity and drug resistance. Studies have confirmed that there are many eccDNAs/ecDNAs in maternal plasma derived from the fetus. Fetal growth restriction (FGR) is a pregnancy-related disease associated with high newborn morbidity and mortality. However, the characteristics and nature of eccDNAs/ecDNAs in FGR are poorly understood. This study aims to deconstruct the properties and potential functions of eccDNAs/ecDNAs in FGR. We performed circle-seq to identify the expression profile of eccDNAs/ecDNAs, analyzed by bioinformatics, and verified by real-time Polymerase Chain Reaction (PCR) combined with southern blot in FGR compared with the normal groups. A total of 45,131 eccDNAs/ecDNAs (including 2,118 unique ones) were identified, which had significantly higher abundance in FRG group than in normal group, and was bimodal in length, peaking at ~146bp and ~340bp, respectively. Gestational age may be one independent factor affecting the production of eccDNAs/ecDNAs, most of which come from genomic regions with high gene density, with a 4~12bp repeat around the junction, and their origin had a certain genetic preference. In addition, some of the host-genes overlapped with non-coding RNAs (ncRNAs) partially or even completely. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that host-genes on the differentially expressed eccDNAs/ecDNAs (DEEECs/DEECs) were mainly enriched in immune-related functions and pathways. The presence of some ecDNAs were verified, and whose variability were consistent with the circle-seq results. We identified and characterized eccDNAs/ecDNAs in placentas with FGR, and elucidated the formation mechanisms and the networks with ncRNAs, which provide a new vision for the screening of new biomarkers and therapeutic targets for FGR.

Identification and Characterization of Extrachromosomal Circular DNA in Plasma of Lung Adenocarcinoma Patients

“…Additionally, both maternal and fetal eccDNA profiles had a 10 bp periodicity, which is consistent with our findings. 19 , 22 The shift in eccDNA size distribution in cancer patients may be caused by changes in the microenvironment, and the underlying mechanisms warrant further research. According to prior research, eccDNA may play important roles in tumor incidence and progression, tumor heterogeneity and tumor oncogene amplification.…”

Extrachromosomal circular DNA: biogenesis, structure, functions and diseases

“…It provided a new vision for the screening of new biomarkers for FGR. 286 Neidlinger C et al detected significantly more spcDNAs in the angiofibroma-derived cell cultures of patients with tuberous sclerosis (TS) than in the skin of these patients or in the skin of 11 healthy donors. 287 Motejlek K et al further found that the spcDNA from angiofibroma cultures was much longer than that from skin fibroblast cultures.…”

Extrachromosomal circular DNA: Current status and future prospects

“…However, important differences were identified between normal pregnancy and fetal growth restriction patients. A noticeable difference was the total number of eccDNAs, which was slightly higher than the control group ( Yang et al, 2021a ). Biological function analysis revealed apoptosis might play an important role in fetal growth restriction, which could, to some extent, relate to the shallow implantation of placental trophoblast cells ( Paules et al, 2019 ).…”

“…Such findings are not restricted to the plasma. According to a study by Yang et al, human placenta-derived eccDNAs also contained two peaks at 146 and 340 bp, and double-repeated trinucleotide sequences were equally present on both sides of these circular molecules ( Yang et al, 2021a ). In addition, their sequencing data revealed that the repertoires of eccDNAs in the placenta overlapped considerably with chromosomal regions, including gene regions, CpG islands, introns, and transposable elements (TEs).…”

“…To date, studies have been primarily focused on the mechanism and function of eccDNA in cancer. Considering the large amount of research devoted to determining the function of eccDNA under different conditions, we classified the functions of eccDNA into the following categories: (1) oncogene amplification and transcription, (2) hijacking or mobile enhancers, (3) gene fusion and reintegration, (4) molecular sponge and transcriptional regulation ( Paulsen et al, 2019 ; Yerlici et al, 2019 ), (5) telomere stability, and (6) cell signaling/communication ( Yang et al, 2021a ).…”