Publications that have received funding from the CIRCULAR VISION project is marked with ★

Published in 2020

Gerovska D, Larrinaga G, Solano-Iturri JD, Márquez J, García Gallastegi P, Khatib AM, Poschmann G, Stühler K, Armesto M, Lawrie CH, Badiola I, Araúzo-Bravo MJ. An Integrative Omics Approach Reveals Involvement of BRCA1 in Hepatic Metastatic Progression of Colorectal Cancer. Cancers (Basel). 2020 Aug 22;12(9):2380. doi: 10.3390/cancers12092380. PMID: 32842712; PMCID: PMC7565528.

Published in 2021

Hernandez LI, Araúzo-Bravo MJ, Gerovska D, Solaun RR, Machado I, Balian A, Botero J, Jiménez T, Zuriarrain Bergara O, Larburu Gurruchaga L, Urruticoechea A, Hernandez FJ. Discovery and Proof-of-Concept Study of Nuclease Activity as a Novel Biomarker for Breast Cancer Tumors. Cancers (Basel). 2021 Jan 13;13(2):276. doi: 10.3390/cancers13020276. PMID: 33451046; PMCID: PMC7828568.

★ Cabau-Laporta J, Ascensión AM, Arrospide-Elgarresta M, Gerovska D, Araúzo-Bravo MJ. FOntCell: Fusion of Ontologies of Cells. Front Cell Dev Biol. 2021 Feb 11;9:562908. doi: 10.3389/fcell.2021.562908. PMID: 33644039; PMCID: PMC7905052.

★ Gerovska D, García-Gallastegi P, Descarpentrie J, Crende O, Casado-Andrés M, Martín A, Eguia J, Khatib AM, Araúzo-Bravo MJ, Badiola I. Proprotein convertases blockage up-regulates specifically metallothioneins coding genes in human colon cancer stem cells. Biochim Biophys Acta Mol Cell Res. 2021 Mar;1868(3):118912. doi: 10.1016/j.bbamcr.2020.118912. Epub 2020 Nov 26. PMID: 33249002.

★ Gerovska D, Garcia-Gallastegi P, Crende O, Márquez J, Larrinaga G, Unzurrunzaga M, Araúzo-Bravo MJ, Badiola I. GeromiRs Are Downregulated in the Tumor Microenvironment during Colon Cancer Colonization of the Liver in a Murine Metastasis Model. Int J Mol Sci. 2021 May 1;22(9):4819. doi: 10.3390/ijms22094819. PMID: 34062897; PMCID: PMC8124834.

★ Xiang X, Corsi GI, Anthon C, Qu K, Pan X, Liang X, Han P, Dong Z, Liu L, Zhong J, Ma T, Wang J, Zhang X, Jiang H, Xu F, Liu X, Xu X, Wang J, Yang H, Bolund L, Church GM, Lin L, Gorodkin J, Luo Y. Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning. Nature Communications. 2021 May 28;12(1):3238. doi: 10.1038/s41467-021-23576-0. PMID: 34050182; PMCID: PMC8163799. Yonglun is the senior and corresponding author of the study.

★ Frades I, Foguet C, Cascante M, Araúzo-Bravo MJ. Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment. Cancers (Basel). 2021 Sep 14;13(18):4609. doi: 10.3390/cancers13184609. PMID: 34572839; PMCID: PMC8470216.

Published in 2022

★ Henriksen R.A., Jenjaroenpun P., Sjøstrøm I.B., Jensen K.R., Prada-Luengo I., Wongsurawat T., Nookaew I., Regenberg B.* (2021) Circular DNA in the human germline and its association with recombination. Molecular Cell. 82 (1):209- 217.e7, doi: 10.1016/j.molcel.2021.11.027. IF: 19.3

★ Santourlidis S, Schulz WA, Araúzo-Bravo MJ, Gerovska D, Ott P, Bendhack ML, Hassan M, Erichsen L. Epigenetics in the Diagnosis and Therapy of Malignant Melanoma. Int J Mol Sci. 2022 Jan 28;23(3):1531. doi: 10.3390/ijms23031531. PMID: 35163453; PMCID: PMC8835790.

★ Descarpentrie J, Araúzo-Bravo MJ, He Z, François A, González Á, Garcia-Gallastegi P, Badiola I, Evrard S, Pernot S, Creemers JWM, Khatib AM. Role of Furin in Colon Cancer Stem Cells Malignant Phenotype and Expression of LGR5 and NANOG in KRAS and BRAF-Mutated Colon Tumors. Cancers (Basel). 2022 Feb 25;14(5):1195. doi: 10.3390/cancers14051195. PMID: 35267511; PMCID: PMC8909039.

Ascensión AM, Araúzo-Bravo MJ, Izeta A. The need to reassess single-cell RNA sequencing datasets: the importance of biological sample processing. F1000Res. 2022 Mar 8;10:767. doi: 10.12688/f1000research.54864.2. PMCID: PMC8984215.

★ Noer JB, Hørsdal OK, Xiang X, Luo Y, Regenberg B. Extrachromosomal circular DNA in cancer: history, current knowledge, and methods. Trends Genet. 2022 Jul;38(7):766-781. doi: 10.1016/j.tig.2022.02.007. Epub 2022 Mar 8. PMID: 35277298. AU and UCPH are joint corresponding for the publication.

★ Anne C. Meinema, Anna Marzelliusardottir, Mihailo Mirkovic, Theo Aspert, Sung Sik Lee, Gilles Charvin, Yves Barral (2022). DNA circles promote yeast ageing in part through stimulating the reorganization of nuclear pore complexes. Elife. 2022 Apr 4;11:e71196.

★ 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. (2022) Circle-Seq Reveals Genomic and Disease Specific Hallmarks in Urinary Cell Free eccDNAs. Clin Transl Med. 2022 Apr;12(4):e817. doi: 10.1002/ctm2.817. AU and UCPH collaborate on conducting this study.

★ Corsi GI, Qu K, Alkan F, Pan X, Luo Y, Gorodkin J. CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context. Nat Commun. 2022 May 30;13(1):3006. doi: 10.1038/s41467-022-30515-0. PMID: 35637227; PMCID: PMC9151727.

Ascension AM, Arauzo-Bravo MJ. BigMPI4py: Python Module for Parallelization of Big Data Objects Discloses Germ Layer Specific DNA Demethylation Motifs. IEEE/ACM Trans Comput Biol Bioinform. 2022 MayJun;19(3):1507-1522. doi: 10.1109/TCBB.2020.3043979. Epub 2022 Jun 3. PMID: 33301409.

★ Feng W, Arrey G, Zole E, Lv W, Liang X, Han P, Mohiyuddin M, Pilegaard H, Regenberg B. Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas9. Comput Struct Biotechnol J. 2022 Jun 15;20:3059-3067.

★ Wang F, Ding P, Liang X, Ding X, Brandt CB, Sjöstedt E, Zhu J, Bolund S, Zhang L, de Rooij LPMH, Luo L, Wei Y, Zhao W, Lv Z, Haskó J, Li R, Qin Q, Jia Y, Wu W, Yuan Y, Pu M, Wang H, Wu A, Xie L, Liu P, Chen F, Herold J, Kalucka J, Karlsson M, Zhang X, Helmig RB, Fagerberg L, Lindskog C, Pontén F, Uhlen M, Bolund L, Jessen N, Jiang H, Xu X, Yang H, Carmeliet P, Mulder J, Chen D, Lin L, Luo Y. Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level. Nat Commun. 2022 Jun 24;13(1):3620. doi: 10.1038/s41467-022-31388-z. Erratum in: Nat Commun. 2022 Nov 8;13(1):6748. PMID: 35750885; PMCID: PMC9232580.

★ Arrey G., Keating S. and Regenberg B.* (2022) A unifying model for extrachromosomal circular DNA load in eukaryotic cells. Seminars in Cell and Developmental Biology. https://doi.org/10.1016/j.semcdb.2022.03.002. IF: 7.7

Ott P, Araúzo-Bravo MJ, Hoffmann MJ, Poyet C, Bendhack ML, Santourlidis S, Erichsen L. Differential DNA Methylation of THOR and hTAPAS in the Regulation of hTERT and the Diagnosis of Cancer. Cancers (Basel). 2022 Sep 8;14(18):4384. doi: 10.3390/cancers14184384. PMID: 36139544; PMCID: PMC9497117.

★ Wanchai V, Jenjaroenpun P, Leangapichart T, Arrey G, Burnham CM, Tümmler MC, Delgado-Calle J, Regenberg B, Nookaew I. CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences. Brief Bioinform. 2022 Oct 4:bbac422. doi: 10.1093/bib/bbac422. Epub ahead of print. PMID: 36198068.

★ Araúzo-Bravo MJ, Erichsen L, Ott P, Beermann A, Sheikh J, Gerovska D, Thimm C, Bendhack ML, Santourlidis S. Consistent DNA Hypomethylations in Prostate Cancer. Int J Mol Sci. 2022 Dec 26;24(1):386. doi: 10.3390/ijms24010386. PMID: 36613831; PMCID: PMC9820221.

Published in 2023

★ Gerovska D, Araúzo-Bravo MJ. Skeletal Muscles of Sedentary and Physically Active Aged People Have Distinctive Genic Extrachromosomal Circular DNA Profiles. Int J Mol Sci. 2023 Feb 1;24(3):2736. doi: 10.3390/ijms24032736. PMID: 36769072; PMCID: PMC9917053.

★ Gerovska D, Araúzo-Bravo MJ. Systemic Lupus Erythematosus Patients with DNASE1L3·Deficiency Have a Distinctive and Specific Genic Circular DNA Profile in Plasma. Cells. 2023 Mar 31;12(7):1061. doi: 10.3390/cells12071061. PMID: 37048133; PMCID: PMC10093232.

Holt S, Arrey G, Regenberg B. Did circular DNA shape the evolution of mammalian genomes? Trends Biochem Sci. 2023 Apr;48(4):317-320. doi: 10.1016/j.tibs.2022.09.010. Epub 2022 Oct 21. PMID: 36280496.

★ Di Vincenzo F, Yadid Y, Petito V, Emoli V, Masi L, Gerovska D, Araúzo-Bravo MJ, Gasbarrini A, Regenberg B, Scaldaferri F. Circular and Circulating DNA in Inflammatory Bowel Disease: From Pathogenesis to Potential Molecular Therapies. Cells. 2023 Jul 27;12(15):1953. doi: 10.3390/cells12151953. PMID: 37566032; PMCID: PMC10417561.

★ Dos Santos CR, Hansen LB, Rojas-Triana M, Johansen AZ, Perez-Moreno M, Regenberg B. Variation of extrachromosomal circular DNA in cancer cell lines. Comput Struct Biotechnol J. 2023 Aug 28;21:4207-4214. doi: 10.1016/j.csbj.2023.08.027. PMID: 37705597; PMCID: PMC10495552.

Fiévet L, Espagnolle N, Gerovska D, Bernard D, Syrykh C, Laurent C, Layrolle P, De Lima J, Justo A, Reina N, Casteilla L, Araúzo-Bravo MJ, Naji A, Pagès JC, Deschaseaux F. Single-cell RNA sequencing of human non-hematopoietic bone marrow cells reveals a unique set of inter-species conserved biomarkers for native mesenchymal stromal cells. Stem Cell Res Ther. 2023 Aug 30;14(1):229. doi: 10.1186/s13287-023-03437-x. PMID: 37649081; PMCID: PMC10469496.

★ Bøllehuus Hansen L, Jakobsen SF, Zole E, Noer JB, Fang LT, Alizadeh S, Johansen JS, Mohiyuddin M, Regenberg B. Methods for the purification and detection of single nucleotide KRAS mutations on extrachromosomal circular DNA in human plasma. Cancer Med. 2023 Sep;12(17):17679-17691. doi: 10.1002/cam4.6385. Epub 2023 Aug 21. PMID: 37602814; PMCID: PMC10523981.

★ Gerovska D, Noer JB, Qin Y, Ain Q, Januzi D, Schwab M, Witte OW, Araúzo-Bravo MJ, Kretz A. A distinct circular DNA profile intersects with proteome changes in the genotoxic stress-related hSOD1G93A model of ALS. Cell Biosci. 2023 Sep 13;13(1):170. doi: 10.1186/s13578-023-01116-1. PMID: 37705092; PMCID: PMC10498603.

★ Gerovska D, Fernández Moreno P, Zabala A, Araúzo-Bravo MJ. Cell-Free Genic Extrachromosomal Circular DNA Profiles of DNase Knockouts Associated with Systemic Lupus Erythematosus and Relation with Common Fragile Sites. Biomedicines. 2023 Dec 28;12(1):80. doi: 10.3390/biomedicines12010080. PMID: 38255187; PMCID: PMC10813657.

Published in 2024

★ Petito V, Di Vincenzo F, Putignani L, Abreu MT, Regenberg B, Gasbarrini A, Scaldaferri F. Extrachromosomal Circular DNA: An Emerging Potential Biomarker for Inflammatory Bowel Diseases? Genes (Basel). 2024 Mar 26;15(4):414. doi: 10.3390/genes15040414. PMID: 38674347; PMCID: PMC11049804.