Circular DNA in diagnosis and disease models

Informacje na temat projektu

CIRCULAR VISION

Identyfikator umowy o grant: 899417

DOI

10.3030/899417

Projekt został zamknięty

Data podpisania przez KE 28 Lipca 2020

Data rozpoczęcia 1 Października 2020

Data zakończenia 31 Marca 2024

Finansowanie w ramach

• EXCELLENT SCIENCE - Future and Emerging Technologies (FET)

Koszt całkowity

€ 4 195 697,50

Wkład UE

€ 3 998 822,50

Koordynowany przez

KOBENHAVNS UNIVERSITET
Denmark

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

Other (1)

Software, circular DNA methylome, SNP, long-read analysis

Websites, patent fillings, videos etc. (4)

Dissemination material
Dissemination material first update
Dissemination material second update
Public website and project logo

Demonstrators, pilots, prototypes (4)

Sensitive screen for T cell receptor circles in IBD patients
Mapping of circular DNA from LC tumor and blood
Mapping of global circular DNA profiles in IBD patients
Application of circular DNA models demonstrated

Documents, reports (4)

Detailed communication, dissemination plan - 2nd update

Detailed communication dissemination plan 2nd update

Detailed communication, dissemination plan - 3rd update

Detailed communication, dissemination plan – 3rd update

Detailed communication, dissemination plan

Detailed communication dissemination plan

Detailed communication, dissemination plan – 1st update

Detailed communication dissemination plan 1st update

Publikacje

Peer reviewed articles (26)

Targeted removal of mitochondrial DNA from mouse and humanextrachromosomal circular DNA with CRISPR-Cas9

Autorzy: Weijia Feng , Gerard Arrey , Egija Zole , Wei Lv , Xue Liang , Peng Han , Marghoob Mohiyuddin , Henriette Pilegaard , Birgitte Regenberg
Opublikowane w: Computational and Structural Biotechnology Journal, Numer Volume 20, 2022, Pages 3059-3067, 2022, ISSN 2001-0370
Wydawca: Elsevier
DOI: 10.1016/j.csbj.2022.06.028

Variation of extrachromosomal circular DNA in cancer cell lines

Autorzy: Carl Rung dos Santos, Lasse Bøllehuus Hansen, Monica Rojas-Triana, Astrid Zedlitz Johansen, Mirna Perez-Moreno, and Birgitte Regenberg
Opublikowane w: Computational and Structural Biotechnology Journal, Numer Volume 21, 2023, Strona(/y) 4207–4214, ISSN 2001-0370
Wydawca: Elsevier
DOI: 10.1016/j.csbj.2023.08.027

Skeletal Muscles of Sedentary and Physically Active Aged People Have Distinctive Genic Extrachromosomal Circular DNA Profiles

Autorzy: Daniela Gerovska; Marcos J. Araúzo-Bravo
Opublikowane w: International Journal of Molecular Sciences, Numer Volume 24; Numer 3, 2023, Strona(/y) 2736, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24032736

Extrachromosomal Circular DNA: An Emerging Potential Biomarker for Inflammatory Bowel Diseases?

Autorzy: Petito V, Di Vincenzo F, Putignani L, Abreu MT, Regenberg B, Gasbarrini A, Scaldaferri F.
Opublikowane w: Genes, Numer Volume 15, Numer 4, 2024, Strona(/y) 414, ISSN 2073-4425
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes15040414

Systemic Lupus Erythematosus Patients with DNASE1L3·Deficiency Have a Distinctive and Specific Genic Circular DNA Profile in Plasma

Autorzy: Daniela Gerovska; Marcos J. Araúzo-Bravo
Opublikowane w: Cells, Numer Volume 12; Numer 7, 2023, Strona(/y) 1061, ISSN 2073-4409
Wydawca: MDPI
DOI: 10.3390/cells12071061

Circular and Circulating DNA in Inflammatory Bowel Disease: From Pathogenesis to Potential Molecular Therapies

Autorzy: Federica Di Vincenzo; Ylenia Yadid; Valentina Petito; Valeria Emoli; Letizia Masi; Daniela Gerovska; Marcos Jesus Araúzo-Bravo; Antonio Gasbarrini; Birgitte Regenberg; Franco Scaldaferri
Opublikowane w: Cells, Numer Volume 12; Numer 15, 2023, Strona(/y) 1953, ISSN 2073-4409
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cells12151953

Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

Autorzy: Xi Xiang, Giulia I. Corsi, Christian Anthon, Kunli Qu, Xiaoguang Pan, Xue Liang, Peng Han, Zhanying Dong, Lijun Liu, Jiayan Zhong, Tao Ma, Jinbao Wang, Xiuqing Zhang, Hui Jiang, Fengping Xu, Xin Liu, Xun Xu, Jian Wang, Huanming Yang, Lars Bolund, George M. Church, Lin Lin, Jan Gorodkin, Yonglun Luo
Opublikowane w: Nature Communications, Numer 12/1, 2021, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-021-23576-0

Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

Autorzy: Fei Wang; Peiwen Ding; Xue Liang; Xiangning Ding; Camilla Blunk Brandt; Evelina Sjöstedt; Jiacheng Zhu; Saga Bolund; Lijing Zhang; Laura P. M. H. de Rooij; Lihua Luo; Yanan Wei; Wandong Zhao; Zhiyuan Lv; János Haskó; Runchu Li; Qiuyu Qin; Yi Jia; Wendi Wu; Yuting Yuan; Mingyi Pu; Haoyu Wang; Aiping Wu; Lin Xie; Ping Liu; Fang Chen; Jacqueline Herold; Joanna Kalucka; Max Karlsson; Xiuqing Zhang;
Opublikowane w: Nature Communications, Numer vol. 13 , 3620, 2022, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-31388-z

FOntCell: Fusion of Ontologies of Cells

Autorzy: Javier Cabau-Laporta, Alex M. Ascensión, Mikel Arrospide-Elgarresta, Daniela Gerovska, Marcos J. Araúzo-Bravo
Opublikowane w: Frontiers in Cell and Developmental Biology, Numer 9, 2021, ISSN 2296-634X
Wydawca: Frontiers in Cell and Developmental Biology
DOI: 10.3389/fcell.2021.562908

Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment

Autorzy: Itziar Frades, Carles Foguet, Marta Cascante, Marcos J. Araúzo-Bravo
Opublikowane w: Cancers, 2021, ISSN 2072-6694
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13184609

Circular DNA in the human germline and its association with recombination

Autorzy: Rasmus Amund Henriksen, Piroon Jenjaroenpun, Ida Borup Sjøstrøm, Kristian Reveles Jensen, Iñigo Prada-Luengo, Thidathip Wongsurawat, Intawat Nookae, BirgitteRegenberg
Opublikowane w: Molecular Cell, Numer Volume 82, Numer 1, 6 January 2022, 2022, Strona(/y) Pages 209-217.e7, ISSN 1097-4164
Wydawca: Elsevier
DOI: 10.1016/j.molcel.2021.11.027

DNA circles promote yeast ageing in part through stimulating the reorganization of nuclear pore complexes

Autorzy: Mihailo Mirkovic; Anna Marzelliusardottir; Anne C Meinema; Théo Aspert; Sung Sik Lee; Gilles Charvin; Yves Barral
Opublikowane w: eLife, Numer 11, 4, 2022, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/elife.71196

Circle-Seq reveals genomic and disease-specific hallmarksin urinary cell-free extrachromosomal circular DNAs

Autorzy: Wei Lv, Xiaoguang Pan, Peng Han, Ziyu Wang, Weijia Feng, Xue Xing, Qingqing Wang, Kunli Qu, Yuchen Zeng, Cailin Zhang, Zhe Xu, Yi Li, Tianyu Zheng, Ling Lin, Chengxun Liu, Xuemei Liu, Hanbo Li, Rasmus Amund Henriksen, Lars Bolund, Lin Lin, Xin Jin, Huanming Yang, Xiuqing Zhang, Tailang Yin, Birgitte Regenberg, Fan He, Yonglun Luo
Opublikowane w: Clin. Transl. Med. 2022, Numer 12:e817, 2022, ISSN 2001-1326
Wydawca: Wiley
DOI: 10.1002/ctm2.817

Extrachromosomal circular DNA in cancer: history, current knowledge, and methods

Autorzy: Birgitte Regenberg; Julie Noer; Oskar Hørsdal; Yonglun Luo; Xi Xiang
Opublikowane w: Trends in Genetics, Numer Vol. 38 , no. 7 , pp. 766-781, 2022, ISSN 0168-9525
Wydawca: Elsevier BV
DOI: 10.1016/j.tig.2022.02.007

Methods for the purification and detection of single nucleotide KRAS mutations on extrachromosomal circular DNA in human plasma

Autorzy: Lasse Bøllehuus Hansen, Sandra Fugl Jakobsen, Egija Zole, Julie Boertmann Noer, Li Tai Fang, Sefa Alizadeh, Julia Sidenius Johansen, Marghoob Mohiyuddin, Birgitte Regenberg
Opublikowane w: Cancer Medicine, Numer Volume 12; Numer 17, 2023, Strona(/y) 17679-17691, ISSN 2045-7634
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/cam4.6385

CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context

Autorzy: Giulia I. Corsi, Kunli Qu, Ferhat Alkan, Xiaoguang Pan, Yonglun Luo, Jan Gorodkin
Opublikowane w: Nature Communications, Numer 13, 2022, Strona(/y) Article number: 3006, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-30515-0

GeromiRs Are Downregulated in the Tumor Microenvironment during Colon Cancer Colonization of the Liver in a Murine Metastasis Model

Autorzy: Daniela Gerovska, Patricia Garcia-Gallastegi, Olatz Crende, Joana Márquez, Gorka Larrinaga, Maite Unzurrunzaga, Marcos J. Araúzo-Bravo, Iker Badiola
Opublikowane w: International Journal of Molecular Sciences, Numer 22/9, 2021, Strona(/y) 4819, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22094819

Proprotein convertases blockage up-regulates specifically metallothioneins coding genes in human colon cancer stem cells

Autorzy: Daniela Gerovska, Patricia García-Gallastegi, Jean Descarpentrie, Olatz Crende, María Casado-Andrés, Ander Martín, Jokin Eguia, Abdel-Majid Khatib, Marcos J. Araúzo-Bravo, Iker Badiola
Opublikowane w: Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Numer 1868/3, 2021, Strona(/y) 118912, ISSN 0167-4889
Wydawca: Elsevier BV
DOI: 10.1016/j.bbamcr.2020.118912

Cell-Free Genic Extrachromosomal Circular DNA Profiles of DNase Knockouts Associated with Systemic Lupus Erythematosus and Relation with Common Fragile Sites

Autorzy: Gerovska D, Fernández Moreno P, Zabala A, Araúzo-Bravo MJ
Opublikowane w: Biomedicines, Numer Volume 12, Numer 1, 2023, Strona(/y) 80, ISSN 2227-9059
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/biomedicines12010080

A unifying model for extrachromosomal circular DNA load in eukaryotic cells

Autorzy: Gerard Arrey , Samuel T Keating , Birgitte Regenberg
Opublikowane w: Seminars in Cell & Developmental Biology, Numer Volume 128, August 2022, Pages 40-50, 2022, ISSN 1084-9521
Wydawca: Academic Press
DOI: 10.1016/j.semcdb.2022.03.002

Microfluidic isolation of extrachromosomal circular DNA through selective digestion of plasmids and linear DNA using immobilized nucleases

Autorzy: Egija Zole, Gowtham Sathyanarayanan, Birgitte Regenberg and Jörg P. Kutter
Opublikowane w: Lab on a Chip, 2024, ISSN 1473-0189
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d3lc01028g

CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences

Autorzy: Visanu Wanchai, Piroon Jenjaroenpun, Thongpan Leangapichart, Gerard Arrey, Charles M Burnham, Maria C Tümmler, Jesus Delgado-Calle, Birgitte Regenberg, Intawat Nookaew
Opublikowane w: Briefings in Bioinformatics, Numer Volume 23, Numer 6, November 2022, bbac422, 2022, ISSN 1477-4054
Wydawca: Oxford Academic
DOI: 10.1093/bib/bbac422

Consistent DNA Hypomethylations in Prostate Cancer

Autorzy: Marcos J. Araúzo-Bravo; Lars Erichsen; Pauline Ott; Agnes Beermann; Jamal Sheikh; Daniela Gerovska; Chantelle Thimm; Marcelo L. Bendhack; Simeon Santourlidis
Opublikowane w: International Journal of Molecular Sciences, Numer Volume 24; Numer 1, 2023, Strona(/y) 386, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24010386

Epigenetics in the Diagnosis and Therapy of Malignant Melanoma

Autorzy: Simeon Santourlidis; Wolfgang A. Schulz; Marcos J. Araúzo-Bravo; Daniela Gerovska; Pauline Ott; Marcelo L. Bendhack; Mohamed Hassan; Lars Erichsen
Opublikowane w: International Journal of Molecular Sciences, Numer Volume 23; Numer 3, 2022, Strona(/y) 1531, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23031531

Role of Furin in Colon Cancer Stem Cells Malignant Phenotype and Expression of LGR5 and NANOG in KRAS and BRAF-Mutated Colon Tumors

Autorzy: Jean Descarpentrie; Marcos J. Araúzo-Bravo; Zongsheng He; Alexia François; Álvaro González; Patricia Garcia-Gallastegi; Iker Badiola; Serge Evrard; Simon Pernot; John W. M. Creemers; Abdel-Majid Khatib
Opublikowane w: Cancers, Numer 14(5): 1195, 2022, ISSN 2072-6694
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14051195

A distinct circular DNA profile intersects with proteome changes in the genotoxic stress-related hSOD1G93A model of ALS

Autorzy: Daniela Gerovska, Julie B Noer, Yating Qin, Quratul Ain, Donjetë Januzi, Matthias Schwab, Otto W Witte, Marcos J Araúzo-Bravo, Alexandra Kretz
Opublikowane w: Cell & Bioscience, Numer Volume 13; Numer 1, 2023, Strona(/y) 170, ISSN 2045-3701
Wydawca: Society of Chinese Bioscientists in America
DOI: 10.1186/s13578-023-01116-1

Conference proceedings (1)

P096 Human extrachromosomal circular DNA is an emerging biomarker in Inflammatory Bowel Disease

Autorzy: V Petito, F DI VINCENZO, D Gerovska, A Piazzesi, A Russo, L Turchini, L Masi, L R Lopetuso, M T Abreu, B Regenberg, A Gasbarrini, L Putignani, M J Bravo Araúzo, F Scaldaferri
Opublikowane w: Journal of Crohn's and Colitis, Numer Volume 18, Numer supplement 1, 2024, Strona(/y) i375, ISSN 1876-4479
Wydawca: Oxford Academic
DOI: 10.1093/ecco-jcc/jjad212.0226

Prawa własności intelektualnej

Trademark (1)

Circle-Pure

Numer wniosku/publikacji: VA 2023 02129
Data: 2023-11-17
Wnioskodawca/wnioskodawcy: KOBENHAVNS UNIVERSITET

Patent (1)

ASSESSMENT OF BIOLOGICAL PARTICLES IMMOBILIZED IN A HYDROGEL

Numer wniosku/publikacji: 22 714391
Data: 2022-03-11
Wnioskodawca/wnioskodawcy: CHEMOMETEC