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Rouhani FJ, Zou X, Danecek P, Badja C, Amarante TD, Koh G, Wu Q, Memari Y, Durbin R, Martincorena I, Bassett AR, Gaffney D, Nik-Zainal S. Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells. Nat Genet 2022; 54:1406-1416. [PMID: 35953586 PMCID: PMC9470532 DOI: 10.1038/s41588-022-01147-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/24/2022] [Indexed: 12/27/2022]
Abstract
We explored human induced pluripotent stem cells (hiPSCs) derived from different tissues to gain insights into genomic integrity at single-nucleotide resolution. We used genome sequencing data from two large hiPSC repositories involving 696 hiPSCs and daughter subclones. We find ultraviolet light (UV)-related damage in ~72% of skin fibroblast-derived hiPSCs (F-hiPSCs), occasionally resulting in substantial mutagenesis (up to 15 mutations per megabase). We demonstrate remarkable genomic heterogeneity between independent F-hiPSC clones derived during the same round of reprogramming due to oligoclonal fibroblast populations. In contrast, blood-derived hiPSCs (B-hiPSCs) had fewer mutations and no UV damage but a high prevalence of acquired BCOR mutations (26.9% of lines). We reveal strong selection pressure for BCOR mutations in F-hiPSCs and B-hiPSCs and provide evidence that they arise in vitro. Directed differentiation of hiPSCs and RNA sequencing showed that BCOR mutations have functional consequences. Our work strongly suggests that detailed nucleotide-resolution characterization is essential before using hiPSCs.
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Affiliation(s)
- Foad J Rouhani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Xueqing Zou
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cherif Badja
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Tauanne Dias Amarante
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Gene Koh
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Qianxin Wu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yasin Memari
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Inigo Martincorena
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andrew R Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Daniel Gaffney
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genomics plc, King Charles House, Oxford, UK
| | - Serena Nik-Zainal
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
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Degasperi A, Zou X, Amarante TD, Martinez-Martinez A, Koh GCC, Dias JML, Heskin L, Chmelova L, Rinaldi G, Wang VYW, Nanda AS, Bernstein A, Momen SE, Young J, Perez-Gil D, Memari Y, Badja C, Shooter S, Czarnecki J, Brown MA, Davies HR, Nik-Zainal S. Substitution mutational signatures in whole-genome-sequenced cancers in the UK population. Science 2022; 376:science.abl9283. [PMID: 35949260 PMCID: PMC7613262 DOI: 10.1126/science.abl9283] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Whole-genome sequencing (WGS) permits comprehensive cancer genome analyses, revealing mutational signatures, imprints of DNA damage and repair processes that have arisen in each patient's cancer. We performed mutational signature analyses on 12,222 WGS tumor-normal matched pairs, from patients recruited via the UK National Health Service. We contrasted our results to two independent cancer WGS datasets, the International Cancer Genome Consortium (ICGC) and Hartwig Foundation, involving 18,640 WGS cancers in total. Our analyses add 40 single and 18 double substitution signatures to the current mutational signature tally. Critically, we show for each organ, that cancers have a limited number of 'common' signatures and a long tail of 'rare' signatures. We provide a practical solution for utilizing this concept of common versus rare signatures in future analyses.
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Affiliation(s)
- Andrea Degasperi
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Xueqing Zou
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Tauanne Dias Amarante
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Andrea Martinez-Martinez
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Gene Ching Chiek Koh
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - João M. L. Dias
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Laura Heskin
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Lucia Chmelova
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Giuseppe Rinaldi
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Valerie Ya Wen Wang
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Arjun S. Nanda
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Aaron Bernstein
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Sophie E. Momen
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Jamie Young
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Daniel Perez-Gil
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Yasin Memari
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Cherif Badja
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Scott Shooter
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Jan Czarnecki
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Matthew A. Brown
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK
- Faculty of Life Sciences and Medicine, King’s College London, London SE19RT, UK
| | - Helen R. Davies
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
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Zou X, Koh GCC, Nanda AS, Degasperi A, Urgo K, Roumeliotis TI, Agu CA, Badja C, Momen S, Young J, Amarante TD, Side L, Brice G, Perez-Alonso V, Rueda D, Gomez C, Bushell W, Harris R, Choudhary JS, Jiricny J, Skarnes WC, Nik-Zainal S. A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage. Nat Cancer 2021; 2:643-657. [PMID: 34164627 PMCID: PMC7611045 DOI: 10.1038/s43018-021-00200-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023]
Abstract
Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. We generated isogenic CRISPR-Cas9 knockouts (Δ) of 43 genes in human induced pluripotent stem cells, cultured them in the absence of added DNA damage, and performed whole-genome sequencing of 173 subclones. ΔOGG1, ΔUNG, ΔEXO1, ΔRNF168, ΔMLH1, ΔMSH2, ΔMSH6, ΔPMS1, and ΔPMS2 produced marked mutational signatures indicative of being critical mitigators of endogenous DNA modifications. Detailed analyses revealed mutational mechanistic insights, including how 8-oxo-dG elimination is sequence-context-specific while uracil clearance is sequence-context-independent. Mismatch repair (MMR) deficiency signatures are engendered by oxidative damage (C>A transversions), differential misincorporation by replicative polymerases (T>C and C>T transitions), and we propose a 'reverse template slippage' model for T>A transversions. ΔMLH1, ΔMSH6, and ΔMSH2 signatures were similar to each other but distinct from ΔPMS2. Finally, we developed a classifier, MMRDetect, where application to 7,695 WGS cancers showed enhanced detection of MMR-deficient tumors, with implications for responsiveness to immunotherapies.
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Affiliation(s)
- Xueqing Zou
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Gene Ching Chiek Koh
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Arjun Scott Nanda
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Andrea Degasperi
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Cherif Badja
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Sophie Momen
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Jamie Young
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Tauanne Dias Amarante
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Lucy Side
- UCL Institute for Women's Health, Great Ormond Street Hospital, London, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Glen Brice
- Southwest Thames Regional Genetics Service, St George's University of London, London, UK
| | - Vanesa Perez-Alonso
- Pediatrics Department, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain
| | - Daniel Rueda
- Hereditary Cancer Laboratory, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain
| | | | | | - Rebecca Harris
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Jyoti S Choudhary
- The Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Josef Jiricny
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - William C Skarnes
- Wellcome Sanger Institute, Hinxton, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- MRC Cancer Unit, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
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4
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Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G, Momen SE, Georgakopoulos-Soares I, Dias JML, Young J, Memari Y, Davies H, Nik-Zainal S. Author Correction: A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies. Nat Cancer 2020; 1:748. [PMID: 35122044 DOI: 10.1038/s43018-020-0093-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Andrea Degasperi
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tauanne Dias Amarante
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan Czarnecki
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Scott Shooter
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xueqing Zou
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dominik Glodzik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Clinical Sciences, Lund University, Lund, Sweden
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sandro Morganella
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Congenica Ltd, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Arjun S Nanda
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Cherif Badja
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gene Koh
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sophie E Momen
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | | | - João M L Dias
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Jamie Young
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yasin Memari
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Helen Davies
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Serena Nik-Zainal
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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5
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Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G, Momen SE, Georgakopoulos-Soares I, Dias JML, Young J, Memari Y, Davies H, Nik-Zainal S. A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies. Nat Cancer 2020; 1:249-263. [PMID: 32118208 PMCID: PMC7048622 DOI: 10.1038/s43018-020-0027-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
Abstract
Mutational signatures are patterns of mutations that arise during tumorigenesis. We present an enhanced, practical framework for mutational signature analyses. Applying these methods on 3,107 whole genome sequenced (WGS) primary cancers of 21 organs reveals known signatures and nine previously undescribed rearrangement signatures. We highlight inter-organ variability of signatures and present a way of visualizing that diversity, reinforcing our findings in an independent analysis of 3,096 WGS metastatic cancers. Signatures with a high level of genomic instability are dependent on TP53 dysregulation. We illustrate how uncertainty in mutational signature identification and assignment to samples affects tumor classification, reinforcing that using multiple orthogonal mutational signature data is not only beneficial, it is essential for accurate tumor stratification. Finally, we present a reference web-based tool for cancer and experimentally-generated mutational signatures, called Signal (https://signal.mutationalsignatures.com), that also supports performing mutational signature analyses.
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Affiliation(s)
- Andrea Degasperi
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tauanne Dias Amarante
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan Czarnecki
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Scott Shooter
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xueqing Zou
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dominik Glodzik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Clinical Sciences, Lund University, Lund, Sweden
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sandro Morganella
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Congenica Ltd, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Arjun S Nanda
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Cherif Badja
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gene Koh
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sophie E Momen
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | | | - João M L Dias
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Jamie Young
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yasin Memari
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Helen Davies
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Serena Nik-Zainal
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
- Academic Laboratory of Medical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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6
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Staaf J, Glodzik D, Bosch A, Vallon-Christersson J, Reuterswärd C, Häkkinen J, Degasperi A, Amarante TD, Saal LH, Hegardt C, Stobart H, Ehinger A, Larsson C, Rydén L, Loman N, Malmberg M, Kvist A, Ehrencrona H, Davies HR, Borg Å, Nik-Zainal S. Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study. Nat Med 2019; 25:1526-1533. [PMID: 31570822 PMCID: PMC6859071 DOI: 10.1038/s41591-019-0582-4] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/15/2019] [Indexed: 01/12/2023]
Abstract
Whole-genome sequencing (WGS) brings comprehensive insights to cancer genome interpretation. To explore the clinical value of WGS, we sequenced 254 triple-negative breast cancers (TNBCs) for which associated treatment and outcome data were collected between 2010 and 2015 via the population-based Sweden Cancerome Analysis Network-Breast (SCAN-B) project (ClinicalTrials.gov ID:NCT02306096). Applying the HRDetect mutational-signature-based algorithm to classify tumors, 59% were predicted to have homologous-recombination-repair deficiency (HRDetect-high): 67% explained by germline/somatic mutations of BRCA1/BRCA2, BRCA1 promoter hypermethylation, RAD51C hypermethylation or biallelic loss of PALB2. A novel mechanism of BRCA1 abrogation was discovered via germline SINE-VNTR-Alu retrotransposition. HRDetect provided independent prognostic information, with HRDetect-high patients having better outcome on adjuvant chemotherapy for invasive disease-free survival (hazard ratio (HR) = 0.42; 95% confidence interval (CI) = 0.2-0.87) and distant relapse-free interval (HR = 0.31, CI = 0.13-0.76) compared to HRDetect-low, regardless of whether a genetic/epigenetic cause was identified. HRDetect-intermediate, some possessing potentially targetable biological abnormalities, had the poorest outcomes. HRDetect-low cancers also had inadequate outcomes: ~4.7% were mismatch-repair-deficient (another targetable defect, not typically sought) and they were enriched for (but not restricted to) PIK3CA/AKT1 pathway abnormalities. New treatment options need to be considered for now-discernible HRDetect-intermediate and HRDetect-low categories. This population-based study advocates for WGS of TNBC to better inform trial stratification and improve clinical decision-making.
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Affiliation(s)
- Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.
| | - Dominik Glodzik
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ana Bosch
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Christel Reuterswärd
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Andrea Degasperi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Tauanne Dias Amarante
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Lao H Saal
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | | | - Anna Ehinger
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Clinical Genetics and Pathology, Department of Laboratory Medicine, Office for Medical Services, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Niklas Loman
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics and Pathology, Department of Laboratory Medicine, Office for Medical Services, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Helen R Davies
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK.
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
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De Mattos-Arruda L, Sammut SJ, Ross EM, Bashford-Rogers R, Greenstein E, Markus H, Morganella S, Teng Y, Maruvka Y, Pereira B, Rueda OM, Chin SF, Contente-Cuomo T, Mayor R, Arias A, Ali HR, Cope W, Tiezzi D, Dariush A, Dias Amarante T, Reshef D, Ciriaco N, Martinez-Saez E, Peg V, Ramon Y Cajal S, Cortes J, Vassiliou G, Getz G, Nik-Zainal S, Murtaza M, Friedman N, Markowetz F, Seoane J, Caldas C. The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer. Cell Rep 2019; 27:2690-2708.e10. [PMID: 31141692 PMCID: PMC6546974 DOI: 10.1016/j.celrep.2019.04.098] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 12/13/2018] [Accepted: 04/22/2019] [Indexed: 02/07/2023] Open
Abstract
The detailed molecular characterization of lethal cancers is a prerequisite to understanding resistance to therapy and escape from cancer immunoediting. We performed extensive multi-platform profiling of multi-regional metastases in autopsies from 10 patients with therapy-resistant breast cancer. The integrated genomic and immune landscapes show that metastases propagate and evolve as communities of clones, reveal their predicted neo-antigen landscapes, and show that they can accumulate HLA loss of heterozygosity (LOH). The data further identify variable tumor microenvironments and reveal, through analyses of T cell receptor repertoires, that adaptive immune responses appear to co-evolve with the metastatic genomes. These findings reveal in fine detail the landscapes of lethal metastatic breast cancer.
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Affiliation(s)
- Leticia De Mattos-Arruda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain
| | - Stephen-John Sammut
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Edith M Ross
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Erez Greenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Havell Markus
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Mayo Clinic Center for Individualized Medicine, Scottsdale, AZ, USA
| | - Sandro Morganella
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yvonne Teng
- Cancer Molecular Diagnosis Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Yosef Maruvka
- The Broad Institute, Cambridge, MA 02142, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Charlestown, MA 02129, USA
| | - Bernard Pereira
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Oscar M Rueda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Tania Contente-Cuomo
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Mayo Clinic Center for Individualized Medicine, Scottsdale, AZ, USA
| | - Regina Mayor
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - Alexandra Arias
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - H Raza Ali
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Wei Cope
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Daniel Tiezzi
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Aliakbar Dariush
- Institute of Astronomy, University of Cambridge, Cambridge CB3 0HA, UK
| | - Tauanne Dias Amarante
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Dan Reshef
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nikaoly Ciriaco
- Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Elena Martinez-Saez
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Vicente Peg
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain; Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Santiago Ramon Y Cajal
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain; Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Javier Cortes
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Ramon y Cajal Hospital, 28034 Madrid, Spain
| | - George Vassiliou
- Cancer Molecular Diagnosis Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust/MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Gad Getz
- The Broad Institute, Cambridge, MA 02142, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Charlestown, MA 02129, USA
| | - Serena Nik-Zainal
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Muhammed Murtaza
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Mayo Clinic Center for Individualized Medicine, Scottsdale, AZ, USA
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Florian Markowetz
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 2QQ, UK.
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8
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Ceolin L, Romitti M, Rodrigues Siqueira D, Vaz Ferreira C, Oliboni Scapineli J, Assis-Brazil B, Vieira Maximiano R, Dias Amarante T, de Souza Nunes MC, Weber G, Maia AL. Effect of 3'UTR RET Variants on RET mRNA Secondary Structure and Disease Presentation in Medullary Thyroid Carcinoma. PLoS One 2016; 11:e0147840. [PMID: 26829565 PMCID: PMC4734678 DOI: 10.1371/journal.pone.0147840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/08/2016] [Indexed: 12/21/2022] Open
Abstract
Background The RET S836S variant has been associated with early onset and increased risk for metastatic disease in medullary thyroid carcinoma (MTC). However, the mechanism by which this variant modulates MTC pathogenesis is still open to discuss. Of interest, strong linkage disequilibrium (LD) between RET S836S and 3'UTR variants has been reported in Hirschsprung's disease patients. Objective To evaluate the frequency of the RET 3’UTR variants (rs76759170 and rs3026785) in MTC patients and to determine whether these variants are in LD with S836S polymorphism. Methods Our sample comprised 152 patients with sporadic MTC. The RET S836S and 3’UTR (rs76759170 and rs3026785) variants were genotyped using Custom TaqMan Genotyping Assays. Haplotypes were inferred using the phase 2.1 program. RET mRNA structure was assessed by Vienna Package. Results The mean age of MTC diagnosis was 48.5±15.5 years and 57.9% were women. The minor allele frequencies of RET polymorphisms were as follows: S836S, 5.6%; rs76759170, 5.6%; rs3026785, 6.2%. We observed a strong LD among S836S and 3’UTR variants (|D’| = -1, r2 = 1 and |D’| = -1, r2 = 0,967). Patients harboring the S836S/3’UTR variants presented a higher percentage of lymph node and distant metastasis (P = 0.013 and P<0.001, respectively). Accordingly, RNA folding analyses demonstrated different RNA secondary structure predictions for WT(TCCGT), S836S(TTCGT) or 3’UTR(GTCAC) haplotypes. The S836S/3’UTR haplotype presented a greater number of double helices sections and lower levels of minimal free energy when compared to the wild-type haplotype, suggesting that these variants provides the most thermodynamically stable mRNA structure, which may have functional consequences on the rate of mRNA degradation. Conclusion The RET S836S polymorphism is in LD with 3’UTR variants. In silico analysis indicate that the 3’UTR variants may affect the secondary structure of RET mRNA, suggesting that these variants might play a role in posttranscriptional control of the RET transcripts.
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Affiliation(s)
- Lucieli Ceolin
- Thyroid Section, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Mirian Romitti
- Thyroid Section, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Débora Rodrigues Siqueira
- Thyroid Section, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Carla Vaz Ferreira
- Thyroid Section, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Jessica Oliboni Scapineli
- Thyroid Section, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
| | - Beatriz Assis-Brazil
- Pathology Department, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rodolfo Vieira Maximiano
- Department of Physics, Computational Biophysics Group, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Tauanne Dias Amarante
- Department of Physics, Computational Biophysics Group, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Miriam Celi de Souza Nunes
- Department of Physics, Computational Biophysics Group, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gerald Weber
- Department of Physics, Computational Biophysics Group, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ana Luiza Maia
- Thyroid Section, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
- * E-mail:
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