Extrachromosomal circular DNA (eccDNA) in immune regulation and autoimmunity: From mechanisms to clinical applications.

Extrachromosomal DNA circularization is a common event in cancer cells and frequently serves as a vehicle for cancer oncogene amplification. Random segregation of oncogene-containing extrachromosomal circular DNA promotes rapid intercellular heterogeneity, conferring tumors the ability to rapidly evolve and escape therapy. Smaller, copy-number neutral extrachromosomal circular DNAs are also abundantly identified in both healthy and malignant tissues, but their function in cancer is still unknown. Understanding how extrachromosomal circular DNAs contribute to intercellular heterogeneity in cancer cells remains crucial, however methods for an unbiased characterization of extrachromosomal circular DNAs in single cells are lacking. We introduce scEC&T-seq (single cell extrachromosomal circular DNA and transcriptomic sequencing), a method for parallel detection of extrachromosomal circular DNAs and full-length mRNA in single cells. We demonstrate the ability of our method to isolate and detect extrachromosomal circular DNAs genome-wide from all range of sizes in single cells. We observed that whereas large oncogene-containing circular DNAs are clonally present in most cancer cells, only a very small fraction of small circular DNAs are recurrently identified in single cells, indicating yet unknown prerequisites for maintenance and propagation. Our method was able to capture and recapitulate the structural complexity of oncogene-containing extrachromosomal circular DNAs in single cells, and the matching transcriptomic data allowed us to identify fusion transcripts resulting from the rearranged extrachromosomal structures. In addition, we observed that whereas the main structure of extrachromosomal circular DNAs is mostly stable in single cells, intercellular differences in extrachromosomal circular DNAs’ content can drive differences in oncogene transcription levels in single cells. We envision that by integrating extrachromosomal circular DNA and mRNA sequencing, our method will not only be useful to investigate the impact of intercellular heterogeneity in extrachromosomal circular DNA in tumor evolution, but also to interrogate its function in other biological and pathological processes. Citation Format: Rocio Chamorro Gonzalez, Thomas Conrad, Robin Xu, Madalina Giurgiu, Maja Cwikla, Katharina Kasack, Lotte Brückner, Eric van Leen, Elias Rodriguez-Fos, Konstantin Helmsauer, Heathcliff Dorado Garcia, Yi Bei, Karin Schmelz, Sascha Sauer, Angelika Eggert, Johannes H. Schulte, Roland F. Schwarz, Kerstin Haase, Richard P. Koche, Anton G. Henssen. Dissecting intercellular extrachromosomal circular DNA heterogeneity in single cancer cells with scEC&T-seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1693.

Autoimmunity--promoting and stabilizing innate immunity 'UNWUCHT'.

Introduction: Evolution of inflammatory arthritis from innate to adaptive immune mechanisms.

Rationale: Extrachromosomal circular DNA is a hallmark of cancer, but its role in shaping the genome heterogeneity of urothelial bladder carcinoma (UBC) remains poorly understood. Here, we comprehensively analyzed the features of extrachromosomal circular DNA in 80 UBC patients.Methods: We performed whole-genome/exome sequencing (WGS/WES), Circle-Seq, single-molecule real-time (SMRT) long-read sequencing of circular DNA, and RNA sequencing (RNA-Seq) on 80 pairs of tumor and AT samples. We used our newly developed circular DNA analysis software, Circle-Map++ to detect small extrachromosomal circular DNA from Circle-Seq data.Results: We observed a high load and significant heterogeneity of extrachromosomal circular DNAs in UBC, including numerous single-locus and complex chimeric circular DNAs originating from different chromosomes. This includes highly chimeric circular DNAs carrying seven oncogenes and circles from nine chromosomes. We also found that large tumor-specific extrachromosomal circular DNAs could influence genome-wide gene expression, and are detectable in time-matched urinary sediments. Additionally, we found that the extrachromosomal circular DNA correlates with hypermutation, copy number variation, oncogene amplification, and clinical outcome.Conclusions: Overall, our study provides a comprehensive extrachromosomal circular DNA map of UBC, along with valuable data resources and bioinformatics tools for future cancer and extrachromosomal circular DNA research.

Sexually transmitted diseases (STDs) are a major worldwide health problem that compromise reproductive fecundity as well as cut short the lives of millions of men, women and children.1,2 Despite extensive efforts, only limited success has been achieved in dealing with STDs, including herpes simplex virus type 2 (HSV-2), Chlamydia trachomatis, group B streptococcus and human immunodeficiency virus [(HIV), the causative agent of acquired immune-deficiency syndrome (AIDS)],3 which collectively devastate both adults and newborns. It is now well recognized that the heterosexual transmission of HIV, which is reponsible for 70–80% of the new cases identified in the last 2 years, is the major route of infection worldwide.4,5 With the identification of HIV in semen and cervical secretions,6–8 AIDS is now the major life-threatening STD.9,10 As strategies are developed to prevent and effectively treat this growing global health problem, understanding the immune system in the female reproductive tract and the way it is regulated by the endocrine system has particular importance.

S2k guideline: Diagnosis and management of cutaneous lupus erythematosus - Part1: Classification, diagnosis, prevention, activity scores.

Genome-wide characterization of extrachromosomal circular DNA in SLE and functional analysis reveal their association with apoptosis

Measuring Inflammatory Arthritis in Patients with Systemic Lupus Erythematosus using Clinical Disease Activity Index

Extrachromosomal circular DNA was recently found to be particularly abundant in multiple human cancer cells, although its frequency varies among different tumor types. Elevated levels of extrachromosomal circular DNA have been considered an effective biomarker of cancer pathogenesis. Multiple reports have demonstrated that the amplification of oncogenes and therapeutic resistance genes located on extrachromosomal DNA is a frequent event that drives intratumoral genetic heterogeneity and provides a potential evolutionary advantage. This review highlights the current understanding of the extrachromosomal circular DNA present in the tissues and circulation of patients with advanced cancers and provides a detailed discussion of their substantial roles in tumor regulation. Confirming the presence of cancer-related extrachromosomal circular DNA would provide a putative testing strategy for the precision diagnosis and treatment of human malignancies in clinical practice.

This paper presents a study of the flow of ice in wedge-shaped converging channels. Such flows are encountered in the relatively constricted waters of the Canadian Arctic Archipelago. Ridging, lead opening patterns, development of a highpressure area, and arch formation are some of the processes which take place during ice flow through converging channels. An idealized geometry and steady wind forcing were used in the testing. The results give ice cover velocity, distribution of stresses, ice thickness, area coverage and ridging. Some of the conditions leading to arch formation at the constricted exit of the channel are explored.

AB0233 ATTAINING CDAI REMISSION IS THE FIRST GATEWAY TO ATTAIN BOOLEAN REMISSION

Extrachromosomal circular DNA is an emerging regulatory element implicated in genomic stability and gene regulation, yet its role in preimplantation development remains elusive. Here, we report the widespread presence of extrachromosomal circular DNA in preimplantation embryos, characterized by homologous junction sequences and originating from genomic regions enriched for active histone marks and RNA Polymerase II occupancy. Functional perturbations demonstrate that RNA Polymerase II inhibition suppresses extrachromosomal circular DNA production, whereas disruption of the Fanconi anemia pathway elevates it, suggesting that transcription-replication conflicts affect its biogenesis. Notably, extrachromosomal circular DNA levels surge during major zygotic genome activation. Synthetic extrachromosomal circular DNAs carrying putative enhancers for the zygotic genome activation genes Mycn and Egfl7, and the developmental gene Emx1, significantly upregulate the expression of their respective genes upon transfection into fibroblasts and zygotes. Collectively, this study unveils the extrachromosomal circular DNA landscape in preimplantation embryos, elucidates a transcription-replication conflict mechanism underlying its generation, and establishes its regulatory potential during mammalian preimplantation development.

Background Inflammatory Bowel Diseases (IBD), comprising Ulcerative Colitis (UC) and Crohn’s Disease (CD), are chronic, relapsing-remitting disorders of the gastrointestinal tract with unclear etiology. Identifying reliable biomarkers for predicting disease progression and treatment response remains a priority. Extrachromosomal circular DNA (eccDNA) has shown promise as a diagnostic and prognostic biomarker in oncology, but its potential in IBD patients, including the gene fragments involved, has not been extensively studied. Methods This monocentric, observational case-control study enrolled IBD patients and healthy controls (HC) undergoing colonoscopy for colorectal cancer screening at our center. IBD disease activity was assessed using the Partial Mayo Score and Mayo Endoscopic Subscore (MES) for UC, and the Harvey-Bradshaw Index and Simple Endoscopic Score (SES-CD) for CD. Colonic biopsies were collected from both inflamed and healthy mucosa of IBD patients, and from HCs. eccDNA was purified using the Circle-Seq method; detection was performed with the Circle Finder pipeline. The study analyzed differences in eccDNA abundances between IBD patients and HCs, focusing on Differentially Produced per Gene eccDNAs (DPpGCs). Results In total, 93 IBD patients (38 CD, 39 UC) and 16 HC were included. IBD patients showed a significantly higher abundance of eccDNAs compared to HC, with this increase observed across all chromosomes, suggesting a global upregulation of eccDNA production throughout the human genome. There was also a statistically significant trend towards larger eccDNA fragments in IBD biopsies. Notably, even when considering only eccDNA derived from genic elements ("genic eccDNAs") IBD patients exhibited a significantly higher abundance of eccDNA compared to HCs. Analysis of DPpGCs (fold change >1 log2, p < 0.01) identified 152 genes enriched in IBD, including GRID2 and NRG1. In CD patients, 70 genes, such as FGF14, SOX5, and ZBTB20, were enriched, while UC patients had 123 enriched genes, including NRG1, SPOCK3, and ATP13A4. Patients in endoscopic remission (SES-CD< 3, MES 0-1) exhibited fewer eccDNAs, though this reduction was not statistically significant. Among identified DPpGCs, key genes included FARS2, HERC3, and PNK2. When analyzing UC and CD seperately, we found a statistically significant increase of eccDNA production in active UC, but not in CD, with NRG1 being notably overrepresented, suggesting its potential as a UC-specific biomarker. Conclusion Our study unveils a unique pattern of eccDNA production in IBD. We showed that circles harboring specific genes can distinguish UC and CD from HCs with statistical significance (p<0.01), indicating that eccDNA profiling may represent a novel diagnostic tool for IBD patients.

AB1070 Comparison of Ultrasound Disease Activity Score in Assessing Joint Inflammation in RA: Comparison with CDAI

Systemic Lupus Erythematosus: Genomics, Mechanisms, and Therapies