1
|
Lang T, Geaghan S, Loh TP, Mak C, Papassotiriou I, Kyriakopoulou LG. Considerations for applying emerging technologies in paediatric laboratory medicine. Clin Chem Lab Med 2024; 62:1938-1949. [PMID: 39044644 DOI: 10.1515/cclm-2023-1408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024]
Abstract
Emerging technology in laboratory medicine can be defined as an analytical method (including biomarkers) or device (software, applications, and algorithms) that by its stage of development, translation into broad routine clinical practice, or geographical adoption and implementation has the potential to add value to clinical diagnostics. Paediatric laboratory medicine itself may be considered an emerging area of specialisation that is established relatively recently following increased appreciation and understanding of the unique physiology and healthcare needs of the children. Through four clinical (neonatal hypoglycaemia, neonatal hyperbilirubinaemia, sickle cell disorder, congenital adrenal hyperplasia) and six technological (microassays, noninvasive testing, alternative matrices, next generation sequencing, exosome analysis, machine learning) illustrations, key takeaways of application of emerging technology for each area are summarised. Additionally, nine key considerations when applying emerging technology in paediatric laboratory medicine setting are discussed.
Collapse
Affiliation(s)
- Tim Lang
- Department of Blood Sciences, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Sharon Geaghan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Chloe Mak
- Division of Chemical Pathology, Hong Kong Children's Hospital, Kowloon, Hong Kong SAR, China
| | - Ioannis Papassotiriou
- First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | | |
Collapse
|
2
|
Geoerger B, Bautista F, André N, Berlanga P, Gatz SA, Marshall LV, Rubino J, Archambaud B, Marchais A, Rubio-San-Simón A, Ducassou S, Zwaan CM, Casanova M, Nysom K, Pellegrino S, Hoog-Labouret N, Buzyn A, Blanc P, Paoletti X, Vassal G. Precision cancer medicine platform trials: Concepts and design of AcSé-ESMART. Eur J Cancer 2024; 208:114201. [PMID: 39018630 DOI: 10.1016/j.ejca.2024.114201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/23/2024] [Accepted: 06/27/2024] [Indexed: 07/19/2024]
Abstract
Precision cancer medicine brought the promise of improving outcomes for patients with cancer. High-throughput molecular profiling of tumors at treatment failure aims to direct a patient to a treatment matched to the tumor profile. In this way, improved outcome has been achieved in a small number of patients whose tumors exhibit unique targetable oncogenic drivers. Most cancers, however, contain multiple genetic alterations belonging to and of various hallmarks of cancer; for most of these alterations, there is limited knowledge on the level of evidence, their hierarchical roles in oncogenicity, and utility as biomarkers for response to targeted treatment(s). We developed a proof-of-concept trial that explores new treatment strategies in a molecularly-enriched tumor-agnostic, pediatric population. The evaluation of novel agents, including first-in-child molecules, alone or in combination, is guided by the available understanding of or hypotheses for the mechanisms of action of the diverse cancer events. Main objectives are: to determine 1) recommended phase 2 doses, 2) activity signals to provide the basis for disease specific development, and 3) to define new predictive biomarkers. Here we outline concepts, rationales and designs applied in the European AcSé-ESMART trial and highlight the feasibility but also complexity and challenges of such innovative platform trials.
Collapse
Affiliation(s)
- Birgit Geoerger
- Gustave Roussy Cancer Campus, Department of Pediatric and Adolescent Oncology, Université Paris-Saclay, Villejuif, France; Gustave Roussy Cancer Campus, INSERM U1015, Université Paris-Saclay, Villejuif, France.
| | - Francisco Bautista
- Hospital Niño Jesús, Department of Pediatric Oncology, Hematology and Stem Cell Transplantation, Madrid, Spain; Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Nicolas André
- Hôpital de la Timone, Department of Pediatric Oncology, AP-HM, Marseille, France; UMR INSERM 1068, CNRS UMR 7258, Aix Marseille Université U105, Marseille Cancer Research Center (CRCM), France; Metronomics Global Health Initiative, Marseille, France
| | - Pablo Berlanga
- Gustave Roussy Cancer Campus, Department of Pediatric and Adolescent Oncology, Université Paris-Saclay, Villejuif, France
| | - Susanne A Gatz
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Lynley V Marshall
- Royal Marsden Hospital NHS Foundation Trust Paediatric and Adolescent Oncology Drug Development Unit, and & The Institute of Cancer Research, Division of Clinical Studies, London, United Kingdom
| | - Jonathan Rubino
- Gustave Roussy Cancer Campus, Clinical Research Direction, Université Paris-Saclay, Villejuif, France
| | - Baptiste Archambaud
- Inserm, Université Paris-Saclay, CESP U1018, Oncostat, labeled Ligue Contre le Cancer, Villejuif, France; Gustave Roussy Cancer Campus, Office of Biostatistics and Epidemiology, Université Paris-Saclay, Villejuif, France, Université Paris-Saclay, CESP U1018, Oncostat, labeled Ligue Contre le Cancer, Villejuif, France
| | - Antonin Marchais
- Gustave Roussy Cancer Campus, Department of Pediatric and Adolescent Oncology, Université Paris-Saclay, Villejuif, France; Gustave Roussy Cancer Campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Alba Rubio-San-Simón
- Hospital Niño Jesús, Department of Pediatric Oncology, Hematology and Stem Cell Transplantation, Madrid, Spain
| | - Stephane Ducassou
- Centre Hospitalier Universitaire Pellegrin - Hôpital des Enfants, Bordeaux, France
| | - C Michel Zwaan
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Michela Casanova
- Fondazione IRCCS Istituto Nazionale dei Tumori, Pediatric Oncology Unit, Milan, Italy
| | - Karsten Nysom
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Sophie Pellegrino
- Gustave Roussy Cancer Campus, Clinical Research Direction, Université Paris-Saclay, Villejuif, France
| | | | - Agnes Buzyn
- Institut National de Cancer, Boulogne, France
| | | | - Xavier Paoletti
- Inserm, Université Paris-Saclay, CESP U1018, Oncostat, labeled Ligue Contre le Cancer, Villejuif, France; Gustave Roussy Cancer Campus, Office of Biostatistics and Epidemiology, Université Paris-Saclay, Villejuif, France, Université Paris-Saclay, CESP U1018, Oncostat, labeled Ligue Contre le Cancer, Villejuif, France
| | - Gilles Vassal
- Gustave Roussy Cancer Campus, Department of Pediatric and Adolescent Oncology, Université Paris-Saclay, Villejuif, France; Gustave Roussy Cancer Campus, Clinical Research Direction, Université Paris-Saclay, Villejuif, France
| |
Collapse
|
3
|
Wong D, Tageldein M, Luo P, Ensminger E, Bruce J, Oldfield L, Gong H, Fischer NW, Laverty B, Subasri V, Davidson S, Khan R, Villani A, Shlien A, Kim RH, Malkin D, Pugh TJ. Cell-free DNA from germline TP53 mutation carriers reflect cancer-like fragmentation patterns. Nat Commun 2024; 15:7386. [PMID: 39191772 DOI: 10.1038/s41467-024-51529-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Germline pathogenic TP53 variants predispose individuals to a high lifetime risk of developing multiple cancers and are the hallmark feature of Li-Fraumeni syndrome (LFS). Our group has previously shown that LFS patients harbor shorter plasma cell-free DNA fragmentation; independent of cancer status. To understand the functional underpinning of cfDNA fragmentation in LFS, we conducted a fragmentomic analysis of 199 cfDNA samples from 82 TP53 mutation carriers and 30 healthy TP53-wildtype controls. We find that LFS individuals exhibit an increased prevalence of A/T nucleotides at fragment ends, dysregulated nucleosome positioning at p53 binding sites, and loci-specific changes in chromatin accessibility at development-associated transcription factor binding sites and at cancer-associated open chromatin regions. Machine learning classification resulted in robust differentiation between TP53 mutant versus wildtype cfDNA samples (AUC-ROC = 0.710-1.000) and intra-patient longitudinal analysis of ctDNA fragmentation signal enabled early cancer detection. These results suggest that cfDNA fragmentation may be a useful diagnostic tool in LFS patients and provides an important baseline for cancer early detection.
Collapse
Affiliation(s)
- Derek Wong
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Maha Tageldein
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ping Luo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Erik Ensminger
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey Bruce
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Leslie Oldfield
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Haifan Gong
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | | | - Brianne Laverty
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Vallijah Subasri
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Scott Davidson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Torotno, Ontario, Canada
| | - Reem Khan
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Torotno, Ontario, Canada
| | - Anita Villani
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Toroton, Ontario, Canada
| | - Adam Shlien
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Torotno, Ontario, Canada
| | - Raymond H Kim
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
- Toronto General Hospital Research Institute, Toronto, Ontario, Canada.
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada.
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Pediatrics, University of Toronto, Torotno, Ontario, Canada.
- Toronto General Hospital Research Institute, Toronto, Ontario, Canada.
| | - Trevor J Pugh
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada.
| |
Collapse
|
4
|
Luo M, Wong D, Zelley K, Wu J, Schubert J, Denenberg EH, Fanning EA, Chen J, Gallo D, Golenberg N, Patel M, Conlin LK, Maxwell KN, Wertheim GB, Surrey LF, Zhong Y, Brodeur GM, MacFarland SP, Li MM. Identification of TP53 germline variants in pediatric patients undergoing tumor testing: strategy and prevalence. J Natl Cancer Inst 2024; 116:1356-1365. [PMID: 38702830 DOI: 10.1093/jnci/djae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/08/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND TP53 alterations are common in certain pediatric cancers, making identification of putative germline variants through tumor genomic profiling crucial for disease management. METHODS We analyzed TP53 alterations in 3123 tumors from 2788 pediatric patients sequenced using tumor-only or tumor-normal paired panels. Germline confirmatory testing was performed when indicated. Somatic and germline variants were classified based on published guidelines. RESULTS In 248 tumors from 222 patients, 284 tier 1/2 TP53 sequence and small copy number variants were detected. Following germline classification, 86.6% of 142 unique variants were pathogenic or likely pathogenic. Confirmatory testing on 118 patients revealed germline TP53 variants in 28 of them (23 pathogenic or likely pathogenic and 5 of uncertain significance), suggesting a minimum Li-Fraumeni syndrome incidence of 0.8% (23/2788) in this cohort, 10.4% (23/222) in patients with TP53 variant-carrying tumors, and 19.5% (23/118) with available normal samples. About 25% (7/28) of patients with germline TP53 variants did not meet Li-Fraumeni syndrome diagnostic or testing criteria, while 20.9% (28/134) with confirmed or inferred somatic origins did. TP53 biallelic inactivation occurred in 75% of germline carrier tumors and was also prevalent in other groups, causing an elevated tumor-observed variant allelic fraction. Somatic evidence, however, including low variant allele fraction correctly identified only 27.8% (25/90) of patients with confirmed somatic TP53 variants. CONCLUSION The high incidence and variable phenotype of Li-Fraumeni syndrome in this cohort highlights the importance of assessing germline status of TP53 variants identified in all pediatric tumors. Without clear somatic evidence, distinguishing somatic from germline origins is challenging. Classifying germline and somatic variants should follow appropriate guidelines.
Collapse
Affiliation(s)
- Minjie Luo
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Derek Wong
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristin Zelley
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jinhua Wu
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jeffery Schubert
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth H Denenberg
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth A Fanning
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiani Chen
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel Gallo
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Netta Golenberg
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maha Patel
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kara N Maxwell
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA
| | - Gerald B Wertheim
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lea F Surrey
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yiming Zhong
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Garrett M Brodeur
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Suzanne P MacFarland
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marilyn M Li
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
5
|
Khincha PP, Savage SA. When the somatic genome informs the germline: the example of TP53. J Natl Cancer Inst 2024; 116:1190-1192. [PMID: 38908000 PMCID: PMC11308161 DOI: 10.1093/jnci/djae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024] Open
Affiliation(s)
- Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| |
Collapse
|
6
|
Dholaria H, Tran B. Time to diversify: germline exome sequencing for men with testicular germ cell tumour. Transl Androl Urol 2024; 13:1329-1332. [PMID: 39100820 PMCID: PMC11291399 DOI: 10.21037/tau-24-85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 08/06/2024] Open
Affiliation(s)
- Hetal Dholaria
- Department of Paediatric Oncology and Hematology, Perth Children’s Hospital, Perth, Australia
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, Australia
- Paediatrics, School of Medicine, University of Western Australia, Perth, Australia
| | - Ben Tran
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| |
Collapse
|
7
|
Mangum R, Lin FY, Parsons DW. Recent Advancements and Innovations in Pediatric Precision Oncology. J Pediatr Hematol Oncol 2024; 46:262-271. [PMID: 38857189 DOI: 10.1097/mph.0000000000002871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/29/2024] [Indexed: 06/12/2024]
Abstract
Precision oncology incorporates comprehensive genomic profiling into the individualized clinical care of pediatric cancer patients. In recent years, comprehensive pan-cancer analyses have led to the successful implementation of genomics-based pediatric trials and accelerated approval of novel targeted agents. In addition, disease-specific studies have resulted in molecular subclassification of myriad cancer types with subsequent tailoring of treatment intensity based on the patient's prognostic factors. This review discusses the progress of the field and highlights developments that are leading to more personalized cancer care and improved patient outcomes. Increased understanding of the evolution of precision oncology over recent decades emphasizes the tremendous impact of improved genomic applications. New technologies and improved diagnostic modalities offer further promise for future advancements within the field.
Collapse
Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ
| | - Frank Y Lin
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
| | - D Williams Parsons
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| |
Collapse
|
8
|
Hodder A, Leiter SM, Kennedy J, Addy D, Ahmed M, Ajithkumar T, Allinson K, Ancliff P, Bailey S, Barnard G, Burke GAA, Burns C, Cano-Flanagan J, Chalker J, Coleman N, Cheng D, Clinch Y, Dryden C, Ghorashian S, Griffin B, Horan G, Hubank M, May P, McDerra J, Nagrecha R, Nicholson J, O'Connor D, Pavasovic V, Quaegebeur A, Rao A, Roberts T, Samarasinghe S, Stasevich I, Tadross JA, Trayers C, Trotman J, Vora A, Watkins J, Chitty LS, Bowdin S, Armstrong R, Murray MJ, Hook CE, Tarpey P, Vedi A, Bartram J, Behjati S. Benefits for children with suspected cancer from routine whole-genome sequencing. Nat Med 2024; 30:1905-1912. [PMID: 38956197 PMCID: PMC11271414 DOI: 10.1038/s41591-024-03056-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/08/2024] [Indexed: 07/04/2024]
Abstract
Clinical whole-genome sequencing (WGS) has been shown to deliver potential benefits to children with cancer and to alter treatment in high-risk patient groups. It remains unknown whether offering WGS to every child with suspected cancer can change patient management. We collected WGS variant calls and clinical and diagnostic information from 281 children (282 tumors) across two English units (n = 152 from a hematology center, n = 130 from a solid tumor center) where WGS had become a routine test. Our key finding was that variants uniquely attributable to WGS changed the management in ~7% (20 out of 282) of cases while providing additional disease-relevant findings, beyond standard-of-care molecular tests, in 108 instances for 83 (29%) cases. Furthermore, WGS faithfully reproduced every standard-of-care molecular test (n = 738) and revealed several previously unknown genomic features of childhood tumors. We show that WGS can be delivered as part of routine clinical care to children with suspected cancer and can change clinical management by delivering unexpected genomic insights. Our experience portrays WGS as a clinically impactful assay for routine practice, providing opportunities for assay consolidation and for delivery of molecularly informed patient care.
Collapse
Affiliation(s)
- Angus Hodder
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sarah M Leiter
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Jonathan Kennedy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Dilys Addy
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Munaza Ahmed
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Kieren Allinson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Phil Ancliff
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Shivani Bailey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gemma Barnard
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - G A Amos Burke
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Charlotte Burns
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Danny Cheng
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Caryl Dryden
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Sara Ghorashian
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Blanche Griffin
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
| | - Gail Horan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Michael Hubank
- North Thames Genomic Laboratory Hub, London, UK
- The Institute of Cancer Research, London, UK
| | - Phillippa May
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Joanna McDerra
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Rajvi Nagrecha
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David O'Connor
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Vesna Pavasovic
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Annelies Quaegebeur
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anupama Rao
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Thomas Roberts
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | | | - Iryna Stasevich
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - John A Tadross
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Claire Trayers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jamie Trotman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ajay Vora
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - James Watkins
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Lyn S Chitty
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
- North Thames Genomic Laboratory Hub, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sarah Bowdin
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- East Genomics Laboratory Hub, Cambridge, UK
| | - Ruth Armstrong
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew J Murray
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Catherine E Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Patrick Tarpey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- East Genomics Laboratory Hub, Cambridge, UK.
| | - Aditi Vedi
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| | - Jack Bartram
- Great Ormond Street Hospital NHS Foundation Trust, London, UK.
- North Thames Genomic Laboratory Hub, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| |
Collapse
|
9
|
Hansford JR, Das A, McGee RB, Nakano Y, Brzezinski J, Scollon SR, Rednam SP, Schienda J, Michaeli O, Kim SY, Greer MLC, Weksberg R, Stewart DR, Foulkes WD, Tabori U, Pajtler KW, Pfister SM, Brodeur GM, Kamihara J. Update on Cancer Predisposition Syndromes and Surveillance Guidelines for Childhood Brain Tumors. Clin Cancer Res 2024; 30:2342-2350. [PMID: 38573059 PMCID: PMC11147702 DOI: 10.1158/1078-0432.ccr-23-4033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/27/2024] [Accepted: 04/04/2024] [Indexed: 04/05/2024]
Abstract
Tumors of the central nervous system (CNS) comprise the second most common group of neoplasms in childhood. The incidence of germline predisposition among children with brain tumors continues to grow as our knowledge on disease etiology increases. Some children with brain tumors may present with nonmalignant phenotypic features of specific syndromes (e.g., nevoid basal cell carcinoma syndrome, neurofibromatosis type 1 and type 2, DICER1 syndrome, and constitutional mismatch-repair deficiency), while others may present with a strong family history of cancer (e.g., Li-Fraumeni syndrome) or with a rare tumor commonly found in the context of germline predisposition (e.g., rhabdoid tumor predisposition syndrome). Approximately 50% of patients with a brain tumor may be the first in a family identified to have a predisposition. The past decade has witnessed a rapid expansion in our molecular understanding of CNS tumors. A significant proportion of CNS tumors are now well characterized and known to harbor specific genetic changes that can be found in the germline. Additional novel predisposition syndromes are also being described. Identification of these germline syndromes in individual patients has not only enabled cascade testing of family members and early tumor surveillance but also increasingly affected cancer management in those patients. Therefore, the AACR Cancer Predisposition Working Group chose to highlight these advances in CNS tumor predisposition and summarize and/or generate surveillance recommendations for established and more recently emerging pediatric brain tumor predisposition syndromes.
Collapse
Affiliation(s)
- Jordan R Hansford
- Michael Rice Children's Hematology and Oncology Center, Women's and Children's Hospital; South Australia Health and Medical Research Institute; South Australia ImmunoGenomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Anirban Das
- Division of Hematology/Oncology, The Hospital for Sick Children; SickKids Research Institute; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Rose B McGee
- Department of Oncology, Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yoshiko Nakano
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Houston, Texas
| | - Jack Brzezinski
- Division of Hematology/Oncology, The Hospital for Sick Children; SickKids Research Institute; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Sarah R Scollon
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Houston, Texas
| | - Surya P Rednam
- Department of Pediatrics, Division of Hematology/Oncology, Baylor College of Medicine, Houston, Texas
| | - Jaclyn Schienda
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Orli Michaeli
- Division of Hematology/Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Sun Young Kim
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Center, Cincinnati, Ohio
| | - Mary-Louise C Greer
- Department of Diagnostic and Interventional Radiology, The Hospital for Sick Children/Department of Medical Imaging, University of Toronto, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - William D Foulkes
- Department of Human Genetics, McGill University, and Division of Medical Genetics, Departments of Specialized Medicine, McGill University Health Centre and Jewish General Hospital, Montreal, Quebec, Canada
| | - Uri Tabori
- Division of Hematology/Oncology, The Hospital for Sick Children; SickKids Research Institute; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Kristian W Pajtler
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center Heidelberg (KiTZ); German Cancer Research Center Heidelberg (DKFZ) and Heidelberg University Hospital, Heidelberg; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, Hopp Children's Cancer Center Heidelberg (KiTZ); German Cancer Research Center Heidelberg (DKFZ) and Heidelberg University Hospital, Heidelberg; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Garrett M Brodeur
- Department of Pediatrics, Division of Oncology, the Children's Hospital of Philadelphia, and the University of Pennsylvania/Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Junne Kamihara
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
10
|
Church AJ, Wakefield CE, Hetherington K, Shern JF. Promise and Perils of Precision Oncology for Patients With Pediatric and Young Adult Sarcomas. Am Soc Clin Oncol Educ Book 2024; 44:e432794. [PMID: 38924707 DOI: 10.1200/edbk_432794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
The completion of multiple national pediatric precision oncology platform trials and the incorporation of standardized molecular profiling into the diagnostic care of pediatric and young adult patients with sarcomas have proven the feasibility and potential of the approach. In this work, we explore the current state of the art of precision oncology for pediatric and young adults with sarcoma. We highlight important lessons learned and the challenges that should be addressed in the next generation of trials. The chapter outlines current efforts to improve standardization of molecular assays, harmonization of data collection, and novel molecular tools such as cell-free DNA analyses. Finally, we discuss the impacts and psychosocial outcomes experienced by patients and communication strategies for providers.
Collapse
Affiliation(s)
- Alanna J Church
- Department of Pathology, Boston Children's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Claire E Wakefield
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Randwick, NSW, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Kate Hetherington
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Randwick, NSW, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| |
Collapse
|
11
|
Linga BG, Mohammed SGAA, Farrell T, Rifai HA, Al-Dewik N, Qoronfleh MW. Genomic Newborn Screening for Pediatric Cancer Predisposition Syndromes: A Holistic Approach. Cancers (Basel) 2024; 16:2017. [PMID: 38893137 PMCID: PMC11171256 DOI: 10.3390/cancers16112017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
As next-generation sequencing (NGS) has become more widely used, germline and rare genetic variations responsible for inherited illnesses, including cancer predisposition syndromes (CPSs) that account for up to 10% of childhood malignancies, have been found. The CPSs are a group of germline genetic disorders that have been identified as risk factors for pediatric cancer development. Excluding a few "classic" CPSs, there is no agreement regarding when and how to conduct germline genetic diagnostic studies in children with cancer due to the constant evolution of knowledge in NGS technologies. Various clinical screening tools have been suggested to aid in the identification of individuals who are at greater risk, using diverse strategies and with varied outcomes. We present here an overview of the primary clinical and molecular characteristics of various CPSs and summarize the existing clinical genomics data on the prevalence of CPSs in pediatric cancer patients. Additionally, we discuss several ethical issues, challenges, limitations, cost-effectiveness, and integration of genomic newborn screening for CPSs into a healthcare system. Furthermore, we assess the effectiveness of commonly utilized decision-support tools in identifying patients who may benefit from genetic counseling and/or direct genetic testing. This investigation highlights a tailored and systematic approach utilizing medical newborn screening tools such as the genome sequencing of high-risk newborns for CPSs, which could be a practical and cost-effective strategy in pediatric cancer care.
Collapse
Affiliation(s)
- BalaSubramani Gattu Linga
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | | | - Thomas Farrell
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
| | - Hilal Al Rifai
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | - Nader Al-Dewik
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Genomics and Precision Medicine (GPM), College of Health & Life Science (CHLS), Hamad Bin Khalifa University (HBKU), Doha 0974, Qatar
- Faculty of Health and Social Care Sciences, Kingston University and St George’s University of London, Kingston upon Thames, Surrey, London KT1 2EE, UK
| | - M. Walid Qoronfleh
- Healthcare Research & Policy Division, Q3 Research Institute (QRI), Ann Arbor, MI 48197, USA
| |
Collapse
|
12
|
Deyell RJ, Shen Y, Titmuss E, Dixon K, Williamson LM, Pleasance E, Nelson JMT, Abbasi S, Krzywinski M, Armstrong L, Bonakdar M, Ch'ng C, Chuah E, Dunham C, Fok A, Jones M, Lee AF, Ma Y, Moore RA, Mungall AJ, Mungall KL, Rogers PC, Schrader KA, Virani A, Wee K, Young SS, Zhao Y, Jones SJM, Laskin J, Marra MA, Rassekh SR. Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers. Nat Commun 2024; 15:4165. [PMID: 38755180 PMCID: PMC11099106 DOI: 10.1038/s41467-024-48363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21.2 y) are included. Germline pathogenic/likely pathogenic variants are identified in 12% of participants, of which 60% were not known prior. Therapeutically actionable variants are identified by targeted gene report and whole genome in 32% and 62% of participants, respectively, and increase to 96% after integrating transcriptome analyses. Thirty-two molecularly informed therapies are pursued in 28 participants with 54% achieving a clinical benefit rate; objective response or stable disease ≥6 months. Integrated WGTA identifies therapeutically actionable variants in almost all tumors and are directly translatable to clinical care of children with poor prognosis cancers.
Collapse
Affiliation(s)
- Rebecca J Deyell
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Katherine Dixon
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Jessica M T Nelson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sanna Abbasi
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Chris Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alexandra Fok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Martin Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Paul C Rogers
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kathleen Wee
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Sean S Young
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Cancer Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Shahrad R Rassekh
- Department of Pediatrics, BC Children's Hospital and Research Institute, Vancouver, BC, Canada.
| |
Collapse
|
13
|
Kratz CP, Lupo PJ, Zelley K, Schienda J, Nichols KE, Stewart DR, Malkin D, Brodeur GM, Maxwell K, Plon SE, Walsh MF. Adult-Onset Cancer Predisposition Syndromes in Children and Adolescents-To Test or not to Test? Clin Cancer Res 2024; 30:1733-1738. [PMID: 38411636 DOI: 10.1158/1078-0432.ccr-23-3683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/17/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
With the increasing use of comprehensive germline genetic testing of children and adolescents with cancer, it has become evident that pathogenic variants (PV) in adult-onset cancer predisposition genes (aoCPG) underlying adult-onset cancer predisposition syndromes, such as Lynch syndrome or hereditary breast and ovarian cancer, are enriched and reported in 1% to 2% of children and adolescents with cancer. However, the causal relationship between PVs in aoCPGs and childhood cancer is still under investigation. The best-studied examples include heterozygous PVs in mismatch repair genes associated with Lynch syndrome in children with mismatch repair deficient high-grade glioma, heterozygous PVs in BARD1 in childhood neuroblastoma, and heterozygous PVs in BRCA2 in children with rhabdomyosarcoma. The low penetrance for pediatric cancers is considered to result from a combination of the low baseline risk of cancer in childhood and the report of only a modest relative risk of disease in childhood. Therefore, we do not advise that healthy children empirically be tested for PVs in an aoCPG before adulthood outside a research study. However, germline panel testing is increasingly being performed in children and adolescents with cancer, and exome and genome sequencing may be offered more commonly in this population in the future. The precise pediatric cancer risks and spectra associated with PVs in aoCPGs, underlying cellular mechanisms and somatic mutational signatures, as well as treatment response, second neoplasm risks, and psycho-oncological aspects require further research.
Collapse
Affiliation(s)
- Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Philip J Lupo
- Department of Pediatrics, Division of Hematology/Oncology, Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Kristin Zelley
- Division of Oncology at the Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jaclyn Schienda
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Kim E Nichols
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, Maryland
| | - David Malkin
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Garrett M Brodeur
- Division of Oncology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kara Maxwell
- Department of Medicine, Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sharon E Plon
- Department of Pediatrics, Division of Hematology/Oncology, Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Michael F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
14
|
Tesi B, Robinson KL, Abel F, Díaz de Ståhl T, Orrsjö S, Poluha A, Hellberg M, Wessman S, Samuelsson S, Frisk T, Vogt H, Henning K, Sabel M, Ek T, Pal N, Nyman P, Giraud G, Wille J, Pronk CJ, Norén-Nyström U, Borssén M, Fili M, Stålhammar G, Herold N, Tettamanti G, Maya-Gonzalez C, Arvidsson L, Rosén A, Ekholm K, Kuchinskaya E, Hallbeck AL, Nordling M, Palmebäck P, Kogner P, Smoler GK, Lähteenmäki P, Fransson S, Martinsson T, Shamik A, Mertens F, Rosenquist R, Wirta V, Tham E, Grillner P, Sandgren J, Ljungman G, Gisselsson D, Taylan F, Nordgren A. Diagnostic yield and clinical impact of germline sequencing in children with CNS and extracranial solid tumors-a nationwide, prospective Swedish study. THE LANCET REGIONAL HEALTH. EUROPE 2024; 39:100881. [PMID: 38803632 PMCID: PMC11129334 DOI: 10.1016/j.lanepe.2024.100881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/04/2024] [Accepted: 02/23/2024] [Indexed: 05/29/2024]
Abstract
Background Childhood cancer predisposition (ChiCaP) syndromes are increasingly recognized as contributing factors to childhood cancer development. Yet, due to variable availability of germline testing, many children with ChiCaP might go undetected today. We report results from the nationwide and prospective ChiCaP study that investigated diagnostic yield and clinical impact of integrating germline whole-genome sequencing (gWGS) with tumor sequencing and systematic phenotyping in children with solid tumors. Methods gWGS was performed in 309 children at diagnosis of CNS (n = 123, 40%) or extracranial (n = 186, 60%) solid tumors and analyzed for disease-causing variants in 189 known cancer predisposing genes. Tumor sequencing data were available for 74% (227/309) of patients. In addition, a standardized clinical assessment for underlying predisposition was performed in 95% (293/309) of patients. Findings The prevalence of ChiCaP diagnoses was 11% (35/309), of which 69% (24/35) were unknown at inclusion (diagnostic yield 8%, 24/298). A second-hit and/or relevant mutational signature was observed in 19/21 (90%) tumors with informative data. ChiCaP diagnoses were more prevalent among patients with retinoblastomas (50%, 6/12) and high-grade astrocytomas (37%, 6/16), and in those with non-cancer related features (23%, 20/88), and ≥2 positive ChiCaP criteria (28%, 22/79). ChiCaP diagnoses were autosomal dominant in 80% (28/35) of patients, yet confirmed de novo in 64% (18/28). The 35 ChiCaP findings resulted in tailored surveillance (86%, 30/35) and treatment recommendations (31%, 11/35). Interpretation Overall, our results demonstrate that systematic phenotyping, combined with genomics-based diagnostics of ChiCaP in children with solid tumors is feasible in large-scale clinical practice and critically guides personalized care in a sizable proportion of patients. Funding The study was supported by the Swedish Childhood Cancer Fund and the Ministry of Health and Social Affairs.
Collapse
Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Frida Abel
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresita Díaz de Ståhl
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Orrsjö
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Poluha
- Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Maria Hellberg
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Sandra Wessman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sofie Samuelsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Tony Frisk
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Hartmut Vogt
- Crown Princess Victoria Children’s Hospital, and Division of Children’s and Women’s Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Karin Henning
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Sabel
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
- Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Torben Ek
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
- Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Niklas Pal
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Per Nyman
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Centre for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Geraldine Giraud
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Pediatric Oncology, Uppsala University Children’s Hospital, Uppsala, Sweden
- Department of Women’s and Children’s Health, Uppsala University, Sweden
| | - Joakim Wille
- Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
| | - Cornelis Jan Pronk
- Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
- Division of Molecular Hematology/Wallenberg Center for Molecular Medicine, Lund University, Sweden
| | | | - Magnus Borssén
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Maria Fili
- Division of Eye and Vision, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- St. Erik Eye Hospital, Stockholm, Sweden
| | - Gustav Stålhammar
- Division of Eye and Vision, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- St. Erik Eye Hospital, Stockholm, Sweden
| | - Nikolas Herold
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Giorgio Tettamanti
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Linda Arvidsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Anna Rosén
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Katja Ekholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | | | - Anna-Lotta Hallbeck
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Margareta Nordling
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Pia Palmebäck
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Per Kogner
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Gunilla Kanter Smoler
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Päivi Lähteenmäki
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Fransson
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alia Shamik
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Pernilla Grillner
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Gustaf Ljungman
- Pediatric Oncology, Uppsala University Children’s Hospital, Uppsala, Sweden
- Department of Women’s and Children’s Health, Uppsala University, Sweden
| | - David Gisselsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
15
|
Mosquera Orgueira A, Krali O, Pérez Míguez C, Peleteiro Raíndo A, Díaz Arias JÁ, González Pérez MS, Pérez Encinas MM, Fernández Sanmartín M, Sinnet D, Heyman M, Lönnerholm G, Norén-Nyström U, Schmiegelow K, Nordlund J. Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling. Clin Epigenetics 2024; 16:49. [PMID: 38549146 PMCID: PMC10976833 DOI: 10.1186/s13148-024-01662-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/16/2024] [Indexed: 04/02/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most prevalent cancer in children, and despite considerable progress in treatment outcomes, relapses still pose significant risks of mortality and long-term complications. To address this challenge, we employed a supervised machine learning technique, specifically random survival forests, to predict the risk of relapse and mortality using array-based DNA methylation data from a cohort of 763 pediatric ALL patients treated in Nordic countries. The relapse risk predictor (RRP) was constructed based on 16 CpG sites, demonstrating c-indexes of 0.667 and 0.677 in the training and test sets, respectively. The mortality risk predictor (MRP), comprising 53 CpG sites, exhibited c-indexes of 0.751 and 0.754 in the training and test sets, respectively. To validate the prognostic value of the predictors, we further analyzed two independent cohorts of Canadian (n = 42) and Nordic (n = 384) ALL patients. The external validation confirmed our findings, with the RRP achieving a c-index of 0.667 in the Canadian cohort, and the RRP and MRP achieving c-indexes of 0.529 and 0.621, respectively, in an independent Nordic cohort. The precision of the RRP and MRP models improved when incorporating traditional risk group data, underscoring the potential for synergistic integration of clinical prognostic factors. The MRP model also enabled the definition of a risk group with high rates of relapse and mortality. Our results demonstrate the potential of DNA methylation as a prognostic factor and a tool to refine risk stratification in pediatric ALL. This may lead to personalized treatment strategies based on epigenetic profiling.
Collapse
Affiliation(s)
- Adrián Mosquera Orgueira
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain.
- Health Research Institute of Santiago de Compostela, Compostela, Spain.
| | - Olga Krali
- Department of Medical Sciences, Molecular Precision Medicine, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Andrés Peleteiro Raíndo
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - José Ángel Díaz Arias
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - Marta Sonia González Pérez
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - Manuel Mateo Pérez Encinas
- Department of Hematology, University Hospital of Santiago de Compostela, Compostela, Spain
- Health Research Institute of Santiago de Compostela, Compostela, Spain
| | - Manuel Fernández Sanmartín
- Health Research Institute of Santiago de Compostela, Compostela, Spain
- Department of Pediatric Medicine, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel Sinnet
- Research Center, CHU Sainte-Justine, Montréal, Canada
- Department of Pediatrics, Université de Montréal, Montreal, Canada
| | - Mats Heyman
- Childhood Cancer Research Unit, Karolinska Institutet, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Ulrika Norén-Nyström
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Kjeld Schmiegelow
- Pediatrics and Adolescent Medicine, Rigshospitalet, and the Medical Faculty, Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- For the Nordic Society of Pediatric Hematology and Oncology (NOPHO), Stockholm, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| |
Collapse
|
16
|
Stoltze UK, Foss-Skiftesvik J, Hansen TVO, Rasmussen S, Karczewski KJ, Wadt KAW, Schmiegelow K. The evolutionary impact of childhood cancer on the human gene pool. Nat Commun 2024; 15:1881. [PMID: 38424437 PMCID: PMC10904397 DOI: 10.1038/s41467-024-45975-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Germline pathogenic variants associated with increased childhood mortality must be subject to natural selection. Here, we analyze publicly available germline genetic metadata from 4,574 children with cancer [11 studies; 1,083 whole exome sequences (WES), 1,950 whole genome sequences (WGS), and 1,541 gene panel] and 141,456 adults [125,748 WES and 15,708 WGS]. We find that pediatric cancer predisposition syndrome (pCPS) genes [n = 85] are highly constrained, harboring only a quarter of the loss-of-function variants that would be expected. This strong indication of selective pressure on pCPS genes is found across multiple lines of germline genomics data from both pediatric and adult cohorts. For six genes [ELP1, GPR161, VHL and SDHA/B/C], a clear lack of mutational constraint calls the pediatric penetrance and/or severity of associated cancers into question. Conversely, out of 23 known pCPS genes associated with biallelic risk, two [9%, DIS3L2 and MSH2] show significant constraint, indicating that they may monoallelically increase childhood cancer risk. In summary, we show that population genetic data provide empirical evidence that heritable childhood cancer leads to natural selection powerful enough to have significantly impacted the present-day gene pool.
Collapse
Affiliation(s)
- Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark.
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark.
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA, 02142, USA.
| | - Jon Foss-Skiftesvik
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
- Department of Neurosurgery, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA, 02142, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA
| | - Karin A W Wadt
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark.
| |
Collapse
|
17
|
Capasso M, Brignole C, Lasorsa VA, Bensa V, Cantalupo S, Sebastiani E, Quattrone A, Ciampi E, Avitabile M, Sementa AR, Mazzocco K, Cafferata B, Gaggero G, Vellone VG, Cilli M, Calarco E, Giusto E, Perri P, Aveic S, Fruci D, Tondo A, Luksch R, Mura R, Rabusin M, De Leonardis F, Cellini M, Coccia P, Iolascon A, Corrias MV, Conte M, Garaventa A, Amoroso L, Ponzoni M, Pastorino F. From the identification of actionable molecular targets to the generation of faithful neuroblastoma patient-derived preclinical models. J Transl Med 2024; 22:151. [PMID: 38351008 PMCID: PMC10863144 DOI: 10.1186/s12967-024-04954-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/03/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Neuroblastoma (NB) represents the most frequent and aggressive form of extracranial solid tumor of infants. Although the overall survival of patients with NB has improved in the last years, more than 50% of high-risk patients still undergo a relapse. Thus, in the era of precision/personalized medicine, the need for high-risk NB patient-specific therapies is urgent. METHODS Within the PeRsonalizEd Medicine (PREME) program, patient-derived NB tumors and bone marrow (BM)-infiltrating NB cells, derived from either iliac crests or tumor bone lesions, underwent to histological and to flow cytometry immunophenotyping, respectively. BM samples containing a NB cells infiltration from 1 to 50 percent, underwent to a subsequent NB cells enrichment using immune-magnetic manipulation. Then, NB samples were used for the identification of actionable targets and for the generation of 3D/tumor-spheres and Patient-Derived Xenografts (PDX) and Cell PDX (CPDX) preclinical models. RESULTS Eighty-four percent of NB-patients showed potentially therapeutically targetable somatic alterations (including point mutations, copy number variations and mRNA over-expression). Sixty-six percent of samples showed alterations, graded as "very high priority", that are validated to be directly targetable by an approved drug or an investigational agent. A molecular targeted therapy was applied for four patients, while a genetic counseling was suggested to two patients having one pathogenic germline variant in known cancer predisposition genes. Out of eleven samples implanted in mice, five gave rise to (C)PDX, all preserved in a local PDX Bio-bank. Interestingly, comparing all molecular alterations and histological and immunophenotypic features among the original patient's tumors and PDX/CPDX up to second generation, a high grade of similarity was observed. Notably, also 3D models conserved immunophenotypic features and molecular alterations of the original tumors. CONCLUSIONS PREME confirms the possibility of identifying targetable genomic alterations in NB, indeed, a molecular targeted therapy was applied to four NB patients. PREME paves the way to the creation of clinically relevant repositories of faithful patient-derived (C)PDX and 3D models, on which testing precision, NB standard-of-care and experimental medicines.
Collapse
Affiliation(s)
- Mario Capasso
- Department of Medical Biotechnology, University of Naples Federico II, 80138, Naples, Italy
- CEINGE Advanced Biotecnology, 80138, Naples, Italy
| | - Chiara Brignole
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | | | - Veronica Bensa
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Sueva Cantalupo
- Department of Medical Biotechnology, University of Naples Federico II, 80138, Naples, Italy
- CEINGE Advanced Biotecnology, 80138, Naples, Italy
| | | | | | - Eleonora Ciampi
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Marianna Avitabile
- Department of Medical Biotechnology, University of Naples Federico II, 80138, Naples, Italy
- CEINGE Advanced Biotecnology, 80138, Naples, Italy
| | - Angela R Sementa
- Pathological Anatomy, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Katia Mazzocco
- Pathological Anatomy, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Barbara Cafferata
- Pathological Anatomy, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Gabriele Gaggero
- Pathological Anatomy, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Valerio G Vellone
- Pathological Anatomy, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Michele Cilli
- Animal Facility, IRCCS Policlinico San Martino, 16100, Genoa, Italy
| | - Enzo Calarco
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Elena Giusto
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Patrizia Perri
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Sanja Aveic
- Pediatric Research Institute Città Della Speranza, 35127, Padua, Italy
| | - Doriana Fruci
- Department of Emato-Oncology, Bambino Gesù Children's Hospital, 00146, -Rome, Italy
| | - Annalisa Tondo
- Department of Emato-Oncology, Anna Meyer Children's Hospital, 50139, Florence, Italy
| | - Roberto Luksch
- Emato-Oncology Unit, Fondazione IRCCS Istituto Nazionale Dei Tumori, 20133, Milan, Italy
| | - Rossella Mura
- Emato-Oncology Unit, Azienda Ospedaliera Brotzu, 09047, Cagliari, Italy
| | - Marco Rabusin
- Pediatric Department, Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137, Trieste, Italy
| | | | - Monica Cellini
- Emato-Oncology Unit, University-Hospital Polyclinic of Modena, 41124, Modena, Italy
| | - Paola Coccia
- University-Hospital of Marche, Presidio Ospedaliero "G. Salesi", 60126, Ancona, Italy
| | - Achille Iolascon
- Department of Medical Biotechnology, University of Naples Federico II, 80138, Naples, Italy
- CEINGE Advanced Biotecnology, 80138, Naples, Italy
| | - Maria V Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Massimo Conte
- Clinical Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147, -Genoa, Italy
| | - Alberto Garaventa
- Clinical Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147, -Genoa, Italy
| | - Loredana Amoroso
- Clinical Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147, -Genoa, Italy
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy.
| | - Fabio Pastorino
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| |
Collapse
|
18
|
Andrew EC, Lewin J, Desai J, Orme L, Hamilton A, Bae S, Zhu W, Nicolson S, Varghese LN, Mitchell CB, Vissers JHA, Xu H, Grimmond SM, Fox SB, Luen SJ. Clinical Impact of Comprehensive Molecular Profiling in Adolescents and Young Adults with Sarcoma. J Pers Med 2024; 14:128. [PMID: 38392562 PMCID: PMC10890624 DOI: 10.3390/jpm14020128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Sarcomas are a heterogenous group of tumours that commonly carry poor prognosis with limited therapeutic options. Adolescents and young adults (AYAs) with sarcoma are a unique and understudied patient population that have only achieved modest survival gains compared to other groups. We present our institutional experience of AYAs with sarcoma who underwent comprehensive molecular profiling (CMP) via either large-panel targeted DNA sequencing or whole genome and transcriptome sequencing and evaluated the feasibility and clinical impact of this approach. Genomic variants detected were determined to be clinically relevant and actionable following evaluation by the Molecular Tumour Board. Clinicians provided feedback regarding the utility of testing three months after reporting. Twenty-five patients who were recruited for CMP are included in this analysis. The median time from consent to final molecular report was 45 days (interquartile range: 37-57). Potentially actionable variants were detected for 14 patients (56%), and new treatment recommendations were identified for 12 patients (48%). Pathogenic germline variants were identified in three patients (12%), and one patient had a change in diagnosis. The implementation of CMP for AYAs with sarcoma is clinically valuable, feasible, and should be increasingly integrated into routine clinical practice as technologies and turnaround times continue to improve.
Collapse
Affiliation(s)
- Eden C Andrew
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC 3052, Australia
- Victorian Adolescent and Young Adult Cancer Service, Parkville, VIC 3000, Australia
| | - Jeremy Lewin
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Victorian Adolescent and Young Adult Cancer Service, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jayesh Desai
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lisa Orme
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Children's Cancer Centre, Royal Children's Hospital, Parkville, VIC 3052, Australia
- Victorian Adolescent and Young Adult Cancer Service, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Anne Hamilton
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Susie Bae
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Wenying Zhu
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shannon Nicolson
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Leila N Varghese
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Camilla B Mitchell
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Joseph H A Vissers
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Huiling Xu
- Department of Pathology and Cancer Research Division, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sean M Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stephen B Fox
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Pathology and Cancer Research Division, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
| | - Stephen J Luen
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Parkville, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC 3010, Australia
| |
Collapse
|
19
|
Wong D, Luo P, Oldfield LE, Gong H, Brunga L, Rabinowicz R, Subasri V, Chan C, Downs T, Farncombe KM, Luu B, Norman M, Sobotka JA, Uju P, Eagles J, Pedersen S, Wellum J, Danesh A, Prokopec SD, Stutheit-Zhao EY, Znassi N, Heisler LE, Jovelin R, Lam B, Lujan Toro BE, Marsh K, Sundaravadanam Y, Torti D, Man C, Goldenberg A, Xu W, Veit-Haibach P, Doria AS, Malkin D, Kim RH, Pugh TJ. Early Cancer Detection in Li-Fraumeni Syndrome with Cell-Free DNA. Cancer Discov 2024; 14:104-119. [PMID: 37874259 PMCID: PMC10784744 DOI: 10.1158/2159-8290.cd-23-0456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
People with Li-Fraumeni syndrome (LFS) harbor a germline pathogenic variant in the TP53 tumor suppressor gene, face a near 100% lifetime risk of cancer, and routinely undergo intensive surveillance protocols. Liquid biopsy has become an attractive tool for a range of clinical applications, including early cancer detection. Here, we provide a proof-of-principle for a multimodal liquid biopsy assay that integrates a targeted gene panel, shallow whole-genome, and cell-free methylated DNA immunoprecipitation sequencing for the early detection of cancer in a longitudinal cohort of 89 LFS patients. Multimodal analysis increased our detection rate in patients with an active cancer diagnosis over uni-modal analysis and was able to detect cancer-associated signal(s) in carriers prior to diagnosis with conventional screening (positive predictive value = 67.6%, negative predictive value = 96.5%). Although adoption of liquid biopsy into current surveillance will require further clinical validation, this study provides a framework for individuals with LFS. SIGNIFICANCE By utilizing an integrated cell-free DNA approach, liquid biopsy shows earlier detection of cancer in patients with LFS compared with current clinical surveillance methods such as imaging. Liquid biopsy provides improved accessibility and sensitivity, complementing current clinical surveillance methods to provide better care for these patients. See related commentary by Latham et al., p. 23. This article is featured in Selected Articles from This Issue, p. 5.
Collapse
Affiliation(s)
- Derek Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ping Luo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Leslie E. Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Haifan Gong
- The Hospital for Sick Children, Toronto, Canada
| | | | | | - Vallijah Subasri
- The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Clarissa Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Tiana Downs
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | - Beatrice Luu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Maia Norman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Julia A. Sobotka
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Precious Uju
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Jenna Eagles
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Stephanie Pedersen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Johanna Wellum
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Nadia Znassi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Bernard Lam
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Kayla Marsh
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Dax Torti
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Carina Man
- The Hospital for Sick Children, Toronto, Canada
| | - Anna Goldenberg
- The Hospital for Sick Children, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Patrick Veit-Haibach
- Joint Department of Medical Imaging, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada
| | | | - David Malkin
- The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Raymond H. Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- The Hospital for Sick Children, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| |
Collapse
|
20
|
McCabe MG, Geoerger B, Chesler L, Hargrave D, Parsons DW, van Tilburg CM, Schleiermacher G, Hickman JA, George SL. Precision Medicine for Childhood Cancer: Current Limitations and Future Perspectives. JCO Precis Oncol 2024; 8:e2300117. [PMID: 38207228 DOI: 10.1200/po.23.00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/19/2023] [Accepted: 10/19/2023] [Indexed: 01/13/2024] Open
Abstract
Greater collaboration needed to realize potential of molecular profiling initiatives for pediatric cancers.
Collapse
Affiliation(s)
- Martin G McCabe
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Birgit Geoerger
- Gustave Roussy Cancer Campus, Department of Pediatric and Adolescent Oncology, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Louis Chesler
- Paediatric Oncology Experimental Medicine Centre, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, The Royal Marsden Hospital, London, United Kingdom
| | - Darren Hargrave
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - D Williams Parsons
- Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX
| | - Cornelis M van Tilburg
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology & Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Gudrun Schleiermacher
- SiRIC RTOP (Recherche Translationelle en Oncologie Pédiatrique), Translational Research Department, Institut Curie Research Center, PSL Research University, Institut Curie, Parbe the only one citing a postcodeis, France
| | - John A Hickman
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Sally L George
- Paediatric Oncology Experimental Medicine Centre, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, The Royal Marsden Hospital, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| |
Collapse
|
21
|
Carcel C, Haupt S, Arnott C, Yap ML, Henry A, Hirst JE, Woodward M, Norton R. A life-course approach to tackling noncommunicable diseases in women. Nat Med 2024; 30:51-60. [PMID: 38242981 DOI: 10.1038/s41591-023-02738-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/27/2023] [Indexed: 01/21/2024]
Abstract
Women's health has been critically underserved by a failure to look beyond women's sexual and reproductive systems to adequately consider their broader health needs. In almost every country in the world, noncommunicable diseases are the leading causes of death for women. Among these, cardiovascular disease (including heart disease and stroke) and cancer are the major causes of mortality. Risks for these conditions exist at each stage of women's lives, but recognition of the unique needs of women for the prevention and management of noncommunicable diseases is relatively recent and still emerging. Once they are diagnosed, treatments for these diseases are often costly and noncurative. Therefore, we call for a strategic, innovative life-course approach to identifying disease triggers and instigating cost-effective measures to minimize exposure in a timely manner. Prohibitive barriers to implementing this holistic approach to women's health exist in both the social arena and the medical arena. Recognizing these impediments and implementing practical approaches to surmounting them is a rational approach to advancing health equity for women, with ultimate benefits for society as a whole.
Collapse
Affiliation(s)
- Cheryl Carcel
- The George Institute for Global Health, UNSW, Sydney, New South Wales, Australia.
- Department of Neurology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia.
| | - Sue Haupt
- The George Institute for Global Health, UNSW, Sydney, New South Wales, Australia
| | - Clare Arnott
- The George Institute for Global Health, UNSW, Sydney, New South Wales, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Mei Ling Yap
- The George Institute for Global Health, UNSW, Sydney, New South Wales, Australia
- Liverpool and Macarthur Cancer Therapy Centres, South-West Sydney Local Health District, Sydney, New South Wales, Australia
- Collaboration for Cancer Outcomes, Research and Evaluation (CCORE), South-Western Sydney Clinical School, Ingham Institute, UNSW, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Amanda Henry
- The George Institute for Global Health, UNSW, Sydney, New South Wales, Australia
- Discipline of Women's Health, School of Clinical Medicine, UNSW Medicine and Health, UNSW, Sydney, New South Wales, Australia
- Department of Women's and Children's Health, St George Hospital, Sydney, New South Wales, Australia
| | - Jane E Hirst
- The George Institute for Global Health, School of Public Health, Imperial College London, London, UK
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Mark Woodward
- The George Institute for Global Health, UNSW, Sydney, New South Wales, Australia
- The George Institute for Global Health, School of Public Health, Imperial College London, London, UK
| | - Robyn Norton
- The George Institute for Global Health, UNSW, Sydney, New South Wales, Australia
- The George Institute for Global Health, School of Public Health, Imperial College London, London, UK
| |
Collapse
|
22
|
Helms L, Guimera AE, Janeway KA, Bailey KM. Innovations in Cancer Treatment of Children. Pediatrics 2023; 152:e2023061539. [PMID: 37920939 PMCID: PMC10657776 DOI: 10.1542/peds.2023-061539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2023] [Indexed: 11/04/2023] Open
Abstract
Pediatric cancer outcomes have significantly improved, and yet this success is not spread equally across cancer types or patients. Disparities data in pediatric oncology highlight needed improvements in access to care, including clinical trials and advanced testing for all patients. For cancers such as brain tumors and sarcomas, continued advancement in understanding the biology of tumor heterogeneity is an essential step toward finding new therapeutic combinations to improve outcomes. Pediatric cancer survivors need access to emerging technologies aimed at reducing or better managing toxicities from therapy. With advances in treatment and survival, pediatric oncology patients continue to need longitudinal, multidisciplinary subspecialty care. Refining the communication between pediatric oncologists, primary pediatricians, survivorship clinics, and adult primary care is key in ensuring the best lifelong care of pediatric cancer survivors. In this State-of-The-Art review, we discuss 5 major domains in pediatric oncology: reducing toxicity, cancer biology, novel therapies, detection and monitoring, and access to care, to highlight recent advances and areas for continued improvement.
Collapse
Affiliation(s)
- Lauren Helms
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan
| | - Allison E. Guimera
- Department of Pediatrics, University of California Los Angeles, Los Angeles, California
| | - Katherine A. Janeway
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Kelly M. Bailey
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| |
Collapse
|
23
|
Tibout P, Livingston J, Kanwar N, Yuki KE, Shlien A, Ngan B, Irwin MS, Morgenstern DA, Hitzler J, Villani A, Cohen-Gogo S. Synchronous T-lymphoblastic lymphoma and neuroblastoma in a 3-yr-old with novel germline SMARCA4 and EZH2 variants. Cold Spring Harb Mol Case Stud 2023; 9:a006286. [PMID: 37932047 PMCID: PMC10815281 DOI: 10.1101/mcs.a006286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023] Open
Abstract
T-lymphoblastic lymphoma (T-LLy) is the most common lymphoblastic lymphoma in children and often presents with a mediastinal mass. Lymphomatous suprarenal masses are possible but rare. Here, we discuss the case of a previously healthy 3-yr-old male who presented with mediastinal T-LLy with bilateral suprarenal masses. Following initial treatment, surgical biopsy of persisting adrenal masses revealed bilateral neuroblastoma (NBL). A clinical genetics panel for germline cancer predisposition did not identify any pathogenic variants. Combination large panel (864 genes) profiling analysis in the context of a precision oncology study revealed two novel likely pathogenic heterozygous variants: SMARCA4 c.1420-1G > T p.? and EZH2 c.1943G > C p.(Ile631Phefs*44). Somatic analysis revealed potential second hits/somatic variants in EZH2 (in the T-LLy) and a segmental loss in Chromosome 19p encompassing SMARCA4 (in the NBL). Synchronous cancers, especially at a young age, warrant genetic evaluation for cancer predisposition; enrollment in a precision oncology program assessing germline and tumor DNA can fulfill that purpose, particularly when standard first-line genetic testing is negative and in the setting of tumors that are not classic for common cancer predisposition syndromes.
Collapse
Affiliation(s)
- Pauline Tibout
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
| | - Joel Livingston
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
| | - Nisha Kanwar
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
| | - Kyoko E Yuki
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
| | - Adam Shlien
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, M5G 1E8 Canada
| | - Bo Ngan
- Division of Pathology, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
| | - Meredith S Irwin
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario M5R 0A3, Canada
| | - Daniel A Morgenstern
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario M5R 0A3, Canada
| | - Johann Hitzler
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario M5R 0A3, Canada
| | - Anita Villani
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario M5R 0A3, Canada
| | - Sarah Cohen-Gogo
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario M5G 1E8, Canada;
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, M5G 1E8 Canada
| |
Collapse
|
24
|
L'Yi S, Maziec D, Stevens V, Manz T, Veit A, Berselli M, Park PJ, Głodzik D, Gehlenborg N. Chromoscope: interactive multiscale visualization for structural variation in human genomes. Nat Methods 2023; 20:1834-1835. [PMID: 37914857 PMCID: PMC10883074 DOI: 10.1038/s41592-023-02056-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Affiliation(s)
- Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Dominika Maziec
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Victoria Stevens
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Trevor Manz
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michele Berselli
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Dominik Głodzik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
25
|
Freycon C, Lupo PJ, Witkowski L, Budd C, Foulkes WD, Goudie C. A systematic review of the prevalence of pathogenic or likely pathogenic germline variants in individuals with FOXO1 fusion-positive rhabdomyosarcoma. Pediatr Blood Cancer 2023; 70:e30651. [PMID: 37638828 DOI: 10.1002/pbc.30651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/20/2023] [Indexed: 08/29/2023]
Abstract
Several cancer predisposition syndromes (CPS) are reported to predispose to rhabdomyosarcoma, most frequently in children with embryonal rhabdomyosarcoma. There are lingering questions over the role of CPS in individuals with alveolar rhabdomyosarcoma (ARMS), which are frequently driven by FOXO1 fusion oncoproteins. We conducted a systematic review to identify patients with FOXO1 fusion-positive ARMS (FP-ARMS) who underwent germline DNA sequencing. We estimated the prevalence of pathogenic/likely pathogenic (P/LP) variants in cancer predisposing genes (CPGs) and of CPSs. We included 19 publications reporting on 191 patients with FP-ARMS. P/LP variants in CPGs were identified in 26/191 (13.6%) patients, nine (4.9%) of which were associated with a CPS diagnosis. Evidence for causal associations between CPSs and FP-ARMS could not be assessed with available data from this review. Only one patient was affected with a CPS known to predispose to rhabdomyosarcoma, Li-Fraumeni syndrome. Typical CPS associations with rhabdomyosarcoma are rare, but not nonexistent, in patients with FP-ARMS. FOXO1 fusion status, alone, is insufficient for clinicians to rely on to distinguish between patients with/without CPS.
Collapse
Affiliation(s)
- Claire Freycon
- Department of Pediatrics, Division of Hematology-Oncology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
- Department of Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Philip J Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Leora Witkowski
- Department of Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University Health Centre, Montreal, Quebec, Canada
| | - Crystal Budd
- Department of Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Catherine Goudie
- Department of Pediatrics, Division of Hematology-Oncology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
- Department of Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| |
Collapse
|
26
|
Brenner C, Sanders C, Vokuhl C. [Receptor tyrosine kinase- fusions in paediatric spindle cell tumors]. PATHOLOGIE (HEIDELBERG, GERMANY) 2023; 44:357-365. [PMID: 37819532 DOI: 10.1007/s00292-023-01228-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 10/13/2023]
Abstract
Pediatric spindle cell tumors are rare and often difficult to diagnose due to a similar morphology and a non-specific immunohistochemical profile. Genetic characterization of these lesions has been constantly improving, which has led to the identification of new subgroups that were partly included in the WHO classification. Receptor tyrosine kinase fusions play a special role in these tumors and their verification has diagnostic relevance and can be an option for target-oriented therapies. In the case of pediatric spindle cell tumors, genetic fusions form especially with NTRK1‑3, ALK, RET, and ROS1. Overall, pediatric tumors with receptor tyrosine kinase fusions are predominantly low-grade tumors, which are often subdivided into the group of intermediate-malign tumors.
Collapse
Affiliation(s)
- Christiane Brenner
- Sektion Kinderpathologie, Institut für Pathologie, Universitätsklinikum Bonn, Venusberg-Campus 1, 53127, Bonn, Deutschland.
| | - Christine Sanders
- Institut für Pathologie, Universitätsklinikum Bonn, Bonn, Deutschland
| | - Christian Vokuhl
- Sektion Kinderpathologie, Institut für Pathologie, Universitätsklinikum Bonn, Venusberg-Campus 1, 53127, Bonn, Deutschland
| |
Collapse
|
27
|
Witkowski L, Nichols KE, Jongmans M, van Engelen N, de Krijger RR, Herrera-Mullar J, Tytgat L, Bahrami A, Mar Fan H, Davidson AL, Robertson T, Anderson M, Hasselblatt M, Plon SE, Foulkes WD. Germline pathogenic SMARCA4 variants in neuroblastoma. J Med Genet 2023; 60:987-992. [PMID: 36813544 PMCID: PMC10570933 DOI: 10.1136/jmg-2022-108854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
Heterozygous germline pathogenic variants (GPVs) in SMARCA4, the gene encoding the ATP-dependent chromatin remodelling protein SMARCA4 (previously known as BRG1), predispose to several rare tumour types, including small cell carcinoma of the ovary, hypercalcaemic type, atypical teratoid and malignant rhabdoid tumour, and uterine sarcoma. The increase in germline testing of SMARCA4 in recent years has revealed putative GPVs affecting SMARCA4 in patients with other cancer types. Here we describe 11 patients with neuroblastoma (NBL), including 4 previously unreported cases, all of whom were found to harbour heterozygous germline variants in SMARCA4 Median age at diagnosis was 5 years (range 2 months-26 years); nine were male; and eight of nine cases had tumour location information in the adrenal gland. Eight of the germline variants were expected to result in loss of function of SMARCA4 (large deletion, truncating and canonical splice variants), while the remaining four were missense variants. Loss of heterozygosity of the wild-type SMARCA4 allele was found in all eight cases where somatic testing was performed, supporting the notion that SMARCA4 functions as a classic tumour suppressor. Altogether, these findings strongly suggest that NBL should be included in the spectrum of SMARCA4-associated tumours.
Collapse
Affiliation(s)
- Leora Witkowski
- Core Molecular Diagnostic Laboratory, McGill University Health Centre, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Kim E Nichols
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Marjolijn Jongmans
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Ronald R de Krijger
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Lieve Tytgat
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Armita Bahrami
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Helen Mar Fan
- Genetic Health Queensland, The University of Queensland, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Aimee L Davidson
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Thomas Robertson
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Queensland Health, Brisbane, Queensland, Australia
| | | | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Sharon E Plon
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - William D Foulkes
- Lady Davis Institute and Segal Cancer Centre, Sir Mortimer B Davis Jewish General Hospital, Montreal, Québec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Québec, Canada
| |
Collapse
|
28
|
Sultan I, Al-Abdallat H, Alnajjar Z, Ismail L, Abukhashabeh R, Bitar L, Abu Shanap M. Using ChatGPT to Predict Cancer Predisposition Genes: A Promising Tool for Pediatric Oncologists. Cureus 2023; 15:e47594. [PMID: 38021917 PMCID: PMC10666922 DOI: 10.7759/cureus.47594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Determining genetic susceptibility for cancer predisposition syndromes (CPS) through cancer predisposition genes (CPGs) testing is critical in facilitating appropriate prevention and surveillance strategies. This study investigates the use of ChatGPT, a large language model, in predicting CPGs using clinical notes. METHODS Our study involved 53 patients with pathogenic CPG mutations. Two kinds of clinical notes were used: the first visit note, containing a thorough history and physical exam, and the genetic clinic note, summarizing the patient's diagnosis and family history. We asked ChatGPT to recommend CPS genes based on these notes and compared these predictions with previously identified mutations. RESULTS Rb1 was the most frequently mutated gene in our cohort (34%), followed by NF1 (9.4%), TP53 (5.7%), and VHL (5.7%). Out of 53 patients, 30 had genetic clinic notes of a median length of 54 words. ChatGPT correctly predicted the gene in 93% of these cases. However, it failed to predict EPCAM and VHL genes in specific patients. For the first visit notes (median length: 461 words), ChatGPT correctly predicted the gene in 64% of these cases. CONCLUSION ChatGPT shows promise in predicting CPGs from clinical notes, particularly genetic clinic notes. This approach may be useful in enhancing CPG testing, especially in areas lacking genetic testing resources. With further training, there is a possibility for ChatGPT to improve its predictive potential and expand its clinical applicability. However, additional research is needed to explore the full potential and applicability of ChatGPT.
Collapse
Affiliation(s)
- Iyad Sultan
- Department of Pediatrics, King Hussein Cancer Center, Amman, JOR
| | | | - Zaina Alnajjar
- Department of Medicine, Hashemite University, Zarqa, JOR
| | - Layan Ismail
- Department of Medicine, University of Jordan, Amman, JOR
| | - Razan Abukhashabeh
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, JOR
| | - Layla Bitar
- Department of Pediatric Oncology, King Hussein Cancer Center, Amman, JOR
| | - Mayada Abu Shanap
- Department of Pediatric Oncology, King Hussein Cancer Center, Amman, JOR
| |
Collapse
|
29
|
Tozzi AE, Gesualdo F, Pandolfi E, Ferro D, Cinelli G, Bozzola E, Aversa T, Di Mauro A, Mameli C, Croci I. Prioritizing educational initiatives on emerging technologies for Italian pediatricians: bibliometric review and a survey. Ital J Pediatr 2023; 49:112. [PMID: 37667297 PMCID: PMC10478260 DOI: 10.1186/s13052-023-01512-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Emerging technologies have demonstrated outstanding potential in improving healthcare, yet their full integration remains a challenge for all medical specialties, including pediatrics. To support the swift implementation of technologies, we identified the current trends through a bibliometric review, and we conducted a survey on Italian pediatricians to gauge educational needs and willingness to integrate technologies into clinical practice. METHODS A working group of pediatricians representing various backgrounds designed and coordinated the study. To identify relevant topics for educational strategy development, we focused on virtual reality, telehealth, natural language processing, smartphone applications, robotics, genomics, and artificial intelligence. A bibliometric analysis limited to 2018-2023 was performed to identify trends and emerging applications within each topic. Based on the results, a questionnaire was developed and made available online to all Italian pediatricians. The results were analyzed through descriptive analysis and a multivariable logistic regression to explore associations between technology adoption and sociodemographic characteristics. RESULTS A total of 3,253 publications were found, with Telehealth and Telemedicine having the highest number of publications and Natural Language Processing the lowest. The number of respondents to the online questionnaire was 1,540, predominantly medical doctors with over 20 years of experience working as family pediatricians. Telehealth had the highest level of knowledge (95.2%), followed by smartphone applications (89.1%) and genomics (63.2%). The greatest potential for increased use through education programs was projected for natural language processing (+ 43.1%), artificial intelligence (+ 39.6%), and virtual and mixed reality (+ 38.1%). Female respondents and older individuals were less likely to use emerging technologies. Hospital pediatricians and residents were more likely to use AI. CONCLUSIONS We developed a replicable strategy to identify emerging themes in medical technologies relevant to pediatrics and assess the educational needs of pediatricians. A significant gap still exists between current and potential usage of emerging technologies among Italian pediatricians although they showed a positive attitude towards implementing these technologies following specific education programs. The study highlights the need for comprehensive education programs on emerging technologies in pediatrics and recommends addressing gender and age disparities in technology adoption.
Collapse
Affiliation(s)
- Alberto Eugenio Tozzi
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy.
| | - Francesco Gesualdo
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Elisabetta Pandolfi
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Diana Ferro
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Giulia Cinelli
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Elena Bozzola
- Pediatric Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Tommaso Aversa
- Department of Human Pathology of Adulthood and Childhood "G. Barresi", University of Messina, Messina, Italy
- Pediatric Unit, University Hospital "G. Martino", Messina, Italy
| | | | - Chiara Mameli
- Department of Pediatrics, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Ileana Croci
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| |
Collapse
|
30
|
Salokas K, Dashi G, Varjosalo M. Decoding Oncofusions: Unveiling Mechanisms, Clinical Impact, and Prospects for Personalized Cancer Therapies. Cancers (Basel) 2023; 15:3678. [PMID: 37509339 PMCID: PMC10377698 DOI: 10.3390/cancers15143678] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Cancer-associated gene fusions, also known as oncofusions, have emerged as influential drivers of oncogenesis across a diverse range of cancer types. These genetic events occur via chromosomal translocations, deletions, and inversions, leading to the fusion of previously separate genes. Due to the drastic nature of these mutations, they often result in profound alterations of cellular behavior. The identification of oncofusions has revolutionized cancer research, with advancements in sequencing technologies facilitating the discovery of novel fusion events at an accelerated pace. Oncofusions exert their effects through the manipulation of critical cellular signaling pathways that regulate processes such as proliferation, differentiation, and survival. Extensive investigations have been conducted to understand the roles of oncofusions in solid tumors, leukemias, and lymphomas. Large-scale initiatives, including the Cancer Genome Atlas, have played a pivotal role in unraveling the landscape of oncofusions by characterizing a vast number of cancer samples across different tumor types. While validating the functional relevance of oncofusions remains a challenge, even non-driver mutations can hold significance in cancer treatment. Oncofusions have demonstrated potential value in the context of immunotherapy through the production of neoantigens. Their clinical importance has been observed in both treatment and diagnostic settings, with specific fusion events serving as therapeutic targets or diagnostic markers. However, despite the progress made, there is still considerable untapped potential within the field of oncofusions. Further research and validation efforts are necessary to understand their effects on a functional basis and to exploit the new targeted treatment avenues offered by oncofusions. Through further functional and clinical studies, oncofusions will enable the advancement of precision medicine and the drive towards more effective and specific treatments for cancer patients.
Collapse
Affiliation(s)
- Kari Salokas
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Giovanna Dashi
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00790 Helsinki, Finland
| |
Collapse
|
31
|
Kratz CP, Smirnov D, Autry R, Jäger N, Waszak SM, Großhennig A, Berutti R, Wendorff M, Hainaut P, Pfister SM, Prokisch H, Ripperger T, Malkin D. Reply to Li and Colleagues. J Natl Cancer Inst 2023; 115:760-761. [PMID: 37004196 PMCID: PMC10248829 DOI: 10.1093/jnci/djad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 04/03/2023] Open
Affiliation(s)
- Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Dmitrii Smirnov
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Robert Autry
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic European Molecular Biology Laboratory (EMBL) Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Anika Großhennig
- Institute of Biostatistics, Hannover Medical School, Hannover, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Inserm 1209 CNRS 5309 UGA, Grenoble, France
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - David Malkin
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
32
|
Subasri V, Light N, Kanwar N, Brzezinski J, Luo P, Hansford JR, Cairney E, Portwine C, Elser C, Finlay JL, Nichols KE, Alon N, Brunga L, Anson J, Kohlmann W, de Andrade KC, Khincha PP, Savage SA, Schiffman JD, Weksberg R, Pugh TJ, Villani A, Shlien A, Goldenberg A, Malkin D. Multiple Germline Events Contribute to Cancer Development in Patients with Li-Fraumeni Syndrome. CANCER RESEARCH COMMUNICATIONS 2023; 3:738-754. [PMID: 37377903 PMCID: PMC10150777 DOI: 10.1158/2767-9764.crc-22-0402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/19/2023] [Accepted: 03/29/2023] [Indexed: 06/29/2023]
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal dominant cancer-predisposition disorder. Approximately 70% of individuals who fit the clinical definition of LFS harbor a pathogenic germline variant in the TP53 tumor suppressor gene. However, the remaining 30% of patients lack a TP53 variant and even among variant TP53 carriers, approximately 20% remain cancer-free. Understanding the variable cancer penetrance and phenotypic variability in LFS is critical to developing rational approaches to accurate, early tumor detection and risk-reduction strategies. We leveraged family-based whole-genome sequencing and DNA methylation to evaluate the germline genomes of a large, multi-institutional cohort of patients with LFS (n = 396) with variant (n = 374) or wildtype TP53 (n = 22). We identified alternative cancer-associated genetic aberrations in 8/14 wildtype TP53 carriers who developed cancer. Among variant TP53 carriers, 19/49 who developed cancer harbored a pathogenic variant in another cancer gene. Modifier variants in the WNT signaling pathway were associated with decreased cancer incidence. Furthermore, we leveraged the noncoding genome and methylome to identify inherited epimutations in genes including ASXL1, ETV6, and LEF1 that confer increased cancer risk. Using these epimutations, we built a machine learning model that can predict cancer risk in patients with LFS with an area under the receiver operator characteristic curve (AUROC) of 0.725 (0.633-0.810). Significance Our study clarifies the genomic basis for the phenotypic variability in LFS and highlights the immense benefits of expanding genetic and epigenetic testing of patients with LFS beyond TP53. More broadly, it necessitates the dissociation of hereditary cancer syndromes as single gene disorders and emphasizes the importance of understanding these diseases in a holistic manner as opposed to through the lens of a single gene.
Collapse
Affiliation(s)
- Vallijah Subasri
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Nicholas Light
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Nisha Kanwar
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jack Brzezinski
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Ping Luo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Jordan R. Hansford
- Children's Cancer Centre, Royal Children's Hospital, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, Australia
- Michael Rice Cancer Centre, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australia Immunogenomics Cancer Institute, University of Adelaide, Adelaide, Australia
| | - Elizabeth Cairney
- Department of Paediatrics, London Health Sciences Centre and Western University, London, Ontario, Canada
| | - Carol Portwine
- Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Christine Elser
- Department of Medical Oncology, Princess Margaret Hospital and Mount Sinai Hospital, Toronto, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan L. Finlay
- Neuro-Oncology Program, Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio
| | - Kim E. Nichols
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Noa Alon
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ledia Brunga
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jo Anson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Wendy Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Kelvin C. de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Payal P. Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Joshua D. Schiffman
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
- PEEL Therapeutics, Inc., Salt Lake City, Utah
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Trevor J. Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anita Villani
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anna Goldenberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- CIFAR: Child and Brain Development, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
33
|
Das A, Nobre L. Genomics in pediatric high-grade gliomas: Hope or hype practical implications for resource limited settings. PEDIATRIC HEMATOLOGY ONCOLOGY JOURNAL 2023. [DOI: 10.1016/j.phoj.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
|
34
|
Comitani F, Nash JO, Cohen-Gogo S, Chang AI, Wen TT, Maheshwari A, Goyal B, Tio ES, Tabatabaei K, Mayoh C, Zhao R, Ho B, Brunga L, Lawrence JEG, Balogh P, Flanagan AM, Teichmann S, Huang A, Ramaswamy V, Hitzler J, Wasserman JD, Gladdy RA, Dickson BC, Tabori U, Cowley MJ, Behjati S, Malkin D, Villani A, Irwin MS, Shlien A. Diagnostic classification of childhood cancer using multiscale transcriptomics. Nat Med 2023; 29:656-666. [PMID: 36932241 PMCID: PMC10033451 DOI: 10.1038/s41591-023-02221-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 01/13/2023] [Indexed: 03/19/2023]
Abstract
The causes of pediatric cancers' distinctiveness compared to adult-onset tumors of the same type are not completely clear and not fully explained by their genomes. In this study, we used an optimized multilevel RNA clustering approach to derive molecular definitions for most childhood cancers. Applying this method to 13,313 transcriptomes, we constructed a pediatric cancer atlas to explore age-associated changes. Tumor entities were sometimes unexpectedly grouped due to common lineages, drivers or stemness profiles. Some established entities were divided into subgroups that predicted outcome better than current diagnostic approaches. These definitions account for inter-tumoral and intra-tumoral heterogeneity and have the potential of enabling reproducible, quantifiable diagnostics. As a whole, childhood tumors had more transcriptional diversity than adult tumors, maintaining greater expression flexibility. To apply these insights, we designed an ensemble convolutional neural network classifier. We show that this tool was able to match or clarify the diagnosis for 85% of childhood tumors in a prospective cohort. If further validated, this framework could be extended to derive molecular definitions for all cancer types.
Collapse
Affiliation(s)
- Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Joshua O Nash
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Sarah Cohen-Gogo
- Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Astra I Chang
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Timmy T Wen
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anant Maheshwari
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bipasha Goyal
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Earvin S Tio
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kevin Tabatabaei
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Regis Zhao
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ben Ho
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ledia Brunga
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Petra Balogh
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital, Brockley Hill, Stanmore, UK
| | - Adrienne M Flanagan
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital, Brockley Hill, Stanmore, UK
- Research Department of Pathology, University College London Cancer Institute, London, UK
| | | | - Annie Huang
- Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Vijay Ramaswamy
- Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
- Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Johann Hitzler
- Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Jonathan D Wasserman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Rebecca A Gladdy
- Department of Surgical Oncology, Princess Margaret Cancer Centre/Mount Sinai Hospital, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Brendan C Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Uri Tabori
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David Malkin
- Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
- Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Anita Villani
- Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Meredith S Irwin
- Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
- Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
35
|
Enhancing childhood cancer targetability. NATURE CANCER 2023; 4:153-155. [PMID: 36585448 DOI: 10.1038/s43018-022-00472-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
36
|
Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis. Nat Commun 2023; 14:77. [PMID: 36604421 PMCID: PMC9816166 DOI: 10.1038/s41467-022-35727-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 12/08/2022] [Indexed: 01/06/2023] Open
Abstract
Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome associated with germline TP53 pathogenic variants. Here, we perform whole-genome sequence (WGS) analysis of tumors from 22 patients with TP53 germline pathogenic variants. We observe somatic mutations affecting Wnt, PI3K/AKT signaling, epigenetic modifiers and homologous recombination genes as well as mutational signatures associated with prior chemotherapy. We identify near-ubiquitous early loss of heterozygosity of TP53, with gain of the mutant allele. This occurs earlier in these tumors compared to tumors with somatic TP53 mutations, suggesting the timing of this mark may distinguish germline from somatic TP53 mutations. Phylogenetic trees of tumor evolution, reconstructed from bulk and multi-region WGS, reveal that LFS tumors exhibit comparatively limited heterogeneity. Overall, our study delineates early copy number gains of mutant TP53 as a characteristic mutational process in LFS tumorigenesis, likely arising years prior to tumor diagnosis.
Collapse
|