1
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de Klaver W, de Wit M, Bolijn A, Tijssen M, Delis-van Diemen P, Lemmens M, Spaander MC, Dekker E, van Leerdam ME, Coupé VM, van Boxtel R, Clevers H, Carvalho B, Meijer GA. Polyketide synthase positive Escherichia coli one-time measurement in stool is not informative of colorectal cancer risk in a screening setting. J Pathol 2024; 263:217-225. [PMID: 38551073 DOI: 10.1002/path.6276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/21/2023] [Accepted: 02/22/2024] [Indexed: 05/12/2024]
Abstract
Environmental factors like the pathogenicity island polyketide synthase positive (pks+) Escherichia coli (E. coli) could have potential for risk stratification in colorectal cancer (CRC) screening. The association between pks+ E. coli measured in fecal immunochemical test (FIT) samples and the detection of advanced neoplasia (AN) at colonoscopy was investigated. Biobanked FIT samples were analyzed for both presence of E. coli and pks+ E. coli and correlated with colonoscopy findings; 5020 CRC screening participants were included. Controls were participants in which no relevant lesion was detected because of FIT-negative results (cut-off ≥15 μg Hb/g feces), a negative colonoscopy, or a colonoscopy during which only a nonadvanced polyp was detected. Cases were participants with AN [CRC, advanced adenoma (AA), or advanced serrated polyp (ASP)]. Existing DNA isolation and quantitative polymerase chain reaction (qPCR) procedures were used for the detection of E. coli and pks+ E. coli in stool. A total of 4542 (90.2%) individuals were E. coli positive, and 1322 (26.2%) were pks+ E. coli positive. The prevalence of E. coli in FIT samples from individuals with AN was 92.9% compared to 89.7% in FIT samples of controls (p = 0.010). The prevalence of pks+ E. coli in FIT samples from individuals with AN (28.6%) and controls (25.9%) was not significantly different (p = 0.13). The prevalences of pks+ E. coli in FIT samples from individuals with CRC, AA, or ASP were 29.6%, 28.3%, and 32.1%, respectively. In conclusion, the prevalence of pks+ E. coli in a screening population was 26.2% and did not differ significantly between individuals with AN and controls. These findings disqualify the straightforward option of using a snapshot measurement of pks+ E. coli in FIT samples as a stratification biomarker for CRC risk. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Willemijn de Klaver
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Location University of Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Meike de Wit
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anne Bolijn
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marianne Tijssen
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Margriet Lemmens
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Manon Cw Spaander
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Location University of Amsterdam, Amsterdam, The Netherlands
| | - Monique E van Leerdam
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Veerle Mh Coupé
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Location VU Medical Center, Amsterdam, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for pediatric oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Hans Clevers
- Princess Máxima Center for pediatric oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, the Netherlands
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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2
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van Soest DMK, Polderman PE, den Toom WTF, Keijer JP, van Roosmalen MJ, Leyten TMF, Lehmann J, Zwakenberg S, De Henau S, van Boxtel R, Burgering BMT, Dansen TB. Mitochondrial H 2O 2 release does not directly cause damage to chromosomal DNA. Nat Commun 2024; 15:2725. [PMID: 38548751 PMCID: PMC10978998 DOI: 10.1038/s41467-024-47008-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Reactive Oxygen Species (ROS) derived from mitochondrial respiration are frequently cited as a major source of chromosomal DNA mutations that contribute to cancer development and aging. However, experimental evidence showing that ROS released by mitochondria can directly damage nuclear DNA is largely lacking. In this study, we investigated the effects of H2O2 released by mitochondria or produced at the nucleosomes using a titratable chemogenetic approach. This enabled us to precisely investigate to what extent DNA damage occurs downstream of near- and supraphysiological amounts of localized H2O2. Nuclear H2O2 gives rise to DNA damage and mutations and a subsequent p53 dependent cell cycle arrest. Mitochondrial H2O2 release shows none of these effects, even at levels that are orders of magnitude higher than what mitochondria normally produce. We conclude that H2O2 released from mitochondria is unlikely to directly damage nuclear genomic DNA, limiting its contribution to oncogenic transformation and aging.
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Affiliation(s)
- Daan M K van Soest
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
| | - Paulien E Polderman
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
| | - Wytze T F den Toom
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
| | - Janneke P Keijer
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
| | - Markus J van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, Utrecht, 3584 CS, The Netherlands
| | - Tim M F Leyten
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
| | - Johannes Lehmann
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
| | - Susan Zwakenberg
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
| | - Sasha De Henau
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, Utrecht, 3584 CS, The Netherlands
- Oncode Institute, Jaarbeursplein 6, Utrecht, 3521 AL, The Netherlands
| | - Boudewijn M T Burgering
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
- Oncode Institute, Jaarbeursplein 6, Utrecht, 3521 AL, The Netherlands
| | - Tobias B Dansen
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands.
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3
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Struys I, Velázquez C, Devriendt K, Godderis L, Segers H, Thienpont B, van Boxtel R, Van Calsteren K, Voet T, Wolters V, Lenaerts L, Amant F. Evaluating offspring Genomic and Epigenomic alterations after prenatal exposure to Cancer treatment In Pregnancy (GE-CIP): a multicentric observational study. BMJ Open 2024; 14:e081833. [PMID: 38548357 PMCID: PMC10982724 DOI: 10.1136/bmjopen-2023-081833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/05/2024] [Indexed: 04/02/2024] Open
Abstract
INTRODUCTION Around 1 in 1000-2000 pregnancies are affected by a cancer diagnosis. Previous studies have shown that chemotherapy during pregnancy has reassuring cognitive and cardiac neonatal outcomes, and hence has been proposed as standard of care. However, although these children perform within normal ranges for their age, subtle differences have been identified. Given that chemotherapeutic compounds can cross the placenta, the possibility that prenatal chemotherapy exposure mutates the offspring's genome and/or epigenome, with potential deleterious effects later in life, urges to be investigated. METHODS AND ANALYSES This multicentric observational study aims to collect cord blood, meconium and neonatal buccal cells at birth, as well as peripheral blood, buccal cells and urine from infants when 6, 18 and/or 36 months of age. Using bulk and single-cell approaches, we will compare samples from chemotherapy-treated pregnant patients with cancer, pregnant patients with cancer not treated with chemotherapy and healthy pregnant women. Potential chemotherapy-related newborn genomic and/or epigenomic alterations, such as single nucleotide variants, copy number variants and DNA-methylation alterations, will be identified in mononuclear and epithelial cells, isolated from blood, buccal swabs and urine. DNA from maternal peripheral blood and paternal buccal cells will be used to determine de novo somatic mutations in the neonatal blood and epithelial cells. Additionally, the accumulated exposure of the fetus, and biological effective dose of alkylating agents, will be assessed in meconium and cord blood via mass spectrometry approaches. ETHICS AND DISSEMINATION The Ethics Committee Research of UZ/KU Leuven (EC Research) and the Medical Ethical Review Committee of University Medical Center Amsterdam have approved the study. Results of this study will be disseminated via presentations at (inter)national conferences, through peer-reviewed, open-access publications, via social media platforms aimed to inform patients and healthcare workers, and through the website of the International Network on Cancer, Infertility and Pregnancy (www.cancerinpregnancy.org).
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Affiliation(s)
- Ilana Struys
- Department of Oncology, KU Leuven, Leuven, Flanders, Belgium
| | | | - Koenraad Devriendt
- Department of Human Genetics, University Hospital Leuven, Leuven, Belgium
| | - Lode Godderis
- Department of Public Health and Primary Care, KU Leuven, Leuven, Flanders, Belgium
- External Service for Prevention and Protection at Work, Heverlee, Belgium
| | - Heidi Segers
- Department of Paediatric Oncology, University Hospital Leuven, Leuven, Belgium
| | | | - Ruben van Boxtel
- Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Kristel Van Calsteren
- Department of Obstetrics and Gynecology, University Hospital Leuven, Leuven, Belgium
| | - Thierry Voet
- Department of Human Genetics, KU Leuven, Leuven, Flanders, Belgium
- Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium
| | - Vera Wolters
- Gynecologic Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Frederic Amant
- Department of Oncology, KU Leuven, Leuven, Flanders, Belgium
- Department of Obstetrics and Gynecology, University Hospital Leuven, Leuven, Belgium
- Gynecologic Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
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Rosendahl Huber A, Pleguezuelos-Manzano C, Puschhof J, Ubels J, Boot C, Saftien A, Verheul M, Trabut LT, Groenen N, van Roosmalen M, Ouyang KS, Wood H, Quirke P, Meijer G, Cuppen E, Clevers H, van Boxtel R. Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer. Cancer Cell 2024; 42:487-496.e6. [PMID: 38471458 DOI: 10.1016/j.ccell.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/26/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Co-culture of intestinal organoids with a colibactin-producing pks+E. coli strain (EcC) revealed mutational signatures also found in colorectal cancer (CRC). E. coli Nissle 1917 (EcN) remains a commonly used probiotic, despite harboring the pks operon and inducing double strand DNA breaks. We determine the mutagenicity of EcN and three CRC-derived pks+E. coli strains with an analytical framework based on sequence characteristic of colibactin-induced mutations. All strains, including EcN, display varying levels of mutagenic activity. Furthermore, a machine learning approach attributing individual mutations to colibactin reveals that patients with colibactin-induced mutations are diagnosed at a younger age and that colibactin can induce a specific APC mutation. These approaches allow the sensitive detection of colibactin-induced mutations in ∼12% of CRC genomes and even in whole exome sequencing data, representing a crucial step toward pinpointing the mutagenic activity of distinct pks+E. coli strains.
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Affiliation(s)
- Axel Rosendahl Huber
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Joske Ubels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Charelle Boot
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Aurelia Saftien
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Laurianne T Trabut
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Niels Groenen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Markus van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Kyanna S Ouyang
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Henry Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Phil Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Gerrit Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Edwin Cuppen
- University Medical Center Utrecht, Utrecht, the Netherlands; Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Roche Pharmaceutical Research and Early Development, 4058 Basel, Switzerland.
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
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5
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Derks LLM, van Boxtel R. Stem cell mutations, associated cancer risk, and consequences for regenerative medicine. Cell Stem Cell 2023; 30:1421-1433. [PMID: 37832550 PMCID: PMC10624213 DOI: 10.1016/j.stem.2023.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Mutation accumulation in stem cells has been associated with cancer risk. However, the presence of numerous mutant clones in healthy tissues has raised the question of what limits cancer initiation. Here, we review recent developments in characterizing mutation accumulation in healthy tissues and compare mutation rates in stem cells during development and adult life with corresponding cancer risk. A certain level of mutagenesis within the stem cell pool might be beneficial to limit the size of malignant clones through competition. This knowledge impacts our understanding of carcinogenesis with potential consequences for the use of stem cells in regenerative medicine.
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Affiliation(s)
- Lucca L M Derks
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands.
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6
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Middelkamp S, Manders F, Peci F, van Roosmalen MJ, González DM, Bertrums EJ, van der Werf I, Derks LL, Groenen NM, Verheul M, Trabut L, Pleguezuelos-Manzano C, Brandsma AM, Antoniou E, Reinhardt D, Bierings M, Belderbos ME, van Boxtel R. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox. Cell Genom 2023; 3:100389. [PMID: 37719152 PMCID: PMC10504672 DOI: 10.1016/j.xgen.2023.100389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/30/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023]
Abstract
Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole-genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole-genome sequencing (WGS) but still generate hundreds of artifacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolbox (PTATO), to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data. PTATO includes a machine learning approach and filtering based on recurrence to distinguish PTA artifacts from true mutations with high sensitivity (up to 90%), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that hematopoietic stem cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS, have normal somatic single base substitution burdens but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.
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Affiliation(s)
- Sjors Middelkamp
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Flavia Peci
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Markus J. van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Diego Montiel González
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Eline J.M. Bertrums
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Department of Pediatric Oncology, Erasmus Medical Center – Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Inge van der Werf
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lucca L.M. Derks
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Niels M. Groenen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Laurianne Trabut
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, the Netherlands
| | - Arianne M. Brandsma
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Evangelia Antoniou
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Marc Bierings
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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7
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Geurts MH, Gandhi S, Boretto MG, Akkerman N, Derks LLM, van Son G, Celotti M, Harshuk-Shabso S, Peci F, Begthel H, Hendriks D, Schürmann P, Andersson-Rolf A, Chuva de Sousa Lopes SM, van Es JH, van Boxtel R, Clevers H. One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids. Nat Commun 2023; 14:4998. [PMID: 37591832 PMCID: PMC10435570 DOI: 10.1038/s41467-023-40701-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Optimization of CRISPR/Cas9-mediated genome engineering has resulted in base editors that hold promise for mutation repair and disease modeling. Here, we demonstrate the application of base editors for the generation of complex tumor models in human ASC-derived organoids. First we show efficacy of cytosine and adenine base editors in modeling CTNNB1 hot-spot mutations in hepatocyte organoids. Next, we use C > T base editors to insert nonsense mutations in PTEN in endometrial organoids and demonstrate tumorigenicity even in the heterozygous state. Moreover, drug sensitivity assays on organoids harboring either PTEN or PTEN and PIK3CA mutations reveal the mechanism underlying the initial stages of endometrial tumorigenesis. To further increase the scope of base editing we combine SpCas9 and SaCas9 for simultaneous C > T and A > G editing at individual target sites. Finally, we show that base editor multiplexing allow modeling of colorectal tumorigenesis in a single step by simultaneously transfecting sgRNAs targeting five cancer genes.
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Affiliation(s)
- Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands.
- Oncode Institute, 3521AL, Utrecht, the Netherlands.
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands.
| | - Shashank Gandhi
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, 94720, USA
| | - Matteo G Boretto
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Ninouk Akkerman
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Lucca L M Derks
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Gijs van Son
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Martina Celotti
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Sarina Harshuk-Shabso
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Flavia Peci
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Paul Schürmann
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Amanda Andersson-Rolf
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | | | - Johan H van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands
- Oncode Institute, 3521AL, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Oncode Institute, 3521AL, Utrecht, the Netherlands
- Princess Maxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Utrecht, the Netherlands.
- Oncode Institute, 3521AL, Utrecht, the Netherlands.
- Pharma Research Early Development, Basel, Switzerland.
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8
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McKinley KL, van Boxtel R, Finley LWS, Peña CJ, Nowakowski TJ. New York Stem Cell Foundation Robertson Investigators. Cell Stem Cell 2022; 29:1621-1623. [PMID: 36459965 DOI: 10.1016/j.stem.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
As the stem cell community mourns the loss of New York Stem Cell Foundation founder Susan Solomon, we also look to celebrate her legacy. In this Voices, members of the 2022 class of NYSCF Roberston Investigators share how NYSCF community support will impact them and the bold ideas they will pursue as a result.
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9
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de Kanter JK, Margaritis T, Beishuizen A, Scheijde-Vermeulen M, Westera L, Brandsma AM, van Boxtel R, Meyer-Wentrup F. Abstract A37: Single-cell RNA sequencing reveals that childhood classical Hodgkin Lymphoma resembles normal inflammation except for T cell exhaustion. Blood Cancer Discov 2022. [DOI: 10.1158/2643-3249.lymphoma22-a37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Cure rates of classical Hodgkin Lymphoma (cHL) in children and young adult patients currently exceed 90%. Nonetheless, survivors are confronted with chronic therapy-related health conditions such as infertility, cardiovascular disease, and high rates of novel second cancers. This calls for development of new targeted and less toxic treatments. cHL is characterized by a low frequency (~0.1-5%) of malignant Hodgkin Reed-Sternberg (HRS) cells, while most of the tissue is composed of nonmalignant immune cells. It is thought that the HRS cells depend on interactions with the tumor microenvironment (TME) for their survival. Indeed, a vast number of interactions between different immune and HRS cells have been reported; however, most of these reports are based on immunohistochemistry or in vitro studies. Here, we systematically characterized the in vivo interactions by applying single-cell RNA sequencing (scRNAseq) to nine primary pediatric and adolescent cHL biopsies and three noncancerous control biopsies of reactive lymph nodes. With scRNAseq, we first sorted live cells to get an unbiased overview of the TME. Then we used a previously published flow cytometry antibody panel to enrich for HRS cells, allowing us to directly assess interactions on a per-tumor basis. Tumor cell identity was confirmed by marker expression as identified by pathology, single-cell copy-number status and the ratio of immunoglobulin kappa/lambda expression. Immune cell identity was determined by canonical marker expression. Using the scRNAseq data, we found that the TME expression profiles in cHL and control biopsies mostly overlap but harbor some differences. First, we identified genes that are consistently overexpressed in HRS cells. These included transcription factors, neural markers, multiple interleukins and other signaling molecules. Second, the extensively described immunosuppressive interactions between HRS, T and NK cells (expressing CTLA-4, TIM-3, and LAG-3) were the strongest and most common interactions that we could identify in HL but not in noncancerous reactive lymph nodes. Third, while the inflammation in the reactive lymph nodes was driven by IFN-g signaling, this pathway was inactive in HL tumors. Other interactions like recruitment of CXCR3+ and CCR4+ T cells, CD47 signaling and interleukin signaling were less pronounced in cHL compared to the controls or were less consistent between tumors. These findings were validated in bulk RNA sequencing of 45 HL tumors. A model arises in which the presence of HRS cells induces inflammation that in most ways resembles lymph node infections. This inflammation and HRS survival are controled by patient-specific interactions between HRS cells and the TME, and by T cell exhaustion, which is universal and the most essential interaction in cHL.
Citation Format: Jurrian K. de Kanter, Thanasis Margaritis, Auke Beishuizen, Marijn Scheijde-Vermeulen, Liset Westera, Arianne M. Brandsma, Ruben van Boxtel, Friederike Meyer-Wentrup. Single-cell RNA sequencing reveals that childhood classical Hodgkin Lymphoma resembles normal inflammation except for T cell exhaustion [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A37.
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Affiliation(s)
| | | | - Auke Beishuizen
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Liset Westera
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Ruben van Boxtel
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
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10
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Peci F, Dekker L, Pagliaro A, van Boxtel R, Nierkens S, Belderbos M. The cellular composition and function of the bone marrow niche after allogeneic hematopoietic cell transplantation. Bone Marrow Transplant 2022; 57:1357-1364. [PMID: 35690693 PMCID: PMC9187885 DOI: 10.1038/s41409-022-01728-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 04/29/2022] [Accepted: 05/26/2022] [Indexed: 11/09/2022]
Abstract
Allogeneic hematopoietic cell transplantation (HCT) is a potentially curative therapy for patients with a variety of malignant and non-malignant diseases. Despite its life-saving potential, HCT is associated with significant morbidity and mortality. Reciprocal interactions between hematopoietic stem cells (HSCs) and their surrounding bone marrow (BM) niche regulate HSC function during homeostatic hematopoiesis as well as regeneration. However, current pre-HCT conditioning regimens, which consist of high-dose chemotherapy and/or irradiation, cause substantial short- and long-term toxicity to the BM niche. This damage may negatively affect HSC function, impair hematopoietic regeneration after HCT and predispose to HCT-related morbidity and mortality. In this review, we summarize current knowledge on the cellular composition of the human BM niche after HCT. We describe how pre-HCT conditioning affects the cell types in the niche, including endothelial cells, mesenchymal stromal cells, osteoblasts, adipocytes, and neurons. Finally, we discuss therapeutic strategies to prevent or repair conditioning-induced niche damage, which may promote hematopoietic recovery and improve HCT outcome.
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Affiliation(s)
- Flavia Peci
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Linde Dekker
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Anna Pagliaro
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mirjam Belderbos
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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11
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Bertrums EJ, Rosendahl Huber AK, de Kanter JK, Brandsma AM, van Leeuwen AJ, Verheul M, van den Heuvel-Eibrink MM, Oka R, van Roosmalen MJ, de Groot-Kruseman HA, Zwaan CM, Goemans BF, van Boxtel R. Elevated Mutational Age in Blood of Children Treated for Cancer Contributes to Therapy-Related Myeloid Neoplasms. Cancer Discov 2022; 12:1860-1872. [PMID: 35678530 PMCID: PMC7613255 DOI: 10.1158/2159-8290.cd-22-0120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/28/2022] [Revised: 05/06/2022] [Accepted: 06/07/2022] [Indexed: 01/07/2023]
Abstract
Childhood cancer survivors are confronted with various chronic health conditions like therapy-related malignancies. However, it is unclear how exposure to chemotherapy contributes to the mutation burden and clonal composition of healthy tissues early in life. Here, we studied mutation accumulation in hematopoietic stem and progenitor cells (HSPC) before and after cancer treatment of 24 children. Of these children, 19 developed therapy-related myeloid neoplasms (t-MN). Posttreatment HSPCs had an average mutation burden increase comparable to what treatment-naïve cells accumulate during 16 years of life, with excesses up to 80 years. In most children, these additional mutations were induced by clock-like processes, which are also active during healthy aging. Other patients harbored mutations that could be directly attributed to treatments like platinum-based drugs and thiopurines. Using phylogenetic inference, we demonstrate that most t-MN in children originate after the start of treatment and that leukemic clones become dominant during or directly after chemotherapy exposure. SIGNIFICANCE Our study shows that chemotherapy increases the mutation burden of normal blood cells in cancer survivors. Only few drugs damage the DNA directly, whereas in most patients, chemotherapy-induced mutations are caused by processes similar to those present during normal aging. This article is highlighted in the In This Issue feature, p. 1825.
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Affiliation(s)
- Eline J.M. Bertrums
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands.,Department of Pediatric Oncology, Erasmus Medical Center – Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Axel K.M. Rosendahl Huber
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Jurrian K. de Kanter
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Arianne M. Brandsma
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Anaïs J.C.N. van Leeuwen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | - Rurika Oka
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Markus J. van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | - C. Michel Zwaan
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pediatric Oncology, Erasmus Medical Center – Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Bianca F. Goemans
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands.,Corresponding Author: Ruben van Boxtel, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands. Phone: 0031 (0)889727272; E-mail:
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12
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Meister MT, Groot Koerkamp MJA, de Souza T, Breunis WB, Frazer‐Mendelewska E, Brok M, DeMartino J, Manders F, Calandrini C, Kerstens HHD, Janse A, Dolman MEM, Eising S, Langenberg KPS, van Tuil M, Knops RRG, van Scheltinga ST, Hiemcke‐Jiwa LS, Flucke U, Merks JHM, van Noesel MM, Tops BBJ, Hehir‐Kwa JY, Kemmeren P, Molenaar JJ, van de Wetering M, van Boxtel R, Drost J, Holstege FCP. Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes. EMBO Mol Med 2022; 14:e16001. [PMID: 35916583 PMCID: PMC9549731 DOI: 10.15252/emmm.202216001] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 03/11/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 02/05/2023] Open
Abstract
Rhabdomyosarcomas (RMS) are mesenchyme-derived tumors and the most common childhood soft tissue sarcomas. Treatment is intense, with a nevertheless poor prognosis for high-risk patients. Discovery of new therapies would benefit from additional preclinical models. Here, we describe the generation of a collection of 19 pediatric RMS tumor organoid (tumoroid) models (success rate of 41%) comprising all major subtypes. For aggressive tumors, tumoroid models can often be established within 4-8 weeks, indicating the feasibility of personalized drug screening. Molecular, genetic, and histological characterization show that the models closely resemble the original tumors, with genetic stability over extended culture periods of up to 6 months. Importantly, drug screening reflects established sensitivities and the models can be modified by CRISPR/Cas9 with TP53 knockout in an embryonal RMS model resulting in replicative stress drug sensitivity. Tumors of mesenchymal origin can therefore be used to generate organoid models, relevant for a variety of preclinical and clinical research questions.
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Affiliation(s)
- Michael T Meister
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Marian J A Groot Koerkamp
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Terezinha de Souza
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Willemijn B Breunis
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Department of Oncology and Children's Research CenterUniversity Children's Hospital ZürichZürichSwitzerland
| | - Ewa Frazer‐Mendelewska
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Mariël Brok
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Jeff DeMartino
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Camilla Calandrini
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | | | - Alex Janse
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - M Emmy M Dolman
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Children's Cancer Institute, Lowy Cancer CentreUNSW SydneyKensingtonNSWAustralia,School of Women's and Children's Health, Faculty of MedicineUNSW SydneyKensingtonNSWAustralia
| | - Selma Eising
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | | | - Marc van Tuil
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Rutger R G Knops
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | | | | | - Uta Flucke
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | | | - Max M van Noesel
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | | | | | - Patrick Kemmeren
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Center for Molecular MedicineUMC Utrecht and Utrecht UniversityUtrechtThe Netherlands
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Marc van de Wetering
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Oncode InstituteUtrechtThe Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands,Center for Molecular MedicineUMC Utrecht and Utrecht UniversityUtrechtThe Netherlands
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13
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Abstract
From conception to death, human cells accumulate somatic mutations in their genomes. These mutations can contribute to the development of cancer and non-malignant diseases and have also been associated with aging. Rapid technological developments in sequencing approaches in the last few years and their application to normal tissues have greatly advanced our knowledge about the accumulation of these mutations during healthy aging. Whole genome sequencing studies have revealed that there are significant differences in mutation burden and patterns across tissues, but also that the mutation rates within tissues are surprisingly constant during adult life. In contrast, recent lineage-tracing studies based on whole-genome sequencing have shown that the rate of mutation accumulation is strongly increased early in life before birth. These early mutations, which can be shared by many cells in the body, may have a large impact on development and the origin of somatic diseases. For example, cancer driver mutations can arise early in life, decades before the detection of the malignancy. Here, we review the recent insights in mutation accumulation and mutagenic processes in normal tissues. We compare mutagenesis early and later in life and discuss how mutation rates and patterns evolve during aging. Additionally, we outline the potential impact of these mutations on development, aging and disease.
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Affiliation(s)
- Freek Manders
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Sjors Middelkamp
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
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14
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Allen J, Rosendahl Huber A, Pleguezuelos-Manzano C, Puschhof J, Wu S, Wu X, Boot C, Saftien A, O’Hagan HM, Wang H, van Boxtel R, Clevers H, Sears CL. Colon Tumors in Enterotoxigenic Bacteroides fragilis (ETBF)-Colonized Mice Do Not Display a Unique Mutational Signature but Instead Possess Host-Dependent Alterations in the APC Gene. Microbiol Spectr 2022; 10:e0105522. [PMID: 35587635 PMCID: PMC9241831 DOI: 10.1128/spectrum.01055-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 03/27/2022] [Accepted: 03/31/2022] [Indexed: 12/13/2022] Open
Abstract
Enterotoxigenic Bacteroides fragilis (ETBF) is consistently found at higher frequency in individuals with sporadic and hereditary colorectal cancer (CRC) and induces tumorigenesis in several mouse models of CRC. However, whether specific mutations induced by ETBF lead to colon tumor formation has not been investigated. To determine if ETBF-induced mutations impact the Apc gene, and other tumor suppressors or proto-oncogenes, we performed whole-exome sequencing and whole-genome sequencing on tumors isolated after ETBF and sham colonization of Apcmin/+ and Apcmin/+Msh2fl/flVC mice, as well as whole-genome sequencing of organoids cocultured with ETBF. Our results indicate that ETBF-induced tumor formation results from loss of heterozygosity (LOH) of Apc, unless the mismatch repair system is disrupted, in which case, tumor formation results from new acquisition of protein-truncating mutations in Apc. In contrast to polyketide synthase-positive Escherichia coli (pks+ E. coli), ETBF does not produce a unique mutational signature; instead, ETBF-induced tumors arise from errors in DNA mismatch repair and homologous recombination DNA damage repair, established pathways of tumor formation in the colon, and the same genetic mechanism accounting for sham tumors in these mouse models. Our analysis informs how this procarcinogenic bacterium may promote tumor formation in individuals with inherited predispositions to CRC, such as Lynch syndrome or familial adenomatous polyposis (FAP). IMPORTANCE Many studies have shown that microbiome composition in both the mucosa and the stool differs in individuals with sporadic and hereditary colorectal cancer (CRC). Both human and mouse models have established a strong association between particular microbes and colon tumor induction. However, the genetic mechanisms underlying putative microbe-induced colon tumor formation are not well established. In this paper, we applied whole-exome sequencing and whole-genome sequencing to investigate the impact of ETBF-induced genetic changes on tumor formation. Additionally, we performed whole-genome sequencing of human colon organoids exposed to ETBF to validate the mutational patterns seen in our mouse models and begin to understand their relevance in human colon epithelial cells. The results of this study highlight the importance of ETBF colonization in the development of sporadic CRC and in individuals with hereditary tumor conditions, such as Lynch syndrome and familial adenomatous polyposis (FAP).
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Affiliation(s)
- Jawara Allen
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Axel Rosendahl Huber
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Shaoguang Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xinqun Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charelle Boot
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Aurelia Saftien
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Heather M. O’Hagan
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
- Cell, Molecular and Cancer Biology Program, Indiana University School of Medicine, Bloomington, Indiana, USA
| | - Hao Wang
- Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine Institutions, Baltimore, Maryland, USA
| | - Ruben van Boxtel
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Cynthia L. Sears
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Institutions, Baltimore, Maryland, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine Institutions, Baltimore, Maryland, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine Institutions, Baltimore, Maryland, USA
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15
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Rosendahl Huber A, van Leeuwen AJCN, Peci F, de Kanter JK, Bertrums EJM, van Boxtel R. Whole-genome sequencing and mutational analysis of human cord-blood derived stem and progenitor cells. STAR Protoc 2022; 3:101361. [PMID: 35573477 PMCID: PMC9092504 DOI: 10.1016/j.xpro.2022.101361] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 12/01/2022] Open
Abstract
Mutational signatures have been identified in cancer genomes, providing information about the causes of cancer and treatment vulnerabilities. This protocol describes an assay to determine the genotoxic mechanisms underlying these signatures using cord-blood derived hematopoietic stem and progenitor cells (CB-HSPCs). CB-HSPCs have a low mutation background, enabling sensitive detection of mutations. First, CB-HSPCs are exposed in vitro, sorted, and clonally expanded. This expansion enables whole-genome sequencing to detect the mutation load and respective patterns induced during genotoxic exposure. For complete details on the use and execution of this protocol, please refer to de Kanter et al. (2021). Experimentally defining mutational signatures in cord blood-derived stem cells Whole genome sequencing of exposed stem cell allows detection of all mutation types Low intrinsic mutation burden of cord blood-derived stem cells increases sensitivity
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Affiliation(s)
- Axel Rosendahl Huber
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Anaïs J C N van Leeuwen
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Flavia Peci
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jurrian K de Kanter
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Eline J M Bertrums
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands.,Department of Pediatric Oncology, Erasmus Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
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16
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Vougioukalaki M, Demmers J, Vermeij WP, Baar M, Bruens S, Magaraki A, Kuijk E, Jager M, Merzouk S, Brandt RM, Kouwenberg J, van Boxtel R, Cuppen E, Pothof J, Hoeijmakers JHJ. Different responses to DNA damage determine ageing differences between organs. Aging Cell 2022; 21:e13562. [PMID: 35246937 PMCID: PMC9009128 DOI: 10.1111/acel.13562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/21/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Organs age differently, causing wide heterogeneity in multimorbidity, but underlying mechanisms are largely elusive. To investigate the basis of organ-specific ageing, we utilized progeroid repair-deficient Ercc1Δ /- mouse mutants and systematically compared at the tissue, stem cell and organoid level two organs representing ageing extremes. Ercc1Δ /- intestine shows hardly any accelerated ageing. Nevertheless, we found apoptosis and reduced numbers of intestinal stem cells (ISCs), but cell loss appears compensated by over-proliferation. ISCs retain their organoid-forming capacity, but organoids perform poorly in culture, compared with WT. Conversely, liver ages dramatically, even causing early death in Ercc1-KO mice. Apoptosis, p21, polyploidization and proliferation of various (stem) cells were prominently elevated in Ercc1Δ /- liver and stem cell populations were either largely unaffected (Sox9+), or expanding (Lgr5+), but were functionally exhausted in organoid formation and development in vitro. Paradoxically, while intestine displays less ageing, repair in WT ISCs appears inferior to liver as shown by enhanced sensitivity to various DNA-damaging agents, and lower lesion removal. Our findings reveal organ-specific anti-ageing strategies. Intestine, with short lifespan limiting time for damage accumulation and repair, favours apoptosis of damaged cells relying on ISC plasticity. Liver with low renewal rates depends more on repair pathways specifically protecting the transcribed compartment of the genome to promote sustained functionality and cell preservation. As shown before, the hematopoietic system with intermediate self-renewal mainly invokes replication-linked mechanisms, apoptosis and senescence. Hence, organs employ different genome maintenance strategies, explaining heterogeneity in organ ageing and the segmental nature of DNA-repair-deficient progerias.
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Affiliation(s)
- Maria Vougioukalaki
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Joris Demmers
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric Oncology Oncode Institute Utrecht The Netherlands
| | - Marjolein Baar
- Center for Molecular Medicine University Medical Center Utrecht Utrecht The Netherlands
| | - Serena Bruens
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Aristea Magaraki
- Department of Developmental Biology Oncode Institute Rotterdam The Netherlands
| | - Ewart Kuijk
- Division Biomedical Genetics Center for Molecular Medicine and Cancer Genomics Netherlands University Medical Center Utrecht Utrecht University Utrecht The Netherlands
| | - Myrthe Jager
- Department of Genetics Center for Molecular Medicine University Medical Center Utrecht Utrecht University Utrecht The Netherlands
| | - Sarra Merzouk
- Department of Developmental Biology Oncode Institute Rotterdam The Netherlands
| | - Renata M.C. Brandt
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Janneke Kouwenberg
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology Oncode Institute Utrecht The Netherlands
| | - Edwin Cuppen
- Division Biomedical Genetics Center for Molecular Medicine and Cancer Genomics Netherlands University Medical Center Utrecht Utrecht University Utrecht The Netherlands
- Hartwig Medical Foundation Amsterdam Netherlands
| | - Joris Pothof
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Jan H. J. Hoeijmakers
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
- Princess Máxima Center for Pediatric Oncology Oncode Institute Utrecht The Netherlands
- Institute for Genome Stability in Ageing and Disease Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University Hospital of Cologne Cologne Germany
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17
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Hasaart KA, Manders F, Ubels J, Verheul M, van Roosmalen MJ, Groenen NM, Oka R, Kuijk E, Lopes SMCDS, Boxtel RV. Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells in vivo. iScience 2022; 25:103736. [PMID: 35118356 PMCID: PMC8792070 DOI: 10.1016/j.isci.2022.103736] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/01/2021] [Revised: 12/03/2021] [Accepted: 01/02/2022] [Indexed: 11/30/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) hold great promise for regenerative medicine, but genetic instability is a major concern. Embryonic pluripotent cells also accumulate mutations during early development, but how this relates to the mutation burden in iPSCs remains unknown. Here, we directly compared the mutation burden of cultured iPSCs with their isogenic embryonic cells during human embryogenesis. We generated developmental lineage trees of human fetuses by phylogenetic inference from somatic mutations in the genomes of multiple stem cells, which were derived from different germ layers. Using this approach, we characterized the mutations acquired pre-gastrulation and found a rate of 1.65 mutations per cell division. When cultured in hypoxic conditions, iPSCs generated from fetal stem cells of the assessed fetuses displayed a similar mutation rate and spectrum. Our results show that iPSCs maintain a genomic integrity during culture at a similar degree as their pluripotent counterparts do in vivo.
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Affiliation(s)
- Karlijn A.L. Hasaart
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Joske Ubels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Markus J. van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Niels M. Groenen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Rurika Oka
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Ewart Kuijk
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | | | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
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18
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Manders F, Brandsma AM, de Kanter J, Verheul M, Oka R, van Roosmalen MJ, van der Roest B, van Hoeck A, Cuppen E, van Boxtel R. MutationalPatterns: the one stop shop for the analysis of mutational processes. BMC Genomics 2022; 23:134. [PMID: 35168570 PMCID: PMC8845394 DOI: 10.1186/s12864-022-08357-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [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: 11/08/2021] [Accepted: 02/01/2022] [Indexed: 01/01/2023] Open
Abstract
Background The collective of somatic mutations in a genome represents a record of mutational processes that have been operative in a cell. These processes can be investigated by extracting relevant mutational patterns from sequencing data. Results Here, we present the next version of MutationalPatterns, an R/Bioconductor package, which allows in-depth mutational analysis of catalogues of single and double base substitutions as well as small insertions and deletions. Major features of the package include the possibility to perform regional mutation spectra analyses and the possibility to detect strand asymmetry phenomena, such as lesion segregation. On top of this, the package also contains functions to determine how likely it is that a signature can cause damaging mutations (i.e., mutations that affect protein function). This updated package supports stricter signature refitting on known signatures in order to prevent overfitting. Using simulated mutation matrices containing varied signature contributions, we showed that reliable refitting can be achieved even when only 50 mutations are present per signature. Additionally, we incorporated bootstrapped signature refitting to assess the robustness of the signature analyses. Finally, we applied the package on genome mutation data of cell lines in which we deleted specific DNA repair processes and on large cancer datasets, to show how the package can be used to generate novel biological insights. Conclusions This novel version of MutationalPatterns allows for more comprehensive analyses and visualization of mutational patterns in order to study the underlying processes. Ultimately, in-depth mutational analyses may contribute to improved biological insights in mechanisms of mutation accumulation as well as aid cancer diagnostics. MutationalPatterns is freely available at http://bioconductor.org/packages/MutationalPatterns. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08357-3.
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Affiliation(s)
- Freek Manders
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Arianne M Brandsma
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Jurrian de Kanter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Rurika Oka
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Markus J van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands
| | - Bastiaan van der Roest
- Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Arne van Hoeck
- Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Edwin Cuppen
- Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands. .,Oncode Institute, Jaarbeursplein 6, 3521 AL, Utrecht, The Netherlands.
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19
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Bollen Y, Hageman JH, van Leenen P, Derks LLM, Ponsioen B, Buissant des Amorie JR, Verlaan-Klink I, van den Bos M, Terstappen LWMM, van Boxtel R, Snippert HJG. Efficient and error-free fluorescent gene tagging in human organoids without double-strand DNA cleavage. PLoS Biol 2022; 20:e3001527. [PMID: 35089911 PMCID: PMC8827455 DOI: 10.1371/journal.pbio.3001527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 05/10/2021] [Revised: 02/09/2022] [Accepted: 01/05/2022] [Indexed: 12/30/2022] Open
Abstract
CRISPR-associated nucleases are powerful tools for precise genome editing of model systems, including human organoids. Current methods describing fluorescent gene tagging in organoids rely on the generation of DNA double-strand breaks (DSBs) to stimulate homology-directed repair (HDR) or non-homologous end joining (NHEJ)-mediated integration of the desired knock-in. A major downside associated with DSB-mediated genome editing is the required clonal selection and expansion of candidate organoids to verify the genomic integrity of the targeted locus and to confirm the absence of off-target indels. By contrast, concurrent nicking of the genomic locus and targeting vector, known as in-trans paired nicking (ITPN), stimulates efficient HDR-mediated genome editing to generate large knock-ins without introducing DSBs. Here, we show that ITPN allows for fast, highly efficient, and indel-free fluorescent gene tagging in human normal and cancer organoids. Highlighting the ease and efficiency of ITPN, we generate triple fluorescent knock-in organoids where 3 genomic loci were simultaneously modified in a single round of targeting. In addition, we generated model systems with allele-specific readouts by differentially modifying maternal and paternal alleles in one step. ITPN using our palette of targeting vectors, publicly available from Addgene, is ideally suited for generating error-free heterozygous knock-ins in human organoids. A major downside of double-strand break-mediated genome editing is the need to verify the genomic integrity of the targeted locus and confirm the absence of off-target indels. This study shows that in-trans paired nicking is a mutation-free CRISPR strategy to introduce precise knock-ins into human organoids; its genomic fidelity allows all knock-in cells to be pooled, accelerating the establishment of new organoid models.
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Affiliation(s)
- Yannik Bollen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Medical Cell Biophysics, TechMed Centre, University of Twente, Enschede, the Netherlands
| | - Joris H. Hageman
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Petra van Leenen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lucca L. M. Derks
- Oncode Institute, Utrecht, the Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Bas Ponsioen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Julian R. Buissant des Amorie
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ingrid Verlaan-Klink
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Myrna van den Bos
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Ruben van Boxtel
- Oncode Institute, Utrecht, the Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Hugo J. G. Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- * E-mail:
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20
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Nguyen L, Jager M, Lieshout R, de Ruiter PE, Locati MD, Besselink N, van der Roest B, Janssen R, Boymans S, de Jonge J, IJzermans JNM, Doukas M, Verstegen MMA, van Boxtel R, van der Laan LJW, Cuppen E, Kuijk E. Precancerous liver diseases do not cause increased mutagenesis in liver stem cells. Commun Biol 2021; 4:1301. [PMID: 34795391 PMCID: PMC8602268 DOI: 10.1038/s42003-021-02839-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/30/2021] [Indexed: 12/18/2022] Open
Abstract
Inflammatory liver disease increases the risk of developing primary liver cancer. The mechanism through which liver disease induces tumorigenesis remains unclear, but is thought to occur via increased mutagenesis. Here, we performed whole-genome sequencing on clonally expanded single liver stem cells cultured as intrahepatic cholangiocyte organoids (ICOs) from patients with alcoholic cirrhosis, non-alcoholic steatohepatitis (NASH), and primary sclerosing cholangitis (PSC). Surprisingly, we find that these precancerous liver disease conditions do not result in a detectable increased accumulation of mutations, nor altered mutation types in individual liver stem cells. This finding contrasts with the mutational load and typical mutational signatures reported for liver tumors, and argues against the hypothesis that liver disease drives tumorigenesis via a direct mechanism of induced mutagenesis. Disease conditions in the liver may thus act through indirect mechanisms to drive the transition from healthy to cancerous cells, such as changes to the microenvironment that favor the outgrowth of precancerous cells.
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Affiliation(s)
- Luan Nguyen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Myrthe Jager
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Mauro D Locati
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bastiaan van der Roest
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | | | | | | | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
- Hartwig Medical Foundation, Amsterdam, The Netherlands.
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
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21
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Brandsma AM, Bertrums EJM, van Roosmalen MJ, Hofman DA, Oka R, Verheul M, Manders F, Ubels J, Belderbos ME, van Boxtel R. Mutation signatures of pediatric acute myeloid leukemia and normal blood progenitors associated with differential patient outcomes. Blood Cancer Discov 2021; 2:484-499. [PMID: 34642666 PMCID: PMC7611805 DOI: 10.1158/2643-3230.bcd-21-0010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Indexed: 12/30/2022] Open
Abstract
A subset of pediatric AML cases harbors more somatic mutations in their genomes compared to normal blood progenitors. This subset displays expression profiles that resemble more committed progenitors and associates with better patient survival. Acquisition of oncogenic mutations with age is believed to be rate limiting for carcinogenesis. However, the incidence of leukemia in children is higher than in young adults. Here we compare somatic mutations across pediatric acute myeloid leukemia (pAML) patient-matched leukemic blasts and hematopoietic stem and progenitor cells (HSPC), as well as HSPCs from age-matched healthy donors. HSPCs in the leukemic bone marrow have limited genetic relatedness and share few somatic mutations with the cell of origin of the malignant blasts, suggesting polyclonal hematopoiesis in patients with pAML. Compared with normal HSPCs, a subset of pAML cases harbored more somatic mutations and a distinct composition of mutational process signatures. We hypothesize that these cases might have arisen from a more committed progenitor. This subset had better outcomes than pAML cases with mutation burden comparable with age-matched healthy HSPCs. Our study provides insights into the etiology and patient stratification of pAML.
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Affiliation(s)
- Arianne M Brandsma
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Eline J M Bertrums
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Markus J van Roosmalen
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Damon A Hofman
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Rurika Oka
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Joske Ubels
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Mirjam E Belderbos
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
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22
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Geurts MH, de Poel E, Pleguezuelos-Manzano C, Oka R, Carrillo L, Andersson-Rolf A, Boretto M, Brunsveld JE, van Boxtel R, Beekman JM, Clevers H. Evaluating CRISPR-based prime editing for cancer modeling and CFTR repair in organoids. Life Sci Alliance 2021; 4:e202000940. [PMID: 34373320 PMCID: PMC8356249 DOI: 10.26508/lsa.202000940] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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: 10/19/2020] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022] Open
Abstract
Prime editing is a recently reported genome editing tool using a nickase-cas9 fused to a reverse transcriptase that directly synthesizes the desired edit at the target site. Here, we explore the use of prime editing in human organoids. Common TP53 mutations can be correctly modeled in human adult stem cell-derived colonic organoids with efficiencies up to 25% and up to 97% in hepatocyte organoids. Next, we functionally repaired the cystic fibrosis CFTR-F508del mutation and compared prime editing to CRISPR/Cas9-mediated homology-directed repair and adenine base editing on the CFTR-R785* mutation. Whole-genome sequencing of prime editing-repaired organoids revealed no detectable off-target effects. Despite encountering varying editing efficiencies and undesired mutations at the target site, these results underline the broad applicability of prime editing for modeling oncogenic mutations and showcase the potential clinical application of this technique, pending further optimization.
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Affiliation(s)
- Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Eyleen de Poel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Rurika Oka
- Oncode Institute,Princes Maxima Center, Utrecht, The Netherlands
| | - Léo Carrillo
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Amanda Andersson-Rolf
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Matteo Boretto
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Jesse E Brunsveld
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Oncode Institute,Princes Maxima Center, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
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23
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Moore L, Cagan A, Coorens THH, Neville MDC, Sanghvi R, Sanders MA, Oliver TRW, Leongamornlert D, Ellis P, Noorani A, Mitchell TJ, Butler TM, Hooks Y, Warren AY, Jorgensen M, Dawson KJ, Menzies A, O'Neill L, Latimer C, Teng M, van Boxtel R, Iacobuzio-Donahue CA, Martincorena I, Heer R, Campbell PJ, Fitzgerald RC, Stratton MR, Rahbari R. The mutational landscape of human somatic and germline cells. Nature 2021; 597:381-386. [PMID: 34433962 DOI: 10.1038/s41586-021-03822-7] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [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] [Received: 11/23/2020] [Accepted: 07/13/2021] [Indexed: 12/31/2022]
Abstract
Over the course of an individual's lifetime, normal human cells accumulate mutations1. Here we compare the mutational landscape in 29 cell types from the soma and germline using multiple samples from the same individuals. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types, but their absolute and relative contributions varied substantially. SBS18, which potentially reflects oxidative damage2, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The rate of mutation was lowest in spermatogonia, the stem cells from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutational processes and may be partially attributable to a low rate of cell division in basal spermatogonia. These results highlight similarities and differences in the maintenance of the germline and soma.
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Affiliation(s)
- Luiza Moore
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alex Cagan
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D C Neville
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Rashesh Sanghvi
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Thomas R W Oliver
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Peter Ellis
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Inivata, Cambridge, UK
| | - Ayesha Noorani
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Thomas J Mitchell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Yvette Hooks
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Anne Y Warren
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mette Jorgensen
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kevin J Dawson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Laura O'Neill
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mabel Teng
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Urology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | | | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
| | - Raheleh Rahbari
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
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24
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Rothgangl T, Dennis MK, Lin PJC, Oka R, Witzigmann D, Villiger L, Qi W, Hruzova M, Kissling L, Lenggenhager D, Borrelli C, Egli S, Frey N, Bakker N, Walker JA, Kadina AP, Victorov DV, Pacesa M, Kreutzer S, Kontarakis Z, Moor A, Jinek M, Weissman D, Stoffel M, van Boxtel R, Holden K, Pardi N, Thöny B, Häberle J, Tam YK, Semple SC, Schwank G. In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels. Nat Biotechnol 2021; 39:949-957. [PMID: 34012094 PMCID: PMC8352781 DOI: 10.1038/s41587-021-00933-4] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [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: 02/05/2021] [Accepted: 04/23/2021] [Indexed: 02/02/2023]
Abstract
Most known pathogenic point mutations in humans are C•G to T•A substitutions, which can be directly repaired by adenine base editors (ABEs). In this study, we investigated the efficacy and safety of ABEs in the livers of mice and cynomolgus macaques for the reduction of blood low-density lipoprotein (LDL) levels. Lipid nanoparticle-based delivery of mRNA encoding an ABE and a single-guide RNA targeting PCSK9, a negative regulator of LDL, induced up to 67% editing (on average, 61%) in mice and up to 34% editing (on average, 26%) in macaques. Plasma PCSK9 and LDL levels were stably reduced by 95% and 58% in mice and by 32% and 14% in macaques, respectively. ABE mRNA was cleared rapidly, and no off-target mutations in genomic DNA were found. Re-dosing in macaques did not increase editing, possibly owing to the detected humoral immune response to ABE upon treatment. These findings support further investigation of ABEs to treat patients with monogenic liver diseases.
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Affiliation(s)
- Tanja Rothgangl
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | | | | | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Dominik Witzigmann
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Lukas Villiger
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Martina Hruzova
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lucas Kissling
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Daniela Lenggenhager
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Sabina Egli
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Nina Frey
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Noëlle Bakker
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | | | | | | | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
- Genome Engineering and Measurement Laboratory, ETH Zurich, Zurich, Switzerland
| | - Zacharias Kontarakis
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
- Genome Engineering and Measurement Laboratory, ETH Zurich, Zurich, Switzerland
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Markus Stoffel
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | | | - Norbert Pardi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beat Thöny
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Neuroscience Center Zurich, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ying K Tam
- Acuitas Therapeutics Inc., Vancouver, BC, Canada
| | | | - Gerald Schwank
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland.
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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25
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Villiger L, Rothgangl T, Witzigmann D, Oka R, Lin PJC, Qi W, Janjuha S, Berk C, Ringnalda F, Beattie MB, Stoffel M, Thöny B, Hall J, Rehrauer H, van Boxtel R, Tam YK, Schwank G. In vivo cytidine base editing of hepatocytes without detectable off-target mutations in RNA and DNA. Nat Biomed Eng 2021; 5:179-189. [PMID: 33495639 PMCID: PMC7610981 DOI: 10.1038/s41551-020-00671-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [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: 01/09/2020] [Accepted: 12/02/2020] [Indexed: 12/26/2022]
Abstract
Base editors are RNA-programmable deaminases that enable precise single-base conversions in genomic DNA. However, off-target activity is a concern in the potential use of base editors to treat genetic diseases. Here, we report unbiased analyses of transcriptome-wide and genome-wide off-target modifications effected by cytidine base editors in the liver of mice with phenylketonuria. The intravenous delivery of intein-split cytidine base editors by dual adeno-associated viruses led to the repair of the disease-causing mutation without generating off-target mutations in the RNA and DNA of the hepatocytes. Moreover, the transient expression of a cytidine base editor mRNA and a relevant single-guide RNA intravenously delivered by lipid nanoparticles led to ~21% on-target editing and to the reversal of the disease phenotype; there were also no detectable transcriptome-wide and genome-wide off-target edits. Our findings support the feasibility of therapeutic cytidine base editing to treat genetic liver diseases.
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Affiliation(s)
- Lukas Villiger
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Tanja Rothgangl
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Dominik Witzigmann
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Paulo J C Lin
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Sharan Janjuha
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Christian Berk
- Institute for Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Femke Ringnalda
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Markus Stoffel
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Beat Thöny
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Neuroscience Center Zurich, Zurich, Switzerland
- Division of Metabolism, University Children's Hospital Zurich and Children's Research Centre, Zurich, Switzerland
| | - Jonathan Hall
- Institute for Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ying K Tam
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Gerald Schwank
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
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26
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Schene IF, Joore IP, Oka R, Mokry M, van Vugt AHM, van Boxtel R, van der Doef HPJ, van der Laan LJW, Verstegen MMA, van Hasselt PM, Nieuwenhuis EES, Fuchs SA. Prime editing for functional repair in patient-derived disease models. Nat Commun 2020; 11:5352. [PMID: 33097693 PMCID: PMC7584657 DOI: 10.1038/s41467-020-19136-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [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: 05/30/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022] Open
Abstract
Prime editing is a recent genome editing technology using fusion proteins of Cas9-nickase and reverse transcriptase, that holds promise to correct the vast majority of genetic defects. Here, we develop prime editing for primary adult stem cells grown in organoid culture models. First, we generate precise in-frame deletions in the gene encoding β-catenin (CTNNB1) that result in proliferation independent of Wnt-stimuli, mimicking a mechanism of the development of liver cancer. Moreover, prime editing functionally recovers disease-causing mutations in intestinal organoids from patients with DGAT1-deficiency and liver organoids from a patient with Wilson disease (ATP7B). Prime editing is as efficient in 3D grown organoids as in 2D grown cell lines and offers greater precision than Cas9-mediated homology directed repair (HDR). Base editing remains more reliable than prime editing but is restricted to a subgroup of pathogenic mutations. Whole-genome sequencing of four prime-edited clonal organoid lines reveals absence of genome-wide off-target effects underscoring therapeutic potential of this versatile and precise gene editing strategy.
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Affiliation(s)
- Imre F Schene
- Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584, EA, Utrecht, the Netherlands
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584, EA, Utrecht, the Netherlands
- Regenerative Medicine Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands
| | - Indi P Joore
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584, EA, Utrecht, the Netherlands
- Regenerative Medicine Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands
| | - Rurika Oka
- Princess Maxima Center, 3584, CS, Utrecht, the Netherlands
- Oncode Institute, Princess Maxima Center, 3584, CS, Utrecht, the Netherlands
| | - Michal Mokry
- Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584, EA, Utrecht, the Netherlands
| | - Anke H M van Vugt
- Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584, EA, Utrecht, the Netherlands
- Regenerative Medicine Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Maxima Center, 3584, CS, Utrecht, the Netherlands
- Oncode Institute, Princess Maxima Center, 3584, CS, Utrecht, the Netherlands
| | - Hubert P J van der Doef
- Department of Pediatric Gastroenterology, University Medical Center Groningen, Hanzeplein 1, 9713, GZ, Groningen, the Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC-University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Monique M A Verstegen
- Department of Surgery, Erasmus MC-University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Peter M van Hasselt
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584, EA, Utrecht, the Netherlands
| | - Edward E S Nieuwenhuis
- Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584, EA, Utrecht, the Netherlands
- Department of Sciences, University College Roosevelt, Lange Noordstraat 1, 4331, CB, Middelburg, the Netherlands
| | - Sabine A Fuchs
- Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584, EA, Utrecht, the Netherlands.
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584, EA, Utrecht, the Netherlands.
- Regenerative Medicine Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands.
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27
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Hasaart KAL, Manders F, van der Hoorn ML, Verheul M, Poplonski T, Kuijk E, de Sousa Lopes SMC, van Boxtel R. Mutation accumulation and developmental lineages in normal and Down syndrome human fetal haematopoiesis. Sci Rep 2020; 10:12991. [PMID: 32737409 PMCID: PMC7395765 DOI: 10.1038/s41598-020-69822-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 02/06/2020] [Accepted: 07/17/2020] [Indexed: 11/30/2022] Open
Abstract
Children show a higher incidence of leukemia compared to young adolescents, yet their cells have less age-related (oncogenic) somatic mutations. Newborns with Down syndrome have an even higher risk of developing leukemia, which is thought to be driven by mutations that accumulate during fetal development. To characterize mutation accumulation in individual stem and progenitor cells of Down syndrome and karyotypically normal fetuses, we clonally expanded single cells and performed whole-genome sequencing. We found a higher mutation rate in haematopoietic stem and progenitor cells during fetal development compared to the post-infant rate. In fetal trisomy 21 cells the number of somatic mutations is even further increased, which was already apparent during the first cell divisions of embryogenesis before gastrulation. The number and types of mutations in fetal trisomy 21 haematopoietic stem and progenitor cells were similar to those in Down syndrome-associated myeloid preleukemia and could be attributed to mutational processes that were active during normal fetal haematopoiesis. Finally, we found that the contribution of early embryonic cells to human fetal tissues can vary considerably between individuals. The increased mutation rates found in this study, may contribute to the increased risk of leukemia early during life and the higher incidence of leukemia in Down syndrome.
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Affiliation(s)
- Karlijn A L Hasaart
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | | | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | - Tomasz Poplonski
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine, University Medical Center Utrecht and Oncode Institute, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | | | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.
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28
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Calandrini C, Schutgens F, Oka R, Margaritis T, Candelli T, Mathijsen L, Ammerlaan C, van Ineveld R, Derakhshan S, Custers L, Lijnzaad P, Begthel H, Kerstens H, Rookmaker M, Verhaar M, Kemmeren P, de Krijger R, Pritchard-Jones K, Rios A, van den Heuvel-Eibrink M, Holstege F, van Boxtel R, Clevers H, Drost J. Abstract IA27: Patient-derived organoids in pediatric cancer research. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-ia27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent advances in in vitro culture technologies, such as adult stem cell-derived organoids, have opened up new avenues for the development of novel, more physiologic human cancer models. Such preclinical models are essential for efficient translation of basic cancer research into novel treatment regimens. We succeeded in growing organoids from a range of pediatric solid tumors, including Wilms’ tumors, renal cell carcinomas, and different types of rhabdoid tumors (i.e., AT/RT, MRT). Tumor organoids retain many characteristics of parental tumor tissue. For instance, Wilms’ tumor organoids retain the cellular heterogeneity of tumors, as they are composed of an intricate network of different cell types. Moreover, we demonstrate that tumor organoids are amenable to gene editing and high-throughput drug screens. In conclusion, our pediatric cancer organoids capture disease and tissue heterogeneity and provide a platform for basic cancer research, drug screening, and personalized medicine.
Citation Format: Camilla Calandrini, Frans Schutgens, Rurika Oka, Thanasis Margaritis, Tito Candelli, Luka Mathijsen, Carola Ammerlaan, Ravian van Ineveld, Sepideh Derakhshan, Lars Custers, Philip Lijnzaad, Harry Begthel, Hinri Kerstens, Maarten Rookmaker, Marianne Verhaar, Patrick Kemmeren, Ronald de Krijger, Kathy Pritchard-Jones, Anne Rios, Marry van den Heuvel-Eibrink, Frank Holstege, Ruben van Boxtel, Hans Clevers, Jarno Drost. Patient-derived organoids in pediatric cancer research [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr IA27.
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Affiliation(s)
| | | | - Rurika Oka
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Tito Candelli
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | - Luka Mathijsen
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | | | | | - Lars Custers
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | - Philip Lijnzaad
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Hinri Kerstens
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | | | - Patrick Kemmeren
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | - Ronald de Krijger
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Anne Rios
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Frank Holstege
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | - Ruben van Boxtel
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Jarno Drost
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
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29
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Geurts MH, de Poel E, Amatngalim GD, Oka R, Meijers FM, Kruisselbrink E, van Mourik P, Berkers G, de Winter-de Groot KM, Michel S, Muilwijk D, Aalbers BL, Mullenders J, Boj SF, Suen SWF, Brunsveld JE, Janssens HM, Mall MA, Graeber SY, van Boxtel R, van der Ent CK, Beekman JM, Clevers H. CRISPR-Based Adenine Editors Correct Nonsense Mutations in a Cystic Fibrosis Organoid Biobank. Cell Stem Cell 2020; 26:503-510.e7. [PMID: 32084388 DOI: 10.1016/j.stem.2020.01.019] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/11/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
Adenine base editing (ABE) enables enzymatic conversion from A-T into G-C base pairs. ABE holds promise for clinical application, as it does not depend on the introduction of double-strand breaks, contrary to conventional CRISPR/Cas9-mediated genome engineering. Here, we describe a cystic fibrosis (CF) intestinal organoid biobank, representing 664 patients, of which ~20% can theoretically be repaired by ABE. We apply SpCas9-ABE (PAM recognition sequence: NGG) and xCas9-ABE (PAM recognition sequence: NGN) on four selected CF organoid samples. Genetic and functional repair was obtained in all four cases, while whole-genome sequencing (WGS) of corrected lines of two patients did not detect off-target mutations. These observations exemplify the value of large, patient-derived organoid biobanks representing hereditary disease and indicate that ABE may be safely applied in human cells.
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Affiliation(s)
- Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Eyleen de Poel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Gimano D Amatngalim
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Rurika Oka
- Princess Maxima Center, 3584 CS Utrecht, the Netherlands; Oncode Institute, Princess Maxima Center, 3584 CS Utrecht, the Netherlands
| | - Fleur M Meijers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Evelien Kruisselbrink
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Peter van Mourik
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Gitte Berkers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Karin M de Winter-de Groot
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Sabine Michel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Danya Muilwijk
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Bente L Aalbers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | | | - Sylvia F Boj
- Hubrecht Organoid Technology, 3584 CM, Utrecht, the Netherlands
| | - Sylvia W F Suen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Jesse E Brunsveld
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Hettie M Janssens
- Department of Pediatrics, division of Respiratory Medicine and Allergology, ErasmusMC-Sophia Children's Hospital, University Hospital Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Marcus A Mall
- Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Simon Y Graeber
- Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Ruben van Boxtel
- Princess Maxima Center, 3584 CS Utrecht, the Netherlands; Oncode Institute, Princess Maxima Center, 3584 CS Utrecht, the Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands.
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
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30
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Pleguezuelos-Manzano C, Puschhof J, Rosendahl Huber A, van Hoeck A, Wood HM, Nomburg J, Gurjao C, Manders F, Dalmasso G, Stege PB, Paganelli FL, Geurts MH, Beumer J, Mizutani T, Miao Y, van der Linden R, van der Elst S, Garcia KC, Top J, Willems RJL, Giannakis M, Bonnet R, Quirke P, Meyerson M, Cuppen E, van Boxtel R, Clevers H. Mutational signature in colorectal cancer caused by genotoxic pks + E. coli. Nature 2020; 580:269-273. [PMID: 32106218 PMCID: PMC8142898 DOI: 10.1038/s41586-020-2080-8] [Citation(s) in RCA: 522] [Impact Index Per Article: 130.5] [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] [Received: 09/14/2019] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
Various species of the intestinal microbiota have been associated with the development of colorectal cancer1,2, but it has not been demonstrated that bacteria have a direct role in the occurrence of oncogenic mutations. Escherichia coli can carry the pathogenicity island pks, which encodes a set of enzymes that synthesize colibactin3. This compound is believed to alkylate DNA on adenine residues4,5 and induces double-strand breaks in cultured cells3. Here we expose human intestinal organoids to genotoxic pks+ E. coli by repeated luminal injection over five months. Whole-genome sequencing of clonal organoids before and after this exposure revealed a distinct mutational signature that was absent from organoids injected with isogenic pks-mutant bacteria. The same mutational signature was detected in a subset of 5,876 human cancer genomes from two independent cohorts, predominantly in colorectal cancer. Our study describes a distinct mutational signature in colorectal cancer and implies that the underlying mutational process results directly from past exposure to bacteria carrying the colibactin-producing pks pathogenicity island.
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Affiliation(s)
- Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Axel Rosendahl Huber
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Arne van Hoeck
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jason Nomburg
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carino Gurjao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Freek Manders
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Guillaume Dalmasso
- University Clermont Auvergne, Inserm U1071, INRA USC2018, M2iSH, Clermont-Ferrand, France
| | - Paul B Stege
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Joep Beumer
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Tomohiro Mizutani
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Yi Miao
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Reinier van der Linden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Stefan van der Elst
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard Bonnet
- University Clermont Auvergne, Inserm U1071, INRA USC2018, M2iSH, Clermont-Ferrand, France
- Department of Bacteriology, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Phil Quirke
- Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Edwin Cuppen
- Oncode Institute, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation, Amsterdam, The Netherlands
- CPCT Consortium, Rotterdam, The Netherlands
| | - Ruben van Boxtel
- Oncode Institute, Utrecht, The Netherlands.
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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31
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Calandrini C, Schutgens F, Oka R, Margaritis T, Candelli T, Mathijsen L, Ammerlaan C, van Ineveld RL, Derakhshan S, de Haan S, Dolman E, Lijnzaad P, Custers L, Begthel H, Kerstens HHD, Visser LL, Rookmaaker M, Verhaar M, Tytgat GAM, Kemmeren P, de Krijger RR, Al-Saadi R, Pritchard-Jones K, Kool M, Rios AC, van den Heuvel-Eibrink MM, Molenaar JJ, van Boxtel R, Holstege FCP, Clevers H, Drost J. An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity. Nat Commun 2020; 11:1310. [PMID: 32161258 PMCID: PMC7066173 DOI: 10.1038/s41467-020-15155-6] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [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: 01/10/2019] [Accepted: 02/21/2020] [Indexed: 01/02/2023] Open
Abstract
Kidney tumours are among the most common solid tumours in children, comprising distinct subtypes differing in many aspects, including cell-of-origin, genetics, and pathology. Pre-clinical cell models capturing the disease heterogeneity are currently lacking. Here, we describe the first paediatric cancer organoid biobank. It contains tumour and matching normal kidney organoids from over 50 children with different subtypes of kidney cancer, including Wilms tumours, malignant rhabdoid tumours, renal cell carcinomas, and congenital mesoblastic nephromas. Paediatric kidney tumour organoids retain key properties of native tumours, useful for revealing patient-specific drug sensitivities. Using single cell RNA-sequencing and high resolution 3D imaging, we further demonstrate that organoid cultures derived from Wilms tumours consist of multiple different cell types, including epithelial, stromal and blastemal-like cells. Our organoid biobank captures the heterogeneity of paediatric kidney tumours, providing a representative collection of well-characterised models for basic cancer research, drug-screening and personalised medicine. Pre-clinical cell culture models capturing the heterogeneity of childhood kidney tumours are limited. Here, the authors establish and characterise an organoid biobank of tumour and matched normal organoid cultures from over 50 children with different subtypes of kidney cancer.
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Affiliation(s)
- Camilla Calandrini
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Frans Schutgens
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Thanasis Margaritis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Tito Candelli
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Luka Mathijsen
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Carola Ammerlaan
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Ravian L van Ineveld
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Sepide Derakhshan
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Sanne de Haan
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Emmy Dolman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Lars Custers
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Hindrik H D Kerstens
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Lindy L Visser
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Maarten Rookmaaker
- University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Marianne Verhaar
- University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Godelieve A M Tytgat
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,University Medical Center, Department of Pathology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Reem Al-Saadi
- University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Kathy Pritchard-Jones
- University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Hopp Children's Cancer Center (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Anne C Rios
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | | | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Hans Clevers
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Jarno Drost
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
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32
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Waanders E, Gu Z, Dobson SM, Antić Ž, Crawford JC, Ma X, Edmonson MN, Payne-Turner D, van der Vorst M, Jongmans MCJ, McGuire I, Zhou X, Wang J, Shi L, Pounds S, Pei D, Cheng C, Song G, Fan Y, Shao Y, Rusch M, McCastlain K, Yu J, van Boxtel R, Blokzijl F, Iacobucci I, Roberts KG, Wen J, Wu G, Ma J, Easton J, Neale G, Olsen SR, Nichols KE, Pui CH, Zhang J, Evans WE, Relling MV, Yang JJ, Thomas PG, Dick JE, Kuiper RP, Mullighan CG. Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia. Blood Cancer Discov 2020; 1:96-111. [PMID: 32793890 PMCID: PMC7418874 DOI: 10.1158/0008-5472.bcd-19-0041] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Relapse of acute lymphoblastic leukemia (ALL) remains a leading cause of childhood death. Prior studies have shown clonal mutations at relapse often arise from relapse-fated subclones that exist at diagnosis. However, the genomic landscape, evolutionary trajectories and mutational mechanisms driving relapse are incompletely understood. In an analysis of 92 cases of relapsed childhood ALL, incorporating multimodal DNA and RNA sequencing, deep digital mutational tracking and xenografting to formally define clonal structure, we identify 50 significant targets of mutation with distinct patterns of mutational acquisition or enrichment. CREBBP, NOTCH1, and Ras signaling mutations rose from diagnosis subclones, whereas variants in NCOR2, USH2A and NT5C2 were exclusively observed at relapse. Evolutionary modeling and xenografting demonstrated that relapse-fated clones were minor (50%), major (27%) or multiclonal (18%) at diagnosis. Putative second leukemias, including those with lineage shift, were shown to most commonly represent relapse from an ancestral clone rather than a truly independent second primary leukemia. A subset of leukemias prone to repeated relapse exhibited hypermutation driven by at least three distinct mutational processes, resulting in heightened neoepitope burden and potential vulnerability to immunotherapy. Finally, relapse-driving sequence mutations were detected prior to relapse using deep digital PCR at levels comparable to orthogonal approaches to monitor levels of measurable residual disease. These results provide a genomic framework to anticipate and circumvent relapse by earlier detection and targeting of relapse-fated clones.
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Affiliation(s)
- Esmé Waanders
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Zhaohui Gu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stephanie M Dobson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Željko Antić
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Maartje van der Vorst
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marjolijn C J Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Irina McGuire
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kelly McCastlain
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jiangyan Yu
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Francis Blokzijl
- Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ji Wen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Geoffrey Neale
- The Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Scott R Olsen
- The Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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33
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Abstract
Hematopoietic stem and progenitor cells (HSPCs) gradually accumulate DNA mutations during a lifespan, which can contribute to age-associated diseases such as leukemia. Characterizing mutation accumulation can improve understanding of the etiology of age-associated diseases. Presented here is a method to catalogue somatic mutations in individual HSPCs, which is based on whole-genome sequencing (WGS) of clonal primary cell cultures. Mutations that are present in the original cell are shared by all cells in the clonal culture, whereas mutations acquired in vitro after cell sorting are present in a subset of cells. Therefore, this method allows for accurate detection of somatic mutations present in the genomes of individual HSPCs, which accumulate during life. These catalogues of somatic mutations can provide valuable insights into mutational processes active in the hematopoietic tissue and how these processes contribute to leukemogenesis. In addition, by assessing somatic mutations that are shared between multiple HSPCs of the same individual, clonal lineage relationships and population dynamics of blood populations can be determined. As this approach relies on in vitro expansion of single cells, the method is limited to hematopoietic cells with sufficient replicative potential.
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Affiliation(s)
| | | | - Rurika Oka
- Princess Máxima Center for Pediatric Oncology
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34
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Jager M, Blokzijl F, Kuijk E, Bertl J, Vougioukalaki M, Janssen R, Besselink N, Boymans S, de Ligt J, Pedersen JS, Hoeijmakers J, Pothof J, van Boxtel R, Cuppen E. Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer. Genome Res 2019; 29:1067-1077. [PMID: 31221724 PMCID: PMC6633256 DOI: 10.1101/gr.246223.118] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [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: 11/08/2018] [Accepted: 06/07/2019] [Indexed: 12/24/2022]
Abstract
Nucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Disruption of this pathway can contribute to the development of cancer and accelerate aging. Mutational characteristics of NER-deficiency may reveal important diagnostic opportunities, as tumors deficient in NER are more sensitive to certain treatments. Here, we analyzed the genome-wide somatic mutational profiles of adult stem cells (ASCs) from NER-deficient Ercc1 -/Δ mice. Our results indicate that NER-deficiency increases the base substitution load twofold in liver but not in small intestinal ASCs, which coincides with the tissue-specific aging pathology observed in these mice. Moreover, NER-deficient ASCs of both tissues show an increased contribution of Signature 8 mutations, which is a mutational pattern with unknown etiology that is recurrently observed in various cancer types. The scattered genomic distribution of the base substitutions indicates that deficiency of global-genome NER (GG-NER) underlies the observed mutational consequences. In line with this, we observe increased Signature 8 mutations in a GG-NER-deficient human organoid culture, in which XPC was deleted using CRISPR-Cas9 gene-editing. Furthermore, genomes of NER-deficient breast tumors show an increased contribution of Signature 8 mutations compared with NER-proficient tumors. Elevated levels of Signature 8 mutations could therefore contribute to a predictor of NER-deficiency based on a patient's mutational profile.
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Affiliation(s)
- Myrthe Jager
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Francis Blokzijl
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Johanna Bertl
- Department of Molecular Medicine, Aarhus University, 8200 Aarhus N, Denmark
| | | | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Joep de Ligt
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | | | | | - Joris Pothof
- Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Ruben van Boxtel
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
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35
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Abstract
BACKGROUND In the past decade, systematic and comprehensive analyses of cancer genomes have identified cancer driver genes and revealed unprecedented insight into the molecular mechanisms underlying the initiation and progression of cancer. These studies illustrate that although every cancer has a unique genetic make-up, there are only a limited number of mechanisms that shape the mutational landscapes of cancer genomes, as reflected by characteristic computationally-derived mutational signatures. Importantly, the molecular mechanisms underlying specific signatures can now be dissected and coupled to treatment strategies. Systematic characterization of mutational signatures in a cancer patient's genome may thus be a promising new tool for molecular tumor diagnosis and classification. RESULTS In this review, we describe the status of mutational signature analysis in cancer genomes and discuss the opportunities and relevance, as well as future challenges, for further implementation of mutational signatures in clinical tumor diagnostics and therapy guidance. CONCLUSIONS Scientific studies have illustrated the potential of mutational signature analysis in cancer research. As such, we believe that the implementation of mutational signature analysis within the diagnostic workflow will improve cancer diagnosis in the future.
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Affiliation(s)
- Arne Van Hoeck
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
| | - Niels H. Tjoonk
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hartwig Medical Foundation, Science Park 408, 1098XH Amsterdam, The Netherlands
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36
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Driehuis E, Kolders S, Spelier S, Lõhmussaar K, Willems SM, Devriese LA, de Bree R, de Ruiter EJ, Korving J, Begthel H, van Es JH, Geurts V, He GW, van Jaarsveld RH, Oka R, Muraro MJ, Vivié J, Zandvliet MMJM, Hendrickx APA, Iakobachvili N, Sridevi P, Kranenburg O, van Boxtel R, Kops GJPL, Tuveson DA, Peters PJ, van Oudenaarden A, Clevers H. Oral Mucosal Organoids as a Potential Platform for Personalized Cancer Therapy. Cancer Discov 2019; 9:852-871. [PMID: 31053628 DOI: 10.1158/2159-8290.cd-18-1522] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/01/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Previous studies have described that tumor organoids can capture the diversity of defined human carcinoma types. Here, we describe conditions for long-term culture of human mucosal organoids. Using this protocol, a panel of 31 head and neck squamous cell carcinoma (HNSCC)-derived organoid lines was established. This panel recapitulates genetic and molecular characteristics previously described for HNSCC. Organoids retain their tumorigenic potential upon xenotransplantation. We observe differential responses to a panel of drugs including cisplatin, carboplatin, cetuximab, and radiotherapy in vitro. Additionally, drug screens reveal selective sensitivity to targeted drugs that are not normally used in the treatment of patients with HNSCC. These observations may inspire a personalized approach to the management of HNSCC and expand the repertoire of HNSCC drugs. SIGNIFICANCE: This work describes the culture of organoids derived from HNSCC and corresponding normal epithelium. These tumoroids recapitulate the disease genetically, histologically, and functionally. In vitro drug screening of tumoroids reveals responses to therapies both currently used in the treatment of HNSCC and those not (yet) used in clinical practice.See related commentary by Hill and D'Andrea, p. 828.This article is highlighted in the In This Issue feature, p. 813.
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Affiliation(s)
- Else Driehuis
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sigrid Kolders
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sacha Spelier
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kadi Lõhmussaar
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lot A Devriese
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Emma J de Ruiter
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeroen Korving
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Johan H van Es
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Veerle Geurts
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gui-Wei He
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Richard H van Jaarsveld
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rurika Oka
- Princess Maxima Center, Utrecht, the Netherlands
| | - Mauro J Muraro
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.,Single Cell Discoveries, Utrecht, the Netherlands
| | - Judith Vivié
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.,Single Cell Discoveries, Utrecht, the Netherlands
| | - Maurice M J M Zandvliet
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | - Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nino Iakobachvili
- M4I Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Priya Sridevi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Onno Kranenburg
- Utrecht Platform for Organoid Technology (U-PORT), Utrecht Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Peter J Peters
- M4I Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands. .,Princess Maxima Center, Utrecht, the Netherlands
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37
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Kuijk E, Blokzijl F, Jager M, Besselink N, Boymans S, Chuva de Sousa Lopes SM, van Boxtel R, Cuppen E. Early divergence of mutational processes in human fetal tissues. Sci Adv 2019; 5:eaaw1271. [PMID: 31149636 PMCID: PMC6541467 DOI: 10.1126/sciadv.aaw1271] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/23/2019] [Indexed: 05/12/2023]
Abstract
A developing human fetus needs to balance rapid cellular expansion with maintaining genomic stability. Here, we accurately quantified and characterized somatic mutation accumulation in fetal tissues by analyzing individual stem cells from human fetal liver and intestine. Fetal mutation rates were about fivefold higher than in tissue-matched adult stem cells. The mutational landscape of fetal intestinal stem cells resembled that of adult intestinal stem cells, while the mutation spectrum of fetal liver stem cells is distinct from stem cells of the fetal intestine and the adult liver. Our analyses indicate that variation in mutational mechanisms, including oxidative stress and spontaneous deamination of methylated cytosines, contributes to the observed divergence in mutation accumulation patterns and drives genetic mosaicism in humans.
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Affiliation(s)
- Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, Netherlands
| | - Francis Blokzijl
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, Netherlands
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, Netherlands
| | - Myrthe Jager
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, Netherlands
| | | | - Ruben van Boxtel
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, Netherlands
- Princess Máxima Center for Pediatric Oncology, 3584 CT Utrecht, Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, Netherlands
- Hartwig Medical Foundation, Science Park 408, 1098 XH Amsterdam, Netherlands
- Corresponding author.
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38
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Sachs N, de Ligt J, Kopper O, Gogola E, Bounova G, Weeber F, Balgobind AV, Wind K, Gracanin A, Begthel H, Korving J, van Boxtel R, Duarte AA, Lelieveld D, van Hoeck A, Ernst RF, Blokzijl F, Nijman IJ, Hoogstraat M, van de Ven M, Egan DA, Zinzalla V, Moll J, Boj SF, Voest EE, Wessels L, van Diest PJ, Rottenberg S, Vries RGJ, Cuppen E, Clevers H. A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity. Cell 2017; 172:373-386.e10. [PMID: 29224780 DOI: 10.1016/j.cell.2017.11.010] [Citation(s) in RCA: 993] [Impact Index Per Article: 141.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 10/06/2017] [Accepted: 11/03/2017] [Indexed: 12/12/2022]
Abstract
Breast cancer (BC) comprises multiple distinct subtypes that differ genetically, pathologically, and clinically. Here, we describe a robust protocol for long-term culturing of human mammary epithelial organoids. Using this protocol, >100 primary and metastatic BC organoid lines were generated, broadly recapitulating the diversity of the disease. BC organoid morphologies typically matched the histopathology, hormone receptor status, and HER2 status of the original tumor. DNA copy number variations as well as sequence changes were consistent within tumor-organoid pairs and largely retained even after extended passaging. BC organoids furthermore populated all major gene-expression-based classification groups and allowed in vitro drug screens that were consistent with in vivo xeno-transplantations and patient response. This study describes a representative collection of well-characterized BC organoids available for cancer research and drug development, as well as a strategy to assess in vitro drug response in a personalized fashion.
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Affiliation(s)
- Norman Sachs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Foundation Hubrecht Organoid Technology (HUB), Yalelaan 62, 3584 CM Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Joep de Ligt
- Center for Molecular Medicine, Department of Genetics, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Oded Kopper
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Gergana Bounova
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Fleur Weeber
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Anjali Vanita Balgobind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Foundation Hubrecht Organoid Technology (HUB), Yalelaan 62, 3584 CM Utrecht, the Netherlands
| | - Karin Wind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ana Gracanin
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ruben van Boxtel
- Center for Molecular Medicine, Department of Genetics, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Alexandra Alves Duarte
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Daphne Lelieveld
- Cell Screening Core, Department of Cell Biology, Center for Molecular Medicine, University Medical Center, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Arne van Hoeck
- Center for Molecular Medicine, Department of Genetics, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Robert Frans Ernst
- Center for Molecular Medicine, Department of Genetics, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Francis Blokzijl
- Center for Molecular Medicine, Department of Genetics, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Isaac Johannes Nijman
- Center for Molecular Medicine, Department of Genetics, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Marlous Hoogstraat
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging (MCCA), Preclinical Intervention Unit, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David Anthony Egan
- Cell Screening Core, Department of Cell Biology, Center for Molecular Medicine, University Medical Center, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Vittoria Zinzalla
- Pharmacology and Translational Research, Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Jurgen Moll
- Pharmacology and Translational Research, Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Sylvia Fernandez Boj
- Foundation Hubrecht Organoid Technology (HUB), Yalelaan 62, 3584 CM Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Emile Eugene Voest
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Lodewyk Wessels
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands; Faculty of EEMCS, Delft University of Technology, Delft, the Netherlands
| | - Paul Joannes van Diest
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
| | - Robert Gerhardus Jacob Vries
- Foundation Hubrecht Organoid Technology (HUB), Yalelaan 62, 3584 CM Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine, Department of Genetics, University Medical Center Utrecht, Utrecht University, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, Oncode Institute, 3584 CG Utrecht, the Netherlands.
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39
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Drost J, van Boxtel R, Blokzijl F, Mizutani T, Sasaki N, Sasselli V, de Ligt J, Behjati S, Grolleman JE, van Wezel T, Nik-Zainal S, Kuiper RP, Cuppen E, Clevers H. Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer. Science 2017; 358:234-238. [PMID: 28912133 PMCID: PMC6038908 DOI: 10.1126/science.aao3130] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [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] [Received: 07/06/2017] [Accepted: 09/01/2017] [Indexed: 12/11/2022]
Abstract
Mutational processes underlie cancer initiation and progression. Signatures of these processes in cancer genomes may explain cancer etiology and could hold diagnostic and prognostic value. We developed a strategy that can be used to explore the origin of cancer-associated mutational signatures. We used CRISPR-Cas9 technology to delete key DNA repair genes in human colon organoids, followed by delayed subcloning and whole-genome sequencing. We found that mutation accumulation in organoids deficient in the mismatch repair gene MLH1 is driven by replication errors and accurately models the mutation profiles observed in mismatch repair-deficient colorectal cancers. Application of this strategy to the cancer predisposition gene NTHL1, which encodes a base excision repair protein, revealed a mutational footprint (signature 30) previously observed in a breast cancer cohort. We show that signature 30 can arise from germline NTHL1 mutations.
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Affiliation(s)
- Jarno Drost
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Ruben van Boxtel
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
- Center for Molecular Medicine, Department of Genetics, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Francis Blokzijl
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
- Center for Molecular Medicine, Department of Genetics, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Tomohiro Mizutani
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Nobuo Sasaki
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Valentina Sasselli
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Joep de Ligt
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
- Center for Molecular Medicine, Department of Genetics, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Judith E Grolleman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tom van Wezel
- Departments of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | - Roland P Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Princess Máxima Center for Pediatric Oncology, 3584CT Utrecht, Netherlands
| | - Edwin Cuppen
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands.
- Center for Molecular Medicine, Department of Genetics, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands.
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
- Princess Máxima Center for Pediatric Oncology, 3584CT Utrecht, Netherlands
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40
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Fumagalli A, Drost J, Suijkerbuijk SJE, van Boxtel R, de Ligt J, Offerhaus GJ, Begthel H, Beerling E, Tan EH, Sansom OJ, Cuppen E, Clevers H, van Rheenen J. Genetic dissection of colorectal cancer progression by orthotopic transplantation of engineered cancer organoids. Proc Natl Acad Sci U S A 2017; 114:E2357-E2364. [PMID: 28270604 PMCID: PMC5373343 DOI: 10.1073/pnas.1701219114] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In the adenoma-carcinoma sequence, it is proposed that intestinal polyps evolve through a set of defined mutations toward metastatic colorectal cancer (CRC). Here, we dissect this adenoma-carcinoma sequence in vivo by using an orthotopic organoid transplantation model of human colon organoids engineered to harbor different CRC mutation combinations. We demonstrate that sequential accumulation of oncogenic mutations in Wnt, EGFR, P53, and TGF-β signaling pathways facilitates efficient tumor growth, migration, and metastatic colonization. We show that reconstitution of specific niche signals can restore metastatic growth potential of tumor cells lacking one of the oncogenic mutations. Our findings imply that the ability to metastasize-i.e., to colonize distant sites-is the direct consequence of the loss of dependency on specific niche signals.
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Affiliation(s)
- Arianna Fumagalli
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center (UMC) Utrecht, 3584 CT Utrecht, The Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Jarno Drost
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center (UMC) Utrecht, 3584 CT Utrecht, The Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Saskia J E Suijkerbuijk
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center (UMC) Utrecht, 3584 CT Utrecht, The Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
- Department of Medical Genetics, UMC Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Joep de Ligt
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
- Department of Medical Genetics, UMC Utrecht, 3584 CX, Utrecht, The Netherlands
| | - G Johan Offerhaus
- Department of Pathology, UMC Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center (UMC) Utrecht, 3584 CT Utrecht, The Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Evelyne Beerling
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center (UMC) Utrecht, 3584 CT Utrecht, The Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Ee Hong Tan
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Edwin Cuppen
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
- Department of Medical Genetics, UMC Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center (UMC) Utrecht, 3584 CT Utrecht, The Netherlands;
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
- Princess Máxima Center for Pediatric Oncology, 3584 CT, Utrecht, The Netherlands
| | - Jacco van Rheenen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center (UMC) Utrecht, 3584 CT Utrecht, The Netherlands;
- Cancer Genomics Netherlands, UMC Utrecht, 3584 CG, Utrecht, The Netherlands
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41
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Blokzijl F, de Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, Huch M, Boymans S, Kuijk E, Prins P, Nijman IJ, Martincorena I, Mokry M, Wiegerinck CL, Middendorp S, Sato T, Schwank G, Nieuwenhuis EES, Verstegen MMA, van der Laan LJW, de Jonge J, IJzermans JNM, Vries RG, van de Wetering M, Stratton MR, Clevers H, Cuppen E, van Boxtel R. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 2016; 538:260-264. [PMID: 27698416 PMCID: PMC5536223 DOI: 10.1038/nature19768] [Citation(s) in RCA: 605] [Impact Index Per Article: 75.6] [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] [Received: 03/07/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022]
Abstract
The gradual accumulation of genetic mutations in human adult stem cells (ASCs) during life is associated with various age-related diseases, including cancer. Extreme variation in cancer risk across tissues was recently proposed to depend on the lifetime number of ASC divisions, owing to unavoidable random mutations that arise during DNA replication. However, the rates and patterns of mutations in normal ASCs remain unknown. Here we determine genome-wide mutation patterns in ASCs of the small intestine, colon and liver of human donors with ages ranging from 3 to 87 years by sequencing clonal organoid cultures derived from primary multipotent cells. Our results show that mutations accumulate steadily over time in all of the assessed tissue types, at a rate of approximately 40 novel mutations per year, despite the large variation in cancer incidence among these tissues. Liver ASCs, however, have different mutation spectra compared to those of the colon and small intestine. Mutational signature analysis reveals that this difference can be attributed to spontaneous deamination of methylated cytosine residues in the colon and small intestine, probably reflecting their high ASC division rate. In liver, a signature with an as-yet-unknown underlying mechanism is predominant. Mutation spectra of driver genes in cancer show high similarity to the tissue-specific ASC mutation spectra, suggesting that intrinsic mutational processes in ASCs can initiate tumorigenesis. Notably, the inter-individual variation in mutation rate and spectra are low, suggesting tissue-specific activity of common mutational processes throughout life.
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Affiliation(s)
- Francis Blokzijl
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Joep de Ligt
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Myrthe Jager
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Valentina Sasselli
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Sophie Roerink
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Nobuo Sasaki
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Meritxell Huch
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Pjotr Prins
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Isaac J Nijman
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Inigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michal Mokry
- Department of Pediatrics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Caroline L Wiegerinck
- Department of Pediatrics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Sabine Middendorp
- Department of Pediatrics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Toshiro Sato
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Gerald Schwank
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Edward E S Nieuwenhuis
- Department of Pediatrics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Monique M A Verstegen
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Jeroen de Jonge
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Jan N M IJzermans
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Robert G Vries
- Foundation Hubrecht Organoid Technology (HUB), Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Marc van de Wetering
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Ruben van Boxtel
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
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Baker LA, Tiriac H, Corbo V, Boj SF, Hwang CI, Chio IIC, Engle DD, Jager M, Ponz-Sarvise M, Spector MS, Gracanin A, Oni T, Yu KH, Boxtel RV, Huch M, Rivera KD, Wilson JP, Feigin ME, Öhlund D, Handly-Santana A, Ardito-Abraham CM, Ludwig M, Elyada E, Alagesan B, Biffi G, Yordanov GN, Delcuze B, Creighton B, Wright K, Park Y, Morsink FH, Molenaar IQ, Rinkes IHB, Cuppen E, Hao Y, Jin Y, Nijman IJ, Iacobuzio-Donahue C, Leach SD, Pappin DJ, Hammell M, Klimstra DS, Basturk O, Hruban RH, Offerhaus GJ, Vries RG, Clevers H, Tuveson DA. Abstract B16: Using human patient-derived organoids to identify genetic dependencies in pancreatic cancer. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.pdx16-b16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal malignancies due to its late diagnosis and limited response to treatment. Tractable model systems to interrogate pathways involved in pancreatic tumorigenesis and to probe individual responses to novel therapies are urgently needed. To that end, we established methods to culture normal and neoplastic pancreatic duct cells as three-dimensional organoid cultures. Pancreatic organoids can be rapidly generated from resected tumors or fine needle biopsies, survive cryopreservation, and exhibit ductal- and disease-stage-specific characteristics. Following orthotopic transplant, neoplastic organoids recapitulated the full spectrum of tumor development by forming early-grade neoplasms that progressed to locally invasive and metastatic carcinomas, demonstrating the utility of organoids to model the stages of PDA tumorigenesis. Monolayer cell lines were generated from organoid cultures with high efficiency, creating a diverse collection of new PDA cell lines. To better understand pathways involved in PDA progression, we performed transcriptomic and proteomic analyses of murine organoids derived from normal pancreatic ducts, pancreatic intraepithelial neoplasias (PanINs), and PDAs. These datasets revealed expression changes associated with early and late pancreatic tumorigenesis. To identify genes dysregulated during pancreatic tumorigenesis whose depletion impaired human PDA cells, a CRISPR-Cas competition assay was employed. Taken together, pancreatic organoids offer a novel model system for studying pancreatic cancer biology and can be used to screen for genetic dependencies in PDA.
Citation Format: Lindsey A. Baker, Hervé Tiriac, Vincenzo Corbo, Sylvia F. Boj, Chang-il Hwang, Iok In Christine Chio, Danielle D. Engle, Myrthe Jager, Mariano Ponz-Sarvise, Mona S. Spector, Ana Gracanin, Tobiloba Oni, Kenneth H. Yu, Ruben van Boxtel, Meritxell Huch, Keith D. Rivera, John P. Wilson, Michael E. Feigin, Daniel Öhlund, Abram Handly-Santana, Christine M. Ardito-Abraham, Michael Ludwig, Ela Elyada, Brinda Alagesan, Giulia Biffi, Georgi N. Yordanov, Bethany Delcuze, Brianna Creighton, Kevin Wright, Youngkyu Park, Folkert H.M. Morsink, I. Quintus Molenaar, Inne H. Borel Rinkes, Edwin Cuppen, Yuan Hao, Ying Jin, Isaac J. Nijman, Christine Iacobuzio-Donahue, Steven D. Leach, Darryl J. Pappin, Molly Hammell, David S. Klimstra, Olca Basturk, Ralph H. Hruban, George Johan Offerhaus, Robert G.J. Vries, Hans Clevers, David A. Tuveson. Using human patient-derived organoids to identify genetic dependencies in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B16.
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Affiliation(s)
| | - Hervé Tiriac
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - Sylvia F. Boj
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | | | | | | | - Myrthe Jager
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | | | | | - Ana Gracanin
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | - Tobiloba Oni
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Kenneth H. Yu
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Ruben van Boxtel
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | - Meritxell Huch
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | | | | | | | - Daniel Öhlund
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | | | | | - Ela Elyada
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - Giulia Biffi
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | | | | | - Kevin Wright
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Youngkyu Park
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | | | | | - Edwin Cuppen
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | - Yuan Hao
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Ying Jin
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Isaac J. Nijman
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | | | | | | | - Molly Hammell
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - Olca Basturk
- 6Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Robert G.J. Vries
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
| | - Hans Clevers
- 3Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, Netherlands,
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Homberg JR, Olivier JDA, VandenBroeke M, Youn J, Ellenbroek AK, Karel P, Shan L, van Boxtel R, Ooms S, Balemans M, Langedijk J, Muller M, Vriend G, Cools AR, Cuppen E, Ellenbroek BA. The role of the dopamine D1 receptor in social cognition: studies using a novel genetic rat model. Dis Model Mech 2016; 9:1147-1158. [PMID: 27483345 PMCID: PMC5087833 DOI: 10.1242/dmm.024752] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/04/2016] [Indexed: 01/25/2023] Open
Abstract
Social cognition is an endophenotype that is impaired in schizophrenia and several other (comorbid) psychiatric disorders. One of the modulators of social cognition is dopamine, but its role is not clear. The effects of dopamine are mediated through dopamine receptors, including the dopamine D1 receptor (Drd1). Because current Drd1 receptor agonists are not Drd1 selective, pharmacological tools are not sufficient to delineate the role of the Drd1. Here, we describe a novel rat model with a genetic mutation in Drd1 in which we measured basic behavioural phenotypes and social cognition. The I116S mutation was predicted to render the receptor less stable. In line with this computational prediction, this Drd1 mutation led to a decreased transmembrane insertion of Drd1, whereas Drd1 expression, as measured by Drd1 mRNA levels, remained unaffected. Owing to decreased transmembrane Drd1 insertion, the mutant rats displayed normal basic motoric and neurological parameters, as well as locomotor activity and anxiety-like behaviour. However, measures of social cognition like social interaction, scent marking, pup ultrasonic vocalizations and sociability, were strongly reduced in the mutant rats. This profile of the Drd1 mutant rat offers the field of neuroscience a novel genetic rat model to study a series of psychiatric disorders including schizophrenia, autism, depression, bipolar disorder and drug addiction.
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Affiliation(s)
- Judith R Homberg
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen 6525 EZ, The Netherlands
| | - Jocelien D A Olivier
- Department of Neurobiology, Unit Behavioural Neuroscience, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9700 CC, The Netherlands
| | - Marie VandenBroeke
- Victoria University of Wellington, School of Psychology, PO Box 600, Wellington 6040, New Zealand
| | - Jiun Youn
- Victoria University of Wellington, School of Psychology, PO Box 600, Wellington 6040, New Zealand
| | - Arabella K Ellenbroek
- Victoria University of Wellington, School of Psychology, PO Box 600, Wellington 6040, New Zealand
| | - Peter Karel
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen 6525 EZ, The Netherlands
| | - Ling Shan
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen 6525 EZ, The Netherlands
| | - Ruben van Boxtel
- Hubrecht Institute, KNAW and University Medical Centre Utrecht, Utrecht 3584 CT, The Netherlands
| | - Sharon Ooms
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen 6525 EZ, The Netherlands
| | - Monique Balemans
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen 6525 EZ, The Netherlands
| | - Jacqueline Langedijk
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen 6525 EZ, The Netherlands
| | - Mareike Muller
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen 6525 EZ, The Netherlands
| | - Gert Vriend
- CMBI, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, Nijmegen 6525 GA, The Netherlands
| | - Alexander R Cools
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen 6525 EZ, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, KNAW and University Medical Centre Utrecht, Utrecht 3584 CT, The Netherlands
| | - Bart A Ellenbroek
- Victoria University of Wellington, School of Psychology, PO Box 600, Wellington 6040, New Zealand
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Karthaus WR, Iaquinta PJ, Drost J, Gracanin A, van Boxtel R, Wongvipat J, Dowling CM, Gao D, Begthel H, Sachs N, Vries RGJ, Cuppen E, Chen Y, Sawyers CL, Clevers HC. Identification of multipotent luminal progenitor cells in human prostate organoid cultures. Cell 2014; 159:163-175. [PMID: 25201529 DOI: 10.1016/j.cell.2014.08.017] [Citation(s) in RCA: 506] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/08/2014] [Accepted: 08/18/2014] [Indexed: 12/30/2022]
Abstract
The prostate gland consists of basal and luminal cells arranged as pseudostratified epithelium. In tissue recombination models, only basal cells reconstitute a complete prostate gland, yet murine lineage-tracing experiments show that luminal cells generate basal cells. It has remained challenging to address the molecular details of these transitions and whether they apply to humans, due to the lack of culture conditions that recapitulate prostate gland architecture. Here, we describe a 3D culture system that supports long-term expansion of primary mouse and human prostate organoids, composed of fully differentiated CK5+ basal and CK8+ luminal cells. Organoids are genetically stable, reconstitute prostate glands in recombination assays, and can be experimentally manipulated. Single human luminal and basal cells give rise to organoids, yet luminal-cell-derived organoids more closely resemble prostate glands. These data support a luminal multilineage progenitor cell model for prostate tissue and establish a robust, scalable system for mechanistic studies.
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Affiliation(s)
- Wouter R Karthaus
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, Netherlands
| | - Phillip J Iaquinta
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jarno Drost
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, Netherlands
| | - Ana Gracanin
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, Netherlands
| | - Ruben van Boxtel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, Netherlands
| | - John Wongvipat
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Catherine M Dowling
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, Netherlands
| | - Norman Sachs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, Netherlands
| | - Robert G J Vries
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, Netherlands
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute
| | - Hans C Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, Netherlands.
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45
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Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G, Tarpey PS, Roerink S, Blokker J, Maddison M, Mudie L, Robinson B, Nik-Zainal S, Campbell P, Goldman N, van de Wetering M, Cuppen E, Clevers H, Stratton MR. Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature 2014; 513:422-425. [PMID: 25043003 DOI: 10.1038/nature13448] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 05/07/2014] [Indexed: 02/08/2023]
Abstract
The somatic mutations present in the genome of a cell accumulate over the lifetime of a multicellular organism. These mutations can provide insights into the developmental lineage tree, the number of divisions that each cell has undergone and the mutational processes that have been operative. Here we describe whole genomes of clonal lines derived from multiple tissues of healthy mice. Using somatic base substitutions, we reconstructed the early cell divisions of each animal, demonstrating the contributions of embryonic cells to adult tissues. Differences were observed between tissues in the numbers and types of mutations accumulated by each cell, which likely reflect differences in the number of cell divisions they have undergone and varying contributions of different mutational processes. If somatic mutation rates are similar to those in mice, the results indicate that precise insights into development and mutagenesis of normal human cells will be possible.
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Affiliation(s)
- Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.,Department of Paediatrics, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Meritxell Huch
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, CancerGenomiCs.nl & University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands.,Present address: Wellcome Trust / Cancer Research UK Gurdon Institute, Tennis Court Road, CB2 1QN, Cambridge, UK
| | - Ruben van Boxtel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, CancerGenomiCs.nl & University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Wouter Karthaus
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, CancerGenomiCs.nl & University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Asif U Tamuri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Inigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Mia Petljak
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Patrick S Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Sophie Roerink
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Joyce Blokker
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, CancerGenomiCs.nl & University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Mark Maddison
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Laura Mudie
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ben Robinson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.,East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
| | - Peter Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Marc van de Wetering
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, CancerGenomiCs.nl & University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, CancerGenomiCs.nl & University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, CancerGenomiCs.nl & University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
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46
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Abstract
Maintaining an immune balance between a chronic inflammatory state and autoimmunity is regulated at multiple levels by complex cellular signaling mechanisms. Numerous immune stimulatory and inhibitory signals converge on a large variety of transcriptional regulators. One key transcriptional regulator of immune homeostasis is FOXP3, which is a member of the Forkhead Box P subfamily of transcription factors and was shown to be essential for the development and maintenance of regulatory T cells. However, other FOXP members have received less attention in relation to a role in immune regulation. Still, recent developments point toward a general important regulatory role for FOXP proteins in the development and function of the adaptive immune system and establishment of a balanced immune response. Here, we discuss the current knowledge on the role of FOXP proteins in establishing immune homeostasis with an emphasis on T-cell biology. Furthermore, we review and speculate about different modes of regulating general FOXP activity and the function of this in health and disease.
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Affiliation(s)
- Veerle Fleskens
- Department of Cell Biology, University Medical Center Utrecht , Utrecht , The Netherlands
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47
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Vervoort SJ, Lourenço AR, van Boxtel R, Coffer PJ. SOX4 mediates TGF-β-induced expression of mesenchymal markers during mammary cell epithelial to mesenchymal transition. PLoS One 2013; 8:e53238. [PMID: 23301048 PMCID: PMC3536747 DOI: 10.1371/journal.pone.0053238] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [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: 07/02/2012] [Accepted: 11/27/2012] [Indexed: 02/04/2023] Open
Abstract
The epithelial to mensenchymal transition program regulates various aspects of embryonic development and tissue homeostasis, but aberrant activation of this pathway in cancer contributes to tumor progression and metastasis. TGF-β potently induces an epithelial to mensenchymal transition in cancers of epithelial origin by inducing transcriptional changes mediated by several key transcription factors. Here, we identify the developmental transcription factor SOX4 as a transcriptional target of TGF-β in immortalized human mammary epithelial cells. SOX4 expression and activity are rapidly induced in the early stages of the TGF-β-induced epithelial to mensenchymal transition. We demonstrate that conditional activation of Sox4 is sufficient to induce the expression of N-cadherin and additional mesenchymal markers including vimentin and fibronectin, but fails to induce complete EMT as no changes are observed in the expression of E-cadherin and β-catenin. Moreover, shRNA-mediated knockdown of SOX4 significantly delays TGF-β-induced mRNA and protein expression of mesenchymal markers. Taken together, these data suggest that TGF-β-mediated increased expression of SOX4 is required for the induction of a mesenchymal phenotype during EMT in human mammary epithelial cells.
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Affiliation(s)
- Stephin J. Vervoort
- Department of Cell Biology, University Medical Centre, Utrecht, The Netherlands
- Division of Pediatrics, Wilhelmina Children’s Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Ana Rita Lourenço
- Department of Cell Biology, University Medical Centre, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Department of Cell Biology, University Medical Centre, Utrecht, The Netherlands
| | - Paul J. Coffer
- Department of Cell Biology, University Medical Centre, Utrecht, The Netherlands
- Division of Pediatrics, Wilhelmina Children’s Hospital, University Medical Centre, Utrecht, The Netherlands
- * E-mail:
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48
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Eijkelenboom A, Mokry M, de Wit E, Smits LM, Polderman PE, van Triest MH, van Boxtel R, Schulze A, de Laat W, Cuppen E, Burgering BMT. Genome-wide analysis of FOXO3 mediated transcription regulation through RNA polymerase II profiling. Mol Syst Biol 2013; 9:638. [PMID: 23340844 PMCID: PMC3564262 DOI: 10.1038/msb.2012.74] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 12/10/2012] [Indexed: 12/25/2022] Open
Abstract
Forkhead box O (FOXO) transcription factors are key players in diverse cellular processes affecting tumorigenesis, stem cell maintenance and lifespan. To gain insight into the mechanisms of FOXO-regulated target gene expression, we studied genome-wide effects of FOXO3 activation. Profiling RNA polymerase II changes shows that FOXO3 regulates gene expression through transcription initiation. Correlative analysis of FOXO3 and RNA polymerase II ChIP-seq profiles demonstrates FOXO3 to act as a transcriptional activator. Furthermore, this analysis reveals a significant part of FOXO3 gene regulation proceeds through enhancer regions. FOXO3 binds to pre-existing enhancers and further activates these enhancers as shown by changes in histone acetylation and RNA polymerase II recruitment. In addition, FOXO3-mediated enhancer activation correlates with regulation of adjacent genes and pre-existence of chromatin loops between FOXO3 bound enhancers and target genes. Combined, our data elucidate how FOXOs regulate gene transcription and provide insight into mechanisms by which FOXOs can induce different gene expression programs depending on chromatin architecture.
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Affiliation(s)
- Astrid Eijkelenboom
- Department of Molecular Cancer Research, University Medical Centre, Utrecht, The Netherlands
| | - Michal Mokry
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Centre, Utrecht, The Netherlands
| | - Elzo de Wit
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Centre, Utrecht, The Netherlands
| | - Lydia M Smits
- Department of Molecular Cancer Research, University Medical Centre, Utrecht, The Netherlands
| | - Paulien E Polderman
- Department of Molecular Cancer Research, University Medical Centre, Utrecht, The Netherlands
| | - Miranda H van Triest
- Department of Molecular Cancer Research, University Medical Centre, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Department of Cell Biology, University Medical Centre, Utrecht, The Netherlands
| | - Almut Schulze
- Gene Expression Analysis Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Wouter de Laat
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Centre, Utrecht, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Centre, Utrecht, The Netherlands
| | - Boudewijn M T Burgering
- Department of Molecular Cancer Research, University Medical Centre, Utrecht, The Netherlands
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Mul JD, van Boxtel R, Bergen DJM, Brans MAD, Brakkee JH, Toonen PW, Garner KM, Adan RAH, Cuppen E. Melanocortin receptor 4 deficiency affects body weight regulation, grooming behavior, and substrate preference in the rat. Obesity (Silver Spring) 2012; 20:612-21. [PMID: 21527895 PMCID: PMC3286758 DOI: 10.1038/oby.2011.81] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 03/04/2011] [Indexed: 12/14/2022]
Abstract
Obesity is caused by an imbalance between energy intake and expenditure and has become a major health-care problem in western society. The central melanocortin system plays a crucial role in the regulation of feeding and energy expenditure, and functional loss of melanocortin receptor 4 (MC4R) is the most common genetic cause of human obesity. In this study, we present the first functional Mc4r knockout model in the rat, resulting from an N-ethyl-N-nitrosourea mutagenesis-induced point mutation. In vitro observations revealed impaired membrane-binding and subsequent nonfunctionality of the receptor, whereas in vivo observations showed that functional loss of MC4R increased body weight, food intake, white adipose mass, and changed substrate preference. In addition, intracerebroventricular (ICV) administration of Agouti-Related Protein(79-129) (AgRP(79-129)), an MC4R inverse agonist, or Melanotan-II (MTII), an MC4R agonist, did affect feeding behavior in wild-type rats but not in homozygous mutant rats, confirming complete loss of MC4R function in vivo. Finally, ICV administration of MTII induced excessive grooming behavior in wild-type rats, whereas this effect was absent in homozygous mutant rats, indicating that MTII-induced grooming behavior is exclusively regulated via MC4R pathways. Taken together, we expect that the MC4R rat model described here will be a valuable tool for studying monogenic obesity in humans. More specifically, the relative big size and increased cognitive capacity of rats as compared to mice will facilitate complex behavioral studies and detailed mechanistic studies regarding central function of MC4R, both of which ultimately may help to further understand the specific mechanisms that induce obesity during loss of MC4R function.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Disease Models, Animal
- Eating
- Energy Metabolism
- Food Preferences
- Grooming
- Obesity/metabolism
- Obesity/physiopathology
- Peptides, Cyclic/pharmacology
- Rats
- Receptor, Melanocortin, Type 4/agonists
- Receptor, Melanocortin, Type 4/deficiency
- Receptor, Melanocortin, Type 4/genetics
- Receptor, Melanocortin, Type 4/metabolism
- Weight Gain
- alpha-MSH/analogs & derivatives
- alpha-MSH/pharmacology
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Affiliation(s)
- Joram D Mul
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
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van Boxtel R, Kuiper RV, Toonen PW, van Heesch S, Hermsen R, de Bruin A, Cuppen E. Homozygous and heterozygous p53 knockout rats develop metastasizing sarcomas with high frequency. Am J Pathol 2011; 179:1616-22. [PMID: 21854749 DOI: 10.1016/j.ajpath.2011.06.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 06/07/2011] [Accepted: 06/14/2011] [Indexed: 11/17/2022]
Abstract
The TP53 tumor suppressor gene is mutated in the majority of human cancers. Inactivation of p53 in a variety of animal models results in early-onset tumorigenesis, reflecting the importance of p53 as a gatekeeper tumor suppressor. We generated a mutant Tp53 allele in the rat using a target-selected mutagenesis approach. Here, we report that homozygosity for this allele results in complete loss of p53 function. Homozygous mutant rats predominantly develop sarcomas with an onset of 4 months of age with a high occurrence of pulmonary metastases. Heterozygous rats develop sarcomas starting at 8 months of age. Molecular analysis revealed that these tumors exhibit a loss-of-heterozygosity of the wild-type Tp53 allele. These unique features make this rat highly complementary to other rodent p53 knockout models and a versatile tool for investigating tumorigenesis processes as well as genotoxic studies.
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Affiliation(s)
- Ruben van Boxtel
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Cancer Genomics Center, KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
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