1
|
Liu NQ, Paassen I, Custers L, Zeller P, Teunissen H, Ayyildiz D, He J, Buhl JL, Hoving EW, van Oudenaarden A, de Wit E, Drost J. SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors. Nat Commun 2023; 14:7762. [PMID: 38040699 PMCID: PMC10692191 DOI: 10.1038/s41467-023-43498-3] [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: 01/22/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023] Open
Abstract
Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer, yet their contribution to tumorigenesis remains in many cases poorly understood. Here, we study derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids reveals a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently reveal patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 activates patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
Collapse
Affiliation(s)
- Ning Qing Liu
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Hematology, Erasmus Medical Center (MC) Cancer Institute, Rotterdam, the Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Peter Zeller
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Dilara Ayyildiz
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Jiayou He
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Juliane Laura Buhl
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| |
Collapse
|
2
|
Young MD, Mitchell TJ, Custers L, Margaritis T, Morales-Rodriguez F, Kwakwa K, Khabirova E, Kildisiute G, Oliver TRW, de Krijger RR, van den Heuvel-Eibrink MM, Comitani F, Piapi A, Bugallo-Blanco E, Thevanesan C, Burke C, Prigmore E, Ambridge K, Roberts K, Braga FAV, Coorens THH, Del Valle I, Wilbrey-Clark A, Mamanova L, Stewart GD, Gnanapragasam VJ, Rampling D, Sebire N, Coleman N, Hook L, Warren A, Haniffa M, Kool M, Pfister SM, Achermann JC, He X, Barker RA, Shlien A, Bayraktar OA, Teichmann SA, Holstege FC, Meyer KB, Drost J, Straathof K, Behjati S. Single cell derived mRNA signals across human kidney tumors. Nat Commun 2021; 12:3896. [PMID: 34162837 PMCID: PMC8222373 DOI: 10.1038/s41467-021-23949-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 11/06/2020] [Accepted: 05/25/2021] [Indexed: 01/16/2023] Open
Abstract
Tumor cells may share some patterns of gene expression with their cell of origin, providing clues into the differentiation state and origin of cancer. Here, we study the differentiation state and cellular origin of 1300 childhood and adult kidney tumors. Using single cell mRNA reference maps of normal tissues, we quantify reference "cellular signals" in each tumor. Quantifying global differentiation, we find that childhood tumors exhibit fetal cellular signals, replacing the presumption of "fetalness" with a quantitative measure of immaturity. By contrast, in adult cancers our assessment refutes the suggestion of dedifferentiation towards a fetal state in most cases. We find an intimate connection between developmental mesenchymal populations and childhood renal tumors. We demonstrate the diagnostic potential of our approach with a case study of a cryptic renal tumor. Our findings provide a cellular definition of human renal tumors through an approach that is broadly applicable to human cancer.
Collapse
Affiliation(s)
- Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | | | - Francisco Morales-Rodriguez
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Kwasi Kwakwa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Eleonora Khabirova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gerda Kildisiute
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Alice Piapi
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | | | | | - Christina Burke
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kirsty Ambridge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ignacio Del Valle
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Vincent J Gnanapragasam
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Urology Translational Research and Clinical Trials office, Cambridge Biomedical Campus Cambridge CB2 0QQ University of Cambridge, Cambridge, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Neil Sebire
- NIHR Great Ormond Street Hospital BRC and Institute of Child Health, London, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Anne Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Intitute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hopp Children´s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children´s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology, Heidelberg, Germany
- Heidelberg University Hospital, Department of Pediatric Hematology and Oncology, Heidelberg, Germany
| | - John C Achermann
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Xiaoling He
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Roger A Barker
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Omer A Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Frank C Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Karin Straathof
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| |
Collapse
|
3
|
Custers L, Khabirova E, Coorens THH, Oliver TRW, Calandrini C, Young MD, Vieira Braga FA, Ellis P, Mamanova L, Segers H, Maat A, Kool M, Hoving EW, van den Heuvel-Eibrink MM, Nicholson J, Straathof K, Hook L, de Krijger RR, Trayers C, Allinson K, Behjati S, Drost J. Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours. Nat Commun 2021; 12:1407. [PMID: 33658498 PMCID: PMC7930245 DOI: 10.1038/s41467-021-21675-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 06/01/2020] [Accepted: 02/05/2021] [Indexed: 11/08/2022] Open
Abstract
Malignant rhabdoid tumour (MRT) is an often lethal childhood cancer that, like many paediatric tumours, is thought to arise from aberrant fetal development. The embryonic root and differentiation pathways underpinning MRT are not firmly established. Here, we study the origin of MRT by combining phylogenetic analyses and single-cell mRNA studies in patient-derived organoids. Comparison of somatic mutations shared between cancer and surrounding normal tissues places MRT in a lineage with neural crest-derived Schwann cells. Single-cell mRNA readouts of MRT differentiation, which we examine by reverting the genetic driver mutation underpinning MRT, SMARCB1 loss, suggest that cells are blocked en route to differentiating into mesenchyme. Quantitative transcriptional predictions indicate that combined HDAC and mTOR inhibition mimic MRT differentiation, which we confirm experimentally. Our study defines the developmental block of MRT and reveals potential differentiation therapies.
Collapse
Affiliation(s)
- Lars Custers
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Oncode Institute, 3584CS, Utrecht, the Netherlands
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Camilla Calandrini
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Oncode Institute, 3584CS, Utrecht, the Netherlands
| | - Matthew D Young
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | | | - Peter Ellis
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | - Heidi Segers
- Department of Pediatric Hemato-Oncology, University Hospital Leuven, Leuven, Belgium
| | - Arie Maat
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, 69120, Heidelberg, Germany
| | - Eelco W Hoving
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
| | | | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Karin Straathof
- UCL Great Ormond Street Hospital Institute of Child Health Biomedical Research Centre, London, WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Department of Pathology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Claire Trayers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Kieren Allinson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands.
- Oncode Institute, 3584CS, Utrecht, the Netherlands.
| |
Collapse
|
4
|
Abstract
A subset of pediatric tumors affects very young children and are thought to arise during fetal life. A common theme is that these embryonal tumors hijack developmental programs, causing a block in differentiation and, as a consequence, unrestricted proliferation. Embryonal tumors, therefore typically maintain an embryonic gene signature not found in their differentiated progeny. Still, the processes underpinning malignant transformation remain largely unknown, which is hampering therapeutic innovation. To gain more insight into these processes, in vitro and in vivo research models are indispensable. However, embryonic development is an extremely dynamic process with continuously changing cellular identities, making it challenging to define cells-of-origin. This is crucial for the development of representative models, as targeting the wrong cell or targeting a cell within an incorrect developmental time window can result in completely different phenotypes. Recent innovations in in vitro cell models may provide more versatile platforms to study embryonal tumors in a scalable manner. In this review, we outline different in vitro models that can be explored to study embryonal tumorigenesis and for therapy development.
Collapse
Affiliation(s)
- Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| |
Collapse
|
5
|
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.
Collapse
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,
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|