Mădălina Giurgiu
PhD student Mădălina holds a B.Sc. and M.Sc. Bioinformatics degree from Technical University Munich and Ludwig-Maximilians University of Munich. She also holds a B.Eng. Computer Science degree from University “Politehnica” Timisoara, Romania. She worked on developing diagnostics pipelines, with focus on detection of tandem-repeats from nanopore long-read sequencing data, in the R&D department of the […]
Lotte Brückner
PhD student She did her bachelor and master’s in biomedical science at the University of York in the United Kingdom. Her master thesis focused on the role of ion channels in breast cancer metastasis. Lotte joined the lab in January 2021 as a PhD student to study the causes and consequences of the micronucleation of […]
Micronuclear ecDNA constrains tumor cell fitness and is associated with favorable patient survival
Brückner L, Xu R, Tang J, Gnanasekar A, Herrmann A, Tsz-Lo Wong I, Zhang S, Tu F, Pilon M, Kukalev A, Pardon K, Sidorova O, Atta J, Yu Q, Montouri G, Pradella D, Ilić M, Suina K, Novais-Cruz M, Kaltenbach S, Treue D, Giurgiu-Kraljič M, Herzog S, Hollinger A, Wittstruck N, Fernandez M, Wolozyn N, Becker F, Louma V, Yan X, Schmargon R, Dörr J, Gamlin D, Lehmann A, Gürgen D, Richter M, Dubois F, Simeoni F, Pennycook BR, Hamilton A, Lindemann RK, Dawes C, Balmus G, Hero B, Fischer M, Bafna V, Verhaak R, Wahl G, Liu Y, Koche RP, Papathanasiou S, Medema R, Spanjaard […]
Extrachromosomal DNA–Driven Oncogene Dosage Heterogeneity Promotes Rapid Adaptation to Therapy in MYCN-Amplified Cancers
Montuori G, Tu F, Qin D, Schmargon R, Rodriguez-Fos E, Helmsauer K, Hui H, Mandal S, Purshouse K, Fankhänel L, Bosco B, Spanjaard B, Seyboldt H, Grunewald L, Schmitt M, Gürgen D, Buck V, Rosenfeldt M, Dubois FPB, Schallenberg S, Lehmann A, Theißen J, Taschner-Mandl S, Koch A, Hundsdoerfer P, Künkele A, Eggert A, Fischer […]
Passenger Gene Coamplifications Create Collateral Therapeutic Vulnerabilities in Cancer
Bei Y, Bramé L, Kirchner M, Fritsche-Guenther R, Kunz S, Bhattacharya A, Rusu M, Gürgen D, Dubios FPB, Köppke JKC, Proba J, Wittstruck N, Sidorova OA, Chamorro González R, Dorado Garcia H, Brückner L, Xu R, Giurgiu M, Rodriguez-Fos E, Yu Q, Spanjaard B, Koche RP, Schmitt CA, Schulte JH, Eggert A, Haase K, Kirwan […]
Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil
Giurgiu M, Wittstruck N, Rodriguez-Fos E, Chamorro González R, Brückner L, Krienelke-Szymansky A, Helmsauer K, Hartebrodt A, Euskirchen P, Koche RP, Haase K, Reinert K, Henssen AG Genome Research (2024), Vol. 34 Issue 9, 1355-1364 https://genome.cshlp.org/content/34/9/1355
Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells
Chamorro González R, Conrad T, Stöber MC, Xu R, Giurgiu M, Rodriguez-Fos M, Kasack K, Brückner L, van Leen E, Helmsauer K, Dorado Garcia H, Stefanova ME, Hung KL, Bei Y, Schmelz K, Lodrini M, Mundlos S, Chang HY, Deubzer HE, Sauer S, Eggert A, Schulte JH, Schwarz RF, Haase K, Koche RP, Henssen AG […]
Method development
ecDNA is small and heavily rearranged, and existing methods are not sufficient to characterize it. We have therefore developed our own: scEC&T-seq, an experimental and computational technique that profiles the transcriptome and ecDNA sequence of single cells (Chamorro González et al., Nat. Genetics, 2023), and Decoil, a purely computational technique that reconstructs ecDNA structure from […]
Understanding ecDNA maintenance and transcription
It is remarkable that cancer cells can maintain and transcribe ecDNA, which is non-chromosomal, circular and does not have centromeres. We hypothesize that specific processes are necessary for ecDNA maintenance and transcription, and that disrupting them can cause loss of ecDNA-based transcripts and lead to cell death of ecDNA-positive tumor cells specifically. Together with the […]
Mechanisms and consequences of ecDNA evolution
ecDNA functions as an evolutionary hotspot, allowing cancers to escape therapy after an initially promising response. We have shown that ecDNA in neuroblastoma is a major source of somatic rearrangements, leading to further circularization or to the reintegration of circular DNA into the linear genome (Koche et al., Nat. Genetics, 2020). In collaboration with the […]