Circular DNA in diagnosis and disease models

Informazioni relative al progetto

CIRCULAR VISION

ID dell’accordo di sovvenzione: 899417

DOI

10.3030/899417

Progetto chiuso

Data della firma CE 28 Luglio 2020

Data di avvio 1 Ottobre 2020

Data di completamento 31 Marzo 2024

Finanziato da

• EXCELLENT SCIENCE - Future and Emerging Technologies (FET)

Costo totale

€ 4 195 697,50

Contributo UE

€ 3 998 822,50

Coordinato da

KOBENHAVNS UNIVERSITET
Denmark

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

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

Pubblicazioni

Peer reviewed articles (26)

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

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

Variation of extrachromosomal circular DNA in cancer cell lines

Autori: Carl Rung dos Santos, Lasse Bøllehuus Hansen, Monica Rojas-Triana, Astrid Zedlitz Johansen, Mirna Perez-Moreno, and Birgitte Regenberg
Pubblicato in: Computational and Structural Biotechnology Journal, Numero Volume 21, 2023, Pagina/e 4207–4214, ISSN 2001-0370
Editore: 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

Autori: Daniela Gerovska; Marcos J. Araúzo-Bravo
Pubblicato in: International Journal of Molecular Sciences, Numero Volume 24; Numero 3, 2023, Pagina/e 2736, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24032736

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

Autori: Petito V, Di Vincenzo F, Putignani L, Abreu MT, Regenberg B, Gasbarrini A, Scaldaferri F.
Pubblicato in: Genes, Numero Volume 15, Numero 4, 2024, Pagina/e 414, ISSN 2073-4425
Editore: 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

Autori: Daniela Gerovska; Marcos J. Araúzo-Bravo
Pubblicato in: Cells, Numero Volume 12; Numero 7, 2023, Pagina/e 1061, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells12071061

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

Autori: Federica Di Vincenzo; Ylenia Yadid; Valentina Petito; Valeria Emoli; Letizia Masi; Daniela Gerovska; Marcos Jesus Araúzo-Bravo; Antonio Gasbarrini; Birgitte Regenberg; Franco Scaldaferri
Pubblicato in: Cells, Numero Volume 12; Numero 15, 2023, Pagina/e 1953, ISSN 2073-4409
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cells12151953

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

Autori: 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
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: 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

Autori: 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;
Pubblicato in: Nature Communications, Numero vol. 13 , 3620, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-31388-z

FOntCell: Fusion of Ontologies of Cells

Autori: Javier Cabau-Laporta, Alex M. Ascensión, Mikel Arrospide-Elgarresta, Daniela Gerovska, Marcos J. Araúzo-Bravo
Pubblicato in: Frontiers in Cell and Developmental Biology, Numero 9, 2021, ISSN 2296-634X
Editore: 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

Autori: Itziar Frades, Carles Foguet, Marta Cascante, Marcos J. Araúzo-Bravo
Pubblicato in: Cancers, 2021, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13184609

Circular DNA in the human germline and its association with recombination

Autori: Rasmus Amund Henriksen, Piroon Jenjaroenpun, Ida Borup Sjøstrøm, Kristian Reveles Jensen, Iñigo Prada-Luengo, Thidathip Wongsurawat, Intawat Nookae, BirgitteRegenberg
Pubblicato in: Molecular Cell, Numero Volume 82, Numero 1, 6 January 2022, 2022, Pagina/e Pages 209-217.e7, ISSN 1097-4164
Editore: Elsevier
DOI: 10.1016/j.molcel.2021.11.027

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

Autori: Mihailo Mirkovic; Anna Marzelliusardottir; Anne C Meinema; Théo Aspert; Sung Sik Lee; Gilles Charvin; Yves Barral
Pubblicato in: eLife, Numero 11, 4, 2022, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.71196

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

Autori: 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
Pubblicato in: Clin. Transl. Med. 2022, Numero 12:e817, 2022, ISSN 2001-1326
Editore: Wiley
DOI: 10.1002/ctm2.817

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

Autori: Birgitte Regenberg; Julie Noer; Oskar Hørsdal; Yonglun Luo; Xi Xiang
Pubblicato in: Trends in Genetics, Numero Vol. 38 , no. 7 , pp. 766-781, 2022, ISSN 0168-9525
Editore: 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

Autori: Lasse Bøllehuus Hansen, Sandra Fugl Jakobsen, Egija Zole, Julie Boertmann Noer, Li Tai Fang, Sefa Alizadeh, Julia Sidenius Johansen, Marghoob Mohiyuddin, Birgitte Regenberg
Pubblicato in: Cancer Medicine, Numero Volume 12; Numero 17, 2023, Pagina/e 17679-17691, ISSN 2045-7634
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/cam4.6385

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

Autori: Giulia I. Corsi, Kunli Qu, Ferhat Alkan, Xiaoguang Pan, Yonglun Luo, Jan Gorodkin
Pubblicato in: Nature Communications, Numero 13, 2022, Pagina/e Article number: 3006, ISSN 2041-1723
Editore: 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

Autori: Daniela Gerovska, Patricia Garcia-Gallastegi, Olatz Crende, Joana Márquez, Gorka Larrinaga, Maite Unzurrunzaga, Marcos J. Araúzo-Bravo, Iker Badiola
Pubblicato in: International Journal of Molecular Sciences, Numero 22/9, 2021, Pagina/e 4819, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22094819

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

Autori: 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
Pubblicato in: Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Numero 1868/3, 2021, Pagina/e 118912, ISSN 0167-4889
Editore: 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

Autori: Gerovska D, Fernández Moreno P, Zabala A, Araúzo-Bravo MJ
Pubblicato in: Biomedicines, Numero Volume 12, Numero 1, 2023, Pagina/e 80, ISSN 2227-9059
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/biomedicines12010080

A unifying model for extrachromosomal circular DNA load in eukaryotic cells

Autori: Gerard Arrey , Samuel T Keating , Birgitte Regenberg
Pubblicato in: Seminars in Cell & Developmental Biology, Numero Volume 128, August 2022, Pages 40-50, 2022, ISSN 1084-9521
Editore: 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

Autori: Egija Zole, Gowtham Sathyanarayanan, Birgitte Regenberg and Jörg P. Kutter
Pubblicato in: Lab on a Chip, 2024, ISSN 1473-0189
Editore: Royal Society of Chemistry
DOI: 10.1039/d3lc01028g

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

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

Consistent DNA Hypomethylations in Prostate Cancer

Autori: Marcos J. Araúzo-Bravo; Lars Erichsen; Pauline Ott; Agnes Beermann; Jamal Sheikh; Daniela Gerovska; Chantelle Thimm; Marcelo L. Bendhack; Simeon Santourlidis
Pubblicato in: International Journal of Molecular Sciences, Numero Volume 24; Numero 1, 2023, Pagina/e 386, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24010386

Epigenetics in the Diagnosis and Therapy of Malignant Melanoma

Autori: Simeon Santourlidis; Wolfgang A. Schulz; Marcos J. Araúzo-Bravo; Daniela Gerovska; Pauline Ott; Marcelo L. Bendhack; Mohamed Hassan; Lars Erichsen
Pubblicato in: International Journal of Molecular Sciences, Numero Volume 23; Numero 3, 2022, Pagina/e 1531, ISSN 1422-0067
Editore: 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

Autori: 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
Pubblicato in: Cancers, Numero 14(5): 1195, 2022, ISSN 2072-6694
Editore: 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

Autori: Daniela Gerovska, Julie B Noer, Yating Qin, Quratul Ain, Donjetë Januzi, Matthias Schwab, Otto W Witte, Marcos J Araúzo-Bravo, Alexandra Kretz
Pubblicato in: Cell & Bioscience, Numero Volume 13; Numero 1, 2023, Pagina/e 170, ISSN 2045-3701
Editore: 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

Autori: 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
Pubblicato in: Journal of Crohn's and Colitis, Numero Volume 18, Numero supplement 1, 2024, Pagina/e i375, ISSN 1876-4479
Editore: Oxford Academic
DOI: 10.1093/ecco-jcc/jjad212.0226

Diritti di proprietà intellettuale

Trademark (1)

Circle-Pure

Numero candidatura/pubblicazione: VA 2023 02129
Data: 2023-11-17
Candidato/i: KOBENHAVNS UNIVERSITET

Patent (1)

ASSESSMENT OF BIOLOGICAL PARTICLES IMMOBILIZED IN A HYDROGEL

Numero candidatura/pubblicazione: 22 714391
Data: 2022-03-11
Candidato/i: CHEMOMETEC