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Rausch T, Snajder R, Leger A, Simovic M, Giurgiu M, Villacorta L, Henssen AG, Fröhling S, Stegle O, Birney E, Bonder MJ, Ernst A, Korbel JO. Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures. CELL GENOMICS 2023; 3:100281. [PMID: 37082141 PMCID: PMC10112291 DOI: 10.1016/j.xgen.2023.100281] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/14/2022] [Accepted: 02/22/2023] [Indexed: 04/22/2023]
Abstract
Cancer genomes harbor a broad spectrum of structural variants (SVs) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assembled complex rearrangements, including a 1.55-Mbp chromothripsis event, and we uncover a complex SV pattern termed templated insertion (TI) thread, characterized by short (mostly <1 kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50 kbp in size. TI threads occur in 3% of cancers, with a prevalence up to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read-based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in cancer-driver genes. Our study shows the advantage of long-read sequencing in the discovery and characterization of complex somatic rearrangements.
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Affiliation(s)
- Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), GeneCore, Heidelberg, Germany
| | - Rene Snajder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty for Biosciences, Heidelberg University, Heidelberg, Germany
- HIDSS4Health, Helmholtz Information and Data Science School for Health, Heidelberg, Germany
| | - Adrien Leger
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Milena Simovic
- Group “Genome Instability in Tumors,” German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mădălina Giurgiu
- Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité-Universitätsmedizin, Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Laura Villacorta
- European Molecular Biology Laboratory (EMBL), GeneCore, Heidelberg, Germany
| | - Anton G. Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité-Universitätsmedizin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Fröhling
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Ewan Birney
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Marc Jan Bonder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aurelie Ernst
- Group “Genome Instability in Tumors,” German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan O. Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Bridging Research Division on Mechanisms of Genomic Variation and Data Science, DKFZ, Heidelberg, Germany
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Kiseleva V, Gordon K, Vishnyakova P, Gantsova E, Elchaninov A, Fatkhudinov T. Particle Therapy: Clinical Applications and Biological Effects. Life (Basel) 2022; 12:2071. [PMID: 36556436 PMCID: PMC9785772 DOI: 10.3390/life12122071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Particle therapy is a developing area of radiotherapy, mostly involving the use of protons, neutrons and carbon ions for cancer treatment. The reduction of side effects on healthy tissues in the peritumoral area is an important advantage of particle therapy. In this review, we analyze state-of-the-art particle therapy, as compared to conventional photon therapy, to identify clinical benefits and specify the mechanisms of action on tumor cells. Systematization of published data on particle therapy confirms its successful application in a wide range of cancers and reveals a variety of biological effects which manifest at the molecular level and produce the particle therapy-specific molecular signatures. Given the rapid progress in the field, the use of particle therapy holds great promise for the near future.
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Affiliation(s)
- Viktoriia Kiseleva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 117198 Moscow, Russia
| | - Konstantin Gordon
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
- A. Tsyb Medical Radiological Research Center, 249031 Obninsk, Russia
| | - Polina Vishnyakova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 117198 Moscow, Russia
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Elena Gantsova
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Andrey Elchaninov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 117198 Moscow, Russia
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
- A.P. Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution “Petrovsky National Research Centre of Surgery”, 117418 Moscow, Russia
| | - Timur Fatkhudinov
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
- A.P. Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution “Petrovsky National Research Centre of Surgery”, 117418 Moscow, Russia
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Utilizing Carbon Ions to Treat Medulloblastomas that Exhibit Chromothripsis. CURRENT STEM CELL REPORTS 2022. [DOI: 10.1007/s40778-022-00213-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Abstract
Purpose of Review
Novel radiation therapies with accelerated charged particles such as protons and carbon ions have shown encouraging results in oncology. We present recent applications as well as benefits and risks associated with their use.
Recent Findings
We discuss the use of carbon ion radiotherapy to treat a specific type of aggressive pediatric brain tumors, namely medulloblastomas with chromothripsis. Potential reasons for the resistance to conventional treatment, such as the presence of cancer stem cells with unique properties, are highlighted. Finally, advantages of particle radiation alone and in combination with other therapies to overcome resistance are featured.
Summary
Provided that future preclinical studies confirm the evidence of high effectiveness, favorable toxicity profiles, and no increased risk of secondary malignancy, carbon ion therapy may offer a promising tool in pediatric (neuro)oncology and beyond.
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Khalid U, Simovic M, Hammann LA, Iskar M, Kl Wong J, Kumar R, Jugold M, Sill M, Bolkestein M, Kolb T, Hergt M, Devens F, Ecker J, Kool M, Milde T, Westermann F, Benner A, Lewis J, Dietrich S, Pfister SM, Lichter P, Zapatka M, Ernst A. A synergistic interaction between HDAC- and PARP inhibitors in childhood tumors with chromothripsis. Int J Cancer 2022; 151:590-606. [PMID: 35411591 DOI: 10.1002/ijc.34027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/15/2021] [Accepted: 01/25/2022] [Indexed: 11/06/2022]
Abstract
Chromothripsis is a form of genomic instability characterized by the occurrence of tens to hundreds of clustered DNA double-strand breaks in a one-off catastrophic event. Rearrangements associated with chromothripsis are detectable in numerous tumor entities and linked with poor prognosis in some of these, such as Sonic Hedgehog medulloblastoma, neuroblastoma and osteosarcoma. Hence, there is a need for therapeutic strategies eliminating tumor cells with chromothripsis. Defects in DNA double-strand break repair, and in particular homologous recombination repair, have been linked with chromothripsis. Targeting DNA repair deficiencies by synthetic lethality approaches, we performed a synergy screen using drug libraries (n = 375 compounds, 15 models) combined with either a PARP inhibitor or cisplatin. This revealed a synergistic interaction between the HDAC inhibitor romidepsin and PARP inhibition. Functional assays, transcriptome analyses, and in vivo validation in patient-derived xenograft mouse models confirmed the efficacy of the combinatorial treatment.
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Affiliation(s)
- Umar Khalid
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,University of Heidelberg, Germany
| | - Milena Simovic
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,University of Heidelberg, Germany
| | - Linda A Hammann
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,University of Heidelberg, Germany
| | - Murat Iskar
- Division of Molecular Genetics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John Kl Wong
- Division of Molecular Genetics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rithu Kumar
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manfred Jugold
- Core Facility, Small Animal Imaging Center, DKFZ, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michiel Bolkestein
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thorsten Kolb
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michaela Hergt
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frauke Devens
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany; KiTZ Clinical Trial Unit.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joe Lewis
- European Molecular Biology Laboratory
| | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aurélie Ernst
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
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