Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction

Originating but free from chromosomal DNA,extrachromosomal circular DNAs(eccDNAs)are organized in circular form and have long been found in unicellular and multicellular eukaryotes.Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA,for which few detection methods are available.Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation,evolution,and drug resistance as well as aging,genomic diversity,and other biological processes,bringing it back to the research hotspot.Several mechanisms of eccDNA formation have been proposed,including the breakage-fusion-bridge(BFB)and translocation-deletion-amplification models.Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health.The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites.The present review summarized the research history,biogenesis,and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction.We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection,prognosis,and treatment of gynecologic tumors.This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.

Identification and characterization of extrachromosomal circular DNA in the silk gland of Bombyx mori

The silk gland cells of silkworm are special cells which only replicate DNA in the nucleus without cell division throughout the larval stage. The extrachromosomal circular DNAs (eccDNAs) have not yet been reported in the silk gland of silkworms. Herein, we have explored the characterization of eccDNAs in the posterior silk gland of silkworms. A total of 35 346 eccDNAs were identified with sizes ranging from 30 to 13 569 549 bp. Motif analysis revealed that dual direct repeats are flanking the 5′ and 3′ breaking points of eccDNA. The sequences exceeding 1 kb length in eccDNAs present palindromic sequence characteristics flanking the 5′ and 3′ breaking points of the eccDNA. These motifs might support possible models for eccDNA generation. Genomic annotation of the eccDNA population revealed that most eccDNAs (58.6%) were derived from intergenic regions, whereas full or partial genes were carried by 41.4% of eccDNAs. It was found that silk protein genes fib-H, fib-L, and P25, as well as the transcription factors SGF and sage, which play an important regulatory role in silk protein synthesis, could be carried by eccDNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the genes carried by eccDNAs were mainly associated with the development and metabolism-related signaling pathways. Moreover, it was found that eccDNAfib-L could promote the transcription of fib-L gene. Overall, the results of the present study not only provide a novel perspective on the mechanism of silk gland development and silk protein synthesis but also complement previously reported genome-scale eccDNA data supporting that eccDNAs are common in eukaryotes.

DNA sequences homologous to hepatitis C virus(HCV) in the extrachromosomal circular DNA in peripheral blood mononuclear cells of HCV-negative subjects

Objective: This study aimed to investigate DNA sequences that are substantially homologous to the corresponding RNA sequence sections of the hepatitis C virus (HCV). These DNA sequences are present in the whole DNA extracted from peripheral blood mononuclear cells (PBMCs) of HCV-negative subjects. We presumed that these experimentally proven 5'-noncoding region (5'-NCR) homologous DNA sequences could be contained in the extrachromosomal circular DNA (eccDNA) fraction as part of the whole cellular DNA. Methods: Home-made polymerase chain reaction (PCR) with whole cellular and isolated eccDNA, nucleotide basic local alignment search tool (BLASTn) alignments, and tests for patterns of methylation in selected sequence sections were performed. Results: The PCR tests revealed DNA sequences of up to 320 bp that broadly matched the corresponding sequence sections of known HCV genotypes. In contrast, BLASTn alignment searches of published HCV 5'-NCR sequences with human genome databases revealed only sequence segments of up to 36 bp of the 5'-NCR. The composition of these sequences shows missing base pairs, base pair mismatches as well as complete homology with HCV reference sequences. These short sequence sections are present in numerous copies on both the same and different chromosomes. The selected sequence region within the DNA sequences of the 5'-NCR revealed a broad diversity of individual patterns of methylation. Conclusions: The experimental results confirm our assumption that parts of the HCV 5'-NCR genomic RNA sequences are present at the DNA level in the eccDNA fraction of PBMCs. The tests for methylation patterns therein revealed individual methylomes which could represent an epigenetic feature. The respective sequence section might be subject to genetic regulation.

DNA plasticity and damage in amyotrophic lateral sclerosis

The pathophysiology of amyotrophic lateral sclerosis （ALS） is particularly challenging due to the heteroge- neity of its clinical presentation and the diversity of cellular, molecular and genetic peculiarities involved. Molecular insights unveiled several novel genetic factors to be inherent in both familial and sporadic dis- ease entities, whose characterizations in terms of phenotype prediction, pathophysiological impact and putative prognostic value are a topic of current researches. However, apart from genetically well-defined high-confidence and other susceptibility loci, the role of DNA damage and repair strategies of the genome as a whole, either elicited as a direct consequence of the underlying genetic mutation or seen as an autono- mous parameter, in the initiation and progression of ALS, and the different cues involved in either process are still incompletely understood. This mini review summarizes current knowledge on DNA alterations and counteracting DNA repair strategies in ALS pathology and discusses the putative role of unconventional DNA entities including transposable elements and extrachromosomal circular DNA in the disease process. Focus is set on SODl-related pathophysiology, with extension to FUS, TDP-43 and C90RF72 mutations. Advancing our knowledge in the field will contribute to an improved understanding of this relentless dis- ease, for which therapeutic options others than symptomatic approaches are almost unavailable.

Candidate therapeutic agents in a newly established triple wild-typemucosalmelanoma cell line

Background:Mucosalmelanoma has characteristically distinct genetic features and typically poor prognosis.The lack of representativemucosal melanoma models,especially cell lines,has hindered translational research on this melanoma subtype.In this study,we aimed to establish and provide the biological properties,genomic features and the pharmacological profiles of a mucosal melanoma cell line that would contribute to the understanding and treatment optimization of molecularly-defined mucosal melanoma subtype.Methods:The sample was collected from a 67-year-old mucosal melanoma patient and processed into pieces for the establishment of cell line and patientderived xenograft(PDX)model.The proliferation and tumorigenic property of cancer cells from different passageswere evaluated,andwhole-genome sequencing(WGS)was performed on the original tumor,PDX,established cell line,and the matched blood to confirm the establishment and define the genomic features of this cell line.AmpliconArchitect was conducted to depict the architecture of amplified regions detected by WGS.High-throughput drug screening(HTDS)assay including a total of 103 therapeutic agents was implemented on the established cell line,and selected candidate agents were validated in the corresponding PDX model.Results:A mucosal melanoma cell line,MM9H-1,was established which exhibited robust proliferation and tumorigenicity after more than 100 serial passages.Genomic analysis of MM9H-1,corresponding PDX,and the original tumor showed genetic fidelity across genomes,and MM9H-1 was defined as a triple wild-type(TWT)melanoma subtype lacking well-characterized“driver mutations”.Instead,the amplification of several oncogenes,telomerase reverse transcriptase(TERT),v-Rafmurine sarcoma viral oncogene homolog B1(BRAF),melanocyte Inducing transcription factor(MITF)and INO80 complex ATPase subunit(INO80),via large-scale genomic rearrangement potentially contributed to oncogenesis of MM9H-1.Moreover,HTDS identified proteasome inhibitors,especially bortezomib,as promising therapeutic candidates for MM9H-1,which was verified in the corresponding PDX model in vivo.Conclusions:We established and characterized a new mucosal melanoma cell line,MM9H-1,and defined this cell line as a TWT melanoma subtype lacking well-characterized“driver mutations”.The MM9H-1 cell line could be adopted as a unique model for the preclinical investigation of mucosal melanoma.

Construction of transgenic mice producing CAT to milk by co-injection of two overlapping fragments of bovine αs1-casein-CAT gene

Two αs1-casein/chloramphenicol acetyltransferase (CAT) gene constructs overlapping by 3.0kb were constructed and co-injected into murine zygotes. In 9 of 10 lines of transgenic mice obtained, based on analysis of structure and expression of the transgene, accurate extrachromosomal homologous recombination (ECR) between the two overlapping DNA fragments was found. Different levels of CAT activity were detected in milk from these lines. The highest CAT activity was about 25-50μg/mL milk. In some mice. CAT activity was found in salvia gland, thymus and spleen extracts. The high frequency and accuracy of ECR reported here will be applicable in the experimental manipulation for generation of relatively large transgene.

Prediction and verifcation of the key ingredients and molecular targets of Guizhi Fuling capsule against tumour metastasis and resistance

Purpose:The well-known traditional Chinese formula Guizhi Fuling capsule(GFC)has been reported to reverse ovarian cancer drug resistance.Extrachromosomal DNA(ecDNA)plays an important role in tumour metastasis and resistance.The purpose of this study was to investigate the potential mechanisms by which GFC blocks tumour metastasis and reverses drug resistance by targeting ecDNA.Methods:CNKI and PubMed were used to obtain pharmacokinetic research data on GFC in rats,and the bioactive ingredients detected in rat serum or plasma were collected.Network databases were used to screen the abnormally expressed genes in ecDNA,tumour metastasis genes,resistance genes,and the active ingredient targets of GFC.The KOBAS3.0 database was used to enrich the KEGG pathways and GO functions;the STRING platform was used to construct the core protein interaction network;and the molecular docking online tool SwissDock was used to analyse the binding activity of the core targets and the active ingredients.RT-qPCR,Western blotting and laser confocal microscopy were used to verify the efect of the sera containing GFC on ecDNA,mRNA and protein expression of key targets.Results:Twenty-three bioactive ingredients of GFC were retrieved from PubMed and CNKI.Nine shared targets were simultaneously involved in abnormal genes in ecDNA,tumour metastasis and resistance and the active ingredient targets of GFC.GO functional analysis indicated that the cotargets involved cell proliferation,apoptotic regulation,nuclear functions,etc.The potential pathways involved in the reversal of tumour metastasis and drug resistance of GFC were the PI3K-Akt signalling,cancer,and platinum drug resistance pathways.Three shared proteins targeting ecDNA(AKT1,EGFR and MYC)stand out from the top 20 PPI targets,and all of the bioactive ingredients of GFC have strong binding afnity to the three proteins.The active ingredients can reduce the expression of MYC,EGFR and AKT1 mRNA and protein and the amount of ecDNA in drug-resistant OC cells.Conclusions:GFC targeting ecDNA to reverse tumour metastasis and drug resistance has the characteristics of multiple ingredients,multiple targets,and multiple pathways,which provides a new perspective for the development of new drugs targeting ecDNA to beneft tumour treatment.