Circular DNA in diagnosis and disease models

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Detailed communication dissemination plan 1st update

Publicaciones

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

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

Variation of extrachromosomal circular DNA in cancer cell lines

Autores: Carl Rung dos Santos, Lasse Bøllehuus Hansen, Monica Rojas-Triana, Astrid Zedlitz Johansen, Mirna Perez-Moreno, and Birgitte Regenberg
Publicado en: Computational and Structural Biotechnology Journal, Edición Volume 21, 2023, Página(s) 4207–4214, ISSN 2001-0370
Editor: Elsevier
DOI: 10.1016/j.csbj.2023.08.027

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

Autores: 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
Publicado en: Cancers, Edición 14(5): 1195, 2022, ISSN 2072-6694
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14051195

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

Autores: Daniela Gerovska; Marcos J. Araúzo-Bravo
Publicado en: Cells, Edición Volume 12; Edición 7, 2023, Página(s) Pages: 1061, ISSN 2073-4409
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cells12071061

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

Autores: Petito V, Di Vincenzo F, Putignani L, Abreu MT, Regenberg B, Gasbarrini A, Scaldaferri F.
Publicado en: Genes, Edición Volume 15, Edición 4, 2024, Página(s) 414, ISSN 2073-4425
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes15040414

Epigenetics in the Diagnosis and Therapy of Malignant Melanoma

Autores: Simeon Santourlidis; Wolfgang A. Schulz; Marcos J. Araúzo-Bravo; Daniela Gerovska; Pauline Ott; Marcelo L. Bendhack; Mohamed Hassan; Lars Erichsen
Publicado en: International Journal of Molecular Sciences, Edición Volume 23; Edición 3, 2022, Página(s) 1531, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23031531

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

Autores: Federica Di Vincenzo; Ylenia Yadid; Valentina Petito; Valeria Emoli; Letizia Masi; Daniela Gerovska; Marcos Jesus Araúzo-Bravo; Antonio Gasbarrini; Birgitte Regenberg; Franco Scaldaferri
Publicado en: Cells, Edición Volume 12; Edición 15, 2023, Página(s) 1953, ISSN 2073-4409
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cells12151953

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

Autores: 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
Publicado en: Nature Communications, Edición 12/1, 2021, ISSN 2041-1723
Editor: 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

Autores: 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;
Publicado en: Nature Communications, Edición vol. 13 , 3620, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-31388-z

FOntCell: Fusion of Ontologies of Cells

Autores: Javier Cabau-Laporta, Alex M. Ascensión, Mikel Arrospide-Elgarresta, Daniela Gerovska, Marcos J. Araúzo-Bravo
Publicado en: Frontiers in Cell and Developmental Biology, Edición 9, 2021, ISSN 2296-634X
Editor: 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

Autores: Itziar Frades, Carles Foguet, Marta Cascante, Marcos J. Araúzo-Bravo
Publicado en: Cancers, 2021, ISSN 2072-6694
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13184609

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

Autores: Daniela Gerovska; Marcos J. Araúzo-Bravo
Publicado en: International Journal of Molecular Sciences, Edición Volume 24; Edición 3, 2023, Página(s) 2736, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24032736

Circular DNA in the human germline and its association with recombination

Autores: Rasmus Amund Henriksen, Piroon Jenjaroenpun, Ida Borup Sjøstrøm, Kristian Reveles Jensen, Iñigo Prada-Luengo, Thidathip Wongsurawat, Intawat Nookae, BirgitteRegenberg
Publicado en: Molecular Cell, Edición Volume 82, Edición 1, 6 January 2022, 2022, Página(s) Pages 209-217.e7, ISSN 1097-4164
Editor: Elsevier
DOI: 10.1016/j.molcel.2021.11.027

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

Autores: Mihailo Mirkovic; Anna Marzelliusardottir; Anne C Meinema; Théo Aspert; Sung Sik Lee; Gilles Charvin; Yves Barral
Publicado en: eLife, Edición 11, 4, 2022, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.71196

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

Autores: 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
Publicado en: Clin. Transl. Med. 2022, Edición 12:e817, 2022, ISSN 2001-1326
Editor: Wiley
DOI: 10.1002/ctm2.817

An Integrative Omics Approach Reveals Involvement of BRCA1 in Hepatic Metastatic Progression of Colorectal Cancer

Autores: Daniela Gerovska, Gorka Larrinaga, Jon Danel Solano-Iturri, Joana Márquez, Patricia García Gallastegi, Abdel-Majid Khatib, Gereon Poschmann, Kai Stühler, María Armesto, Charles H. Lawrie, Iker Badiola, Marcos J. Araúzo-Bravo
Publicado en: Cancers, Edición 12/9, 2020, Página(s) 2380, ISSN 2072-6694
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers12092380

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

Autores: Birgitte Regenberg; Julie Noer; Oskar Hørsdal; Yonglun Luo; Xi Xiang
Publicado en: Trends in Genetics, Edición Vol. 38 , no. 7 , pp. 766-781, 2022, ISSN 0168-9525
Editor: 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

Autores: Lasse Bøllehuus Hansen, Sandra Fugl Jakobsen, Egija Zole, Julie Boertmann Noer, Li Tai Fang, Sefa Alizadeh, Julia Sidenius Johansen, Marghoob Mohiyuddin, Birgitte Regenberg
Publicado en: Cancer Medicine, Edición Volume 12; Edición 17, 2023, Página(s) 17679-17691, ISSN 2045-7634
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/cam4.6385

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

Autores: Giulia I. Corsi, Kunli Qu, Ferhat Alkan, Xiaoguang Pan, Yonglun Luo, Jan Gorodkin
Publicado en: Nature Communications, Edición 13, 2022, Página(s) Article number: 3006, ISSN 2041-1723
Editor: 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

Autores: Daniela Gerovska, Patricia Garcia-Gallastegi, Olatz Crende, Joana Márquez, Gorka Larrinaga, Maite Unzurrunzaga, Marcos J. Araúzo-Bravo, Iker Badiola
Publicado en: International Journal of Molecular Sciences, Edición 22/9, 2021, Página(s) 4819, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22094819

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

Autores: 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
Publicado en: Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Edición 1868/3, 2021, Página(s) 118912, ISSN 0167-4889
Editor: 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

Autores: Gerovska D, Fernández Moreno P, Zabala A, Araúzo-Bravo MJ
Publicado en: Biomedicines, Edición Volume 12, Edición 1, 2023, Página(s) 80, ISSN 2227-9059
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/biomedicines12010080

A unifying model for extrachromosomal circular DNA load in eukaryotic cells

Autores: Gerard Arrey , Samuel T Keating , Birgitte Regenberg
Publicado en: Seminars in Cell & Developmental Biology, Edición Volume 128, August 2022, Pages 40-50, 2022, ISSN 1084-9521
Editor: Academic Press
DOI: 10.1016/j.semcdb.2022.03.002

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

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

Consistent DNA Hypomethylations in Prostate Cancer

Autores: Marcos J. Araúzo-Bravo; Lars Erichsen; Pauline Ott; Agnes Beermann; Jamal Sheikh; Daniela Gerovska; Chantelle Thimm; Marcelo L. Bendhack; Simeon Santourlidis
Publicado en: International Journal of Molecular Sciences, Edición Volume 24; Edición 1, 2023, Página(s) 386, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24010386

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

Autores: Daniela Gerovska, Julie B Noer, Yating Qin, Quratul Ain, Donjetë Januzi, Matthias Schwab, Otto W Witte, Marcos J Araúzo-Bravo, Alexandra Kretz
Publicado en: Cell & Bioscience, Edición Volume 13; Edición 1, 2023, Página(s) 170, ISSN 2045-3701
Editor: Society of Chinese Bioscientists in America
DOI: 10.1186/s13578-023-01116-1

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

Autores: 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
Publicado en: Journal of Crohn's and Colitis, Edición Volume 18, Edición supplement 1, 2024, Página(s) i375, ISSN 1876-4479
Editor: Oxford University Press
DOI: 10.1093/ecco-jcc/jjad212.0226

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