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Gilbertson RJ, Behjati S, Böttcher AL, Bronner ME, Burridge M, Clausing H, Clifford H, Danaher T, Donovan LK, Drost J, Eggermont AMM, Emerson C, Flores MG, Hamerlik P, Jabado N, Jones A, Kaessmann H, Kleinman CL, Kool M, Kutscher LM, Lindberg G, Linnane E, Marioni JC, Maris JM, Monje M, Macaskill A, Niederer S, Northcott PA, Peeters E, Plieger-van Solkema W, Preußner L, Rios AC, Rippe K, Sandford P, Sgourakis NG, Shlien A, Smith P, Straathof K, Sullivan PJ, Suvà ML, Taylor MD, Thompson E, Vento-Tormo R, Wainwright BJ, Wechsler-Reya RJ, Westermann F, Winslade S, Al-Lazikani B, Pfister SM. The Virtual Child. Cancer Discov 2024; 14:663-668. [PMID: 38571421 DOI: 10.1158/2159-8290.cd-23-1500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
SUMMARY We are building the world's first Virtual Child-a computer model of normal and cancerous human development at the level of each individual cell. The Virtual Child will "develop cancer" that we will subject to unlimited virtual clinical trials that pinpoint, predict, and prioritize potential new treatments, bringing forward the day when no child dies of cancer, giving each one the opportunity to lead a full and healthy life.
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Affiliation(s)
- Richard J Gilbertson
- CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Anna-Lisa Böttcher
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | | | | | | | | | - Laura K Donovan
- University College London Great Ormond Street Institute of Child Health, United Kingdom
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | | | | | | | - Nada Jabado
- Department of Paediatrics, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Henrick Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Claudia L Kleinman
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Lena M Kutscher
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Emily Linnane
- CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - John C Marioni
- CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, California
| | | | - Steven Niederer
- Turing Research and Innovation Cluster in Digital Twins (TRIC: DT), The Alan Turing Institute, London, United Kingdom
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | | | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Heidelberg, Germany
| | | | - Nikolaos G Sgourakis
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Adam Shlien
- Genetics and Genomics Program, The Hospital for Sick Children, Toronto, Canada
| | - Pete Smith
- Hula Therapeutics, Philadelphia, Pennsylvania
| | - Karin Straathof
- University College London Cancer Institute, London, United Kingdom
- Great Ormond Street Hospital for Children, London, United Kingdom
| | | | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Boston, Massachusetts
| | - Michael D Taylor
- Texas Children's Cancer Center, Hematology-Oncology Section and Department of Pediatrics - Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, Texas
| | | | | | - Brandon J Wainwright
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Robert J Wechsler-Reya
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Bissan Al-Lazikani
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
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2
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Steffin D, Ghatwai N, Montalbano A, Rathi P, Courtney AN, Arnett AB, Fleurence J, Sweidan R, Wang T, Zhang H, Masand P, Maris JM, Martinez D, Pogoriler J, Varadarajan N, Thakkar SG, Lyon D, Lapteva N, Mei Z, Patel K, Lopez-Terrada D, Ramos C, Lulla P, Armaghany T, Grilley BJ, Dotti G, Metelitsa LS, Heslop HE, Brenner MK, Sumazin P, Heczey A. Interleukin-15-armored GPC3-CAR T cells for patients with solid cancers. Res Sq 2024:rs.3.rs-4103623. [PMID: 38645165 PMCID: PMC11030543 DOI: 10.21203/rs.3.rs-4103623/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Interleukin-15 (IL15) promotes the survival of T lymphocytes and enhances the antitumor properties of CAR T cells in preclinical models of solid neoplasms in which CAR T cells have limited efficacy1-4. Glypican-3 (GPC3) is expressed in a group of solid cancers5-10, and here we report the first evaluation in humans of the effects of IL15 co-expression on GPC3-CAR T cells. Cohort 1 patients (NCT02905188/NCT02932956) received GPC3-CAR T cells, which were safe but produced no objective antitumor responses and reached peak expansion at two weeks. Cohort 2 patients (NCT05103631/NCT04377932) received GPC3-CAR T cells that co-expressed IL15 (15.CAR), which mediated significantly increased cell expansion and induced a disease control rate of 66% and antitumor response rate of 33%. Infusion of 15.CAR T cells was associated with increased incidence of cytokine release syndrome, which was rapidly ameliorated by activation of the inducible caspase 9 safety switch. Compared to non-responders, tumor-infiltrating 15.CAR T cells from responders showed repression of SWI/SNF epigenetic regulators and upregulation of FOS and JUN family members as well as genes related to type I interferon signaling. Collectively, these results demonstrate that IL15 increases the expansion, intratumoral survival, and antitumor activity of GPC3-CAR T cells in patients.
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Affiliation(s)
- David Steffin
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Center for Advanced Innate Cell Therapy, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
| | - Nisha Ghatwai
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Center for Advanced Innate Cell Therapy, Baylor College of Medicine, Houston, Texas
| | - Antonino Montalbano
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Center for Advanced Innate Cell Therapy, Baylor College of Medicine, Houston, Texas
| | - Purva Rathi
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Center for Advanced Innate Cell Therapy, Baylor College of Medicine, Houston, Texas
| | - Amy N Courtney
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Center for Advanced Innate Cell Therapy, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Azlann B Arnett
- Center for Advanced Innate Cell Therapy, Baylor College of Medicine, Houston, Texas
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Julien Fleurence
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Ramy Sweidan
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Thao Wang
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Huimin Zhang
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Prakash Masand
- Department of Radiology, Baylor College of Medicine, Houston, Texas
| | - John M Maris
- Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel Martinez
- Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer Pogoriler
- Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Navin Varadarajan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas
| | - Sachin G Thakkar
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Deborah Lyon
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Natasha Lapteva
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Baylor College of Medicine, Houston, Texas
| | - Zhuyong Mei
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Kalyani Patel
- Department of Pathology, Baylor College of Medicine, Houston, Texas
| | | | - Carlos Ramos
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Premal Lulla
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Tannaz Armaghany
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Bambi J Grilley
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Center for Advanced Innate Cell Therapy, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
| | - Gianpietro Dotti
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Leonid S Metelitsa
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Center for Advanced Innate Cell Therapy, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Helen E Heslop
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Malcolm K Brenner
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Immunology and Microbiology, Baylor College of Medicine, Texas
| | - Pavel Sumazin
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Andras Heczey
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Center for Advanced Innate Cell Therapy, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital Liver Tumor Program, Houston, Texas
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3
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Huang M, Fang W, Farrel A, Li L, Chronopoulos A, Nasholm N, Cheng B, Zheng T, Yoda H, Barata MJ, Porras T, Miller ML, Zhen Q, Ghiglieri L, McHenry L, Wang L, Asgharzadeh S, Park J, Gustafson WC, Matthay KK, Maris JM, Weiss WA. ALK upregulates POSTN and WNT signaling to drive neuroblastoma. Cell Rep 2024; 43:113927. [PMID: 38451815 PMCID: PMC11101011 DOI: 10.1016/j.celrep.2024.113927] [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: 08/07/2023] [Revised: 12/29/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor of childhood. While MYCN and mutant anaplastic lymphoma kinase (ALKF1174L) cooperate in tumorigenesis, how ALK contributes to tumor formation remains unclear. Here, we used a human stem cell-based model of neuroblastoma. Mis-expression of ALKF1174L and MYCN resulted in shorter latency compared to MYCN alone. MYCN tumors resembled adrenergic, while ALK/MYCN tumors resembled mesenchymal, neuroblastoma. Transcriptomic analysis revealed enrichment in focal adhesion signaling, particularly the extracellular matrix genes POSTN and FN1 in ALK/MYCN tumors. Patients with ALK-mutant tumors similarly demonstrated elevated levels of POSTN and FN1. Knockdown of POSTN, but not FN1, delayed adhesion and suppressed proliferation of ALK/MYCN tumors. Furthermore, loss of POSTN reduced ALK-dependent activation of WNT signaling. Reciprocally, inhibition of the WNT pathway reduced expression of POSTN and growth of ALK/MYCN tumor cells. Thus, ALK drives neuroblastoma in part through a feedforward loop between POSTN and WNT signaling.
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Affiliation(s)
- Miller Huang
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Wanqi Fang
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Linwei Li
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
| | - Antonios Chronopoulos
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
| | - Nicole Nasholm
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Bo Cheng
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
| | - Tina Zheng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Hiroyuki Yoda
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Megumi J Barata
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Tania Porras
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
| | - Matthew L Miller
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Qiqi Zhen
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lisa Ghiglieri
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lauren McHenry
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Linyu Wang
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Shahab Asgharzadeh
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - JinSeok Park
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - W Clay Gustafson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Departments of Pediatrics and Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Katherine K Matthay
- Departments of Pediatrics and Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - William A Weiss
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Departments of Pediatrics and Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
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4
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Mooney B, Negri GL, Shyp T, Delaidelli A, Zhang HF, Spencer Miko SE, Weiner AK, Radaoui AB, Shraim R, Lizardo MM, Hughes CS, Li A, El-Naggar AM, Rouleau M, Li W, Dimitrov DS, Kurmasheva RT, Houghton PJ, Diskin SJ, Maris JM, Morin GB, Sorensen PH. Surface and Global Proteome Analyses Identify ENPP1 and Other Surface Proteins as Actionable Immunotherapeutic Targets in Ewing Sarcoma. Clin Cancer Res 2024; 30:1022-1037. [PMID: 37812652 PMCID: PMC10905525 DOI: 10.1158/1078-0432.ccr-23-2187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/24/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
PURPOSE Ewing sarcoma is the second most common bone sarcoma in children, with 1 case per 1.5 million in the United States. Although the survival rate of patients diagnosed with localized disease is approximately 70%, this decreases to approximately 30% for patients with metastatic disease and only approximately 10% for treatment-refractory disease, which have not changed for decades. Therefore, new therapeutic strategies are urgently needed for metastatic and refractory Ewing sarcoma. EXPERIMENTAL DESIGN This study analyzed 19 unique Ewing sarcoma patient- or cell line-derived xenografts (from 14 primary and 5 metastatic specimens) using proteomics to identify surface proteins for potential immunotherapeutic targeting. Plasma membranes were enriched using density gradient ultracentrifugation and compared with a reference standard of 12 immortalized non-Ewing sarcoma cell lines prepared in a similar manner. In parallel, global proteome analysis was carried out on each model to complement the surfaceome data. All models were analyzed by Tandem Mass Tags-based mass spectrometry to quantify identified proteins. RESULTS The surfaceome and global proteome analyses identified 1,131 and 1,030 annotated surface proteins, respectively. Among surface proteins identified, both approaches identified known Ewing sarcoma-associated proteins, including IL1RAP, CD99, STEAP1, and ADGRG2, and many new cell surface targets, including ENPP1 and CDH11. Robust staining of ENPP1 was demonstrated in Ewing sarcoma tumors compared with other childhood sarcomas and normal tissues. CONCLUSIONS Our comprehensive proteomic characterization of the Ewing sarcoma surfaceome provides a rich resource of surface-expressed proteins in Ewing sarcoma. This dataset provides the preclinical justification for exploration of targets such as ENPP1 for potential immunotherapeutic application in Ewing sarcoma. See related commentary by Bailey, p. 934.
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Affiliation(s)
- Brian Mooney
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Taras Shyp
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alberto Delaidelli
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hai-Feng Zhang
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sandra E. Spencer Miko
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Amber K. Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alexander B. Radaoui
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rawan Shraim
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael M. Lizardo
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Christopher S. Hughes
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy Li
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amal M. El-Naggar
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Rouleau
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wei Li
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Dimiter S. Dimitrov
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Raushan T. Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Peter J. Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregg B. Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Poul H. Sorensen
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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5
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Felipe I, Martínez-de-Villarreal J, Patel K, Martínez-Torrecuadrada J, Grossmann LD, Roncador G, Cubells M, Farrell A, Kendsersky N, Sabroso-Lasa S, Sancho-Temiño L, Torres K, Martinez D, Perez JM, García F, Pogoriler J, Moreno L, Maris JM, Real FX. BPTF cooperates with MYCN and MYC to link neuroblastoma cell cycle control to epigenetic cellular states. bioRxiv 2024:2024.02.11.579816. [PMID: 38405949 PMCID: PMC10888818 DOI: 10.1101/2024.02.11.579816] [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] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The nucleosome remodeling factor BPTF is required for the deployment of the MYC-driven transcriptional program. Deletion of one Bptf allele delays tumor progression in mouse models of pancreatic cancer and lymphoma. In neuroblastoma, MYCN cooperates with the transcriptional core regulatory circuitry (CRC). High BPTF levels are associated with high-risk features and decreased survival. BPTF depletion results in a dramatic decrease of cell proliferation. Bulk RNA-seq, single-cell sequencing, and tissue microarrays reveal a positive correlation of BPTF and CRC transcription factor expression. Immunoprecipitation/mass spectrometry shows that BPTF interacts with MYCN and the CRC proteins. Genome-wide distribution analysis of BPTF and CRC in neuroblastoma reveals a dual role for BPTF: 1) it co-localizes with MYCN/MYC at the promoter of genes involved in cell cycle and 2) it co-localizes with the CRC at super-enhancers to regulate cell identity. The critical role of BPTF across neuroblastoma subtypes supports its relevance as a therapeutic target.
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6
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Randall MP, Egolf LE, Vaksman Z, Samanta M, Tsang M, Groff D, Evans JP, Rokita JL, Layeghifard M, Shlien A, Maris JM, Diskin SJ, Bosse KR. BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma. J Natl Cancer Inst 2024; 116:138-148. [PMID: 37688570 PMCID: PMC10777668 DOI: 10.1093/jnci/djad182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/10/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND High-risk neuroblastoma is a complex genetic disease that is lethal in more than 50% of patients despite intense multimodal therapy. Through genome-wide association studies (GWAS) and next-generation sequencing, we have identified common single nucleotide polymorphisms and rare, pathogenic or likely pathogenic germline loss-of-function variants in BARD1 enriched in neuroblastoma patients. The functional implications of these findings remain poorly understood. METHODS We correlated BARD1 genotype with expression in normal tissues and neuroblastomas, along with the burden of DNA damage in tumors. To validate the functional consequences of germline pathogenic or likely pathogenic BARD1 variants, we used CRISPR-Cas9 to generate isogenic neuroblastoma (IMR-5) and control (RPE1) cellular models harboring heterozygous BARD1 loss-of-function variants (R112*, R150*, E287fs, and Q564*) and quantified genomic instability in these cells via next-generation sequencing and with functional assays measuring the efficiency of DNA repair. RESULTS Both common and rare neuroblastoma-associated BARD1 germline variants were associated with lower levels of BARD1 mRNA and an increased burden of DNA damage. Using isogenic heterozygous BARD1 loss-of-function variant cellular models, we functionally validated this association with inefficient DNA repair. BARD1 loss-of-function variant isogenic cells exhibited reduced efficiency in repairing Cas9-induced DNA damage, ineffective RAD51 focus formation at DNA double-strand break sites, and enhanced sensitivity to cisplatin and poly (ADP-ribose) polymerase (PARP) inhibition both in vitro and in vivo. CONCLUSIONS Taken together, we demonstrate that germline BARD1 variants disrupt DNA repair fidelity. This is a fundamental molecular mechanism contributing to neuroblastoma initiation that may have important therapeutic implications.
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Affiliation(s)
- Michael P Randall
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura E Egolf
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Zalman Vaksman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Current affiliation: New York Genome Center, New York, NY
| | - Minu Samanta
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew Tsang
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - J Perry Evans
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Current affiliation: Genomics and Data Sciences, Spark Therapeutics, Philadelphia, PA
| | - Jo Lynne Rokita
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mehdi Layeghifard
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Adam Shlien
- 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 Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sharon J Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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7
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Kim J, Vaksman Z, Egolf LE, Kaufman R, Evans JP, Conkrite KL, Danesh A, Lopez G, Randall MP, Dent MH, Farra LM, Menghani NL, Dymek M, Desai H, Hausler R, Hicks B, Auvil JG, Gerhard DS, Hakonarson H, Maxwell KN, Cole KA, Pugh TJ, Bosse KR, Khan J, Wei JS, Maris JM, Stewart DR, Diskin SJ. Germline pathogenic variants in neuroblastoma patients are enriched in BARD1 and predict worse survival. J Natl Cancer Inst 2024; 116:149-159. [PMID: 37688579 PMCID: PMC10777667 DOI: 10.1093/jnci/djad183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/09/2023] [Revised: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND Neuroblastoma is an embryonal cancer of the developing sympathetic nervous system. The genetic contribution of rare pathogenic or likely pathogenic germline variants in patients without a family history remains unclear. METHODS Germline DNA sequencing was performed on 786 neuroblastoma patients. The frequency of rare cancer predisposition gene pathogenic or likely pathogenic variants in patients was compared with 2 cancer-free control cohorts. Matched tumor DNA sequencing was evaluated for second hits, and germline DNA array data from 5585 neuroblastoma patients and 23 505 cancer-free control children were analyzed to identify rare germline copy number variants. Patients with germline pathogenic or likely pathogenic variants were compared with those without to test for association with clinical characteristics, tumor features, and survival. RESULTS We observed 116 pathogenic or likely pathogenic variants involving 13.9% (109 of 786) of neuroblastoma patients, representing a statistically significant excess burden compared with cancer-free participants (odds ratio [OR] = 1.60, 95% confidence interval [CI] = 1.27 to 2.00). BARD1 harbored the most statistically significant enrichment of pathogenic or likely pathogenic variants (OR = 32.30, 95% CI = 6.44 to 310.35). Rare germline copy number variants disrupting BARD1 were identified in patients but absent in cancer-free participants (OR = 29.47, 95% CI = 1.52 to 570.70). Patients harboring a germline pathogenic or likely pathogenic variant had a worse overall survival compared with those without (P = 8.6 x 10-3). CONCLUSIONS BARD1 is an important neuroblastoma predisposition gene harboring both common and rare germline pathogenic or likely pathogenic variations. The presence of any germline pathogenic or likely pathogenic variant in a cancer predisposition gene was independently predictive of worse overall survival. As centers move toward paired tumor-normal sequencing at diagnosis, efforts should be made to centralize data and provide an infrastructure to support cooperative longitudinal prospective studies of germline pathogenic variation.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Zalman Vaksman
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura E Egolf
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca Kaufman
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - J Perry Evans
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karina L Conkrite
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, Canada
| | - Gonzalo Lopez
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael P Randall
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maiah H Dent
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lance M Farra
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Neil L Menghani
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malwina Dymek
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Heena Desai
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan Hausler
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Belynda Hicks
- Cancer Genome Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina A Cole
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Kristopher R Bosse
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jun S Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John M Maris
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Sharon J Diskin
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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8
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Weiner AK, Radaoui AB, Tsang M, Martinez D, Sidoli S, Conkrite KL, Delaidelli A, Modi A, Rokita JL, Patel K, Lane MV, Zhang B, Zhong C, Ennis B, Miller DP, Brown MA, Rathi KS, Raman P, Pogoriler J, Bhatti T, Pawel B, Glisovic-Aplenc T, Teicher B, Erickson SW, Earley EJ, Bosse KR, Sorensen PH, Krytska K, Mosse YP, Havenith KE, Zammarchi F, van Berkel PH, Smith MA, Garcia BA, Maris JM, Diskin SJ. A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma. bioRxiv 2024:2023.12.06.570390. [PMID: 38106022 PMCID: PMC10723418 DOI: 10.1101/2023.12.06.570390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cancer immunotherapies have produced remarkable results in B-cell malignancies; however, optimal cell surface targets for many solid cancers remain elusive. Here, we present an integrative proteomic, transcriptomic, and epigenomic analysis of tumor specimens along with normal tissues to identify biologically relevant cell surface proteins that can serve as immunotherapeutic targets for neuroblastoma, an often-fatal childhood cancer of the developing nervous system. We apply this approach to human-derived cell lines (N=9) and cell/patient-derived xenograft (N=12) models of neuroblastoma. Plasma membrane-enriched mass spectrometry identified 1,461 cell surface proteins in cell lines and 1,401 in xenograft models, respectively. Additional proteogenomic analyses revealed 60 high-confidence candidate immunotherapeutic targets and we prioritized Delta-like canonical notch ligand 1 (DLK1) for further study. High expression of DLK1 directly correlated with the presence of a super-enhancer spanning the DLK1 locus. Robust cell surface expression of DLK1 was validated by immunofluorescence, flow cytometry, and immunohistochemistry. Short hairpin RNA mediated silencing of DLK1 in neuroblastoma cells resulted in increased cellular differentiation. ADCT-701, a DLK1-targeting antibody-drug conjugate (ADC), showed potent and specific cytotoxicity in DLK1-expressing neuroblastoma xenograft models. Moreover, DLK1 is highly expressed in several adult cancer types, including adrenocortical carcinoma (ACC), pheochromocytoma/paraganglioma (PCPG), hepatoblastoma, and small cell lung cancer (SCLC), suggesting potential clinical benefit beyond neuroblastoma. Taken together, our study demonstrates the utility of comprehensive cancer surfaceome characterization and credentials DLK1 as an immunotherapeutic target. Highlights Plasma membrane enriched proteomics defines surfaceome of neuroblastomaMulti-omic data integration prioritizes DLK1 as a candidate immunotherapeutic target in neuroblastoma and other cancersDLK1 expression is driven by a super-enhancer DLK1 silencing in neuroblastoma cells results in cellular differentiation ADCT-701, a DLK1-targeting antibody-drug conjugate, shows potent and specific cytotoxicity in DLK1-expressing neuroblastoma preclinical models.
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9
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Batra V, Gikandi A, Pawel B, Martinez D, Granger MM, Marachelian A, Park JR, Maris JM, Vo KT, Matthay KK, DuBois SG. Norepinephrine transporter and vesicular monoamine transporter 2 tumor expression as a predictor of response to 131 I-MIBG in patients with relapsed/refractory neuroblastoma. Pediatr Blood Cancer 2024; 71:e30743. [PMID: 37885116 PMCID: PMC10842219 DOI: 10.1002/pbc.30743] [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: 08/19/2023] [Revised: 10/06/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Prior studies suggest that norepinephrine transporter (NET) and vesicular monoamine transporter 2 (VMAT2) mediate meta-iodobenzylguanidine (MIBG) uptake and retention in neuroblastoma tumors. We evaluated the relationship between NET and VMAT2 tumor expression and clinical response to 131 I-MIBG therapy in patients with neuroblastoma. METHODS Immunohistochemistry (IHC) was used to evaluate NET and VMAT2 protein expression levels on archival tumor samples (obtained at diagnosis or relapse) from patients with relapsed or refractory neuroblastoma treated with 131 I-MIBG. A composite protein expression H-score was determined by multiplying a semi-quantitative intensity value (0-3+) by the percentage of tumor cells expressing the protein. RESULTS Tumor samples and clinical data were available for 106 patients, of whom 28.3% had partial response (PR) or higher. NET H-score was not significantly associated with response (≥PR), though the percentage of tumor cells expressing NET was lower among responders (median 80% for ≥PR vs. 90% for CONCLUSIONS Markers of lower NET and VMAT2 protein expression are associated with higher likelihood of response to 131 I-MIBG therapy in patients with relapsed/refractory neuroblastoma. Increased VMAT2 protein expression is associated with a more differentiated disease phenotype.
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Affiliation(s)
- Vandana Batra
- Children’s Hospital of Philadelphia and Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA
| | | | - Bruce Pawel
- Department of Pathology, Children’s Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA
| | - Daniel Martinez
- Children’s Hospital of Philadelphia and Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA
| | | | - Araz Marachelian
- Department of Pediatrics, Children’s Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA
| | - Julie R. Park
- Department of Pediatrics, Seattle Children’s Hospital and University of Washington School of Medicine, Seattle, WA
| | - John M. Maris
- Children’s Hospital of Philadelphia and Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA
| | - Kieuhoa T. Vo
- Department of Pediatrics, UCSF Benioff Children’s Hospital and UCSF School of Medicine, San Francisco, CA
| | - Katherine K. Matthay
- Department of Pediatrics, UCSF Benioff Children’s Hospital and UCSF School of Medicine, San Francisco, CA
| | - Steven G. DuBois
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
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10
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Weiner AK, Palmer A, Moll MF, Lindberg G, Reidy K, Diskin SJ, Mackall CL, Maris JM, Sullivan PJ. Advancing childhood cancer research through young investigator and advocate collaboration. bioRxiv 2023:2023.12.03.569769. [PMID: 38105944 PMCID: PMC10723281 DOI: 10.1101/2023.12.03.569769] [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] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cancer advocates and researchers share the same goal of driving science forward to create new therapies to cure more patients. The power of combining cancer researchers and advocates has become of increased importance due to their complementary expertise. Therefore, advocacy is a critical component of grant structures and has become embedded into the Stand Up 2 Cancer (SU2C) applications. To date, the optimal way to combine these skillsets and experiences to benefit the cancer community is currently unknown. The Saint Baldrick's Foundation (SBF)-SU2C now called St. Baldrick's Empowering Pediatric Immunotherapies for Childhood Cancer (EPICC) Team is comprised of a collaborative network across nine institutions in the United States and Canada. Since SU2C encourages incorporating advocacy into the team structure, we have assembled a diverse team of advocates and scientists by nominating a young investigator (YI) and advocate from each site. In order to further bridge this interaction beyond virtual monthly and yearly in person meetings, we have developed a questionnaire and conducted interviews. The questionnaire is focused on understanding each member's experience at the intersection between science/advocacy, comparing to previous experiences, providing advice on incorporating advocacy into team science and discussing how we can build on our work. Through creating a YI and advocate infrastructure, we have cultivated a supportive environment for meaningful conversation that impacts the entire research team. We see this as a model for team science by combining expertise to drive innovation forward and positively impact pediatric cancer patients, and perhaps those with adult malignancies. Significance Questionnaire results show both advocates and YI's see this structure to be valuable and beneficial. YI's communicated their research to a non-scientific audience and learned advocate's experience. This was their first advocacy experience for most YIs. Advocates learned more about the research being conducted to provide hope. They can also aid with fundraising, publicity and lobbying. This collaboration improves science communication, designing patient-friendly clinical trials and sharing experience across institutions.
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11
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Sun Y, Florio TJ, Gupta S, Young MC, Marshall QF, Garfinkle SE, Papadaki GF, Truong HV, Mycek E, Li P, Farrel A, Church NL, Jabar S, Beasley MD, Kiefel BR, Yarmarkovich M, Mallik L, Maris JM, Sgourakis NG. Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion. Sci Immunol 2023; 8:eadj5792. [PMID: 38039376 PMCID: PMC10782944 DOI: 10.1126/sciimmunol.adj5792] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
Peptide-centric chimeric antigen receptors (PC-CARs) recognize oncoprotein epitopes displayed by cell-surface human leukocyte antigens (HLAs) and offer a promising strategy for targeted cancer therapy. We have previously developed a PC-CAR targeting a neuroblastoma-associated PHOX2B peptide, leading to robust tumor cell lysis restricted by two common HLA allotypes. Here, we determine the 2.1-angstrom crystal structure of the PC-CAR-PHOX2B-HLA-A*24:02-β2m complex, which reveals the basis for antigen-specific recognition through interactions with CAR complementarity-determining regions (CDRs). This PC-CAR adopts a diagonal docking mode, where interactions with both conserved and polymorphic HLA framework residues permit recognition of multiple HLA allotypes from the A9 serological cross-reactive group, covering a combined global population frequency of up to 46.7%. Biochemical binding assays, molecular dynamics simulations, and structural and functional analyses demonstrate that high-affinity PC-CAR recognition of cross-reactive pHLAs necessitates the presentation of a specific peptide backbone, where subtle structural adaptations of the peptide are critical for high-affinity complex formation, and CAR T cell killing. Our results provide a molecular blueprint for engineering CARs with optimal recognition of tumor-associated antigens in the context of different HLAs, while minimizing cross-reactivity with self-epitopes.
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Affiliation(s)
- Yi Sun
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tyler J. Florio
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sagar Gupta
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michael C. Young
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Quinlen F. Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samuel E. Garfinkle
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Georgia F. Papadaki
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hau V. Truong
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Emily Mycek
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peiyao Li
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | | | | | - Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Leena Mallik
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Nikolaos G. Sgourakis
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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12
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Yarmarkovich M, Marshall QF, Warrington JM, Premaratne R, Farrel A, Groff D, Li W, di Marco M, Runbeck E, Truong H, Toor JS, Tripathi S, Nguyen S, Shen H, Noel T, Church NL, Weiner A, Kendsersky N, Martinez D, Weisberg R, Christie M, Eisenlohr L, Bosse KR, Dimitrov DS, Stevanovic S, Sgourakis NG, Kiefel BR, Maris JM. Retraction Note: Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs. Nature 2023; 623:872. [PMID: 37938785 PMCID: PMC10665177 DOI: 10.1038/s41586-023-06731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Affiliation(s)
- Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Quinlen F Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Warrington
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Erin Runbeck
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hau Truong
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Son Nguyen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena Shen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tiffany Noel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Amber Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nathan Kendsersky
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dan Martinez
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rebecca Weisberg
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Molly Christie
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurence Eisenlohr
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Nikolaos G Sgourakis
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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13
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Yarmarkovich M, Marshall QF, Warrington JM, Premaratne R, Farrel A, Groff D, Li W, di Marco M, Runbeck E, Truong H, Toor JS, Tripathi S, Nguyen S, Shen H, Noel T, Church NL, Weiner A, Kendsersky N, Martinez D, Weisberg R, Christie M, Eisenlohr L, Bosse KR, Dimitrov DS, Stevanovic S, Sgourakis NG, Kiefel BR, Maris JM. Targeting of intracellular oncoproteins with peptide-centric CARs. Nature 2023; 623:820-827. [PMID: 37938771 PMCID: PMC10665195 DOI: 10.1038/s41586-023-06706-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/23/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023]
Abstract
The majority of oncogenic drivers are intracellular proteins, constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes1. However, most cancers have a modest mutational burden that is insufficient for generating responses using neoantigen-based therapies2,3. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks4. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins essential for tumorigenesis. We focused on targeting the unmutated peptide QYNPIRTTF discovered on HLA-A*24:02, which is derived from the neuroblastoma-dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (PC-CARs) through a counter panning strategy using predicted potentially cross-reactive peptides. We further proposed that PC-CARs can recognize peptides on additional HLA allotypes when presenting a similar overall molecular surface. Informed by our computational modelling results, we show that PHOX2B PC-CARs also recognize QYNPIRTTF presented by HLA-A*23:01, the most common non-A2 allele in people with African ancestry. Finally, we demonstrate potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that PC-CARs have the potential to expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and allow targeting through additional HLA allotypes in a clinical setting.
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Affiliation(s)
- Mark Yarmarkovich
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA.
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Quinlen F Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Warrington
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Erin Runbeck
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hau Truong
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Son Nguyen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena Shen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tiffany Noel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Amber Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nathan Kendsersky
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dan Martinez
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rebecca Weisberg
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Molly Christie
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurence Eisenlohr
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Nikolaos G Sgourakis
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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14
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Tian M, Wei JS, Shivaprasad N, Highfill SL, Gryder BE, Milewski D, Brown GT, Moses L, Song H, Wu JT, Azorsa P, Kumar J, Schneider D, Chou HC, Song YK, Rahmy A, Masih KE, Kim YY, Belyea B, Linardic CM, Dropulic B, Sullivan PM, Sorensen PH, Dimitrov DS, Maris JM, Mackall CL, Orentas RJ, Cheuk AT, Khan J. Preclinical development of a chimeric antigen receptor T cell therapy targeting FGFR4 in rhabdomyosarcoma. Cell Rep Med 2023; 4:101212. [PMID: 37774704 PMCID: PMC10591056 DOI: 10.1016/j.xcrm.2023.101212] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 06/12/2023] [Accepted: 09/06/2023] [Indexed: 10/01/2023]
Abstract
Pediatric patients with relapsed or refractory rhabdomyosarcoma (RMS) have dismal cure rates, and effective therapy is urgently needed. The oncogenic receptor tyrosine kinase fibroblast growth factor receptor 4 (FGFR4) is highly expressed in RMS and lowly expressed in healthy tissues. Here, we describe a second-generation FGFR4-targeting chimeric antigen receptor (CAR), based on an anti-human FGFR4-specific murine monoclonal antibody 3A11, as an adoptive T cell treatment for RMS. The 3A11 CAR T cells induced robust cytokine production and cytotoxicity against RMS cell lines in vitro. In contrast, a panel of healthy human primary cells failed to activate 3A11 CAR T cells, confirming the selectivity of 3A11 CAR T cells against tumors with high FGFR4 expression. Finally, we demonstrate that 3A11 CAR T cells are persistent in vivo and can effectively eliminate RMS tumors in two metastatic and two orthotopic models. Therefore, our study credentials CAR T cell therapy targeting FGFR4 to treat patients with RMS.
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Affiliation(s)
- Meijie Tian
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Jun S Wei
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Nityashree Shivaprasad
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Steven L Highfill
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Berkley E Gryder
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - David Milewski
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - G Tom Brown
- Artificial Intelligence Resource, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Larry Moses
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Hannah Song
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Jerry T Wu
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Peter Azorsa
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Jeetendra Kumar
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Dina Schneider
- Lentigen Corporation, Miltenyi Bioindustry, 1201 Clopper Road, Gaithersburg, MD 20878, USA
| | - Hsien-Chao Chou
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Young K Song
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Abdelrahman Rahmy
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Katherine E Masih
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Yong Yean Kim
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Brian Belyea
- Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Corinne M Linardic
- Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Boro Dropulic
- Caring Cross, 708 Quince Orchard Road, Gaithersburg, MD 20878, USA
| | - Peter M Sullivan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, 1100 Olive Way, Seattle, WA 98101, USA
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Dimiter S Dimitrov
- University of Pittsburgh Department of Medicine, Pittsburgh, PA 15261, USA
| | - John M Maris
- Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Crystal L Mackall
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rimas J Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, 1100 Olive Way, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Adam T Cheuk
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA.
| | - Javed Khan
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA.
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15
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Modi A, Lopez G, Conkrite KL, Su C, Leung TC, Ramanan S, Manduchi E, Johnson ME, Cheung D, Gadd S, Zhang J, Smith MA, Guidry Auvil JM, Meshinchi S, Perlman EJ, Hunger SP, Maris JM, Wells AD, Grant SF, Diskin SJ. Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors. Cancer Res 2023; 83:3462-3477. [PMID: 37584517 PMCID: PMC10787516 DOI: 10.1158/0008-5472.can-22-3186] [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: 10/11/2022] [Revised: 03/07/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
Abstract
Long noncoding RNAs (lncRNA) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curated RNA sequencing data for 1,044 pediatric leukemia and extracranial solid tumors and integrated paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. A total of 2,657 lncRNAs were robustly expressed across six pediatric cancers, including 1,142 exhibiting histotype-elevated expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multidimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell type-specific transcription factors further implicated distinct histotype-elevated and developmental lncRNAs. Integration of these analyses prioritized lncRNAs for experimental validation, and silencing of TBX2-AS1, the top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming the computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies. SIGNIFICANCE Comprehensive characterization of lncRNAs in pediatric cancer leads to the identification of highly expressed lncRNAs across childhood cancers, annotation of lncRNAs showing histotype-specific elevated expression, and prediction of lncRNA gene regulatory networks.
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Affiliation(s)
- Apexa Modi
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Genomics and Computational Biology Graduate Group, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Gonzalo Lopez
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Karina L. Conkrite
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tsz Ching Leung
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Sathvik Ramanan
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elisabetta Manduchi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew E. Johnson
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daphne Cheung
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois 60208, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Malcolm A. Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland 20892, USA
| | | | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Elizabeth J. Perlman
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois 60208, USA
| | - Stephen P. Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Divisions of Human Genetics and Endocrinology & Diabetes, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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16
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Rosenberg MI, Greenstein E, Buchkovich M, Peres A, Santoni-Rugiu E, Yang L, Mikl M, Vaksman Z, Gibbs DL, Reshef D, Salovin A, Irwin MS, Naranjo A, Ulitsky I, de Alarcon PA, Matthay KK, Weigman V, Yaari G, Panzer JA, Friedman N, Maris JM. Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma. Cell Rep 2023; 42:112879. [PMID: 37537844 PMCID: PMC10551040 DOI: 10.1016/j.celrep.2023.112879] [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: 04/14/2022] [Revised: 04/25/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023] Open
Abstract
Neuroblastoma is a lethal childhood solid tumor of developing peripheral nerves. Two percent of children with neuroblastoma develop opsoclonus myoclonus ataxia syndrome (OMAS), a paraneoplastic disease characterized by cerebellar and brainstem-directed autoimmunity but typically with outstanding cancer-related outcomes. We compared tumor transcriptomes and tumor-infiltrating T and B cell repertoires from 38 OMAS subjects with neuroblastoma to 26 non-OMAS-associated neuroblastomas. We found greater B and T cell infiltration in OMAS-associated tumors compared to controls and showed that both were polyclonal expansions. Tertiary lymphoid structures (TLSs) were enriched in OMAS-associated tumors. We identified significant enrichment of the major histocompatibility complex (MHC) class II allele HLA-DOB∗01:01 in OMAS patients. OMAS severity scores were associated with the expression of several candidate autoimmune genes. We propose a model in which polyclonal auto-reactive B lymphocytes act as antigen-presenting cells and drive TLS formation, thereby supporting both sustained polyclonal T cell-mediated anti-tumor immunity and paraneoplastic OMAS neuropathology.
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Affiliation(s)
- Miriam I Rosenberg
- Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem 91904, Israel.
| | - Erez Greenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Ayelet Peres
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel; Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital and Department of Clinical Medicine, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Lei Yang
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Martin Mikl
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | | | - David L Gibbs
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA 98109, USA
| | - Dan Reshef
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amy Salovin
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Meredith S Irwin
- Department of Pediatrics and Division of Hematology-Oncology, Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, ON M5G1X8, Canada
| | - Arlene Naranjo
- Department of Biostatistics, University of Florida, Children's Oncology Group Statistics & Data Center, Gainesville, FL, USA
| | - Igor Ulitsky
- Department of Immunology & Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Pedro A de Alarcon
- Department of Pediatrics, Hematology/Oncology, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Katherine K Matthay
- Department of Pediatrics, UCSF School of Medicine, San Francisco, CA 94143, USA
| | | | - Gur Yaari
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel; Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Jessica A Panzer
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - John M Maris
- Department of Pediatrics and Division of Oncology, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Zhang HF, Delaidelli A, Javed S, Turgu B, Morrison T, Hughes CS, Yang X, Pachva M, Lizardo MM, Singh G, Hoffmann J, Huang YZ, Patel K, Shraim R, Kung SH, Morin GB, Aparicio S, Martinez D, Maris JM, Bosse KR, Williams KC, Sorensen PH. A MYCN-independent mechanism mediating secretome reprogramming and metastasis in MYCN-amplified neuroblastoma. Sci Adv 2023; 9:eadg6693. [PMID: 37611092 PMCID: PMC10446492 DOI: 10.1126/sciadv.adg6693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
MYCN amplification (MNA) is a defining feature of high-risk neuroblastoma (NB) and predicts poor prognosis. However, whether genes within or in close proximity to the MYCN amplicon also contribute to MNA+ NB remains poorly understood. Here, we identify that GREB1, a transcription factor encoding gene neighboring the MYCN locus, is frequently coexpressed with MYCN and promotes cell survival in MNA+ NB. GREB1 controls gene expression independently of MYCN, among which we uncover myosin 1B (MYO1B) as being highly expressed in MNA+ NB and, using a chick chorioallantoic membrane (CAM) model, as a crucial regulator of invasion and metastasis. Global secretome and proteome profiling further delineates MYO1B in regulating secretome reprogramming in MNA+ NB cells, and the cytokine MIF as an important pro-invasive and pro-metastatic mediator of MYO1B activity. Together, we have identified a putative GREB1-MYO1B-MIF axis as an unconventional mechanism promoting aggressive behavior in MNA+ NB and independently of MYCN.
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Affiliation(s)
- Hai-Feng Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Alberto Delaidelli
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Sumreen Javed
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Busra Turgu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Taylor Morrison
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Christopher S. Hughes
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Xiaqiu Yang
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Manideep Pachva
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Michael M. Lizardo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gurdeep Singh
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Jennifer Hoffmann
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yue Zhou Huang
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Khushbu Patel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rawan Shraim
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Gregg B. Morin
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Samuel Aparicio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Daniel Martinez
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karla C. Williams
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Poul H. Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
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18
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Farrel A, Li P, Veenbergen S, Patel K, Maris JM, Leonard WJ. ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery. BMC Bioinformatics 2023; 24:303. [PMID: 37516886 PMCID: PMC10386769 DOI: 10.1186/s12859-023-05420-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 07/18/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND The growing power and ever decreasing cost of RNA sequencing (RNA-Seq) technologies have resulted in an explosion of RNA-Seq data production. Comparing gene expression values within RNA-Seq datasets is relatively easy for many interdisciplinary biomedical researchers; however, user-friendly software applications increase the ability of biologists to efficiently explore available datasets. RESULTS Here, we describe ROGUE (RNA-Seq Ontology Graphic User Environment, https://marisshiny. RESEARCH chop.edu/ROGUE/ ), a user-friendly R Shiny application that allows a biologist to perform differentially expressed gene analysis, gene ontology and pathway enrichment analysis, potential biomarker identification, and advanced statistical analyses. We use ROGUE to identify potential biomarkers and show unique enriched pathways between various immune cells. CONCLUSIONS User-friendly tools for the analysis of next generation sequencing data, such as ROGUE, will allow biologists to efficiently explore their datasets, discover expression patterns, and advance their research by allowing them to develop and test hypotheses.
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Affiliation(s)
- Alvin Farrel
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
- Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Peng Li
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon Veenbergen
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Pediatric Gastroenterology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Laboratory of Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Khushbu Patel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
- Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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19
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Cole KA, Ijaz H, Surrey LF, Santi M, Liu X, Minard CG, Maris JM, Voss S, Reid JM, Fox E, Weigel BJ. Pediatric phase 2 trial of a WEE1 inhibitor, adavosertib (AZD1775), and irinotecan for relapsed neuroblastoma, medulloblastoma, and rhabdomyosarcoma. Cancer 2023; 129:2245-2255. [PMID: 37081608 PMCID: PMC10628947 DOI: 10.1002/cncr.34786] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 07/28/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 04/22/2023]
Abstract
BACKGROUND Inhibition of the WEE1 kinase by adavosertib (AZD1775) potentiates replicative stress from genomic instability or chemotherapy. This study reports the pediatric solid tumor phase 2 results of the ADVL1312 trial combining irinotecan and adavosertib. METHODS Pediatric patients with recurrent neuroblastoma (part B), medulloblastoma/central nervous system embryonal tumors (part C), or rhabdomyosarcoma (part D) were treated with irinotecan and adavosertib orally for 5 days every 21 days. The combination was considered effective if there were at least three of 20 responses in parts B and D or six of 19 responses in part C. Tumor tissue was analyzed for alternative lengthening of telomeres and ATRX. Patient's prior tumor genomic analyses were provided. RESULTS The 20 patients with neuroblastoma (part B) had a median of three prior regimens and 95% had a history of prior irinotecan. There were three objective responses (9, 11, and 18 cycles) meeting the protocol defined efficacy end point. Two of the three patients with objective responses had tumors with alternative lengthening of telomeres. One patient with pineoblastoma had a partial response (11 cycles), but parts C and D did not meet the protocol defined efficacy end point. The combination was well tolerated and there were no dose limiting toxicities at cycle 1 or beyond in any parts of ADVL1312 at the recommended phase 2 dose. CONCLUSION This is first phase 2 clinical trial of adavosertib in pediatrics and the first with irinotecan. The combination may be of sufficient activity to consider further study of adavosertib in neuroblastoma.
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Affiliation(s)
- Kristina A. Cole
- Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Heba Ijaz
- Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lea F. Surrey
- Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mariarita Santi
- Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xiaowei Liu
- Children’s Oncology Group, Monravia, California, USA
| | | | - John M. Maris
- Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephan Voss
- Dana‐Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Elizabeth Fox
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA
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20
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Bender HG, Irwin MS, Hogarty MD, Castleberry R, Maris JM, Kao PC, Zhang FF, Naranjo A, Cohn SL, London WB. Survival of Patients With Neuroblastoma After Assignment to Reduced Therapy Because of the 12- to 18-Month Change in Age Cutoff in Children's Oncology Group Risk Stratification. J Clin Oncol 2023; 41:3149-3159. [PMID: 37098238 PMCID: PMC10256433 DOI: 10.1200/jco.22.01946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 08/26/2022] [Revised: 12/01/2022] [Accepted: 02/23/2023] [Indexed: 04/27/2023] Open
Abstract
PURPOSE In 2006, Children's Oncology Group (COG) reclassified subgroups of toddlers diagnosed with neuroblastoma from high-risk to intermediate-risk, when the age cutoff for high-risk assignment was raised from 365 days (12 months) to 547 days (18 months). The primary aim of this retrospective study was to determine if excellent outcome was maintained after assigned reduction of therapy. PATIENTS AND METHODS Children <3 years old at diagnosis, enrolled on a COG biology study from 1990 to 2018, were eligible (n = 9,189). Assigned therapy was reduced for two cohorts of interest on the basis of the age cutoff change: 365-546 days old with International Neuroblastoma Staging System (INSS) stage 4, MYCN not amplified (MYCN-NA), favorable International Neuroblastoma Pathology Classification (INPC), hyperdiploid tumors (12-18mo/Stage4/FavBiology), and 365-546 days old with INSS stage 3, MYCN-NA, and unfavorable INPC tumors (12-18mo/Stage3/MYCN-NA/Unfav). Log-rank tests compared event-free survival (EFS) and overall survival (OS) curves. RESULTS For 12-18mo/Stage4/FavBiology, 5-year EFS/OS (± SE) before (≤2006; n = 40) versus after (>2006; n = 55) assigned reduction in therapy was similar: 89% ± 5.1%/89% ± 5.1% versus 87% ± 4.6%/94% ± 3.2% (P = .7; P = .4, respectively). For 12-18mo/Stage3/MYCN-NA/Unfav, the 5-year EFS and OS were both 100%, before (n = 6) and after (n = 4) 2006. The 12-18mo/Stage4/FavBiology plus 12-18mo/Stage3/MYCN-NA/Unfav classified as high-risk ≤2006 had an EFS/OS of 91% ± 4.4%/91% ± 4.5% versus 38% ± 1.3%/43% ± 1.3% for all other high-risk patients <3 years old (P < .0001; P < .0001, respectively). The 12-18mo/Stage4/FavBiology plus 12-18mo/Stage3/MYCN-NA/Unfav classified as intermediate-risk >2006 had an EFS/OS of 88% ± 4.3%/95% ± 2.9% versus 88% ± 0.9%/95% ± 0.6% for all other intermediate-risk patients <3 years old (P = .87; P = .85, respectively). CONCLUSION Excellent outcome was maintained among subsets of toddlers with neuroblastoma assigned to reduced treatment after reclassification of risk group from high to intermediate on the basis of new age cutoffs. Importantly, as documented in prior trials, intermediate-risk therapy is not associated with the degree of acute toxicity and late effects commonly observed with high-risk regimens.
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Affiliation(s)
- Hannah G. Bender
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Meredith S. Irwin
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, ON, Canada
| | - Michael D. Hogarty
- Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - John M. Maris
- Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Pei-Chi Kao
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Fan F. Zhang
- Department of Biostatistics, Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, FL
| | - Arlene Naranjo
- Department of Biostatistics, Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, FL
| | - Susan L. Cohn
- Department of Pediatrics and Comer Children's Hospital, University of Chicago, Chicago, IL
| | - Wendy B. London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
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21
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Sun Y, Florio TJ, Gupta S, Young MC, Marshall QF, Garfinkle SE, Papadaki GF, Truong HV, Mycek E, Li P, Farrel A, Church NL, Jabar S, Beasley MD, Kiefel BR, Yarmarkovich M, Mallik L, Maris JM, Sgourakis NG. Structural principles of peptide-centric Chimeric Antigen Receptor recognition guide therapeutic expansion. bioRxiv 2023:2023.05.24.542108. [PMID: 37292750 PMCID: PMC10245919 DOI: 10.1101/2023.05.24.542108] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Peptide-Centric Chimeric Antigen Receptors (PC-CARs), which recognize oncoprotein epitopes displayed by human leukocyte antigens (HLAs) on the cell surface, offer a promising strategy for targeted cancer therapy 1 . We have previously developed a PC-CAR targeting a neuroblastoma- associated PHOX2B peptide, leading to robust tumor cell lysis restricted by two common HLA allotypes 2 . Here, we determine the 2.1 Å structure of the PC-CAR:PHOX2B/HLA-A*24:02/β2m complex, which reveals the basis for antigen-specific recognition through interactions with CAR complementarity-determining regions (CDRs). The PC-CAR adopts a diagonal docking mode, where interactions with both conserved and polymorphic HLA framework residues permit recognition of multiple HLA allotypes from the A9 serological cross-reactivity group, covering a combined American population frequency of up to 25.2%. Comprehensive characterization using biochemical binding assays, molecular dynamics simulations, and structural and functional analyses demonstrate that high-affinity PC-CAR recognition of cross-reactive pHLAs necessitates the presentation of a specific peptide backbone, where subtle structural adaptations of the peptide are critical for high-affinity complex formation and CAR-T cell killing. Our results provide a molecular blueprint for engineering CARs with optimal recognition of tumor-associated antigens in the context of different HLAs, while minimizing cross-reactivity with self-epitopes.
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22
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Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic predisposition to neuroblastoma results from a regulatory polymorphism that promotes the adrenergic cell state. J Clin Invest 2023; 133:e166919. [PMID: 37183825 PMCID: PMC10178836 DOI: 10.1172/jci166919] [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: 11/09/2022] [Accepted: 03/14/2023] [Indexed: 05/16/2023] Open
Abstract
Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like mesenchymal cell state and a more differentiated sympathetic adrenergic cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional cofactor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism, G/T, that affects a GATA motif in the first intron of LMO1. Here, we showed that WT zebrafish with the GATA genotype developed adrenergic neuroblastoma, while knock-in of the protective TATA allele at this locus reduced the penetrance of MYCN-driven tumors, which were restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrated that TATA/TATA tumors also exhibited a mesenchymal cell state and were low risk at diagnosis. Thus, conversion of the regulatory GATA to a TATA allele in the first intron of LMO1 reduced the neuroblastoma-initiation rate by preventing formation of the adrenergic cell state. This mechanism was conserved over 400 million years of evolution, separating zebrafish and humans.
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Affiliation(s)
- Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Hui Shi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ting Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Derek A. Oldridge
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adam D. Durbin
- Department of Oncology and Comprehensive Cancer Center, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Brian J. Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mark W. Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota, USA
| | - Andrew C. Wood
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - J. Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Biology Department, MIT, Cambridge, Massachusetts, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
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23
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Berko ER, Witek GM, Matkar S, Petrova ZO, Wu MA, Smith CM, Daniels A, Kalna J, Kennedy A, Gostuski I, Casey C, Krytska K, Gerelus M, Pavlick D, Ghazarian S, Park JR, Marachelian A, Maris JM, Goldsmith KC, Radhakrishnan R, Lemmon MA, Mossé YP. Circulating tumor DNA reveals mechanisms of lorlatinib resistance in patients with relapsed/refractory ALK-driven neuroblastoma. Nat Commun 2023; 14:2601. [PMID: 37147298 PMCID: PMC10163008 DOI: 10.1038/s41467-023-38195-0] [Citation(s) in RCA: 7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
Activating point mutations in Anaplastic Lymphoma Kinase (ALK) have positioned ALK as the only mutated oncogene tractable for targeted therapy in neuroblastoma. Cells with these mutations respond to lorlatinib in pre-clinical studies, providing the rationale for a first-in-child Phase 1 trial (NCT03107988) in patients with ALK-driven neuroblastoma. To track evolutionary dynamics and heterogeneity of tumors, and to detect early emergence of lorlatinib resistance, we collected serial circulating tumor DNA samples from patients enrolled on this trial. Here we report the discovery of off-target resistance mutations in 11 patients (27%), predominantly in the RAS-MAPK pathway. We also identify newly acquired secondary compound ALK mutations in 6 (15%) patients, all acquired at disease progression. Functional cellular and biochemical assays and computational studies elucidate lorlatinib resistance mechanisms. Our results establish the clinical utility of serial circulating tumor DNA sampling to track response and progression and to discover acquired resistance mechanisms that can be leveraged to develop therapeutic strategies to overcome lorlatinib resistance.
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Affiliation(s)
- Esther R Berko
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Hematology and Oncology, Schneider Children's Medical Center, Petach Tikva, Israel, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gabriela M Witek
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Smita Matkar
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zaritza O Petrova
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Megan A Wu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Courtney M Smith
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Alex Daniels
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua Kalna
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Annie Kennedy
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ivan Gostuski
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Colleen Casey
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kateryna Krytska
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mark Gerelus
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Susan Ghazarian
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Julie R Park
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Araz Marachelian
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly C Goldsmith
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.
| | - Yaël P Mossé
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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24
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Goldsmith KC, Park JR, Kayser K, Malvar J, Chi YY, Groshen SG, Villablanca JG, Krytska K, Lai LM, Acharya PT, Goodarzian F, Pawel B, Shimada H, Ghazarian S, States L, Marshall L, Chesler L, Granger M, Desai AV, Mody R, Morgenstern DA, Shusterman S, Macy ME, Pinto N, Schleiermacher G, Vo K, Thurm HC, Chen J, Liyanage M, Peltz G, Matthay KK, Berko ER, Maris JM, Marachelian A, Mossé YP. Lorlatinib with or without chemotherapy in ALK-driven refractory/relapsed neuroblastoma: phase 1 trial results. Nat Med 2023; 29:1092-1102. [PMID: 37012551 DOI: 10.1038/s41591-023-02297-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/09/2023] [Indexed: 04/05/2023]
Abstract
Neuroblastomas harbor ALK aberrations clinically resistant to crizotinib yet sensitive pre-clinically to the third-generation ALK inhibitor lorlatinib. We conducted a first-in-child study evaluating lorlatinib with and without chemotherapy in children and adults with relapsed or refractory ALK-driven neuroblastoma. The trial is ongoing, and we report here on three cohorts that have met pre-specified primary endpoints: lorlatinib as a single agent in children (12 months to <18 years); lorlatinib as a single agent in adults (≥18 years); and lorlatinib in combination with topotecan/cyclophosphamide in children (<18 years). Primary endpoints were safety, pharmacokinetics and recommended phase 2 dose (RP2D). Secondary endpoints were response rate and 123I-metaiodobenzylguanidine (MIBG) response. Lorlatinib was evaluated at 45-115 mg/m2/dose in children and 100-150 mg in adults. Common adverse events (AEs) were hypertriglyceridemia (90%), hypercholesterolemia (79%) and weight gain (87%). Neurobehavioral AEs occurred mainly in adults and resolved with dose hold/reduction. The RP2D of lorlatinib with and without chemotherapy in children was 115 mg/m2. The single-agent adult RP2D was 150 mg. The single-agent response rate (complete/partial/minor) for <18 years was 30%; for ≥18 years, 67%; and for chemotherapy combination in <18 years, 63%; and 13 of 27 (48%) responders achieved MIBG complete responses, supporting lorlatinib's rapid translation into active phase 3 trials for patients with newly diagnosed high-risk, ALK-driven neuroblastoma. ClinicalTrials.gov registration: NCT03107988 .
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Affiliation(s)
- Kelly C Goldsmith
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Julie R Park
- Seattle Children's Hospital, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Kimberly Kayser
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jemily Malvar
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Yueh-Yun Chi
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Susan G Groshen
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Judith G Villablanca
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kateryna Krytska
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lillian M Lai
- Department of Radiology, University of Iowa Hospital and Clinics, Iowa City, IA, USA
| | - Patricia T Acharya
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Radiology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Fariba Goodarzian
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Radiology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Bruce Pawel
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Hiroyuki Shimada
- Department of Pathology and Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan Ghazarian
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Lisa States
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Lynley Marshall
- The Royal Marsden Hospital, London, UK
- The Institute of Cancer Research, London, UK
| | - Louis Chesler
- The Royal Marsden Hospital, London, UK
- The Institute of Cancer Research, London, UK
| | | | - Ami V Desai
- Department of Pediatrics, Section of Hematology/Oncology/Stem Cell Transplantation, University of Chicago, Chicago, IL, USA
| | - Rajen Mody
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Daniel A Morgenstern
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Suzanne Shusterman
- Dana-Farber Cancer Institute, Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Margaret E Macy
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
| | - Navin Pinto
- Seattle Children's Hospital, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Gudrun Schleiermacher
- RTOP (Recherche Translationelle en Oncologie Pédiatrique), INSERM U830, Research Center, PSL Research University, Institut Curie, Paris, France
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), Institut Curie, Paris, France
| | - Kieuhoa Vo
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Holger C Thurm
- Global Product Development, Clinical Pharmacology, Pfizer Oncology, Pfizer, Inc., New York, NY, USA
| | - Joseph Chen
- Global Product Development, Clinical Pharmacology, Pfizer Oncology, Pfizer, Inc., New York, NY, USA
| | - Marlon Liyanage
- Global Product Development, Clinical Pharmacology, Pfizer Oncology, Pfizer, Inc., New York, NY, USA
| | - Gerson Peltz
- Global Product Development, Clinical Pharmacology, Pfizer Oncology, Pfizer, Inc., New York, NY, USA
| | - Katherine K Matthay
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Esther R Berko
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Hematology and Oncology, Schneider Children's Medical Center, Petach Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Araz Marachelian
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yael P Mossé
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State. bioRxiv 2023:2023.02.28.530457. [PMID: 36909587 PMCID: PMC10002714 DOI: 10.1101/2023.02.28.530457] [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] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like "mesenchymal" cell state and a more differentiated sympathetic "adrenergic" cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional co-factor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism G/T that affects a G ATA motif in the first intron of LMO1. Here we show that wild-type zebrafish with the G ATA genotype develop adrenergic neuroblastoma, while knock-in of the protective T ATA allele at this locus reduces the penetrance of MYCN-driven tumors, which are restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrates that T ATA/ T ATA tumors also exhibit a mesenchymal cell state and are low risk at diagnosis. Thus, conversion of the regulatory G ATA to a T ATA allele in the first intron of LMO1 reduces the neuroblastoma initiation rate by preventing formation of the adrenergic cell state, a mechanism that is conserved over 400 million years of evolution separating zebrafish and humans.
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Maris JM. In memoriam: Dr. Audrey E. Evans. Pediatr Blood Cancer 2023; 70:e30113. [PMID: 36524612 DOI: 10.1002/pbc.30113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 12/23/2022]
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Randall MP, Egolf LE, Vaksman Z, Samanta M, Tsang M, Groff D, Evans JP, Rokita JL, Layeghifard M, Shlien A, Maris JM, Diskin SJ, Bosse KR. BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma. bioRxiv 2023:2023.01.31.525066. [PMID: 36778420 PMCID: PMC9915690 DOI: 10.1101/2023.01.31.525066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Importance High-risk neuroblastoma is a complex genetic disease that is lethal in 50% of patients despite intense multimodal therapy. Our genome-wide association study (GWAS) identified single-nucleotide polymorphisms (SNPs) within the BARD1 gene showing the most significant enrichment in neuroblastoma patients, and also discovered pathogenic (P) or likely pathogenic (LP) rare germline loss-of-function variants in this gene. The functional implications of these findings remain poorly understood. Objective To define the functional relevance of BARD1 germline variation in children with neuroblastoma. Design We correlated BARD1 genotype with BARD1 expression in normal and tumor cells and the cellular burden of DNA damage in tumors. To validate the functional consequences of rare germline P-LP BARD1 variants, we generated isogenic cellular models harboring heterozygous BARD1 loss-of-function (LOF) variants and conducted multiple complementary assays to measure the efficiency of DNA repair. Setting (N/A). Participants (N/A). Interventions/Exposures (N/A). Main Outcomes and Measures BARD1 expression, efficiency of DNA repair, and genome-wide burden of DNA damage in neuroblastoma tumors and cellular models harboring disease-associated BARD1 germline variants. Results Both common and rare neuroblastoma associated BARD1 germline variants were significantly associated with lower levels of BARD1 mRNA and an increased burden of DNA damage. Using neuroblastoma cellular models engineered to harbor disease-associated heterozygous BARD1 LOF variants, we functionally validated this association with inefficient DNA repair. These BARD1 LOF variant isogenic models exhibited reduced efficiency in repairing Cas9-induced DNA damage, ineffective RAD51 focus formation at DNA doublestrand break sites, and enhanced sensitivity to cisplatin and poly-ADP ribose polymerase (PARP) inhibition. Conclusions and Relevance Considering that at least 1 in 10 children diagnosed with cancer carry a predicted pathogenic mutation in a cancer predisposition gene, it is critically important to understand their functional relevance. Here, we demonstrate that germline BARD1 variants disrupt DNA repair fidelity. This is a fundamental molecular mechanism contributing to neuroblastoma initiation that may have important therapeutic implications, and these findings may also extend to other cancers harboring germline variants in genes essential for DNA damage repair. Key Points Question: How do neuroblastoma patient BRCA1-associated RING domain 1 ( BARD1 ) germline variants impact DNA repair? Findings: Neuroblastoma-associated germline BARD1 variants disrupt DNA repair fidelity. Common risk variants correlate with decreased BARD1 expression and increased DNA double-strand breaks in neuroblastoma tumors and rare heterozygous loss-of-function variants induce BARD1 haploinsufficiency, resulting in defective DNA repair and genomic instability in neuroblastoma cellular models. Meaning: Germline variation in BARD1 contributes to neuroblastoma pathogenesis via dysregulation of critical cellular DNA repair functions, with implications for neuroblastoma treatment, risk stratification, and cancer predisposition.
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Affiliation(s)
- Michael P. Randall
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Laura E. Egolf
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zalman Vaksman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Minu Samanta
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew Tsang
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - J. Perry Evans
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jo Lynne Rokita
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, PA 19104, USA
| | - Mehdi Layeghifard
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Adam Shlien
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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Erbe AK, Diccianni MB, Mody R, Naranjo A, Zhang FF, Birstler J, Kim K, Feils AS, Hung JT, London WB, Shulkin BL, Mathew V, Parisi MT, Servaes S, Asgharzadeh S, Maris JM, Park J, Yu AL, Sondel PM, Bagatell R. KIR/KIR-ligand genotypes and clinical outcomes following chemoimmunotherapy in patients with relapsed or refractory neuroblastoma: a report from the Children's Oncology Group. J Immunother Cancer 2023; 11:e006530. [PMID: 36822669 PMCID: PMC9950969 DOI: 10.1136/jitc-2022-006530] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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] [Accepted: 01/25/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND In the Children's Oncology Group ANBL1221 phase 2 trial for patients with first relapse/first declaration of refractory high-risk neuroblastoma, irinotecan and temozolomide (I/T) combined with either temsirolimus (TEMS) or immunotherapy (the anti-GD2 antibody dinutuximab (DIN) and granulocyte macrophage colony stimulating factory (GM-CSF)) was administered. The response rate among patients treated with I/T/DIN/GM-CSF in the initial cohort (n=17) was 53%; additional patients were enrolled to permit further evaluation of this chemoimmunotherapy regimen. Potential associations between immune-related biomarkers and clinical outcomes including response and survival were evaluated. METHODS Patients were evaluated for specific immunogenotypes that influence natural killer (NK) cell activity, including killer immunoglobulin-like receptors (KIRs) and their ligands, Fc gamma receptors, and NCR3. Total white cells and leucocyte subsets were assessed via complete blood counts, and flow cytometry of peripheral blood mononuclear cells was performed to assess the potential association between immune cell subpopulations and surface marker expression and clinical outcomes. Appropriate statistical tests of association were performed. The Bonferroni correction for multiple comparisons was performed where indicated. RESULTS Of the immunogenotypes assessed, the presence or absence of certain KIR and their ligands was associated with clinical outcomes in patients treated with chemoimmunotherapy rather than I/T/TEMS. While median values of CD161, CD56, and KIR differed in responders and non-responders, statistical significance was not maintained in logistic regression models. White cell and neutrophil counts were associated with differences in survival outcomes, however, increases in risk of event in patients assigned to chemoimmunotherapy were not clinically significant. CONCLUSIONS These findings are consistent with those of prior studies showing that KIR/KIR-ligand genotypes are associated with clinical outcomes following anti-GD2 immunotherapy in children with neuroblastoma. The current study confirms the importance of KIR/KIR-ligand genotype in the context of I/T/DIN/GM-CSF chemoimmunotherapy administered to patients with relapsed or refractory disease in a clinical trial. These results are important because this regimen is now widely used for treatment of patients at time of first relapse/first declaration of refractory disease. Efforts to assess the role of NK cells and genes that influence their function in response to immunotherapy are ongoing. TRIAL REGISTRATION NUMBER NCT01767194.
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Affiliation(s)
- Amy K Erbe
- Department of Human Oncology, University of Wisconsin, Madison, Wisconsin, USA
| | - Mitch B Diccianni
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Rajen Mody
- C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan, USA
| | - Arlene Naranjo
- Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, Florida, USA
| | - Fan F Zhang
- Children's Oncology Group Statistics and Data Center, Monrovia, California, USA
| | - Jen Birstler
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, USA
| | - KyungMann Kim
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, USA
| | - Arika S Feils
- Department of Human Oncology, University of Wisconsin, Madison, Wisconsin, USA
| | - Jung-Tung Hung
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wendy B London
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Barry L Shulkin
- Departments of Diagnostic Imaging and Comprehensive Cancer Center, St. Jude Children's Research Hospital and the University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Varsha Mathew
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Marguerite T Parisi
- Department of Pediatrics, Seattle Children's Hospital and the University, Seattle, Washington, USA
| | - Sabah Servaes
- Department of Pediatrics, The Children's Hospital, Philadelphia, Pennsylvania, USA
| | - Shahab Asgharzadeh
- Department Cancer and Blood Disease Institute, Childrens Hospital of Los Angeles, Los Angeles, California, USA
| | - John M Maris
- Department of Pediatrics, The Children's Hospital, Philadelphia, Pennsylvania, USA
| | - Julie Park
- Department of Pediatrics, Seattle Children's Hospital and the University, Seattle, Washington, USA
| | - Alice L Yu
- Department of Pediatrics, University of California, San Diego, California, USA
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital Linkou Main Branch, Taoyuan, Taiwan
| | - Paul M Sondel
- Department of Human Oncology, University of Wisconsin, Madison, Wisconsin, USA
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, USA
| | - Rochelle Bagatell
- Department of Pediatrics, The Children's Hospital, Philadelphia, Pennsylvania, USA
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29
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Kim J, Vaksman Z, Egolf LE, Kaufman R, Evans JP, Conkrite KL, Danesh A, Lopez G, Randall MP, Dent MH, Farra LM, Menghani N, Dymek M, Desai H, Hausler R, Auvil JG, Gerhard DS, Hakonarson H, Maxwell KN, Cole KA, Pugh TJ, Bosse KR, Khan J, Wei JS, Maris JM, Stewart DR, Diskin SJ. Germline pathogenic variants in 786 neuroblastoma patients. medRxiv 2023:2023.01.23.23284864. [PMID: 36747619 PMCID: PMC9901064 DOI: 10.1101/2023.01.23.23284864] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Importance Neuroblastoma accounts for 12% of childhood cancer deaths. The genetic contribution of rare pathogenic germline variation in patients without a family history remains unclear. Objective To define the prevalence, spectrum, and clinical significance of pathogenic germline variation in cancer predisposition genes (CPGs) in neuroblastoma patients. Design Setting and Participants Germline DNA sequencing was performed on the peripheral blood from 786 neuroblastoma patients unselected for family history. Rare variants mapping to CPGs were evaluated for pathogenicity and the percentage of cases harboring pathogenic (P) or likely pathogenic (LP) variants was quantified. The frequency of CPG P-LP variants in neuroblastoma cases was compared to two distinct cancer-free control cohorts to assess enrichment. Matched tumor DNA sequencing was evaluated for "second hits" at CPGs and germline DNA array data from 5,585 neuroblastoma cases and 23,505 cancer-free control children was analyzed to identify rare germline copy number variants (CNVs) affecting genes with an excess burden of P-LP variants in neuroblastoma. Neuroblastoma patients with germline P-LP variants were compared to those without P-LP variants to test for association with clinical characteristics, tumor features, and patient survival. Main Outcomes and Measures Rare variant prevalence, pathogenicity, enrichment, and association with clinical characteristics, tumor features, and patient survival. Results We observed 116 P-LP variants in CPGs involving 13.9% (109/786) of patients, representing a significant excess burden of P-LP variants compared to controls (9.1%; P = 5.14 × 10-5, Odds Ratio: 1.60, 95% confidence interval: 1.27-2.00). BARD1 harbored the most significant burden of P-LP variants compared to controls (1.0% vs. 0.03%; P = 8.18 × 10-7; Odds Ratio: 32.30, 95% confidence interval: 6.44-310.35). Rare germline CNVs disrupting BARD1 were also identified in neuroblastoma patients (0.05%) but absent in controls (P = 7.08 × 10-3; Odds Ratio: 29.47, 95% confidence interval: 1.52 - 570.70). Overall, P-LP variants in DNA repair genes in this study were enriched in cases compared to controls (8.1% vs. 5.7%; P = 0.01; Odds Ratio: 1.45, 95% confidence interval: 1.08-1.92). Neuroblastoma patients harboring a germline P-LP variant had a worse overall survival when compared to patients without P-LP variants (P = 8.6 × 10-3), and this remained significant in a multivariate Cox proportional-hazards model (P = 0.01). Conclusions and Relevance Neuroblastoma patients harboring germline P-LP variants in CPGs have worse overall survival and BARD1 is an important predisposition gene affected by both common and rare pathogenic variation. Germline sequencing should be performed for all neuroblastoma patients at diagnosis to inform genetic counseling and support future longitudinal and mechanistic studies. Patients with a germline P-LP variant should be closely monitored, regardless of risk group assignment.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Zalman Vaksman
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura E. Egolf
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca Kaufman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - J. Perry Evans
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karina L. Conkrite
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, M5S Canada
| | - Gonzalo Lopez
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael P. Randall
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maiah H. Dent
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lance M. Farra
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Neil Menghani
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malwina Dymek
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Heena Desai
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan Hausler
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Penn Medicine BioBank
- Penn Medicine BioBank, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kara N. Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina A. Cole
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, M5S Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, ON, M5S Canada
| | - Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jun S. Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Sharon J. Diskin
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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30
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Desai AV, Gilman AL, Ozkaynak MF, Naranjo A, London WB, Tenney SC, Diccianni M, Hank JA, Parisi MT, Shulkin BL, Smith M, Moscow JA, Shimada H, Matthay KK, Cohn SL, Maris JM, Bagatell R, Sondel PM, Park JR, Yu AL. Outcomes Following GD2-Directed Postconsolidation Therapy for Neuroblastoma After Cessation of Random Assignment on ANBL0032: A Report From the Children's Oncology Group. J Clin Oncol 2022; 40:4107-4118. [PMID: 35839426 PMCID: PMC9746736 DOI: 10.1200/jco.21.02478] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 10/19/2021] [Revised: 03/31/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Postconsolidation immunotherapy including dinutuximab, granulocyte-macrophage colony-stimulating factor, and interleukin-2 improved outcomes for patients with high-risk neuroblastoma enrolled on the randomized portion of Children's Oncology Group study ANBL0032. After random assignment ended, all patients were assigned to immunotherapy. Survival and toxicities were assessed. PATIENTS AND METHODS Patients with a pre-autologous stem cell transplant (ASCT) response (excluding bone marrow) of partial response or better were eligible. Demographics, stage, tumor biology, pre-ASCT response, and adverse events were summarized using descriptive statistics. Event-free survival (EFS) and overall survival (OS) from time of enrollment (up to day +200 from last ASCT) were evaluated. RESULTS From 2009 to 2015, 1,183 patients were treated. Five-year EFS and OS for the entire cohort were 61.1 ± 1.9% and 71.9 ± 1.7%, respectively. For patients ≥ 18 months old at diagnosis with International Neuroblastoma Staging System stage 4 disease (n = 662) 5-year EFS and OS were 57.0 ± 2.4% and 70.9 ± 2.2%, respectively. EFS was superior for patients with complete response/very good partial response pre-ASCT compared with those with PR (5-year EFS: 64.2 ± 2.2% v 55.4 ± 3.2%, P = .0133); however, OS was not significantly different. Allergic reactions, capillary leak, fever, and hypotension were more frequent during interleukin-2-containing cycles than granulocyte-macrophage colony-stimulating factor-containing cycles (P < .0001). EFS was superior in patients with higher peak dinutuximab levels during cycle 1 (P = .034) and those with a high affinity FCGR3A genotype (P = .0418). Human antichimeric antibody status did not correlate with survival. CONCLUSION Analysis of a cohort assigned to immunotherapy after cessation of random assignment on ANBL0032 confirmed previously described survival and toxicity outcomes. EFS was highest among patients with end-induction complete response/very good partial response. Among patients with available data, higher dinutuximab levels and FCGR3A genotype were associated with superior EFS. These may be predictive biomarkers for dinutuximab therapy.
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Affiliation(s)
| | | | - Mehmet Fevzi Ozkaynak
- Maria Fareri Children's Hospital Westchester Medical Center, New York Medical College, Valhalla, NY
| | - Arlene Naranjo
- Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, FL
| | - Wendy B. London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Sheena C. Tenney
- Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, FL
| | | | | | - Marguerite T. Parisi
- Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA
| | | | - Malcolm Smith
- Clinical Investigations Branch, National Cancer Institute, Bethesda, MD
| | - Jeffrey A. Moscow
- Investigational Drug Branch, National Cancer Institute, Bethesda, MD
| | | | | | | | - John M. Maris
- Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA
| | - Rochelle Bagatell
- Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA
| | - Paul M. Sondel
- University of Wisconsin Carbone Cancer Center, Madison, WI
| | - Julie R. Park
- Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA
| | - Alice L. Yu
- University of California in San Diego, San Diego, CA
- Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
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31
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Bosse KR, Giudice AM, Lane MV, McIntyre B, Schürch PM, Pascual-Pasto G, Buongervino SN, Suresh S, Fitzsimmons A, Hyman A, Gemino-Borromeo M, Saggio J, Berko ER, Daniels AA, Stundon J, Friedrichsen M, Liu X, Margolis ML, Li MM, Tierno MB, Oxnard GR, Maris JM, Mossé YP. Serial Profiling of Circulating Tumor DNA Identifies Dynamic Evolution of Clinically Actionable Genomic Alterations in High-Risk Neuroblastoma. Cancer Discov 2022; 12:2800-2819. [PMID: 36108156 PMCID: PMC9722579 DOI: 10.1158/2159-8290.cd-22-0287] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 03/17/2022] [Revised: 07/21/2022] [Accepted: 09/13/2022] [Indexed: 01/12/2023]
Abstract
Neuroblastoma evolution, heterogeneity, and resistance remain inadequately defined, suggesting a role for circulating tumor DNA (ctDNA) sequencing. To define the utility of ctDNA profiling in neuroblastoma, 167 blood samples from 48 high-risk patients were evaluated for ctDNA using comprehensive genomic profiling. At least one pathogenic genomic alteration was identified in 56% of samples and 73% of evaluable patients, including clinically actionable ALK and RAS-MAPK pathway variants. Fifteen patients received ALK inhibition (ALKi), and ctDNA data revealed dynamic genomic evolution under ALKi therapeutic pressure. Serial ctDNA profiling detected disease evolution in 15 of 16 patients with a recurrently identified variant-in some cases confirming disease progression prior to standard surveillance methods. Finally, ctDNA-defined ERRFI1 loss-of-function variants were validated in neuroblastoma cellular models, with the mutant proteins exhibiting loss of wild-type ERRFI1's tumor-suppressive functions. Taken together, ctDNA is prevalent in children with high-risk neuroblastoma and should be followed throughout neuroblastoma treatment. SIGNIFICANCE ctDNA is prevalent in children with neuroblastoma. Serial ctDNA profiling in patients with neuroblastoma improves the detection of potentially clinically actionable and functionally relevant variants in cancer driver genes and delineates dynamic tumor evolution and disease progression beyond that of standard tumor sequencing and clinical surveillance practices. See related commentary by Deubzer et al., p. 2727. This article is highlighted in the In This Issue feature, p. 2711.
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Affiliation(s)
- Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
| | - Anna Maria Giudice
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Maria V. Lane
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Brendan McIntyre
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Patrick M. Schürch
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Guillem Pascual-Pasto
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Samantha N. Buongervino
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Sriyaa Suresh
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Alana Fitzsimmons
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Adam Hyman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Maria Gemino-Borromeo
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Jennifer Saggio
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Esther R. Berko
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Alexander A. Daniels
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Jennifer Stundon
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | | | - Xin Liu
- Foundation Medicine, Inc. Cambridge, MA 02141; USA
| | | | - Marilyn M. Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and the Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | | | | | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
| | - Yael P. Mossé
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
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Van Egeren D, Kohli K, Warner JL, Bedard PL, Riely G, Lepisto E, Schrag D, LeNoue-Newton M, Catalano P, Kehl KL, Michor F, Fiandalo M, Foti M, Khotskaya Y, Lee J, Peters N, Sweeney S, Abraham J, Brenton JD, Caldas C, Doherty G, Nimmervoll B, Pinilla K, Martin JE, Rueda OM, Sammut SJ, Silva D, Cao K, Heath AP, Li M, Lilly J, MacFarland S, Maris JM, Mason JL, Morgan AM, Resnick A, Welsh M, Zhu Y, Johnson B, Li Y, Sholl L, Beaudoin R, Biswas R, Cerami E, Cushing O, Dand D, Ducar M, Gusev A, Hahn WC, Haigis K, Hassett M, Janeway KA, Jänne P, Jawale A, Johnson J, Kehl KL, Kumari P, Laucks V, Lepisto E, Lindeman N, Lindsay J, Lueders A, Macconaill L, Manam M, Mazor T, Miller D, Newcomb A, Orechia J, Ovalle A, Postle A, Quinn D, Reardon B, Rollins B, Shivdasani P, Tramontano A, Van Allen E, Van Nostrand SC, Bell J, Datto MB, Green M, Hubbard C, McCall SJ, Mettu NB, Strickler JH, Andre F, Besse B, Deloger M, Dogan S, Italiano A, Loriot Y, Ludovic L, Michels S, Scoazec J, Tran-Dien A, Vassal G, Freeman CE, Hsiao SJ, Ingham M, Pang J, Rabadan R, Roman LC, Carvajal R, DuBois R, Arcila ME, Benayed R, Berger MF, Bhuiya M, Brannon AR, Brown S, Chakravarty D, Chu C, de Bruijn I, Galle J, Gao J, Gardos S, Gross B, Kundra R, Kung AL, Ladanyi M, Lavery JA, Li X, Lisman A, Mastrogiacomo B, McCarthy C, Nichols C, Ochoa A, Panageas KS, Philip J, Pillai S, Riely GJ, Rizvi H, Rudolph J, Sawyers CL, Schrag D, Schultz N, Schwartz J, Sheridan R, Solit D, Wang A, Wilson M, Zehir A, Zhang H, Zhao G, Ahmed L, Bedard PL, Bruce JP, Chow H, Cooke S, Del Rossi S, Felicen S, Hakgor S, Jagannathan P, Kamel-Reid S, Krishna G, Leighl N, Lu Z, Nguyen A, Oldfield L, Plagianakos D, Pugh TJ, Rizvi A, Sabatini P, Shah E, Singaravelan N, Siu L, Srivastava G, Stickle N, Stockley T, Tang M, Virtaenen C, Watt S, Yu C, Bernard B, Bifulco C, Cramer JL, Lee S, Piening B, Reynolds S, Slagel J, Tittel P, Urba W, VanCampen J, Weerasinghe R, Acebedo A, Guinney J, Guo X, Hunter-Zinck H, Yu T, Dang K, Anagnostou V, Baras A, Brahmer J, Gocke C, Scharpf RB, Tao J, Velculescu VE, Alexander S, Bailey N, Gold P, Bierkens M, de Graaf J, Hudeček J, Meijer GA, Monkhorst K, Samsom KG, Sanders J, Sonke G, ten Hoeve J, van de Velde T, van den Berg J, Voest E, Steinhardt G, Kadri S, Pankhuri W, Wang P, Segal J, Moung C, Espinosa-Mendez C, Martell HJ, Onodera C, Quintanar Alfaro A, Sweet-Cordero EA, Talevich E, Turski M, Van’t Veer L, Wren A, Aguilar S, Dienstmann R, Mancuso F, Nuciforo P, Tabernero J, Viaplana C, Vivancos A, Anderson I, Chaugai S, Coco J, Fabbri D, Johnson D, Jones L, Li X, Lovly C, Mishra S, Mittendorf K, Wen L, Yang YJ, Ye C, Holt M, LeNoue-Newton ML, Micheel CM, Park BH, Rubinstein SM, Stricker T, Wang L, Warner J, Guan M, Jin G, Liu L, Topaloglu U, Urtis C, Zhang W, D’Eletto M, Hutchison S, Longtine J, Walther Z. Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis. Sci Rep 2022; 12:19055. [PMID: 36351964 PMCID: PMC9646734 DOI: 10.1038/s41598-022-21448-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.
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Affiliation(s)
- Debra Van Egeren
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Systems Biology, Harvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Stem Cell Program, Boston Children’s Hospital, Boston, MA USA ,grid.5386.8000000041936877XDepartment of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Khushi Kohli
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Jeremy L. Warner
- grid.152326.10000 0001 2264 7217Department of Medicine, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA
| | - Philippe L. Bedard
- grid.17063.330000 0001 2157 2938Department of Medicine, University of Toronto, Toronto, ON Canada
| | - Gregory Riely
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Eva Lepisto
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.429426.f0000 0000 9350 5788Present Address: Multiple Myeloma Research Foundation, Norwalk, CT USA
| | - Deborah Schrag
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Michele LeNoue-Newton
- grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Paul Catalano
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Kenneth L. Kehl
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Franziska Michor
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.65499.370000 0001 2106 9910The Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XThe Ludwig Center at Harvard, Boston, MA USA
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Coppes MJ, Maris JM. Dr Audrey E. Evans (1925-2022): academic trailblazer par excellence. Pediatr Res 2022:10.1038/s41390-022-02368-2. [PMID: 36335266 DOI: 10.1038/s41390-022-02368-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Max J Coppes
- Departments of Pediatrics and Internal Medicine, University of Nevada Reno School of Medicine, Reno, NV, USA.
| | - John M Maris
- Pediatric Oncology Perelman School of Medicine at the University of Pennsylvania, Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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Lynch HM, Beslow LA, Treat JR, Corcoran A, Lin JH, Gunawardena N, Maris JM, Behrens EM. Paraneoplastic myasthenia gravis and pemphigus associated with follicular dendritic cell sarcoma leading to cardiorespiratory collapse in a 7-year-old. Pediatr Blood Cancer 2022; 69:e29723. [PMID: 35484988 DOI: 10.1002/pbc.29723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Hayley M Lynch
- Division of General Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lauren A Beslow
- Division of Child Neurology, Departments of Neurology and Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James R Treat
- Division of General Pediatrics, Department of Dermatology, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aoife Corcoran
- Division of Pulmonary and Sleep Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jenny H Lin
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Perelman School of Medicine Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Naomi Gunawardena
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward M Behrens
- Division of Rheumatology, Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Shraim R, Weiner AK, Conkrite KL, Radaoui AB, Maris JM, Mosse YP, Diskin SJ, Sacan A, Garcia BA, Houghton PJ, Kurmasheva RT, Sorensen P, Morin GB, Mooney B. Abstract A009: Proteogenomic prioritization of immunotherapeutic targets in rhabdomyosarcoma nominate MEGF10 for preclinical development. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-a009] [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
Background: Rhabdomyosarcoma (RMS) has a high unmet need in terms of precision therapy development as there are currently no approved immunotherapies or targeted therapies, and few in the developmental pipeline. Here we sought to identify cell surface oncoproteins as a target for novel RMS-directed immunotherapies. Methods: We first performed plasma membrane enrichment followed by mass spectrometry to define the cell surface landscape of 7 fusion(+) and 14 fusion(-) RMS patient-derived xenograft (PDX) models. The surfaceome data was filtered to only “high confidence” surface proteins by querying protein localization databases, Compartments (https://compartments.jensenlab.org/) and CIRFESS (https://gundrylab.shinyapps.io/cirfess/). We then developed a prioritization algorithm that uses a rank-product approach to score surface proteins. The input to the algorithm is a matrix that integrates multiple datasets to score the surface proteins based on their suitability to be an optimal immunotherapeutic target. In addition to the surfaceome data generated here, we also integrated matched RNA-sequencing data from eleven of the RMS PDX models, RNA-sequencing data from GTEx (n=15,253) and a recently developed normal tissue proteomics dataset (n=201) [Jiang. Cell. 2020], a list from Gene Ontology that included genes involved in muscle development pathways, and the gene dependency list for RMS in DepMap (https://depmap.org/portal/). Results: A total of 913 and 937 high confidence surface proteins were annotated from the mass spectrometry data for fusion(+) and fusion(−) samples, respectively. A dendrogram separated the surface protein profiles into two clusters based on fusion(+) and fusion(−) RMS subtypes, thus the algorithm was run separately on each subtype. Within the top 50% of prioritized targets, 88% and 86% of the targets overlapped and 12% and 14% were identified exclusively in fusion(+) and fusion(−) subtypes, respectively. ALK, a previously putative protein marker in fusion(+) RMS, scored in the top 10% of the fusion(+) targets based on the algorithm, and surprisingly we saw abundant ALK expression in 6/14 fusion(−) PDX samples. MEGF10, a novel target, was ranked as the top target for both fusion(+) and fusion(−) RMS. MEGF10 plays a role in cell adhesion, motility, and proliferation. It scored as a significant dependency in DepMap for RMS (p-value=0.0002). Based on RNA-sequencing and proteomics, MEGF10 shows no expression in most healthy tissues surveyed, with several orders of magnitude lower expression detected in RNASeq in muscle and brain tissue, but not in the proteomic datasets. Conclusion: Here, we defined the surfaceome of RMS, and found substantial overlap in surface proteins between fusion(+) and fusion(−) RMS subtypes. We validated previous observations that ALK is expressed in RMS, here verifying that the protein is expressed on the plasma membrane. MEGF10 appears to be a strong novel candidate target for RMS immunotherapies, and ongoing work to validate our proteogenomic findings will be reported.
Citation Format: Rawan Shraim, Amber K. Weiner, Karina L. Conkrite, Alexander B. Radaoui, John M. Maris, Yael P. Mosse, Sharon J. Diskin, Ahmet Sacan, Benjamin A. Garcia, Peter J. Houghton, Raushan T. Kurmasheva, Poul Sorensen, Gregg B. Morin, Brian Mooney. Proteogenomic prioritization of immunotherapeutic targets in rhabdomyosarcoma nominate MEGF10 for preclinical development [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A009.
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Affiliation(s)
- Rawan Shraim
- 1Children's Hospital of Philadelphia, Philadelphia, PA,
| | | | | | | | - John M. Maris
- 1Children's Hospital of Philadelphia, Philadelphia, PA,
| | - Yael P. Mosse
- 1Children's Hospital of Philadelphia, Philadelphia, PA,
| | | | | | | | | | | | - Poul Sorensen
- 5University of British Columbia, Vancouver, BC, Canada
| | | | - Brian Mooney
- 5University of British Columbia, Vancouver, BC, Canada
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Batra V, Samanta M, Makvandi M, Groff D, Martorano P, Elias J, Ranieri P, Tsang M, Hou C, Li Y, Pawel B, Martinez D, Vaidyanathan G, Carlin S, Pryma DA, Maris JM. Preclinical Development of [211At]meta- astatobenzylguanidine ([211At]MABG) as an Alpha Particle Radiopharmaceutical Therapy for Neuroblastoma. Clin Cancer Res 2022; 28:4146-4157. [PMID: 35861867 PMCID: PMC9475242 DOI: 10.1158/1078-0432.ccr-22-0400] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/09/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE [131I]meta-iodobenzylguanidine ([131I]MIBG) is a targeted radiotherapeutic administered systemically to deliver beta particle radiation in neuroblastoma. However, relapses in the bone marrow are common. [211At]meta-astatobenzylguanidine ([211At] MABG) is an alpha particle emitter with higher biological effectiveness and short path length which effectively sterilizes microscopic residual disease. Here we investigated the safety and antitumor activity [211At]MABG in preclinical models of neuroblastoma. EXPERIMENTAL DESIGN We defined the maximum tolerated dose (MTD), biodistribution, and toxicity of [211At]MABG in immunodeficient mice in comparison with [131I]MIBG. We compared the antitumor efficacy of [211At]MABG with [131I]MIBG in three murine xenograft models. Finally, we explored the efficacy of [211At]MABG after tail vein xenografting designed to model disseminated neuroblastoma. RESULTS The MTD of [211At]MABG was 66.7 MBq/kg (1.8 mCi/kg) in CB17SC scid-/- mice and 51.8 MBq/kg (1.4 mCi/kg) in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice. Biodistribution of [211At]MABG was similar to [131I]MIBG. Long-term toxicity studies on mice administered with doses up to 41.5 MBq/kg (1.12 mCi/kg) showed the radiotherapeutic to be well tolerated. Both 66.7 MBq/kg (1.8 mCi/kg) single dose and fractionated dosing 16.6 MBq/kg/fraction (0.45 mCi/kg) × 4 over 11 days induced marked tumor regression in two of the three models studied. Survival was significantly prolonged for mice treated with 12.9 MBq/kg/fraction (0.35 mCi/kg) × 4 doses over 11 days [211At]MABG in the disseminated disease (IMR-05NET/GFP/LUC) model (P = 0.003) suggesting eradication of microscopic disease. CONCLUSIONS [211At]MABG has significant survival advantage in disseminated models of neuroblastoma. An alpha particle emitting radiopharmaceutical may be effective against microscopic disseminated disease, warranting clinical development.
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Affiliation(s)
- Vandana Batra
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Minu Samanta
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mehran Makvandi
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Paul Martorano
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jimmy Elias
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pietro Ranieri
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Matthew Tsang
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Catherine Hou
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yimei Li
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bruce Pawel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Daniel Martinez
- Division of Anatomic Pathology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Sean Carlin
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel A. Pryma
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Corresponding Author: John M. Maris, Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, 3501 Civic Center Boulevard, Philadelphia, PA 19104. Phone: 215-590-5242; E-mail:
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Foster JB, Griffin C, Rokita JL, Stern A, Brimley C, Rathi K, Lane MV, Buongervino SN, Smith T, Madsen PJ, Martinez D, Delaidelli A, Sorensen PH, Wechsler-Reya RJ, Karikó K, Storm PB, Barrett DM, Resnick AC, Maris JM, Bosse KR. Development of GPC2-directed chimeric antigen receptors using mRNA for pediatric brain tumors. J Immunother Cancer 2022; 10:e004450. [PMID: 36167467 PMCID: PMC9516314 DOI: 10.1136/jitc-2021-004450] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Pediatric brain tumors are the leading cause of cancer death in children with an urgent need for innovative therapies. Glypican 2 (GPC2) is a cell surface oncoprotein expressed in neuroblastoma for which targeted immunotherapies have been developed. This work aimed to characterize GPC2 expression in pediatric brain tumors and develop an mRNA CAR T cell approach against this target. METHODS We investigated GPC2 expression across a cohort of primary pediatric brain tumor samples and cell lines using RNA sequencing, immunohistochemistry, and flow cytometry. To target GPC2 in the brain with adoptive cellular therapies and mitigate potential inflammatory neurotoxicity, we used optimized mRNA to create transient chimeric antigen receptor (CAR) T cells. We developed four mRNA CAR T cell constructs using the highly GPC2-specific fully human D3 single chain variable fragment for preclinical testing. RESULTS We identified high GPC2 expression across multiple pediatric brain tumor types including medulloblastomas, embryonal tumors with multilayered rosettes, other central nervous system embryonal tumors, as well as definable subsets of highly malignant gliomas. We next validated and prioritized CAR configurations using in vitro cytotoxicity assays with GPC2-expressing neuroblastoma cells, where the light-to-heavy single chain variable fragment configurations proved to be superior. We expanded the testing of the two most potent GPC2-directed CAR constructs to GPC2-expressing medulloblastoma and high-grade glioma cell lines, showing significant GPC2-specific cell death in multiple models. Finally, biweekly locoregional delivery of 2-4 million GPC2-directed mRNA CAR T cells induced significant tumor regression in an orthotopic medulloblastoma model and significantly prolonged survival in an aggressive orthotopic thalamic diffuse midline glioma xenograft model. No GPC2-directed CAR T cell related neurologic or systemic toxicity was observed. CONCLUSION Taken together, these data show that GPC2 is a highly differentially expressed cell surface protein on multiple malignant pediatric brain tumors that can be targeted safely with local delivery of mRNA CAR T cells, laying the framework for the clinical translation of GPC2-directed immunotherapies for pediatric brain tumors.
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Affiliation(s)
- Jessica B Foster
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Data-Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Crystal Griffin
- Center for Data-Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Bioinformatics and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Allison Stern
- Center for Data-Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cameron Brimley
- Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Komal Rathi
- Center for Data-Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Bioinformatics and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Maria V Lane
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Samantha N Buongervino
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tiffany Smith
- Center for Data-Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Peter J Madsen
- Center for Data-Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daniel Martinez
- Department of Pathology & Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alberto Delaidelli
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Poul H Sorensen
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | | | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurosurgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John M Maris
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kristopher R Bosse
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Krytska K, Casey CE, Pogoriler J, Martinez D, Rathi KS, Farrel A, Berko ER, Tsang M, Sano RR, Kendsersky N, Erickson SW, Teicher BA, Isse K, Saunders L, Smith MA, Maris JM, Mossé YP. Evaluation of the DLL3-targeting antibody-drug conjugate rovalpituzumab tesirine in preclinical models of neuroblastoma. Cancer Res Commun 2022; 2:616-623. [PMID: 36381237 PMCID: PMC9648412 DOI: 10.1158/2767-9764.crc-22-0137] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/10/2022] [Accepted: 06/20/2022] [Indexed: 06/16/2023]
Abstract
Neuroblastomas have neuroendocrine features and often show similar gene expression patterns to small cell lung cancer including high expression of delta-like ligand 3 (DLL3). Here we determine the efficacy of rovalpituzumab tesirine (Rova-T), an antibody drug conjugated (ADC) with a pyrrolobenzodiazepine (PBD) dimer toxin targeting DLL3, in preclinical models of human neuroblastoma. We evaluated DLL3 expression in RNA sequencing data sets and performed immunohistochemistry (IHC) on neuroblastoma patient derived xenograft (PDX), human neuroblastoma primary tumor and normal childhood tissue microarrays (TMAs). We then evaluated the activity of Rova-T against 11 neuroblastoma PDX models using varying doses and schedules and compared anti-tumor activity to expression levels. DLL3 mRNA was differentially overexpressed in neuroblastoma at comparable levels to small cell lung cancer, as well as Wilms and rhabdoid tumors. DLL3 protein was robustly expressed across the neuroblastoma PDX array, but membranous staining was variable. The human neuroblastoma array, however, showed staining in only 44% of cases, whereas no significant staining was observed in the normal childhood tissue array. Rova-T showed a clear dose response effect across the 11 models tested, with a single dose inducing a complete or partial response in 3/11 and stable disease in another 3/11 models. No overt signs of toxicity were observed, and there was no treatment-related mortality. Strong membranous staining was necessary, but not sufficient, for anti-tumor activity. Rova-T has activity in a subset of neuroblastoma preclinical models, but heterogeneous expression in these models and the near absence of expression seen in human tumors suggests that any DLL3-targeting clinical trial should be only performed with a robust companion diagnostic to evaluate DLL3 expression for patient selection.
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Affiliation(s)
- Kateryna Krytska
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Colleen E. Casey
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jennifer Pogoriler
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel Martinez
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Komal S. Rathi
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics and Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics and Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Esther R. Berko
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Matthew Tsang
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Renata R. Sano
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Nathan Kendsersky
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | - Kumiko Isse
- Abbvie Stemcentrx, South San Francisco, California
| | | | | | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yael P. Mossé
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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Kendsersky NM, Mabe NW, Farrel A, Grossmann LD, Odrobina M, Stegmaier K, Maris JM. Abstract 3889: Identification of ADRN-specific, MES-specific, and pan-subtype therapeutic targets in neuroblastoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3889] [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
Background: Neuroblastoma is an extracranial solid tumor of childhood that arises from the developing sympathetic nervous system. Half of patients with high-risk disease do not survive despite multimodal therapy, and survival after relapse is unlikely. Recent studies have characterized two distinct neuroblastoma cell subtypes: the adrenergic (ADRN) subtype of sympathetic noradrenergic-like identity and the mesenchymal (MES) subtype of neural crest-like identity. ADRN-like cells are more aggressive and proliferative, while the MES-like cells are chemotherapy resistant. Neuroblastoma tumors are heterogenous and comprised of both ADRN and MES cell subtypes, which likely leads to differential responses to therapy. Thus, to eliminate cells that may lead to tumor relapse, it is critical to develop therapies against both neuroblastoma subtypes.
Methods: To identify candidate subtype-specific therapeutic targets, we used ssGSEA to classify human neuroblastoma tumors into ADRN- or MES-dominant and performed differential expression. We validated subtype-specific targets in additional datasets and models, including transdifferentiated neuroblastoma cell lines (ADRN-to-MES) after inducible overexpression of the MES transcription factor PRRX1.
Results: We show ADRN-specific expression of known preclinical and clinical neuroblastoma targets with limited or no expression in MES-dominant tumors. We propose CD276 (B7-H3) and L1CAM as pan-subtype targets with similar expression in both subtypes and stable expression after ADRN-to-MES transdifferentiation. In MES-specific neuroblastoma patient samples and cell lines, we identify the receptor tyrosine kinase AXL as a candidate MES target. MES neuroblastoma cell lines are more sensitive to small molecule AXL inhibitors (Cabozantinib, NPS-1034, and ONO-7475) compared to ADRN cell lines. We also observe higher expression of PDL1 and immunosuppressive chemokines in MES-dominant tumors and cell lines. Finally, we detect AXL and Gas6 transcripts in tumor-resident macrophages and fibroblasts, which may further promote immune evasion.
Conclusion: Here we have identified and prioritized ADRN-specific, MES-specific, and pan-subtype neuroblastoma therapeutic targets and suggest AXL-targeted therapy may eliminate both MES-dominant neuroblastoma cells and immune cell populations that contribute to an immunosuppressive microenvironment.
Citation Format: Nathan M. Kendsersky, Nathaniel W. Mabe, Alvin Farrel, Liron D. Grossmann, Michal Odrobina, Kimberly Stegmaier, John M. Maris. Identification of ADRN-specific, MES-specific, and pan-subtype therapeutic targets in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3889.
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Affiliation(s)
| | - Nathaniel W. Mabe
- 2Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA
| | - Alvin Farrel
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Kimberly Stegmaier
- 2Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA
| | - John M. Maris
- 1Children's Hospital of Philadelphia, Philadelphia, PA
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Groff D, Casey C, krytska K, Tsang M, Acholla C, Maris JM, Mosse YP. Abstract 2006: Preclinical evaluation of dual AURKA (LY3295668) and BCL2 (venetoclax) inhibition in neuroblastoma (NB). Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2006] [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
Introduction: Deregulated expression of the MYCN oncogene is associated with the development of many neural-derived pediatric cancers including NB, medulloblastoma and atypical teratoid rhabdoid tumors. Amplification of the MYCN oncogene is present in over 40% of high-risk NBs that remain lethal in most patients, thus developing better therapies for these patients is essential. While direct therapeutic targeting of MYCN protein remains challenging, we previously demonstrated synergistic activity of dual targeting of BCL-2 (venetoclax) and AURKA (MLN8237) in MYCN-amplified NB (Ham Cancer Cell, 2016). With MLN8237 no longer being developed due to toxicities related to AURKB inhibition, testing of a highly selective AURKA inhibitor, LY3295668, is warranted.
Methods: LY3295668 (Chemie Tek) and venetoclax (Selleck Chem) were tested alone and in combination in six NB PDX models using 2-3 mice/arm. Five Patient Derived Xenograft (PDX) models tested (COG-N-424x, COG-N-453x, NB-1643, Obelix-Rx and Obelix-2x) were MYCN-amplified and one xenograft model (SK-N-AS) was MYCN-non-amplified. First, a comprehensive toxicity study, testing LY3295668 at 30mg/kg with venetoclax at 100mg/kg, 75mg/kg, 50mg/kg, and 25mkg/kg, was performed. Based on tolerability of combination, an optimal dose of 30mg/kg for LY3295668 and 50mg/kg for venetoclax was selected and administered once daily, seven days a week, via oral gavage for 60 days. These were the maximum tolerated doses when tested in combination, that did not result in weight loss greater than 15% or other overt signs of toxicity.
Results: LY3295668 (30mg/kg) and venetoclax (50mg/kg) were well tolerated as monotherapy, and when administered in combination showed a maximum weight loss of 13%. Single agent therapy resulted in minimal if any growth delay. Four of five MYCN-amplified PDX models demonstrated maintained complete responses and one showed significant tumor growth delay. No effect was observed in the MYCN-non-amplified model with single agent or combination treatment compared to vehicle.
Conclusions: Dual targeting of AURKA and BCL2 with LY3295668 and venetoclax is tolerable and demonstrates compelling anti-tumor activity in MYCN-amplified NB PDX models, validating our earlier findings (Ham et al). These preclinical results provisionally support clinical development of this combination for NB patients with MYCN amplification. Assessment of additional PDX models is currently ongoing and will be reported.
Citation Format: David Groff, Colleen Casey, Kateryna krytska, Matthew Tsang, Christina Acholla, John M. Maris, Yael P. Mosse. Preclinical evaluation of dual AURKA (LY3295668) and BCL2 (venetoclax) inhibition in neuroblastoma (NB) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2006.
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Affiliation(s)
- David Groff
- 1The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Colleen Casey
- 1The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Matthew Tsang
- 1The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - John M. Maris
- 2University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yael P. Mosse
- 2University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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Uzun Y, Grossmann LD, Chen CH, Thadi A, Wu CY, Gao P, Diep D, Surrey L, Martinez D, Patel T, Qiu Q, Johnson S, Yu W, Drabings S, Chen C, Hu Y, Chen G, Oldridge DA, Zhang K, Wu H, Bernt K, Zhang N, Maris JM, Tan K. Abstract 6051: Longitudinal single-cell sequencing of high-risk neuroblastoma tumors reveals intrinsic and extrinsic mechanisms of therapy resistance. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6051] [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
Neuroblastoma is a childhood cancer originating from embryonic neuronal progenitor cells and is the most common cancer diagnosed in infants. Although the majority of patients respond to initial chemotherapy, most high-risk patients suffer relapse due to therapy resistance.
Here, we generated single-cell transcriptome and bulk whole-genome sequencing data of diagnosis and post-therapy samples from 23 patients diagnosed with high-risk neuroblastoma. We found two distinct adrenergic populations in the patient samples. Most tumor cells showed a mature sympathoblast phenotype whereas a small fraction was in an undifferentiated state with activation of protein translation, unfolded protein, and oxidative phosphorylation pathways. We found that therapy-resistant tumor cells in these two subpopulations had distinct characteristics. The more mature resistant subpopulation upregulated genes associated with epithelial-to-mesenchymal transition, including TWIST1, PLCB1 and CD276. The undifferentiated resistant subpopulation upregulated Ras signal transduction and TP53 pathway genes.
Analysis of the immune microenvironment revealed that most tumor-associated macrophages became more immunosuppressive post-therapy via multiple newly gained signaling interactions including the complement signaling pathway. We discovered a limited infiltration of T lymphocytes in the tumor microenvironment, and chemotherapy induced an effector state with upregulated mTOR signaling and metabolism. Overall, our study revealed subpopulations of tumor cells in neuroblastoma that responded differently to induction chemotherapy. Our findings uncovered distinct molecular signatures of the resistant cells and their interactions with the immune microenvironment, paving the way for developing novel therapies for high-risk neuroblastoma.
Citation Format: Yasin Uzun, Liron D. Grossmann, Chia-Hui Chen, Anusha Thadi, Chi-Yun Wu, Peng Gao, Dinh Diep, Lea Surrey, Daniel Martinez, Tasleema Patel, Qi Qiu, Sarah Johnson, Wenbao Yu, Shane Drabings, Changya Chen, Yuxuan Hu, Gregory Chen, Derek A. Oldridge, Kun Zhang, Hao Wu, Kathrin Bernt, Nancy Zhang, John M. Maris, Kai Tan. Longitudinal single-cell sequencing of high-risk neuroblastoma tumors reveals intrinsic and extrinsic mechanisms of therapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6051.
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Affiliation(s)
- Yasin Uzun
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Chia-Hui Chen
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - Anusha Thadi
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - Chi-Yun Wu
- 2University of Pennsylvania, Philadelphia, PA
| | - Peng Gao
- 3Xi’an Jiao Tong University, Xi’an, China
| | - Dinh Diep
- 4University of California San Diego, San Diego, CA
| | - Lea Surrey
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Qi Qiu
- 2University of Pennsylvania, Philadelphia, PA
| | | | - Wenbao Yu
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Changya Chen
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | | | - Kun Zhang
- 4University of California San Diego, San Diego, CA
| | - Hao Wu
- 2University of Pennsylvania, Philadelphia, PA
| | - Kathrin Bernt
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - Nancy Zhang
- 2University of Pennsylvania, Philadelphia, PA
| | - John M. Maris
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kai Tan
- 1Children's Hospital of Philadelphia, Philadelphia, PA
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Grossmann LD, Uzun Y, Lindsay J, Chen CH, Wingrove C, Gao P, Thadi A, Marshall Q, Kendsersky NM, Surrey L, Martinez D, Mycek E, Casey C, Krytska K, Tsang M, Wolpaw A, Groff DN, Runbeck E, McDevitt J, Diep D, Patel T, Bernt KM, Dang C, Zhang K, Mosse YP, Tan K, Maris JM. Abstract 699: NF-kB is a master regulator of resistance to therapy in high-risk neuroblastoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-699] [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
BACKGROUND High-risk neuroblastoma is a pediatric cancer arising from the developing sympathetic nervous system with a 50% relapse rate that is typically fatal. At least two subpopulations of neuroblastoma cells exist that can transdifferentiate, adrenergic and mesenchymal, the latter being more resistant to chemotherapy. Mechanisms of therapy resistance are largely unknown and the cells responsible for relapse have not been identified.
METHODS We used single nucleus RNA and ATAC sequencing to identify and characterize the cells that survive chemotherapy, termed here “persister cells”, from a cohort of 20 matched diagnostic and post induction chemotherapyhigh-risk neuroblastoma patients and two patient derived xenograft (PDX) models from diagnostic tumors. Eight representative cell lines derived from neuroblastomas at diagnosis were treated with standard-of-care chemotherapy, and flow cytometry was used to sort for live cells. ML120B and CRISPR-CAS9 were used to modulate NF-kB signaling. An RNA-seq dataset of 153 high-risk neuroblastoma patients was used to determine differentially activated pathways between adrenergic and mesenchymal tumors.
RESULTS Residual malignant cells in the post-chemotherapy tumor samples clustered into three main groups separated by the response to therapy. The most prevalent group of persister cells in responders (N=16/20) displayed low MYC(N) activity even in the presence of MYCN amplification. This group also demonstrated decreased expression of the adrenergic core regulatory circuit genes including PHOX2B, ISL1, HAND2, along with marked activation of TNF-alpha via NF-kB signaling. High NF-kB activity was found in a subpopulation of diagnostic cells in two chemo-refractory patients. We validated decreased expression of MYCN (2-fold decrease, p<0.0001) and PHOX2B (3.13-fold decrease, p<0.0001) in PDXs following chemotherapy. MYCN protein levels were decreased and nuclear p65 levels were increased in cell lines treated with chemotherapy. Pharmacologic inhibition of NF-kB signaling and genetic depletion of p65 resulted in increased killing (3.58-fold increase, p=0.0012) of neuroblastoma cell lines in response to chemotherapy. Finally, we classified 153 diagnostic high-risk neuroblastomas as predominantly adrenergic or mesenchymal using RNA-seq, showing that mesenchymal tumors were enriched with NF-kB pathway activation signatures. We then validated high nuclear p65 levels in 3 mesenchymal cell lines. We tested 6 adrenergic lines, 4 of which had no detectable nuclear p65. Notably, the 2 cell lines with detectable nuclear p65 were derived from diagnostic specimens that showed de novo chemotherapy resistance.
CONCLUSIONS NF-kB activation is a major mediator of de novo and acquired chemotherapy resistance in high-risk neuroblastoma. We postulate that concomitant silencing of this pathway could eliminate persister cells and prevent disease relapse.
Citation Format: Liron D. Grossmann, Yasin Uzun, Jarrett Lindsay, Chia-Hui Chen, Catherine Wingrove, Peng Gao, Anusha Thadi, Quinlen Marshall, Nathan M. Kendsersky, Lea Surrey, Daniel Martinez, Emily Mycek, Colleen Casey, Kateryna Krytska, Matthew Tsang, Adam Wolpaw, David N. Groff, Erin Runbeck, Jayne McDevitt, Dinh Diep, Tasleema Patel, Kathrin M. Bernt, Chi Dang, Kun Zhang, Yael P. Mosse, Kai Tan, John M. Maris. NF-kB is a master regulator of resistance to therapy in high-risk neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 699.
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Affiliation(s)
| | - Yasin Uzun
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Chia-Hui Chen
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Peng Gao
- 3Xidian University, Xi'an, China
| | - Anusha Thadi
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Lea Surrey
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Emily Mycek
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - Colleen Casey
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Matthew Tsang
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - Adam Wolpaw
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Erin Runbeck
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Dinh Diep
- 5University of California San Diego, La Jolla, CA
| | | | | | - Chi Dang
- 2University of Pennsylvania, Philadelphia, PA
| | - Kun Zhang
- 5University of California San Diego, La Jolla, CA
| | - Yael P. Mosse
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kai Tan
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - John M. Maris
- 1Children's Hospital of Philadelphia, Philadelphia, PA
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Scolaro L, Nunes NM, Kushida M, Schultz DC, Cherry S, Whig K, Dirks P, Tabori U, Maris JM. Abstract LB188: Identification of intrinsic molecular vulnerabilities in inherited and treatment-related hypermutant patient-derived glioma cell line models. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-lb188] [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
Background: Hypermutant gliomas in children are caused by inherited or therapy related replication repair deficiency (RRD), the latter typically following treatment with the alkylating agent temozolomide (TMZ). Recently, immune checkpoint inhibitors (ICIs) revealed clinical responses and prolonged survival in 30% of pediatric-inherited hypermutant gliomas but none of the treatment-related adult hypermutant gliomas. We hypothesized that high-throughput screening of hypermutant and RRD patient derived glioma cell lines from both glioma types (PDGCL) would reveal specific molecular vulnerabilities immediately translatable as targeted therapies to be used in combination with ICIs.
Methods: We screened two pediatric hypermutant and RRD PDGCLs (1806, 1260); one pediatric non-hypermutant non-RRD PDGCL (477); an adult non-hypermutant non-RRD PDGCL (189EW); matched recurrent post-TMZ treatment hypermutant RRD PDGCL (248z, 248xy) from patient 189 against a library of 3336 bioactive compounds, including 1500 FDA approved drugs supplemented with 16 additional compounds (BET, PLK1, EZH2, PARP1 inhibitors) at 100nM.Each plate screened contained negative (0.2% DMSO) and positive controls (50nM bortezomib). Cell viability was calculated at 96hr by ATP measurement. Raw values from negative and positive control wells were aggregated and used to calculate Z’-factors for each assay plate, as a measure of assay performance and data quality, with a Z’-factor >0.5 representing high quality data. Only drugs scoring Normalized Percentage of Inhibition (NPI) >50% and z-score>3 were considered potential hits for follow-up evaluation, focusing on those enriched in the pediatric and adult hypermutant PDGCLs.
Results: We identified 45 drugs active in all three of the pediatric PDGCLs and 23 common hits in the adult cell lines. Broad target classes were identified such as microtubule associated inhibitors, heat shock protein inhibitors for PDGCLs and proteasome inhibitors for adult cell lines. Unique targets were also identified. Importantly, the inherited and treatment related mismatch repair deficient glioma cells (MMR1260,248z, 248xy) and the hypermutant pediatric cell line (1806) exhibited significant response to PI3K/mTOR inhibitors. Ultrahypermutant RRD cell line and the treatment-related hypermutant cell lines (1806 248z 248xy ) displayed sensitivity to topoisomerase I inhibitors. Preliminary in vitro data confirm sensitivity to topotecan of hypermutant pediatric and adult cell lines.
Conclusion: We have identified both mechanism specific and common intrinsic vulnerabilities in hypermutant PDGCLs that can be tested as adjuvant therapies for ICI. Functional validation of the lead candidates is ongoing and will be reported.
Citation Format: Laura Scolaro, Nuno Miguel Nunes, Michelle Kushida, David C. Schultz, Sara Cherry, Kanupriya Whig, Peter Dirks, Uri Tabori, John M. Maris. Identification of intrinsic molecular vulnerabilities in inherited and treatment-related hypermutant patient-derived glioma cell line models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB188.
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Affiliation(s)
- Laura Scolaro
- 1Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Nuno Miguel Nunes
- 2Program in Genetics and Genome Biology, The Hospital for Sick Children, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, Ontario, Canada
| | - Michelle Kushida
- 3The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Roronto, Ontario, Canada
| | - David C. Schultz
- 4High-throughput Screening Core, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sara Cherry
- 4High-throughput Screening Core, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kanupriya Whig
- 4High-throughput Screening Core, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Peter Dirks
- 5The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Uri Tabori
- 2Program in Genetics and Genome Biology, The Hospital for Sick Children, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, Ontario, Canada
| | - John M. Maris
- 6Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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Chang X, Liu Y, Glessner J, Hou C, Qu H, Nguyen K, Sleiman P, Lee L, Diskin SJ, Maris JM, Hakonarson H. Identification of Mitochondrial DNA Variants Associated With Risk of Neuroblastoma. J Natl Cancer Inst 2022; 114:910-913. [PMID: 35134187 PMCID: PMC9194614 DOI: 10.1093/jnci/djac012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 07/06/2021] [Revised: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Neuroblastoma is a childhood cancer that originates in the developing sympathetic nervous system. We previously reported a crucial role of mitochondrial DNA haplogroups in the pathology of neuroblastoma. To pinpoint mitochondrial DNA variants associated with neuroblastoma risk, we applied a mitochondrial genome imputation pipeline to the single nucleotide polymorphisms array data of 2 pediatric cohorts containing a total of 2404 neuroblastoma patients and 9310 cancer-free controls. All statistical tests were 2-sided. The single nucleotide variant, rs2853493, was statistically significantly associated with neuroblastoma risk in the discovery cohort (odds ratio = 0.62, 95% confidence interval = 0.53 to 0.72, P < .001) and further confirmed in the replication cohort (odds ratio = 0.75, 95% confidence interval = 0.62 to 0.90, P = .002). Further, expression quantitative trait loci analysis indicated genotypes of rs2853493 were associated with expression levels of MT-CYB gene expression in neuroblastoma cells, suggesting rs2853493 may confer risk to neuroblastoma via regulating the expression level of its nearby genes.
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Affiliation(s)
- Xiao Chang
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yichuan Liu
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph Glessner
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cuiping Hou
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Huiqi Qu
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kenny Nguyen
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Patrick Sleiman
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lobin Lee
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Sharon J Diskin
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Maris
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA , USA
- Division of Oncology and Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine , Philadelphia, PA, USA
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Ph iladelphia, PA, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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London WB, Bender H, Irwin M, Hogarty MD, Castleberry RP, Maris JM, Kao PC, Naranjo A, Cohn SL. Survival of patients with neuroblastoma before versus after reduction of therapy due to the change in age cut-off from 12 to 18 months in Children’s Oncology Group (COG) risk stratification. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.10013] [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: 11/20/2022] Open
Abstract
10013 Background: In 2006, COG reclassified subgroups of toddlers diagnosed with neuroblastoma from high-(HR) to intermediate-risk (IR), when the age cut-off for increased risk was raised from 365 days (12 mo) to 547 days (18 mo) (London, J Clin Onc 2005). The aim of this retrospective study was to determine if excellent outcome was maintained after a reduction of therapy. Methods: Children < 3 yrs old at diagnosis, enrolled on a COG biology study from 1990-2018, were eligible (n = 9,189). Therapy was reduced for two “cohorts of interest” based on the age cut-off change: 365-546 days old with INSS stage 4, MYCN not amplified, favorable INPC, hyperdiploid tumors (12-18mo/Stage4/FavBiology); and, 365-546 days old with INSS stage 3 tumors with non-amplified MYCN and unfavorable INPC (12-18mo/Stage3/NotAmp/UnfavINPC). Log rank tests compared event-free (EFS) and overall survival (OS) curves. Results: In the cohorts of interest, patient (pt) characteristics were similar for ≤2006 vs > 2006. For 12-18mo/Stage4/FavBiology, 5-year EFS and OS (± std error) before (≤2006; n = 40) versus after (> 2006; n = 55) the reduction in therapy were similar: 89±5.1% versus 87±4.6% (p = 0.7), and 89±5.1% versus 94±3.2% (p = 0.4), respectively (Table). For 12-18mo/Stage3/NotAmp/UnfavINPC, the 5-year EFS and OS were both 100%, before (n = 6) and after (n = 4) 2006. For the combined cohorts for ≤2006 versus > 2006, EFS and OS were 91±4.4% versus 88±4.3% (p = 0.6), and 91±4.5% versus 95±2.9% (p = 0.5), respectively. Within HR pts diagnosed ≤2006, EFS/OS were 91±4.4%/91±4.5% for (12-18mo/Stage4/FavBiology plus 12-18mo/Stage3/NotAmp/UnfavINPC) vs 38±1.3%/43±1.3% for all other HR pts < 3 yrs old (p < 0.0001; Table). Within IR pts diagnosed > 2006, EFS/OS were 88±4.3%/95±2.9% for (12-18mo/Stage4/FavBiology plus 12-18mo/Stage3/NotAmp/UnfavINPC) vs 88±0.9%/95±0.6% for all other IR pts < 3 yrs old (p = 0.9). Conclusions: Our 19 year study demonstrates that excellent outcome is maintained among toddlers with Stage4/FavBiology and Stage3/Not Amp/Unfav INPC neuroblastoma with a significant reduction of therapy from high- to intermediate-risk treatment. Importantly, pts were likely spared acute toxicity and late effects known to be associated with HR therapy. Efforts to identify additional pt cohorts who may not require HR therapy to achieve long-term survival are critical to improve the long-term health of children with neuroblastoma. [Table: see text]
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Affiliation(s)
- Wendy B. London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | | | | | | | - John M. Maris
- Children's Hospital of Philadelphia, Philadelphia, PA
| | - Pei-Chi Kao
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Arlene Naranjo
- Children's Oncology Group Statistics and Data Center, University of Florida, Gainesville, FL
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Goldsmith KC, Mosse YP, Kayser K, Chi YY, Chioda M, Thurm HC, Chen J, Krishnaswami S, Peltz G, Granger M, Mody R, Marshall LV, Desai AV, Berko E, Maris JM, Matthay KK, Ghazarian S, Park JR, Marachelian A. Phase I trial of lorlatinib in combination with topotecan/cyclophosphamide in children with ALK-driven refractory or relapsed neuroblastoma: A new approaches to neuroblastoma therapy consortium study. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.10041] [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: 11/20/2022] Open
Abstract
10041 Background: Lorlatinib, a macrocyclic ATP-competitive ALK inhibitor, exerts potent activity against neuroblastoma (NB) xenograftsharboring the most common ALK mutations. We performed a first-in-child phase 1 study of lorlatinib for patients with refractory/relapsed (R/R) ALK aberrant high-risk NB. We previously reported on Part A of the study, where safety of single agent lorlatinib was determined, showing complete responses (CR) to lorlatinib at the recommended phase 2 dose (RP2D) of 115 mg/m2 in pts < 18 years and 150 mg in pts > 18 yrs. Part B of the study aimed to determine the safety, pharmacokinetics (PK), RP2D, and explore the anti-tumor activity of lorlatinib in combination with topotecan and cyclophosphamide in pts with R/R ALK-driven NB. Methods: Patients with R/R NB ages 1-17 years with ALK mutations or amplification were eligible; prior ALK inhibitor (ALKi) treatment was allowed. Lorlatinib was orally administered once daily on days 1-28 with topotecan (0.75 mg/m2/day) and cyclophosphamide (250 mg/m2/day) administered intravenously days 1-5 and GCSF starting day 6. Two lorlatinib dose levels (DL) of 95 mg/m2/day (DL4B) and 115 mg/m2/day (DL5B) were assessed using a 3+3 dose escalation design with the primary endpoint of dose limiting toxicity (DLT) in Course 1. We report lorlatinib safety, PK, and objective response rate (ORR) for patients enrolled on Part B. Results: Between 10FEB2020 and 03DEC2021,9 eligible pts enrolled on Part B with a median age of 6.7 years (3.7-12.7). Three pts were enrolled onto DL4B and six onto DL5B (2/3 pts on DL4B and 4/6 pts on DL5B had received prior ALKi therapy) with no DLT’s observed in course 1. One patient on DL5B experienced a neuropsychological DLT in Course 3. Most common treatment-related adverse events were hematological, febrile neutropenia, high cholesterol, hypertriglyceridemia, and neuropsychological effects. The median number of courses received was 6 with a range of 1-8 on DL4B and 1-7 on DL5B. Of the 8 patients evaluable for response, ORR was 50%: 2/3 pts on DL4B and 2/5 pts on DL5B. Preliminary PK data demonstrate comparable dose level-associated lorlatinib steady state exposure between Part B chemotherapy combination and Part A monotherapy cohorts, supporting that chemotherapy had no effect on lorlatinib exposure that there are no overlapping toxicities. Conclusions: Lorlatinib in combination with topotecan and cyclophosphamide is well tolerated, and early data suggest encouraging objective anti-tumor activity. These data support the current integration of lorlatinib into up-front high risk neuroblastoma therapy for patients with ALK-driven neuroblastoma. Clinical trial information: NCT03107988.
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Affiliation(s)
| | - Yael P. Mosse
- The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Yueh-Yun Chi
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | | | | | | | | | | | | | - Lynley V. Marshall
- Paediatric and Adolescent Drug Development Team, The Royal Marsden Hospital and The Institute of Cancer Research, London, United Kingdom
| | | | - Esther Berko
- Children's Hospital of Philadelphia, Philadelphia, PA
| | - John M. Maris
- Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Julie R. Park
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, WA
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Testori A, Vaksman Z, Diskin SJ, Hakonarson H, Capasso M, Iolascon A, Maris JM, Devoto M. Genetic analysis in African American children supports ancestry specific neuroblastoma susceptibility. Cancer Epidemiol Biomarkers Prev 2022; 31:870-875. [DOI: 10.1158/1055-9965.epi-21-0782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/15/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
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48
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Ferris MA, Smith AM, Heath SE, Duncavage EJ, Oberley M, Freyer D, Wynn R, Douzgou S, Maris JM, Reilly AF, Wu MD, Choo F, Fiets RB, Koene S, Spencer DH, Miller CA, Shinawi M, Ley TJ. DNMT3A overgrowth syndrome is associated with the development of hematopoietic malignancies in children and young adults. Blood 2022; 139:461-464. [PMID: 34788385 PMCID: PMC8777205 DOI: 10.1182/blood.2021014052] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/04/2021] [Indexed: 01/22/2023] Open
Affiliation(s)
| | | | | | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University, St Louis, MO
| | | | - David Freyer
- Children's Hospital Los Angeles, Los Angeles, CA
| | - Robert Wynn
- Paediatric Haematology and Bone Marrow Transplant (BMT), Royal Manchester Children's Hospital, Manchester, United Kingdom
| | - Sofia Douzgou
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - John M Maris
- Children's Hospital of Philadelphia, Philadelphia, PA and
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Anne F Reilly
- Children's Hospital of Philadelphia, Philadelphia, PA and
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Melinda D Wu
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR
| | - Florence Choo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Oregon Health & Science University, Portland, OR
| | - Roel B Fiets
- Department of Internal Medicine, Amphia Hospital, Breda, The Netherlands; and
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Heitzeneder S, Bosse KR, Zhu Z, Zhelev D, Majzner RG, Radosevich MT, Dhingra S, Sotillo E, Buongervino S, Pascual-Pasto G, Garrigan E, Xu P, Huang J, Salzer B, Delaidelli A, Raman S, Cui H, Martinez B, Bornheimer SJ, Sahaf B, Alag A, Fetahu IS, Hasselblatt M, Parker KR, Anbunathan H, Hwang J, Huang M, Sakamoto K, Lacayo NJ, Klysz DD, Theruvath J, Vilches-Moure JG, Satpathy AT, Chang HY, Lehner M, Taschner-Mandl S, Julien JP, Sorensen PH, Dimitrov DS, Maris JM, Mackall CL. GPC2-CAR T cells tuned for low antigen density mediate potent activity against neuroblastoma without toxicity. Cancer Cell 2022; 40:53-69.e9. [PMID: 34971569 PMCID: PMC9092726 DOI: 10.1016/j.ccell.2021.12.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 02/18/2021] [Revised: 10/13/2021] [Accepted: 12/06/2021] [Indexed: 01/12/2023]
Abstract
Pediatric cancers often mimic fetal tissues and express proteins normally silenced postnatally that could serve as immune targets. We developed T cells expressing chimeric antigen receptors (CARs) targeting glypican-2 (GPC2), a fetal antigen expressed on neuroblastoma (NB) and several other solid tumors. CARs engineered using standard designs control NBs with transgenic GPC2 overexpression, but not those expressing clinically relevant GPC2 site density (∼5,000 molecules/cell, range 1-6 × 103). Iterative engineering of transmembrane (TM) and co-stimulatory domains plus overexpression of c-Jun lowered the GPC2-CAR antigen density threshold, enabling potent and durable eradication of NBs expressing clinically relevant GPC2 antigen density, without toxicity. These studies highlight the critical interplay between CAR design and antigen density threshold, demonstrate potent efficacy and safety of a lead GPC2-CAR candidate suitable for clinical testing, and credential oncofetal antigens as a promising class of targets for CAR T cell therapy of solid tumors.
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Affiliation(s)
- Sabine Heitzeneder
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Kristopher R Bosse
- Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhongyu Zhu
- National Cancer Institute, Frederick, MD 21702, USA
| | - Doncho Zhelev
- University of Pittsburgh Department of Medicine, Pittsburgh, PA 15261, USA
| | - Robbie G Majzner
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Molly T Radosevich
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Shaurya Dhingra
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Samantha Buongervino
- Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Guillem Pascual-Pasto
- Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Emily Garrigan
- Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Xu
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Jing Huang
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Benjamin Salzer
- St. Anna Children's Cancer Research Institute, Vienna, Austria; Christian Doppler Laboratory for Next Generation CAR T Cells, Vienna, Austria
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Swetha Raman
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Hong Cui
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Benjamin Martinez
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | | | - Bita Sahaf
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Anya Alag
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Irfete S Fetahu
- University of Pittsburgh Department of Medicine, Pittsburgh, PA 15261, USA
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Hima Anbunathan
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | | | - Min Huang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathleen Sakamoto
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Norman J Lacayo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dorota D Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - Johanna Theruvath
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA
| | - José G Vilches-Moure
- Department of Comparative Medicine, Animal Histology Services, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 941209, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Manfred Lehner
- St. Anna Children's Cancer Research Institute, Vienna, Austria; Christian Doppler Laboratory for Next Generation CAR T Cells, Vienna, Austria
| | | | - Jean-Phillipe Julien
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada; Departments of Biochemistry and Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Dimiter S Dimitrov
- University of Pittsburgh Department of Medicine, Pittsburgh, PA 15261, USA
| | - John M Maris
- Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Lorry Lokey Building, Suite G3141, MC: 5456, 265 Campus Drive, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 941209, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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50
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Das A, Sudhaman S, Morgenstern D, Coblentz A, Chung J, Stone SC, Alsafwani N, Liu ZA, Karsaneh OAA, Soleimani S, Ladany H, Chen D, Zatzman M, Cabric V, Nobre L, Bianchi V, Edwards M, Sambira Nahum LC, Ercan AB, Nabbi A, Constantini S, Dvir R, Yalon-Oren M, Campino GA, Caspi S, Larouche V, Reddy A, Osborn M, Mason G, Lindhorst S, Bronsema A, Magimairajan V, Opocher E, De Mola RL, Sabel M, Frojd C, Sumerauer D, Samuel D, Cole K, Chiaravalli S, Massimino M, Tomboc P, Ziegler DS, George B, Van Damme A, Hijiya N, Gass D, McGee RB, Mordechai O, Bowers DC, Laetsch TW, Lossos A, Blumenthal DT, Sarosiek T, Yen LY, Knipstein J, Bendel A, Hoffman LM, Luna-Fineman S, Zimmermann S, Scheers I, Nichols KE, Zapotocky M, Hansford JR, Maris JM, Dirks P, Taylor MD, Kulkarni AV, Shroff M, Tsang DS, Villani A, Xu W, Aronson M, Durno C, Shlien A, Malkin D, Getz G, Maruvka YE, Ohashi PS, Hawkins C, Pugh TJ, Bouffet E, Tabori U. Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency. Nat Med 2022; 28:125-135. [PMID: 34992263 PMCID: PMC8799468 DOI: 10.1038/s41591-021-01581-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 02/10/2021] [Accepted: 10/15/2021] [Indexed: 02/08/2023]
Abstract
Cancers arising from germline DNA mismatch repair deficiency or polymerase proofreading deficiency (MMRD and PPD) in children harbour the highest mutational and microsatellite insertion–deletion (MS-indel) burden in humans. MMRD and PPD cancers are commonly lethal due to the inherent resistance to chemo-irradiation. Although immune checkpoint inhibitors (ICIs) have failed to benefit children in previous studies, we hypothesized that hypermutation caused by MMRD and PPD will improve outcomes following ICI treatment in these patients. Using an international consortium registry study, we report on the ICI treatment of 45 progressive or recurrent tumors from 38 patients. Durable objective responses were observed in most patients, culminating in a 3 year survival of 41.4%. High mutation burden predicted response for ultra-hypermutant cancers (>100 mutations per Mb) enriched for combined MMRD + PPD, while MS-indels predicted response in MMRD tumors with lower mutation burden (10–100 mutations per Mb). Furthermore, both mechanisms were associated with increased immune infiltration even in ‘immunologically cold’ tumors such as gliomas, contributing to the favorable response. Pseudo-progression (flare) was common and was associated with immune activation in the tumor microenvironment and systemically. Furthermore, patients with flare who continued ICI treatment achieved durable responses. This study demonstrates improved survival for patients with tumors not previously known to respond to ICI treatment, including central nervous system and synchronous cancers, and identifies the dual roles of mutation burden and MS-indels in predicting sustained response to immunotherapy. Hypermutation and microsatellite burden determine responses and long-term survival following PD-1 blockade in children and young adults with refractory cancers resulting from germline DNA replication repair deficiency.
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Affiliation(s)
- Anirban Das
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatric Haematology/ Oncology, Tata Medical Centre, Kolkata, India
| | - Sumedha Sudhaman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniel Morgenstern
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Ailish Coblentz
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jiil Chung
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Simone C Stone
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Noor Alsafwani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University (IAU), Dammam, Saudi Arabia
| | - Zhihui Amy Liu
- Department of Biostatistics, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Ola Abu Al Karsaneh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Shirin Soleimani
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Hagay Ladany
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Tel-Aviv, Israel
| | - David Chen
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew Zatzman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vanja Cabric
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Liana Nobre
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Vanessa Bianchi
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lauren C Sambira Nahum
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ayse B Ercan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Arash Nabbi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shlomi Constantini
- Department of Pediatric Neurosurgery, Dana Children's Hospital, Tel-Aviv, Israel
| | - Rina Dvir
- Department of Pediatric Hematology-Oncology, Tel-Aviv Sourasky Medical Centre, Tel-Aviv, Israel
| | - Michal Yalon-Oren
- Department of Pediatric Hematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | - Gadi Abebe Campino
- Department of Pediatric Hematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | - Shani Caspi
- Department of Pediatric Hematology-Oncology, Sheba Medical Centre, Ramat Gan, Israel
| | - Valerie Larouche
- Department of Paediatric Haematology/Oncology, Centre Hospitalier de Quebec-Universite Laval, Quebec City, Quebec, Canada
| | - Alyssa Reddy
- Departments of Neurology and Pediatrics, University of California, San Francisco, CA, USA
| | - Michael Osborn
- Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Gary Mason
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Scott Lindhorst
- Neuro-Oncology, Department of Neurosurgery, and Department of Medicine, Division of Hematology/Medical Oncology, Medical University of South Carolina, Charleston, SC, USA
| | - Annika Bronsema
- Department of Paediatric Haematology and Oncology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Vanan Magimairajan
- Department of Paediatric Haematology-Oncology, Cancer Care Manitoba, Research Institute in Oncology and Haematology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Enrico Opocher
- Paediatric Haematology, Oncology and Stem Cell Transplant Division, Padua University Hospital, Padua, Italy
| | - Rebecca Loret De Mola
- Pediatric Hematology-Oncology, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Magnus Sabel
- Department of Paediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.,Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Charlotta Frojd
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - David Sumerauer
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - David Samuel
- Department of Pediatric Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Kristina Cole
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelpha, PA, USA
| | - Stefano Chiaravalli
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maura Massimino
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Patrick Tomboc
- Department of Pediatrics, J.W. Ruby Memorial Hospital - West Virginia University, Morgantown, WV, USA
| | - David S Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Ben George
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - An Van Damme
- Department of Paediatric Haematology and Oncology, Saint Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - Nobuko Hijiya
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Centre, New York, NY, USA
| | - David Gass
- Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Rose B McGee
- Cancer Predisposition Division, Oncology Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Oz Mordechai
- Department of Pediatric Hematology Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Daniel C Bowers
- Department of Pediatrics, The University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Theodore W Laetsch
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelpha, PA, USA
| | - Alexander Lossos
- Department of Oncology, Leslie and Michael Gaffin Center for Neuro-Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Deborah T Blumenthal
- Neuro-Oncology Service, Tel-Aviv Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | | | - Lee Yi Yen
- Department of Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jeffrey Knipstein
- Division of Pediatric Hematology/ Oncology/ BMT, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anne Bendel
- Department of Pediatric Hematology-Oncology, Children's Hospitals and Clinics of Minnesota, St Paul, MN, USA
| | | | - Sandra Luna-Fineman
- Department of Pediatrics, Anschutz Medical Campus, Children's Hospital of Colorado, Aurora, CO, USA
| | - Stefanie Zimmermann
- Paediatric Haematology and Oncology, University Hospital Frankfurt, Frankfurt, Germany
| | - Isabelle Scheers
- Paediatric Gastroenterology, Hepatology and Nutrition Unit, Cliniques Universitaires St Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Kim E Nichols
- Cancer Predisposition Division, Oncology Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michal Zapotocky
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelpha, PA, USA
| | - Peter Dirks
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Abhaya V Kulkarni
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Manohar Shroff
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Derek S Tsang
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Anita Villani
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Carol Durno
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gad Getz
- Massachusetts General Hospital Cancer Center and Department of Pathology, Charlestown, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yosef E Maruvka
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Tel-Aviv, Israel
| | - Pamela S Ohashi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Eric Bouffet
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Uri Tabori
- Division of Haematology Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada. .,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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