1
|
Edsjö A, Russnes HG, Lehtiö J, Tamborero D, Hovig E, Stenzinger A, Rosenquist R. High-throughput molecular assays for inclusion in personalised oncology trials - State-of-the-art and beyond. J Intern Med 2024. [PMID: 38698538 DOI: 10.1111/joim.13785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
In the last decades, the development of high-throughput molecular assays has revolutionised cancer diagnostics, paving the way for the concept of personalised cancer medicine. This progress has been driven by the introduction of such technologies through biomarker-driven oncology trials. In this review, strengths and limitations of various state-of-the-art sequencing technologies, including gene panel sequencing (DNA and RNA), whole-exome/whole-genome sequencing and whole-transcriptome sequencing, are explored, focusing on their ability to identify clinically relevant biomarkers with diagnostic, prognostic and/or predictive impact. This includes the need to assess complex biomarkers, for example microsatellite instability, tumour mutation burden and homologous recombination deficiency, to identify patients suitable for specific therapies, including immunotherapy. Furthermore, the crucial role of biomarker analysis and multidisciplinary molecular tumour boards in selecting patients for trial inclusion is discussed in relation to various trial concepts, including drug repurposing. Recognising that today's exploratory techniques will evolve into tomorrow's routine diagnostics and clinical study inclusion assays, the importance of emerging technologies for multimodal diagnostics, such as proteomics and in vivo drug sensitivity testing, is also discussed. In addition, key regulatory aspects and the importance of patient engagement in all phases of a clinical trial are described. Finally, we propose a set of recommendations for consideration when planning a new precision cancer medicine trial.
Collapse
Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Hege G Russnes
- Department of Pathology, Oslo University Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
- Cancer genomics and proteomics, Karolinska University Hospital, Solna, Sweden
| | - David Tamborero
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Eivind Hovig
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Albrecht Stenzinger
- Institute of Pathology, Division of Molecular Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| |
Collapse
|
2
|
Ferrari A, Orbach D, Bergamaschi L, Schoot RA, van Noesel MM, Di Carlo D, Bisogno G, Alaggio R, Milano GM, Chiaravalli S, Fuccillo F, Laurence V, Corradini N, Gasparini P, Vennarini S, Pasquali S, Casanova M. Treatment at relapse for synovial sarcoma of children and adolescents: A multi-institutional European retrospective analysis. Pediatr Blood Cancer 2024:e31038. [PMID: 38679840 DOI: 10.1002/pbc.31038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024]
Abstract
PURPOSE Though the prognosis for pediatric patients with localised synovial sarcoma (SS) is generally good, the chances of being cured after relapse are limited. This study describes a retrospective multi-institutional series of relapsing SS patients treated at six selected European referral centers for pediatric sarcoma. PATIENTS AND METHODS The study included 41 patients <21 years with relapsing SS, treated between 2002 and 2022. The analysis included patient's characteristics at first diagnosis, first-line treatments, clinical findings at relapse, and second-line treatment modalities. RESULTS The first relapse occurred within 3-132 months (median 18 months) after first diagnosis and was local in 34%, metastatic in 54%, and both in 12%. Treatment at first relapse included surgery in 56% of cases, radiotherapy in 34%, and systemic therapy in 88%. In all, 36 patients received second-line medical treatment, that was chemotherapy in 32 cases (with 10 different regimens) and targeted therapy in four. No patient was included in an early-phase clinical trial as second-line therapy-line therapy. Overall response rate was 42%. Median event-free survival (EFS) was 12 months, postrelapse 5-year EFS was 15.8%. Median overall survival (OS) was 30 months, postrelapse 5-year OS was 22.2%. At the Cox's multivariable regression analysis, OS was significantly associated with time and type of relapse. CONCLUSION Pediatric patients with relapsed SS have a poor prognosis and generally receive an individualized approach, due to the lack of a uniform standardized approach. New comprehensive strategies are needed to improve the knowledge on the biologic landscape of SS and develop tailored prospective clinical trials.
Collapse
Affiliation(s)
- Andrea Ferrari
- Pediatric Oncology Unit, Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniel Orbach
- SIREDO Oncology Center Care, (Innovation and Research for Children, Adolescents and Young Adults with Cancer), Institut Curie, PSL University, Paris, France
| | - Luca Bergamaschi
- Pediatric Oncology Unit, Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Reineke A Schoot
- Solid Tumors Department, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Max M van Noesel
- Solid Tumors Department, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Division Imaging & Cancer, Pediatric Oncology Department, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Daniela Di Carlo
- Hematology Oncology Division, Department of Women's and Children's Health, University of Padua, Padua, Italy
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Gianni Bisogno
- Hematology Oncology Division, Department of Women's and Children's Health, University of Padua, Padua, Italy
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Rita Alaggio
- Pathology Department, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Giuseppe Maria Milano
- Hematology/Oncology, Department of Oncohematology, Hematopoietic Transplantation, and Cell Therapy, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Stefano Chiaravalli
- Pediatric Oncology Unit, Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Fernando Fuccillo
- Pediatric Oncology Unit, Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Nadege Corradini
- Department of Pediatric Hematology and Oncology-IHOPe, Léon Bérard Center, Lyon, France
| | - Patrizia Gasparini
- Department of Research, Tumor Genomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sabina Vennarini
- Pediatric Radiotherapy Unit, Radiotherapy Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Sandro Pasquali
- Department of Experimental Oncology, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Surgery, Sarcoma Service, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Michela Casanova
- Pediatric Oncology Unit, Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| |
Collapse
|
3
|
Weijers DD, Hirsch S, Bakhuizen JJ, van Engelen N, Kester LA, Kranendonk MEG, Hiemcke-Jiwa LS, de Vos-Kerkhof E, Loeffen JLC, Autry RJ, Pajtler KW, Jäger N, Jongmans MCJ, Kuiper RP. Molecular analysis of cancer genomes in children with Lynch syndrome: Exploring causal associations. Int J Cancer 2024; 154:1455-1463. [PMID: 38175816 DOI: 10.1002/ijc.34832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Lynch syndrome (LS) predisposes to cancer in adulthood and is caused by heterozygous germline variants in a mismatch repair (MMR) gene. Recent studies show an increased prevalence of LS among children with cancer, suggesting a causal relationship. For LS-spectrum (LSS) cancers, including high-grade gliomas and colorectal cancer, causality has been supported by typical MMR-related tumor characteristics, but for non-LSS cancers, causality is unclear. We characterized 20 malignant tumors of 18 children with LS, including 16 non-LSS tumors. We investigated second hits, tumor mutational load, mutational signatures and MMR protein expression. In all LSS tumors and three non-LSS tumors, we detected MMR deficiency caused by second hit somatic alterations. Furthermore, these MMR-deficient tumors carried driver variants that likely originated as a consequence of MMR deficiency. However, in 13 non-LSS tumors (81%), a second hit and MMR deficiency were absent, thus a causal link between LS and cancer development in these children is lacking. These findings demonstrate that causality of LS in children with cancer, which can be determined by molecular tumor characterization, seems to be restricted to specific tumor types. Large molecular and epidemiological studies are needed to further refine the tumor spectrum in children with LS.
Collapse
Affiliation(s)
- Dilys D Weijers
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Steffen Hirsch
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jette J Bakhuizen
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | | | - Lennart A Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Laura S Hiemcke-Jiwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Jan L C Loeffen
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Robert J Autry
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marjolijn C J Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| |
Collapse
|
4
|
Acanda De La Rocha AM, Berlow NE, Fader M, Coats ER, Saghira C, Espinal PS, Galano J, Khatib Z, Abdella H, Maher OM, Vorontsova Y, Andrade-Feraud CM, Daccache A, Jacome A, Reis V, Holcomb B, Ghurani Y, Rimblas L, Guilarte TR, Hu N, Salyakina D, Azzam DJ. Feasibility of functional precision medicine for guiding treatment of relapsed or refractory pediatric cancers. Nat Med 2024; 30:990-1000. [PMID: 38605166 PMCID: PMC11031400 DOI: 10.1038/s41591-024-02848-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/31/2024] [Indexed: 04/13/2024]
Abstract
Children with rare, relapsed or refractory cancers often face limited treatment options, and few predictive biomarkers are available that can enable personalized treatment recommendations. The implementation of functional precision medicine (FPM), which combines genomic profiling with drug sensitivity testing (DST) of patient-derived tumor cells, has potential to identify treatment options when standard-of-care is exhausted. The goal of this prospective observational study was to generate FPM data for pediatric patients with relapsed or refractory cancer. The primary objective was to determine the feasibility of returning FPM-based treatment recommendations in real time to the FPM tumor board (FPMTB) within a clinically actionable timeframe (<4 weeks). The secondary objective was to assess clinical outcomes from patients enrolled in the study. Twenty-five patients with relapsed or refractory solid and hematological cancers were enrolled; 21 patients underwent DST and 20 also completed genomic profiling. Median turnaround times for DST and genomics were within 10 days and 27 days, respectively. Treatment recommendations were made for 19 patients (76%), of whom 14 received therapeutic interventions. Six patients received subsequent FPM-guided treatments. Among these patients, five (83%) experienced a greater than 1.3-fold improvement in progression-free survival associated with their FPM-guided therapy relative to their previous therapy, and demonstrated a significant increase in progression-free survival and objective response rate compared to those of eight non-guided patients. The findings from our proof-of-principle study illustrate the potential for FPM to positively impact clinical care for pediatric and adolescent patients with relapsed or refractory cancers and warrant further validation in large prospective studies. ClinicalTrials.gov registration: NCT03860376 .
Collapse
Affiliation(s)
- Arlet M Acanda De La Rocha
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | | | - Maggie Fader
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ebony R Coats
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Cima Saghira
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Paula S Espinal
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Jeanette Galano
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ziad Khatib
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Haneen Abdella
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ossama M Maher
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Yana Vorontsova
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Cristina M Andrade-Feraud
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Aimee Daccache
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Alexa Jacome
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Victoria Reis
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Baylee Holcomb
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Yasmin Ghurani
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Lilliam Rimblas
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Tomás R Guilarte
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Nan Hu
- Department of Biostatistics, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Daria Salyakina
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Diana J Azzam
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA.
| |
Collapse
|
5
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [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
|
6
|
Sholler GLS, Bergendahl G, Lewis EC, Kraveka J, Ferguson W, Nagulapally AB, Dykema K, Brown VI, Isakoff MS, Junewick J, Mitchell D, Rawwas J, Roberts W, Eslin D, Oesterheld J, Wada RK, Pastakia D, Harrod V, Ginn K, Saab R, Bielamowicz K, Glover J, Chang E, Hanna GK, Enriquez D, Izatt T, Halperin RF, Moore A, Byron SA, Hendricks WPD, Trent JM. Molecular-guided therapy for the treatment of patients with relapsed and refractory childhood cancers: a Beat Childhood Cancer Research Consortium trial. Genome Med 2024; 16:28. [PMID: 38347552 PMCID: PMC10860258 DOI: 10.1186/s13073-024-01297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Children with relapsed central nervous system (CNS tumors), neuroblastoma, sarcomas, and other rare solid tumors face poor outcomes. This prospective clinical trial examined the feasibility of combining genomic and transcriptomic profiling of tumor samples with a molecular tumor board (MTB) approach to make real‑time treatment decisions for children with relapsed/refractory solid tumors. METHODS Subjects were divided into three strata: stratum 1-relapsed/refractory neuroblastoma; stratum 2-relapsed/refractory CNS tumors; and stratum 3-relapsed/refractory rare solid tumors. Tumor samples were sent for tumor/normal whole-exome (WES) and tumor whole-transcriptome (WTS) sequencing, and the genomic data were used in a multi-institutional MTB to make real‑time treatment decisions. The MTB recommended plan allowed for a combination of up to 4 agents. Feasibility was measured by time to completion of genomic sequencing, MTB review and initiation of treatment. Response was assessed after every two cycles using Response Evaluation Criteria in Solid Tumors (RECIST). Patient clinical benefit was calculated by the sum of the CR, PR, SD, and NED subjects divided by the sum of complete response (CR), partial response (PR), stable disease (SD), no evidence of disease (NED), and progressive disease (PD) subjects. Grade 3 and higher related and unexpected adverse events (AEs) were tabulated for safety evaluation. RESULTS A total of 186 eligible patients were enrolled with 144 evaluable for safety and 124 evaluable for response. The average number of days from biopsy to initiation of the MTB-recommended combination therapy was 38 days. Patient benefit was exhibited in 65% of all subjects, 67% of neuroblastoma subjects, 73% of CNS tumor subjects, and 60% of rare tumor subjects. There was little associated toxicity above that expected for the MGT drugs used during this trial, suggestive of the safety of utilizing this method of selecting combination targeted therapy. CONCLUSIONS This trial demonstrated the feasibility, safety, and efficacy of a comprehensive sequencing model to guide personalized therapy for patients with any relapsed/refractory solid malignancy. Personalized therapy was well tolerated, and the clinical benefit rate of 65% in these heavily pretreated populations suggests that this treatment strategy could be an effective option for relapsed and refractory pediatric cancers. TRIAL REGISTRATION ClinicalTrials.gov, NCT02162732. Prospectively registered on June 11, 2014.
Collapse
Affiliation(s)
- Giselle L Saulnier Sholler
- Division of Pediatric Hematology/Oncology, Penn State Health Children's Hospital, 500 University Drive, MC-H085, Rm. C7621, Hershey, PA, 17033-0850, USA.
| | - Genevieve Bergendahl
- Division of Pediatric Hematology/Oncology, Penn State Health Children's Hospital, 500 University Drive, MC-H085, Rm. C7621, Hershey, PA, 17033-0850, USA
| | | | | | - William Ferguson
- Cardinal Glennon Children's Medical Center, St. Louis University School of Medicine, St. Louis, MO, USA
| | - Abhinav B Nagulapally
- Division of Pediatric Hematology/Oncology, Penn State Health Children's Hospital, 500 University Drive, MC-H085, Rm. C7621, Hershey, PA, 17033-0850, USA
| | - Karl Dykema
- Levine Children's Hospital, Atrium Health, Charlotte, NC, USA
| | - Valerie I Brown
- Division of Pediatric Hematology/Oncology, Penn State Health Children's Hospital, 500 University Drive, MC-H085, Rm. C7621, Hershey, PA, 17033-0850, USA
| | | | - Joseph Junewick
- Helen DeVos Children's Hospital, Spectrum Health, Grand Rapids, MI, USA
| | - Deanna Mitchell
- Helen DeVos Children's Hospital, Spectrum Health, Grand Rapids, MI, USA
| | - Jawhar Rawwas
- Children's Hospitals and Clinics of Minnesota, Minneapolis, USA
| | - William Roberts
- Rady Children's Hospital-San Diego and UC San Diego School of Medicine, San Diego, CA, USA
| | - Don Eslin
- St. Joseph's Children's Hospital, Tampa, FL, USA
| | | | - Randal K Wada
- Kapiolani Medical Center for Women and Children, University of Hawaii, Honolulu, HI, USA
| | | | - Virginia Harrod
- Dell Children's Blood and Cancer Center, Ascension Dell Children's, Austin, TX, USA
| | | | - Raya Saab
- Stanford Medicine Children's Health, Palo Alto, CA, USA
| | | | | | | | - Gina K Hanna
- Orlando Health Cancer Institute, Orlando, FL, USA
| | | | - Tyler Izatt
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Abigail Moore
- Division of Pediatric Hematology/Oncology, Penn State Health Children's Hospital, 500 University Drive, MC-H085, Rm. C7621, Hershey, PA, 17033-0850, USA
| | - Sara A Byron
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | |
Collapse
|
7
|
Mardis ER. Overview of modern genomic tools for diagnosis and precision therapy of childhood solid cancers. Curr Opin Pediatr 2024; 36:71-77. [PMID: 37972971 PMCID: PMC10763706 DOI: 10.1097/mop.0000000000001311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW The application of technology and computational analyses to generate new data types from pediatric solid cancers is transforming diagnostic accuracy. This review provides an overview of such new capabilities in the pursuit of improved treatment for essentially rare and underserved diseases that are the highest cause of mortality in children over one year of age. Sophisticated ways of identifying therapeutic vulnerabilities for highly personalized treatment are presented alongside cutting-edge disease response monitoring by liquid biopsy. RECENT FINDINGS Precision molecular profiling data are now being combined with conventional pathology-based evaluation of pediatric cancer tissues. The resulting diagnostic information can be used to guide therapeutic decision-making, including the use of small molecule inhibitors and of immunotherapies. Integrating somatic and germline variant profiles constitutes a critical component of this emerging paradigm, as does tissue-of-origin derivation from methylation profiling, and rapid screening of potential therapies. These new approaches are poised for use in disease response and therapy resistance monitoring. SUMMARY The integration of clinical molecular profiling data with pathology can provide a highly precise diagnosis, identify therapeutic vulnerabilities, and monitor patient responses, providing next steps toward precision oncology for improved outcomes, including reducing lifelong treatment-related sequelae.
Collapse
Affiliation(s)
- Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio, USA
| |
Collapse
|
8
|
Geoerger B, Bautista F, Gatz SA, Marshall LV, André N. A new generation of comprehensive precision oncology trials. Lancet Oncol 2023; 24:e452. [PMID: 38039994 DOI: 10.1016/s1470-2045(23)00476-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 12/03/2023]
Affiliation(s)
- Birgit Geoerger
- Department of Pediatric and Adolescent Oncology and INSERM U1015, Gustave Roussy Cancer Campus, Universiteé Paris-Saclay, Villejuif 94805, France.
| | - Francisco Bautista
- Department of Pediatric Oncology, Hematology and Stem Cell Transplantation, Hospital Ninño Jesués, Madrid, Spain; Princess Maéxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Susanne A Gatz
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Lynley V Marshall
- Paediatric and Adolescent Oncology Drug Development Unit and Division of Clinical Studies, Royal Marsden NHS Foundation Trust and the Institute of Cancer Research, London, UK
| | - Nicolas André
- Department of Pediatric Oncology, Timone Hospital, AP-HM, Marseille, France; Reverse Molecular Pharmacology in Pediatric Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, CNRS, INSERM, Marseille, France; Metronomics Global Health Initiative, Marseille, France
| |
Collapse
|
9
|
Ferrari A, Berlanga P, Gatz SA, Schoot RA, van Noesel MM, Hovsepyan S, Chiaravalli S, Bergamaschi L, Minard-Colin V, Corradini N, Alaggio R, Gasparini P, Brennan B, Casanova M, Pasquali S, Orbach D. Treatment at Relapse for Synovial Sarcoma of Children, Adolescents and Young Adults: From the State of Art to Future Clinical Perspectives. Cancer Manag Res 2023; 15:1183-1196. [PMID: 37920695 PMCID: PMC10618684 DOI: 10.2147/cmar.s404371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023] Open
Abstract
While the overall prognosis is generally quite satisfactory in children, adolescents and young adults with localised synovial sarcoma at first diagnosis, the outcome remains poor for patients after relapse. Conversely to the front-line standardised treatment options, patients with relapse generally have an individualised approach and to date, there is still a lack of consensus regarding standard treatment approaches. Studies on relapsed synovial sarcoma were able to identify some prognostic variables that influence post-relapse survival, in order to plan risk-adapted salvage protocols. Treatment proposals must consider previous first-line treatments, potential toxicities, and the possibility of achieving an adequate local treatment by new surgery and/or re-irradiation. Effective second-line drug therapies are urgently needed. Notably, experimental treatments such as adoptive engineered TCR-T cell immunotherapy seem promising in adults and are currently under validation also in paediatric patients.
Collapse
Affiliation(s)
- Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Pablo Berlanga
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Susanne Andrea Gatz
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Reineke A Schoot
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Division Imaging & Cancer, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Shushan Hovsepyan
- Pediatric Cancer and Blood Disorders Center of Armenia, Yerevan, Armenia
| | - Stefano Chiaravalli
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Luca Bergamaschi
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Veronique Minard-Colin
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Nadege Corradini
- Department of Pediatric Hematology and Oncology-IHOPe, Léon Bérard Center, Lyon, France
| | - Rita Alaggio
- Pathology Department, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Patrizia Gasparini
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Bernadette Brennan
- Pediatric Oncology, Royal Manchester Children’s Hospital, Manchester, UK
| | - Michela Casanova
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sandro Pasquali
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Sarcoma Service, Department of Surgery, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniel Orbach
- SIREDO Oncology Center(Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), Institut Curie, PSL University, Paris, France
| |
Collapse
|
10
|
Wang Y, Ding Q, Prokopec S, Farncombe KM, Bruce J, Casalino S, McCuaig J, Szybowska M, van Engelen K, Lerner-Ellis J, Pugh TJ, Kim RH. Germline whole genome sequencing in adults with multiple primary tumors. Fam Cancer 2023; 22:513-520. [PMID: 37481477 DOI: 10.1007/s10689-023-00343-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/27/2023] [Indexed: 07/24/2023]
Abstract
Multiple primary tumors (MPTs) are a harbinger of hereditary cancer syndromes. Affected individuals often fit genetic testing criteria for a number of hereditary cancer genes and undergo multigene panel testing. Other genomic testing options, such as whole exome (WES) and whole genome sequencing (WGS) are available, but the utility of these genomic approaches as a second-tier test for those with uninformative multigene panel testing has not been explored. Here, we report our germline sequencing results from WGS in 9 patients with MPTs who had non-informative multigene panel testing. Following germline WGS, sequence (agnostic or 735 selected genes) and copy number variant (CNV) analysis was performed according to the American College of Medical Genetics (ACMG) standards and guidelines for interpreting sequence variants and reporting CNVs. In this cohort, WGS, as a second-tier test, did not identify additional pathogenic or likely pathogenic variants in cancer predisposition genes. Although we identified a CHEK2 likely pathogenic variant and a MUTYH pathogenic variant, both were previously identified in the multigene panels and were not explanatory for the presented type of tumors. CNV analysis also failed to identify any pathogenic or likely pathogenic variants in cancer predisposition genes. In summary, after multigene panel testing, WGS did not reveal any additional pathogenic variants in patients with MPTs. Our study, based on a small cohort of patients with MPT, suggests that germline gene panel testing may be sufficient to investigate these cases. Future studies with larger sample sizes may further elucidate the additional utility of WGS in MPTs.
Collapse
Affiliation(s)
- Yiming Wang
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Qiliang Ding
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephenie Prokopec
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kirsten M Farncombe
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeffrey Bruce
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Selina Casalino
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Jeanna McCuaig
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marta Szybowska
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Kalene van Engelen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- London Health Science Centre, London, Canada
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
- Department of Pediatrics, Western University, London, ON, Canada
| | - Jordan Lerner-Ellis
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Raymond H Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
- Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada.
- Department of Medicine, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
11
|
Affiliation(s)
- Ian F Tannock
- Department of Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada.
| |
Collapse
|
12
|
van Gerven MR, Schild L, van Arkel J, Koopmans B, Broeils LA, Meijs LAM, van Oosterhout R, van Noesel MM, Koster J, van Hooff SR, Molenaar JJ, van den Boogaard ML. Two opposing gene expression patterns within ATRX aberrant neuroblastoma. PLoS One 2023; 18:e0289084. [PMID: 37540673 PMCID: PMC10403137 DOI: 10.1371/journal.pone.0289084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/02/2023] [Indexed: 08/06/2023] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. A subgroup of high-risk patients is characterized by aberrations in the chromatin remodeller ATRX that is encoded by 35 exons. In contrast to other pediatric cancer where ATRX point mutations are most frequent, multi-exon deletions (MEDs) are the most frequent type of ATRX aberrations in neuroblastoma. 75% of these MEDs are predicted to produce in-frame fusion proteins, suggesting a potential gain-of-function effect compared to nonsense mutations. For neuroblastoma there are only a few patient-derived ATRX aberrant models. Therefore, we created isogenic ATRX aberrant models using CRISPR-Cas9 in several neuroblastoma cell lines and one tumoroid and performed total RNA-sequencing on these and the patient-derived models. Gene set enrichment analysis (GSEA) showed decreased expression of genes related to both ribosome biogenesis and several metabolic processes in our isogenic ATRX exon 2-10 MED model systems, the patient-derived MED models and in tumor data containing two patients with an ATRX exon 2-10 MED. In sharp contrast, these same processes showed an increased expression in our isogenic ATRX knock-out and exon 2-13 MED models. Our validations confirmed a role of ATRX in the regulation of ribosome homeostasis. The two distinct molecular expression patterns within ATRX aberrant neuroblastomas that we identified imply that there might be a need for distinct treatment regimens.
Collapse
Affiliation(s)
- Michael R van Gerven
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Linda Schild
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Jennemiek van Arkel
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Bianca Koopmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Luuk A Broeils
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Loes A M Meijs
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Romy van Oosterhout
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
- Department of Cancer and Imaging, University Medical Center Utrecht, Utrecht, Utrecht, The Netherlands
| | - Jan Koster
- Department of Oncogenomics, University Medical Center Amsterdam, Amsterdam, North-Holland, The Netherlands
| | - Sander R van Hooff
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
- Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Utrecht, The Netherlands
| | | |
Collapse
|
13
|
Wadensten E, Wessman S, Abel F, Diaz De Ståhl T, Tesi B, Orsmark Pietras C, Arvidsson L, Taylan F, Fransson S, Vogt H, Poluha A, Pradhananga S, Hellberg M, Lagerstedt-Robinson K, Raj Somarajan P, Samuelsson S, Orrsjö S, Maqbool K, Henning K, Strid T, Ek T, Fagman H, Olsson Bontell T, Martinsson T, Puls F, Kogner P, Wirta V, Pronk CJ, Wille J, Rosenquist R, Nistér M, Mertens F, Sabel M, Norén-Nyström U, Grillner P, Nordgren A, Ljungman G, Sandgren J, Gisselsson D. Diagnostic Yield From a Nationwide Implementation of Precision Medicine for all Children With Cancer. JCO Precis Oncol 2023; 7:e2300039. [PMID: 37384868 PMCID: PMC10581599 DOI: 10.1200/po.23.00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/20/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
PURPOSE Several studies have indicated that broad genomic characterization of childhood cancer provides diagnostically and/or therapeutically relevant information in selected high-risk cases. However, the extent to which such characterization offers clinically actionable data in a prospective broadly inclusive setting remains largely unexplored. METHODS We implemented prospective whole-genome sequencing (WGS) of tumor and germline, complemented by whole-transcriptome sequencing (RNA-Seq) for all children diagnosed with a primary or relapsed solid malignancy in Sweden. Multidisciplinary molecular tumor boards were set up to integrate genomic data in the clinical decision process along with a medicolegal framework enabling secondary use of sequencing data for research purposes. RESULTS During the study's first 14 months, 118 solid tumors from 117 patients were subjected to WGS, with complementary RNA-Seq for fusion gene detection in 52 tumors. There was no significant geographic bias in patient enrollment, and the included tumor types reflected the annual national incidence of pediatric solid tumor types. Of the 112 tumors with somatic mutations, 106 (95%) exhibited alterations with a clear clinical correlation. In 46 of 118 tumors (39%), sequencing only corroborated histopathological diagnoses, while in 59 cases (50%), it contributed to additional subclassification or detection of prognostic markers. Potential treatment targets were found in 31 patients (26%), most commonly ALK mutations/fusions (n = 4), RAS/RAF/MEK/ERK pathway mutations (n = 14), FGFR1 mutations/fusions (n = 5), IDH1 mutations (n = 2), and NTRK2 gene fusions (n = 2). In one patient, the tumor diagnosis was revised based on sequencing. Clinically relevant germline variants were detected in 8 of 94 patients (8.5%). CONCLUSION Up-front, large-scale genomic characterization of pediatric solid malignancies provides diagnostically valuable data in the majority of patients also in a largely unselected cohort.
Collapse
Affiliation(s)
- Elisabeth Wadensten
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| | - Sandra Wessman
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, 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
| | | | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christina Orsmark Pietras
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| | - Linda Arvidsson
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, 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
| | - Hartmut Vogt
- Crown Princess Victoria's Child and Youth Hospital in Linköping, and Division of Children's and Women's Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anna Poluha
- Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sailendra Pradhananga
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
| | - Maria Hellberg
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | | | - Sofie Samuelsson
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, 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
| | - Khurram Maqbool
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Karin Henning
- Section for Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department for Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Strid
- Department of Clinical Pathology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Torben Ek
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg
- Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Henrik Fagman
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tommy Martinsson
- 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
| | - Florian Puls
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Kogner
- Section for Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Valtteri Wirta
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Clinical Genomics Stockholm, Science Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Joakim Wille
- Childhood Cancer Centre, Skåne University Hospital, Lund, Sweden
| | - Richard Rosenquist
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Monica Nistér
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Mertens
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| | - Magnus Sabel
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg
- Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Pernilla Grillner
- Section for Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- 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
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Gustaf Ljungman
- Department of Women's and Children's Health, Uppsala University, Sweden
- Department of Pediatric Oncology, Uppsala University Children's Hospital, 751 35 Uppsala, Sweden
| | - Johanna Sandgren
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - David Gisselsson
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| |
Collapse
|