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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: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [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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