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Ketola K, Kaljunen H, Taavitsainen S, Kaarijärvi R, Järvelä E, Rodríguez-Martín B, Haase K, Woodcock DJ, Tubio J, Wedge DC, Nykter M, Bova GS. Subclone Eradication Analysis Identifies Targets for Enhanced Cancer Therapy and Reveals L1 Retrotransposition as a Dynamic Source of Cancer Heterogeneity. Cancer Res 2021; 81:4901-4909. [PMID: 34348967 PMCID: PMC9397610 DOI: 10.1158/0008-5472.can-21-0371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/03/2021] [Accepted: 08/02/2021] [Indexed: 01/07/2023]
Abstract
Treatment-eradicated cancer subclones have been reported in leukemia and have recently been detected in solid tumors. Here we introduce Differential Subclone Eradication and Resistance (DSER) analysis, a method developed to identify molecular targets for improved therapy by direct comparison of genomic features of eradicated and resistant subclones in pre- and posttreatment samples from a patient with BRCA2-deficient metastatic prostate cancer. FANCI and EYA4 were identified as candidate DNA repair-related targets for converting subclones from resistant to eradicable, and RNAi-mediated depletion of FANCI confirmed it as a potential target. The EYA4 alteration was associated with adjacent L1 transposon insertion during cancer evolution upon treatment, raising questions surrounding the role of therapy in L1 activation. Both carboplatin and enzalutamide turned on L1 transposon machinery in LNCaP and VCaP but not in PC3 and 22Rv1 prostate cancer cell lines. L1 activation in LNCaP and VCaP was inhibited by the antiretroviral drug azidothymidine. L1 activation was also detected postcastration in LuCaP 77 and LuCaP 105 xenograft models and postchemotherapy in previously published time-series transcriptomic data from SCC25 head and neck cancer cells. In conclusion, DSER provides an informative intermediate step toward effective precision cancer medicine and should be tested in future studies, especially those including dramatic but temporary metastatic tumor regression. L1 transposon activation may be a modifiable source of cancer genomic heterogeneity, suggesting the potential of leveraging newly discovered triggers and blockers of L1 activity to overcome therapy resistance. SIGNIFICANCE: Differential analysis of eradicated and resistant subclones following cancer treatment identifies that L1 activity associated with resistance is induced by current therapies and blocked by the antiretroviral drug azidothymidine.
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Affiliation(s)
- Kirsi Ketola
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.,Corresponding Authors: Kirsi Ketola, Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, Kuopio FI-70211, Finland. Phone: 358-503299984; E-mail: ; and G. S. Bova, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, PO Box 100, Tampere FI-33014, Finland. Phone: 358-502945211; E-mail:
| | - Heidi Kaljunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Roosa Kaarijärvi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Emmi Järvelä
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Bernardo Rodríguez-Martín
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Kerstin Haase
- Experimental and Clinical Research Center, Charité and the Max Delbrück Center for Molecular Medicine, Universitätsmedizin Berlin, Berlin, Germany
| | - Dan J. Woodcock
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Jose Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - David C. Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, United Kingdom
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - G. Steven Bova
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.,Corresponding Authors: Kirsi Ketola, Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, Kuopio FI-70211, Finland. Phone: 358-503299984; E-mail: ; and G. S. Bova, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, PO Box 100, Tampere FI-33014, Finland. Phone: 358-502945211; E-mail:
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3
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Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, Grossmann S, Dawson KJ, Ju YS, Iorio F, Tubio JMC, Koh CC, Georgakopoulos-Soares I, Rodríguez-Martín B, Otlu B, O'Meara S, Butler AP, Menzies A, Bhosle SG, Raine K, Jones DR, Teague JW, Beal K, Latimer C, O'Neill L, Zamora J, Anderson E, Patel N, Maddison M, Ng BL, Graham J, Garnett MJ, McDermott U, Nik-Zainal S, Campbell PJ, Stratton MR. Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis. Cell 2020; 176:1282-1294.e20. [PMID: 30849372 PMCID: PMC6424819 DOI: 10.1016/j.cell.2019.02.012] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 09/19/2018] [Accepted: 01/27/2019] [Indexed: 12/20/2022]
Abstract
Multiple signatures of somatic mutations have been identified in cancer genomes. Exome sequences of 1,001 human cancer cell lines and 577 xenografts revealed most common mutational signatures, indicating past activity of the underlying processes, usually in appropriate cancer types. To investigate ongoing patterns of mutational-signature generation, cell lines were cultured for extended periods and subsequently DNA sequenced. Signatures of discontinued exposures, including tobacco smoke and ultraviolet light, were not generated in vitro. Signatures of normal and defective DNA repair and replication continued to be generated at roughly stable mutation rates. Signatures of APOBEC cytidine deaminase DNA-editing exhibited substantial fluctuations in mutation rate over time with episodic bursts of mutations. The initiating factors for the bursts are unclear, although retrotransposon mobilization may contribute. The examined cell lines constitute a resource of live experimental models of mutational processes, which potentially retain patterns of activity and regulation operative in primary human cancers. Annotation of mutational signatures across 1,001 cancer cell lines and 577 PDXs Activities of mutational processes determined over time in cancer cell lines APOBEC-associated mutagenesis is often ongoing and can be episodic Detection of mutational signatures by single-cell sequencing
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Affiliation(s)
- Mia Petljak
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ludmil B Alexandrov
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan S Brammeld
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Stacey Price
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David C Wedge
- Oxford Big Data Institute, Old Road Campus, Oxford OX3 7LF, UK; Oxford NIHR Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - Sebastian Grossmann
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Kevin J Dawson
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Francesco Iorio
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jose M C Tubio
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Mobile Genomes and Disease, Molecular Medicine and Chronic Diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo 36310, Spain
| | - Ching Chiek Koh
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Bernardo Rodríguez-Martín
- Mobile Genomes and Disease, Molecular Medicine and Chronic Diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo 36310, Spain
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sarah O'Meara
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Adam P Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrew Menzies
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Shriram G Bhosle
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Keiran Raine
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David R Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jon W Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Kathryn Beal
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Laura O'Neill
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jorge Zamora
- Mobile Genomes and Disease, Molecular Medicine and Chronic Diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain; The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo 36310, Spain
| | - Elizabeth Anderson
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Nikita Patel
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mark Maddison
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Bee Ling Ng
- Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jennifer Graham
- Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mathew J Garnett
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ultan McDermott
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Serena Nik-Zainal
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
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Rodríguez-Martín B, Palumbo E, Marco-Sola S, Griebel T, Ribeca P, Alonso G, Rastrojo A, Aguado B, Guigó R, Djebali S. ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. BMC Genomics 2017; 18:7. [PMID: 28049418 PMCID: PMC5209911 DOI: 10.1186/s12864-016-3404-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/09/2016] [Indexed: 11/28/2022] Open
Abstract
Background Chimeric transcripts are commonly defined as transcripts linking two or more different genes in the genome, and can be explained by various biological mechanisms such as genomic rearrangement, read-through or trans-splicing, but also by technical or biological artefacts. Several studies have shown their importance in cancer, cell pluripotency and motility. Many programs have recently been developed to identify chimeras from Illumina RNA-seq data (mostly fusion genes in cancer). However outputs of different programs on the same dataset can be widely inconsistent, and tend to include many false positives. Other issues relate to simulated datasets restricted to fusion genes, real datasets with limited numbers of validated cases, result inconsistencies between simulated and real datasets, and gene rather than junction level assessment. Results Here we present ChimPipe, a modular and easy-to-use method to reliably identify fusion genes and transcription-induced chimeras from paired-end Illumina RNA-seq data. We have also produced realistic simulated datasets for three different read lengths, and enhanced two gold-standard cancer datasets by associating exact junction points to validated gene fusions. Benchmarking ChimPipe together with four other state-of-the-art tools on this data showed ChimPipe to be the top program at identifying exact junction coordinates for both kinds of datasets, and the one showing the best trade-off between sensitivity and precision. Applied to 106 ENCODE human RNA-seq datasets, ChimPipe identified 137 high confidence chimeras connecting the protein coding sequence of their parent genes. In subsequent experiments, three out of four predicted chimeras, two of which recurrently expressed in a large majority of the samples, could be validated. Cloning and sequencing of the three cases revealed several new chimeric transcript structures, 3 of which with the potential to encode a chimeric protein for which we hypothesized a new role. Applying ChimPipe to human and mouse ENCODE RNA-seq data led to the identification of 131 recurrent chimeras common to both species, and therefore potentially conserved. Conclusions ChimPipe combines discordant paired-end reads and split-reads to detect any kind of chimeras, including those originating from polymerase read-through, and shows an excellent trade-off between sensitivity and precision. The chimeras found by ChimPipe can be validated in-vitro with high accuracy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3404-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bernardo Rodríguez-Martín
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Joint IRB-BSC Program in Computational Biology, Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona, 08034, Spain
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Santiago Marco-Sola
- Centro Nacional de Análisis Genómico, Baldiri Reixac, 4, Barcelona Science Park - Tower I, Barcelona, 08028, Spain
| | - Thasso Griebel
- Centro Nacional de Análisis Genómico, Baldiri Reixac, 4, Barcelona Science Park - Tower I, Barcelona, 08028, Spain
| | - Paolo Ribeca
- Centro Nacional de Análisis Genómico, Baldiri Reixac, 4, Barcelona Science Park - Tower I, Barcelona, 08028, Spain.,Integrative Biology, The Pirbright Institute, London, GU24 0NF, UK
| | - Graciela Alonso
- Centro de Biología Molecular Severo Ochoa (CSIC - UAM), Nicolás Cabrera 1, Cantoblanco, Madrid, 28049, Spain
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa (CSIC - UAM), Nicolás Cabrera 1, Cantoblanco, Madrid, 28049, Spain
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC - UAM), Nicolás Cabrera 1, Cantoblanco, Madrid, 28049, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, 08003, Spain
| | - Sarah Djebali
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France.
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