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Sun CX, Daniel P, Bradshaw G, Shi H, Loi M, Chew N, Parackal S, Tsui V, Liang Y, Koptyra M, Adjumain S, Sun C, Chong WC, Fernando D, Drinkwater C, Tourchi M, Habarakada D, Sooraj D, Carvalho D, Storm PB, Baubet V, Sayles LC, Fernandez E, Nguyen T, Pörksen M, Doan A, Crombie DE, Panday M, Zhukova N, Dun MD, Ludlow LE, Day B, Stringer BW, Neeman N, Rubens JA, Raabe EH, Vinci M, Tyrrell V, Fletcher JI, Ekert PG, Dumevska B, Ziegler DS, Tsoli M, Syed Sulaiman NF, Loh AHP, Low SYY, Sweet-Cordero EA, Monje M, Resnick A, Jones C, Downie P, Williams B, Rosenbluh J, Gough D, Cain JE, Firestein R. Generation and multi-dimensional profiling of a childhood cancer cell line atlas defines new therapeutic opportunities. Cancer Cell 2023; 41:660-677.e7. [PMID: 37001527 DOI: 10.1016/j.ccell.2023.03.007] [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: 09/28/2022] [Revised: 12/21/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
Abstract
Pediatric solid and central nervous system tumors are the leading cause of cancer-related death among children. Identifying new targeted therapies necessitates the use of pediatric cancer models that faithfully recapitulate the patient's disease. However, the generation and characterization of pediatric cancer models has significantly lagged behind adult cancers, underscoring the urgent need to develop pediatric-focused cell line resources. Herein, we establish a single-site collection of 261 cell lines, including 224 pediatric cell lines representing 18 distinct extracranial and brain childhood tumor types. We subjected 182 cell lines to multi-omics analyses (DNA sequencing, RNA sequencing, DNA methylation), and in parallel performed pharmacological and genetic CRISPR-Cas9 loss-of-function screens to identify pediatric-specific treatment opportunities and biomarkers. Our work provides insight into specific pathway vulnerabilities in molecularly defined pediatric tumor classes and uncovers biomarker-linked therapeutic opportunities of clinical relevance. Cell line data and resources are provided in an open access portal.
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Affiliation(s)
- Claire Xin Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Paul Daniel
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Gabrielle Bradshaw
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Hui Shi
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Melissa Loi
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Nicole Chew
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Sarah Parackal
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Vanessa Tsui
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Yuqing Liang
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Mateusz Koptyra
- Center for Data Driven Discovery in Biomedicine, Neurosurgery Department, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shazia Adjumain
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Christie Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Wai Chin Chong
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Dasun Fernando
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Caroline Drinkwater
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Motahhareh Tourchi
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Dilru Habarakada
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Dhanya Sooraj
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Diana Carvalho
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Phillip B Storm
- Center for Data Driven Discovery in Biomedicine, Neurosurgery Department, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Valerie Baubet
- Center for Data Driven Discovery in Biomedicine, Neurosurgery Department, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Leanne C Sayles
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elisabet Fernandez
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Thy Nguyen
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Mia Pörksen
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia; Department of Paediatrics, University of Lübeck, 23562 Lübeck, Germany
| | - Anh Doan
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Duncan E Crombie
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Monty Panday
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Nataliya Zhukova
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia; Children's Cancer Centre, Monash Children's Hospital, Monash Health, Clayton, VIC 3168, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3168, Australia
| | - Matthew D Dun
- Hunter Cancer Research Alliance, University of Newcastle, Callaghan, NSW 2308, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Louise E Ludlow
- Children's Cancer Centre Biobank, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Bryan Day
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Brett W Stringer
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Naama Neeman
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Jeffrey A Rubens
- Division of Pediatric Oncology, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eric H Raabe
- Division of Pediatric Oncology, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maria Vinci
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital-IRCCS, 00165 Rome, Italy
| | - Vanessa Tyrrell
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Paul G Ekert
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia; Centre for Cancer Immunotherapy, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Department of Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Biljana Dumevska
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - David S Ziegler
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia; Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Maria Tsoli
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Nur Farhana Syed Sulaiman
- Neurosurgical Service, KK Women's and Children's Hospital, Singapore 229899, Singapore; VIVA-KKH Paediatric Brain and Solid Tumours Programme, Singapore 229899, Singapore
| | - Amos Hong Pheng Loh
- VIVA-KKH Paediatric Brain and Solid Tumours Programme, Singapore 229899, Singapore; Duke-NUS Medical School, Singapore 169857, Singapore
| | - Sharon Yin Yee Low
- Neurosurgical Service, KK Women's and Children's Hospital, Singapore 229899, Singapore; VIVA-KKH Paediatric Brain and Solid Tumours Programme, Singapore 229899, Singapore; SingHealth-Duke NUS Neuroscience Academic Clinical Programme, Singapore 308433, Singapore; SingHealth-Duke NUS Paediatrics Academic Clinical Programme, Singapore 229899, Singapore
| | | | - Michelle Monje
- Department of Neurology, Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Adam Resnick
- Center for Data Driven Discovery in Biomedicine, Neurosurgery Department, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chris Jones
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Peter Downie
- Children's Cancer Centre, Monash Children's Hospital, Monash Health, Clayton, VIC 3168, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3168, Australia
| | - Bryan Williams
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Joseph Rosenbluh
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3168, Australia
| | - Daniel Gough
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Jason E Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia.
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Daniel P, Sun C, Koptyra M, Drinkwater C, Chew N, Bradshaw G, Loi M, Shi C, Tourchi M, Parackal S, Chong WC, Fernando D, Adjumain S, Nguyen H, Habarakada D, Sooraj D, Crombie D, Zhukova N, Jones C, Rubens J, Raabe E, Vinci M, Dun M, Ludlow L, Nazarian J, Fletcher J, Ekert P, Ziegler D, Loh AHP, Low SYY, Monje M, Neeman N, Williams B, Resnick A, Gough D, Cain J, Firestein R. MODL-17. The Childhood Brain Cancer Cell Line Atlas: A Resource for Biomarker Identification and Therapeutic Development. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.640] [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: 11/13/2022] Open
Abstract
Abstract
Cell lines represent the most versatile and widely used models of cancer and, as such, are critical for identifying and advancing new therapies. Strikingly, there is a significant gap in both the number of childhood brain cancer cell lines and their characterisation compared to their adult counterparts. To address this inequity, we established a childhood brain cancer cell line atlas (publicly available at vicpcc.org.au/dashboard) encompassing over 180 childhood CNS-derived cell lines, representing 20 tumour types and 11 molecular subtypes. Cell lines are characterized by whole genome, RNA-sequencing, phospho- and total proteomics, DNA methylation and ATAC-seq analyses. Multi-omic factor analysis revealed distinct lineage-specified classification of our cell line cohort. In parallel, high throughput drug and CRISPR/Cas9 screens were conducted to map the functional dependencies in over 70 childhood CNS cell lines, including 47 paediatric high grade glioma models. These screens identified both lineage and molecular-subtype specific genetic and drug dependencies, underscoring the utility of this wide-scale approach. Machine based learning approaches to predict genotype-phenotype correlations uncovered distinct paediatric-specific biomarkers of growth dependency, highlighting the unique genetic wiring underlying paediatric CNS tumours. Finally, by integrating functional, molecular and drug profiles of paediatric CNS cell lines, we construct a system to prioritize investigation of novel therapeutic target-biomarkers pairs in specific CNS tumour types.
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Affiliation(s)
- Paul Daniel
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Claire Sun
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Mateusz Koptyra
- Children's Hospital of Philadelphia , Philadelphia, PA , USA
- Childrens Brain Tumor Network , Philadelphia, PA , USA
| | | | - Nicole Chew
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | | | - Melissa Loi
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Claire Shi
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | | | - Sarah Parackal
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Wai Chin Chong
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Dasun Fernando
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Shazia Adjumain
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Hoang Nguyen
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | | | - Dhanya Sooraj
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Duncan Crombie
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | | | - Chris Jones
- Institute of Cancer Research , London , United Kingdom
| | - Jeffrey Rubens
- Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Eric Raabe
- Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Maria Vinci
- Bambino Gesù Children's Hospital , Rome , Italy
| | - Matt Dun
- University of Newcastle , Newcastle, NSW , Australia
| | - Louise Ludlow
- Royal Children's Hospital , Melbourne, VIC , Australia
| | | | - Jamie Fletcher
- Children's Cancer Institute of Australia , Sydney, NSW , Australia
| | - Paul Ekert
- Children's Cancer Institute of Australia , Sydney, NSW , Australia
| | - David Ziegler
- Children's Cancer Institute of Australia , Sydney, NSW , Australia
| | | | | | | | - Naama Neeman
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Bryan Williams
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Adam Resnick
- Children's Hospital of Philadelphia , Philadelphia, PA , USA
- Childrens Brain Tumor Network , Philadelphia, PA , USA
| | - Daniel Gough
- Hudson Institute of Medical Research , Clayton, VIC , Australia
| | - Jason Cain
- Hudson Institute of Medical Research , Clayton, VIC , Australia
- Childrens Brain Tumor Network , Philadelphia, PA , USA
| | - Ron Firestein
- Hudson Institute of Medical Research , Clayton, VIC , Australia
- Childrens Brain Tumor Network , Philadelphia, PA , USA
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