1
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Slobodyanyuk M, Bahcheli AT, Klein ZP, Bayati M, Strug LJ, Reimand J. Directional integration and pathway enrichment analysis for multi-omics data. Nat Commun 2024; 15:5690. [PMID: 38971800 DOI: 10.1038/s41467-024-49986-4] [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: 09/29/2023] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
Omics techniques generate comprehensive profiles of biomolecules in cells and tissues. However, a holistic understanding of underlying systems requires joint analyses of multiple data modalities. We present DPM, a data fusion method for integrating omics datasets using directionality and significance estimates of genes, transcripts, or proteins. DPM allows users to define how the input datasets are expected to interact directionally given the experimental design or biological relationships between the datasets. DPM prioritises genes and pathways that change consistently across the datasets and penalises those with inconsistent directionality. To demonstrate our approach, we characterise gene and pathway regulation in IDH-mutant gliomas by jointly analysing transcriptomic, proteomic, and DNA methylation datasets. Directional integration of survival information in ovarian cancer reveals candidate biomarkers with consistent prognostic signals in transcript and protein expression. DPM is a general and adaptable framework for gene prioritisation and pathway analysis in multi-omics datasets.
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Affiliation(s)
- Mykhaylo Slobodyanyuk
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Str Suite 15-701, Toronto, ON M5G 1L7, Canada
| | - Alexander T Bahcheli
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle Room 4386, Toronto, ON M5S 1A8, Canada
| | - Zoe P Klein
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle Room 4386, Toronto, ON M5S 1A8, Canada
| | - Masroor Bayati
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Str Suite 15-701, Toronto, ON M5G 1L7, Canada
| | - Lisa J Strug
- Program in Genetics and Genome Biology, the Hospital for Sick Children Research Institute, 686 Bay Str, Toronto, ON M5G 0A4, Canada
- Departments of Statistical Sciences, Computer Science and Division of Biostatistics, University of Toronto, 700 University Avenue, Toronto, ON M5G 1Z5, Canada
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON M5G 0A3, Canada.
- Department of Medical Biophysics, University of Toronto, 101 College Str Suite 15-701, Toronto, ON M5G 1L7, Canada.
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle Room 4386, Toronto, ON M5S 1A8, Canada.
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2
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Biswas A, Rao HR, Wagner MW. Pediatric-type diffuse low-grade gliomas. Childs Nerv Syst 2024:10.1007/s00381-024-06500-x. [PMID: 38926169 DOI: 10.1007/s00381-024-06500-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
The World Health Organization's 5th edition classification of Central Nervous System (CNS) tumors differentiates diffuse gliomas into adult and pediatric variants. Pediatric-type diffuse low-grade gliomas (pDLGGs) are distinct from adult gliomas in their molecular characteristics, biological behavior, clinical progression, and prognosis. Various molecular alterations identified in pDLGGs are crucial for treatment. There are four distinct entities of pDLGGs. All four of these tumor subtypes exhibit diffuse growth and share overlapping histopathological and imaging characteristics. Molecular analysis is essential for differentiating these lesions.
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Affiliation(s)
- Asthik Biswas
- Department of Radiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Harini R Rao
- Department of Pediatric Oncology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Matthias W Wagner
- Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany
- Division of Neuroradiology, The Hospital for Sick Children, Toronto, Canada
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3
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Cases-Cunillera S, Friker LL, Müller P, Becker AJ, Gielen GH. From bedside to bench: New insights in epilepsy-associated tumors based on recent classification updates and animal models on brain tumor networks. Mol Oncol 2024. [PMID: 38899375 DOI: 10.1002/1878-0261.13680] [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: 12/28/2023] [Revised: 12/28/2023] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Low-grade neuroepithelial tumors (LGNTs), particularly those with glioneuronal histology, are highly associated with pharmacoresistant epilepsy. Increasing research focused on these neoplastic lesions did not translate into drug discovery; and anticonvulsant or antitumor therapies are not available yet. During the last years, animal modeling has improved, thereby leading to the possibility of generating brain tumors in mice mimicking crucial genetic, molecular and immunohistological features. Among them, intraventricular in utero electroporation (IUE) has been proven to be a valuable tool for the generation of animal models for LGNTs allowing endogenous tumor growth within the mouse brain parenchyma. Epileptogenicity is mostly determined by the slow-growing patterns of these tumors, thus mirroring intrinsic interactions between tumor cells and surrounding neurons is crucial to investigate the mechanisms underlying convulsive activity. In this review, we provide an updated classification of the human LGNT and summarize the most recent data from human and animal models, with a focus on the crosstalk between brain tumors and neuronal function.
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Affiliation(s)
- Silvia Cases-Cunillera
- INSERM U1266, Neuronal Signaling in Epilepsy and Glioma, Institute of Psychiatry and Neuroscience of Paris (IPNP), Université Paris Cité, Paris, France
- Section for Translational Epilepsy Research, Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Lea L Friker
- Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Philipp Müller
- Section for Translational Epilepsy Research, Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Albert J Becker
- Section for Translational Epilepsy Research, Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Gerrit H Gielen
- Institute of Neuropathology, University Hospital Bonn, Bonn, Germany
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4
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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024; 24:382-398. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [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] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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5
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Brizini M, Drimes T, Bourne C, Streilein J, Drapeau A, Wrogemann J, Archer LA, Del Bigio M, Vanan MI. Case report: Slipped capital femoral epiphysis: a rare adverse event associated with FGFR tyrosine kinase inhibitor therapy in a child. Front Oncol 2024; 14:1399356. [PMID: 38854731 PMCID: PMC11156995 DOI: 10.3389/fonc.2024.1399356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/07/2024] [Indexed: 06/11/2024] Open
Abstract
We report a case of slipped capital femoral epiphysis (SCFE), an on target skeletal toxicity of a pan-FGFR TKI inhibitor, erdafitinib. A 13-year-old boy was diagnosed to have an optic pathway/hypothalamic glioma with signs of increased intracranial pressure and obstructive hydrocephalus requiring placement of ventriculo-peritoneal (VP) shunt. Sequencing of the tumor showed FGFR1-tyrosine kinase domain internal tandem duplication (FGFR1-KD-ITD). He developed hypothalamic obesity with rapid weight gain and BMI >30. At 12 weeks of treatment with erdafitinib, he developed persistent knee pain. X-ray of the right hip showed SCFE. Erdafitinib was discontinued, and he underwent surgical pinning of the right hip. MRI at discontinuation of erdafitinib showed a 30% decrease in the size of the tumor, which has remained stable at 6 months follow-up. Our experience and literature review suggest that pediatric patients who are treated with pan-FGFR TKIs should be regularly monitored for skeletal side effects.
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Affiliation(s)
- Meziane Brizini
- Division of Pediatric Hematology-Oncology, Cancer Care Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Tina Drimes
- Division of Nursing, Cancer Care Manitoba, Winnipeg, MB, Canada
| | | | | | - Annie Drapeau
- Section of Neuro-Surgery, University of Manitoba, Winnipeg, MB, Canada
| | - Jens Wrogemann
- Department of Radiology, University of Manitoba, Winnipeg, MB, Canada
| | - Lori Anne Archer
- Section of Orthopedic Surgery, University of Manitoba, Winnipeg, MB, Canada
| | - Marc Del Bigio
- Department of Pathology, University of Manitoba, Winnipeg, MB, Canada
| | - Magimairajan Issai Vanan
- Division of Pediatric Hematology-Oncology, Cancer Care Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
- Paul Albrechtsen Research Institute, Cancer Care Manitoba, Winnipeg, MB, Canada
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6
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Bennett J, Yeo KK, Tabori U, Hawkins C, Lim-Fat MJ. Pediatric-type low-grade gliomas in adolescents and young adults-challenges and emerging paradigms. Childs Nerv Syst 2024:10.1007/s00381-024-06449-x. [PMID: 38761264 DOI: 10.1007/s00381-024-06449-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/09/2024] [Indexed: 05/20/2024]
Abstract
Pediatric-type low-grade glioma (PLGG) encompasses a heterogeneous group of WHO grade 1 or 2 tumors and is the most common central nervous system tumor found in children. PLGG extends beyond pediatrics, into adolescents and young adults (AYA, ages 15-40). PLGG represents 25% of all gliomas diagnosed in AYA with differences in tumor location and molecular alterations compared to children, resulting in improved outcome for AYAs. Long-term outcome is excellent, though patients may suffer significant morbidity depending on tumor location. There are differences in treatment practices with radiation used to treat PLGG in AYAs more often than in children. Most PLGG in AYA harbor an alteration in the RAS/MAPK pathway, with limited insight into response to targeted therapy in this age group. This review discusses the epidemiology, current therapeutic approaches, and challenges in the management of PLGG in AYA.
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Affiliation(s)
- Julie Bennett
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada.
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada.
- Arthur and Sonia Labbatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Kee Kiat Yeo
- Department of Pediatric Oncology, Dana-Farber / Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | - Uri Tabori
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labbatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Cynthia Hawkins
- Arthur and Sonia Labbatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mary Jane Lim-Fat
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
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7
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Kim JW, Kim SK. The role of surgery for optic pathway gliomas in the era of precision medicine. Childs Nerv Syst 2024:10.1007/s00381-024-06450-4. [PMID: 38743267 DOI: 10.1007/s00381-024-06450-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Optic pathway gliomas (OPGs) represent a unique subset of brain tumours that primarily affect the paediatric population. Traditionally, these tumours are managed conservatively due to their location to and association with vital structures. This article explores the evolving role of surgery in the management of OPGs, particularly in the context of advancements in precision medicine. The advent of targeted therapy, especially for tumours with specific genetic alterations, such as BRAF V600E mutations, has revolutionized the treatment landscape, offering new avenues for patient-specific therapy. However, surgery still plays a crucial role, especially for debulking in cases of hydrocephalus or when standard therapies are ineffective. Advances in surgical techniques, including neuronavigation, endoscopic approaches, and intraoperative neurophysiological monitoring, have enhanced the safety and efficacy of operative interventions. Despite these developments, the complexity of OPGs necessitates a multidisciplinary approach, focusing on long-term outcomes and quality of life. Future research is needed to further elucidate the role of surgery in an era increasingly dominated by molecular genetics and targeted therapies.
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Affiliation(s)
- Joo Whan Kim
- Division of Paediatric Neurosurgery, Seoul National University Children's Hospital, Seoul National University College of Medicine, 03080, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Seung-Ki Kim
- Division of Paediatric Neurosurgery, Seoul National University Children's Hospital, Seoul National University College of Medicine, 03080, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea.
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8
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Boop S, Shimony N, Boop F. How modern treatments have modified the role of surgery in pediatric low-grade glioma. Childs Nerv Syst 2024:10.1007/s00381-024-06412-w. [PMID: 38676718 DOI: 10.1007/s00381-024-06412-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024]
Abstract
Low-grade gliomas are the most common brain tumor of childhood, and complete resection offers a high likelihood of cure. However, in many instances, tumors may not be surgically accessible without substantial morbidity, particularly in regard to gliomas arising from the optic or hypothalamic regions, as well as the brainstem. When gross total resection is not feasible, alternative treatment strategies must be considered. While conventional chemotherapy and radiation therapy have long been the backbone of adjuvant therapy for low-grade glioma, emerging techniques and technologies are rapidly changing the landscape of care for patients with this disease. This article seeks to review the current and emerging modalities of treatment for pediatric low-grade glioma.
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Affiliation(s)
- Scott Boop
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Nir Shimony
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Le Bonheur Neuroscience Institute, LeBonheur Children's Hospital, Memphis, TN, USA
- Department of Neurological Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
- Semmes-Murphey Clinic, Memphis, TN, USA
| | - Frederick Boop
- Department of Neurological Surgery, University of Tennessee Health Science Center, Memphis, TN, USA.
- Global Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
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d’Amati A, Bargiacchi L, Rossi S, Carai A, Bertero L, Barresi V, Errico ME, Buccoliero AM, Asioli S, Marucci G, Del Baldo G, Mastronuzzi A, Miele E, D’Antonio F, Schiavello E, Biassoni V, Massimino M, Gessi M, Antonelli M, Gianno F. Pediatric CNS tumors and 2021 WHO classification: what do oncologists need from pathologists? Front Mol Neurosci 2024; 17:1268038. [PMID: 38544524 PMCID: PMC10966132 DOI: 10.3389/fnmol.2024.1268038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/23/2024] [Indexed: 05/14/2024] Open
Abstract
The fifth edition of the WHO Classification of Tumors of the Central Nervous System (CNS), published in 2021, established new approaches to both CNS tumor nomenclature and grading, emphasizing the importance of integrated diagnoses and layered reports. This edition increased the role of molecular diagnostics in CNS tumor classification while still relying on other established approaches such as histology and immunohistochemistry. Moreover, it introduced new tumor types and subtypes based on novel diagnostic technologies such as DNA methylome profiling. Over the past decade, molecular techniques identified numerous key genetic alterations in CSN tumors, with important implications regarding the understanding of pathogenesis but also for prognosis and the development and application of effective molecularly targeted therapies. This review summarizes the major changes in the 2021 fifth edition classification of pediatric CNS tumors, highlighting for each entity the molecular alterations and other information that are relevant for diagnostic, prognostic, or therapeutic purposes and that patients' and oncologists' need from a pathology report.
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Affiliation(s)
- Antonio d’Amati
- Unit of Anatomical Pathology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, Bari, Italy
- Unit of Human Anatomy and Histology, Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari “Aldo Moro”, Bari, Italy
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
- Neuropathology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica S. Cuore, Roma, Italy
| | - Lavinia Bargiacchi
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Carai
- Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valeria Barresi
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria Elena Errico
- Department of Pathology, AORN Santobono Pausilipon, Pediatric Hospital, Naples, Italy
| | | | - Sofia Asioli
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Gianluca Marucci
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giada Del Baldo
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Angela Mastronuzzi
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Evelina Miele
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Federica D’Antonio
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Elisabetta Schiavello
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Veronica Biassoni
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maura Massimino
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marco Gessi
- Neuropathology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica S. Cuore, Roma, Italy
| | - Manila Antonelli
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Francesca Gianno
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
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10
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Otsuji R, Fujioka Y, Hata N, Kuga D, Hatae R, Sangatsuda Y, Nakamizo A, Mizoguchi M, Yoshimoto K. Liquid Biopsy for Glioma Using Cell-Free DNA in Cerebrospinal Fluid. Cancers (Basel) 2024; 16:1009. [PMID: 38473369 DOI: 10.3390/cancers16051009] [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: 12/25/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Glioma is one of the most common primary central nervous system (CNS) tumors, and its molecular diagnosis is crucial. However, surgical resection or biopsy is risky when the tumor is located deep in the brain or brainstem. In such cases, a minimally invasive approach to liquid biopsy is beneficial. Cell-free DNA (cfDNA), which directly reflects tumor-specific genetic changes, has attracted attention as a target for liquid biopsy, and blood-based cfDNA monitoring has been demonstrated for other extra-cranial cancers. However, it is still challenging to fully detect CNS tumors derived from cfDNA in the blood, including gliomas, because of the unique structure of the blood-brain barrier. Alternatively, cerebrospinal fluid (CSF) is an ideal source of cfDNA and is expected to contribute significantly to the liquid biopsy of gliomas. Several successful studies have been conducted to detect tumor-specific genetic alterations in cfDNA from CSF using digital PCR and/or next-generation sequencing. This review summarizes the current status of CSF-based cfDNA-targeted liquid biopsy for gliomas. It highlights how the approaches differ from liquid biopsies of other extra-cranial cancers and discusses the current issues and prospects.
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Affiliation(s)
- Ryosuke Otsuji
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yutaka Fujioka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Oita University Faculty of Medicine, Yufu 879-5593, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Nakamizo
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Neurosurgery, National Hospital Organization Kyushu Medical Center, Clinical Research Institute, Fukuoka 810-8563, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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11
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Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.27.23299068. [PMID: 38076942 PMCID: PMC10705664 DOI: 10.1101/2023.11.27.23299068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., MYCN for neuroblastoma, CDKN2A and PAX5 for B-/T-ALL, and SMARCB1 for AT/RT), and 7,590 polymorphism sites for interrogating tumors with aneuploidy, such as hyperdiploid and hypodiploid B-ALL or 17q gain neuroblastoma. We used driver alterations reported from an established real-time clinical genomics cohort (n=253) to validate this gene panel. Among the 485 pathogenic variants reported, our panel covered 417 variants (86%). For 90 rearrangements responsible for oncogenic fusions, our panel covered 74 events (82%). We re-sequenced 113 previously characterized clinical specimens at an average depth of 2,500X using SJPedPanel and recovered 354 (91%) of the 389 reported pathogenic variants. We then investigated the power of this panel in detecting mutations from specimens with low tumor purity (as low as 0.1%) using cell line-based dilution experiments and discovered that this gene panel enabled us to detect ∼80% variants with allele fraction of 0.2%, while the detection rate decreases to ∼50% when the allele fraction is 0.1%. We finally demonstrate its utility in disease monitoring on clinical specimens collected from AML patients in morphologic remission. Conclusions SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
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12
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Johns DA, Williams RJ, Smith CM, Nadaminti PP, Samarasinghe RM. Novel insights on genetics and epigenetics as clinical targets for paediatric astrocytoma. Clin Transl Med 2024; 14:e1560. [PMID: 38299304 PMCID: PMC10831580 DOI: 10.1002/ctm2.1560] [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: 07/02/2023] [Revised: 01/07/2024] [Accepted: 01/12/2024] [Indexed: 02/02/2024] Open
Abstract
Paediatric and adult astrocytomas are notably different, where clinical treatments used for adults are not as effective on children with the same form of cancer and these treatments lead to adverse long-term health concerns. Integrative omics-based studies have shown the pathology and fundamental molecular characteristics differ significantly and cannot be extrapolated from the more widely studied adult disease. Recent clinical advances in our understanding of paediatric astrocytomas, with the aid of next-generation sequencing and epigenome-wide profiling, have led to the identification of key canonical mutations that vary based on the tumour location and age of onset. These driver mutations, in particular the identification of the recurrent histone H3 mutations in high-grade tumours, have confirmed the important role epigenetic dysregulations play in cancer progression. This review summarises the current updates of the classification, epidemiology, pathogenesis and clinical management of paediatric astrocytoma based on their grades and the ongoing clinical trials. It also provides novel insights on genetic and epigenetic alterations as diagnostic biomarkers, highlighting the potential of targeting these pathways as therapeutics for this devastating childhood cancer.
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Affiliation(s)
- Dona A. Johns
- School of Medicine, Deakin UniversityGeelongVictoriaAustralia
| | - Richard J. Williams
- School of Medicine, Deakin UniversityGeelongVictoriaAustralia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongVictoriaAustralia
- The Graeme Clark Institute, The University of MelbourneMelbourneVICAustralia
| | - Craig M. Smith
- School of Medicine, Deakin UniversityGeelongVictoriaAustralia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongVictoriaAustralia
| | - Pavani P. Nadaminti
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, ParkvilleMelbourneVictoriaAustralia
| | - Rasika M. Samarasinghe
- School of Medicine, Deakin UniversityGeelongVictoriaAustralia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongVictoriaAustralia
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13
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van Tilburg CM, Kilburn LB, Perreault S, Schmidt R, Azizi AA, Cruz-Martínez O, Zápotocký M, Scheinemann K, Meeteren AYNSV, Sehested A, Opocher E, Driever PH, Avula S, Ziegler DS, Capper D, Koch A, Sahm F, Qiu J, Tsao LP, Blackman SC, Manley P, Milde T, Witt R, Jones DTW, Hargrave D, Witt O. LOGGIC/FIREFLY-2: a phase 3, randomized trial of tovorafenib vs. chemotherapy in pediatric and young adult patients with newly diagnosed low-grade glioma harboring an activating RAF alteration. BMC Cancer 2024; 24:147. [PMID: 38291372 PMCID: PMC10826080 DOI: 10.1186/s12885-024-11820-x] [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: 08/31/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Pediatric low-grade glioma (pLGG) is essentially a single pathway disease, with most tumors driven by genomic alterations affecting the mitogen-activated protein kinase/ERK (MAPK) pathway, predominantly KIAA1549::BRAF fusions and BRAF V600E mutations. This makes pLGG an ideal candidate for MAPK pathway-targeted treatments. The type I BRAF inhibitor, dabrafenib, in combination with the MEK inhibitor, trametinib, has been approved by the United States Food and Drug Administration for the systemic treatment of BRAF V600E-mutated pLGG. However, this combination is not approved for the treatment of patients with tumors harboring BRAF fusions as type I RAF inhibitors are ineffective in this setting and may paradoxically enhance tumor growth. The type II RAF inhibitor, tovorafenib (formerly DAY101, TAK-580, MLN2480), has shown promising activity and good tolerability in patients with BRAF-altered pLGG in the phase 2 FIREFLY-1 study, with an objective response rate (ORR) per Response Assessment in Neuro-Oncology high-grade glioma (RANO-HGG) criteria of 67%. Tumor response was independent of histologic subtype, BRAF alteration type (fusion vs. mutation), number of prior lines of therapy, and prior MAPK-pathway inhibitor use. METHODS LOGGIC/FIREFLY-2 is a two-arm, randomized, open-label, multicenter, global, phase 3 trial to evaluate the efficacy, safety, and tolerability of tovorafenib monotherapy vs. current standard of care (SoC) chemotherapy in patients < 25 years of age with pLGG harboring an activating RAF alteration who require first-line systemic therapy. Patients are randomized 1:1 to either tovorafenib, administered once weekly at 420 mg/m2 (not to exceed 600 mg), or investigator's choice of prespecified SoC chemotherapy regimens. The primary objective is to compare ORR between the two treatment arms, as assessed by independent review per RANO-LGG criteria. Secondary objectives include comparisons of progression-free survival, duration of response, safety, neurologic function, and clinical benefit rate. DISCUSSION The promising tovorafenib activity data, CNS-penetration properties, strong scientific rationale combined with the manageable tolerability and safety profile seen in patients with pLGG led to the SIOPe-BTG-LGG working group to nominate tovorafenib for comparison with SoC chemotherapy in this first-line phase 3 trial. The efficacy, safety, and functional response data generated from the trial may define a new SoC treatment for newly diagnosed pLGG. TRIAL REGISTRATION ClinicalTrials.gov: NCT05566795. Registered on October 4, 2022.
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Affiliation(s)
- 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
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | | | | | - Rene Schmidt
- Institute of Biostatistics and Clinical Research, Münster, Germany
| | - Amedeo A Azizi
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Ofelia Cruz-Martínez
- Neuro-oncology Unit, Pediatric Cancer Center, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Michal Zápotocký
- Department of Paediatric Haematology and Oncology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Katrin Scheinemann
- Division of Oncology-Hematology, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
- Faculty of Health Sciences and Medicine, University of Lucerne, Lucerne, Switzerland
- Department of Pediatrics, McMaster Children's Hospital and McMaster University, Hamilton, Canada
| | | | - Astrid Sehested
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Enrico Opocher
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Padua University Hospital, Padua, Italy
| | - Pablo Hernáiz Driever
- German HIT-LOGGIC-Registry for LGG in Children and Adolescents, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Shivaram Avula
- Department of Radiology, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
| | - David S Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
- Lowy Cancer Research Centre, Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia
- School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- DKTK Partner Site, Berlin, Germany
| | - Arend Koch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Sahm
- Department of Neuropathology, German Cancer Research Center (DKFZ), University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Jiaheng Qiu
- Day One Biopharmaceuticals, Brisbane, CA, USA
| | - Li-Pen Tsao
- Day One Biopharmaceuticals, Brisbane, CA, USA
| | | | | | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ruth Witt
- 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
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Darren Hargrave
- UCL Great Ormond Street Institute of Child Health and Great Ormond Street Hospital for Children, London, UK
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
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14
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Yvone GM, Breunig JJ. Pediatric low-grade glioma models: advances and ongoing challenges. Front Oncol 2024; 13:1346949. [PMID: 38318325 PMCID: PMC10839015 DOI: 10.3389/fonc.2023.1346949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024] Open
Abstract
Pediatric low-grade gliomas represent the most common childhood brain tumor class. While often curable, some tumors fail to respond and even successful treatments can have life-long side effects. Many clinical trials are underway for pediatric low-grade gliomas. However, these trials are expensive and challenging to organize due to the heterogeneity of patients and subtypes. Advances in sequencing technologies are helping to mitigate this by revealing the molecular landscapes of mutations in pediatric low-grade glioma. Functionalizing these mutations in the form of preclinical models is the next step in both understanding the disease mechanisms as well as for testing therapeutics. However, such models are often more difficult to generate due to their less proliferative nature, and the heterogeneity of tumor microenvironments, cell(s)-of-origin, and genetic alterations. In this review, we discuss the molecular and genetic alterations and the various preclinical models generated for the different types of pediatric low-grade gliomas. We examined the different preclinical models for pediatric low-grade gliomas, summarizing the scientific advances made to the field and therapeutic implications. We also discuss the advantages and limitations of the various models. This review highlights the importance of preclinical models for pediatric low-grade gliomas while noting the challenges and future directions of these models to improve therapeutic outcomes of pediatric low-grade gliomas.
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Affiliation(s)
- Griselda Metta Yvone
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Joshua J. Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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15
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Ali RH, Almanabri M, Ali NY, Alsaber AR, Khalifa NM, Hussein R, Alateeqi M, Mohammed EMA, Jama H, Almarzooq A, Benobaid N, Alqallaf Z, Ahmed AA, Bahzad S, Almurshed M. Clinicopathological analysis of BRAF and non-BRAF MAPK pathway-altered gliomas in paediatric and adult patients: a single-institution study of 40 patients. J Clin Pathol 2024:jcp-2023-209318. [PMID: 38195220 DOI: 10.1136/jcp-2023-209318] [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: 11/28/2023] [Accepted: 12/28/2023] [Indexed: 01/11/2024]
Abstract
AIMS Mitogen-activated protein kinase (MAPK) pathway alteration is a major oncogenic driver in paediatric low-grade gliomas (LGG) and some adult gliomas, encompassing BRAF (most common) and non-BRAF alterations. The aim was to determine the frequency, molecular spectrum and clinicopathological features of MAPK-altered gliomas in paediatric and adult patients at our neuropathology site in Kuwait. METHODS We retrospectively searched the data of molecularly sequenced gliomas between 2018 and 2023 for MAPK alterations, revised the pathology in view of the 2021 WHO classification and evaluated the clinicopathological data for possible correlations. RESULTS Of 272 gliomas, 40 (15%) harboured a MAPK pathway alteration in 19 paediatric (median 9.6 years; 1.2-17.6) and 21 adult patients (median 37 years; 18.9-89.2), comprising 42% and 9% of paediatric and adult cases, respectively. Pilocytic astrocytoma and glioblastoma were the most frequent diagnoses in children (47%) and adults (43%), respectively. BRAF V600E (n=17, 43%) showed a wide distribution across age groups, locations and pathological diagnoses while KIAA1549::BRAF fusion (n=8, 20%) was spatially and histologically restricted to cerebellar paediatric LGGs. Non-V600E variants and BRAF amplifications accompanied other molecular aberrations in high-grade tumours. Non-BRAF MAPK alterations (n=8) included mutations and gene fusions involving FGFR1, NTRK2, NF1, ROS1 and MYB. Fusions included KANK1::NTRK2, GOPC::ROS1 (both infant hemispheric gliomas), FGFR1::TACC1 (diffuse LGG), MYB::QKI (angiocentric glioma) and BCR::NTRK2 (glioblastoma). Paradoxical H3 K27M/MAPK co-mutations were observed in two LGGs. CONCLUSION The study provided insights into MAPK-altered gliomas in Kuwait highlighting the differences among paediatric and adult patients and providing a framework for planning therapeutic polices.
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Affiliation(s)
- Rola H Ali
- Department of Pathology, College of Medicine, Kuwait University, Jabriya, Hawalli, Kuwait
- Department of Histopathology, Al Sabah Hospital, Shuwaikh, Al Asimah, Kuwait
| | - Mohamad Almanabri
- Department of Neurosurgery, Ibn Sina Hospital, Shuwaikh, Al Asimah, Kuwait
| | - Nawal Y Ali
- Department of Radiology, Ibn Sina Hospital, Shuwaikh, Al Asimah, Kuwait
| | - Ahmad R Alsaber
- Department of Management, College of Business and Economics, American University of Kuwait, Salmiya, Hawalli, Kuwait
| | - Nisreen M Khalifa
- Department of Pediatric Hematology/Oncology, NBK Children's Hospital, Shuwaikh, Al Asimah, Kuwait
| | - Rania Hussein
- Department of Radiation Oncology, Kuwait Cancer Control Center, Shuwaikh, Al Asimah, Kuwait
| | - Mona Alateeqi
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Al Asimah, Kuwait
| | - Eiman M A Mohammed
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Al Asimah, Kuwait
| | - Hiba Jama
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Al Asimah, Kuwait
| | - Ammar Almarzooq
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Al Asimah, Kuwait
| | - Noelle Benobaid
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Al Asimah, Kuwait
| | - Zainab Alqallaf
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Al Asimah, Kuwait
| | - Amir A Ahmed
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Al Asimah, Kuwait
| | - Shakir Bahzad
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Al Asimah, Kuwait
| | - Maryam Almurshed
- Department of Histopathology, Al Sabah Hospital, Shuwaikh, Al Asimah, Kuwait
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16
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Fangusaro J, Jones DT, Packer RJ, Gutmann DH, Milde T, Witt O, Mueller S, Fisher MJ, Hansford JR, Tabori U, Hargrave D, Bandopadhayay P. Pediatric low-grade glioma: State-of-the-art and ongoing challenges. Neuro Oncol 2024; 26:25-37. [PMID: 37944912 PMCID: PMC10768984 DOI: 10.1093/neuonc/noad195] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
The most common childhood central nervous system (CNS) tumor is pediatric low-grade glioma (pLGG), representing 30%-40% of all CNS tumors in children. Although there is high associated morbidity, tumor-related mortality is relatively rare. pLGG is now conceptualized as a chronic disease, underscoring the importance of functional outcomes and quality-of-life measures. A wealth of data has emerged about these tumors, including a better understanding of their natural history and their molecular drivers, paving the way for the use of targeted inhibitors. While these treatments have heralded tremendous promise, challenges remain about how to best optimize their use, and the long-term toxicities associated with these inhibitors remain unknown. The International Pediatric Low-Grade Glioma Coalition (iPLGGc) is a global group of physicians and scientists with expertise in pLGG focused on addressing key pLGG issues. Here, the iPLGGc provides an overview of the current state-of-the-art in pLGG, including epidemiology, histology, molecular landscape, treatment paradigms, survival outcomes, functional outcomes, imaging response, and ongoing challenges. This paper also serves as an introduction to 3 other pLGG manuscripts on (1) pLGG preclinical models, (2) consensus framework for conducting early-phase clinical trials in pLGG, and (3) pLGG resistance, rebound, and recurrence.
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Affiliation(s)
- Jason Fangusaro
- Department of Hematology and Oncology, Children’s Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA
| | - David T Jones
- Translational Program, Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), University Hospital Heidelberg, Heidelberg, Germany
| | - Roger J Packer
- Brain Tumor Institute, Daniel and Jennifer Gilbert Neurofibromatosis Institute, Neuroscience and Behavioral Medicine, Children’s National Medical Center, Washington, District of Columbia, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Till Milde
- Translational Program, Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Olaf Witt
- Translational Program, Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Sabine Mueller
- Department of Neurological Surgery, University of California, San Francisco, California, USA
- Department of Pediatrics, University of California, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, California, USA
- Department of Oncology, University Children’s Hospital Zürich, Zürich, Switzerland
| | - Michael J Fisher
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jordan R Hansford
- Michael Rice Centre for Hematology and Oncology, Women’s and Children’s Hospital, Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australia ImmunoGENomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Uri Tabori
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Darren Hargrave
- University College London Great Ormond Street Institute of Child Health, London, UK
| | - Pratiti Bandopadhayay
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
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17
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Wongsurawat T, Jenjaroenpun P, Anekwiang P, Arigul T, Thongrattana W, Jamshidi‐Parsian A, Boysen G, Suriyaphol P, Suktitipat B, Srirabheebhat P, Cheunsuchon P, Tanboon J, Nookaew I, Sathornsumetee S. Exploiting nanopore sequencing for characterization and grading of IDH-mutant gliomas. Brain Pathol 2024; 34:e13203. [PMID: 37574201 PMCID: PMC10711254 DOI: 10.1111/bpa.13203] [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: 03/31/2023] [Accepted: 07/28/2023] [Indexed: 08/15/2023] Open
Abstract
The 2021 WHO Classification of Central Nervous System Tumors recommended evaluation of cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) deletion in addition to codeletion of 1p/19q to characterize IDH-mutant gliomas. Here, we demonstrated the use of a nanopore-based copy-number variation sequencing (nCNV-seq) approach to simultaneously identify deletions of CDKN2A/B and 1p/19q. The nCNV-seq approach was initially evaluated on three distinct glioma cell lines and then applied to 19 IDH-mutant gliomas (8 astrocytomas and 11 oligodendrogliomas) from patients. The whole-arm 1p/19q codeletion was detected in all oligodendrogliomas with high concordance among nCNV-seq, FISH, DNA methylation profiling, and whole-genome sequencing. For the CDKN2A/B deletion, nCNV-seq detected the loss in both astrocytoma and oligodendroglioma, with strong correlation with the CNV profiles derived from whole-genome sequencing (Pearson correlation (r) = 0.95, P < 2.2 × 10-16 to r = 0.99, P < 2.2 × 10-16 ) and methylome profiling. Furthermore, nCNV-seq can differentiate between homozygous and hemizygous deletions of CDKN2A/B. Taken together, nCNV-seq holds promise as a new, alternative approach for a rapid and simultaneous detection of the molecular signatures of IDH-mutant gliomas without capital expenditure for a sequencer.
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Affiliation(s)
- Thidathip Wongsurawat
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Panatna Anekwiang
- Department of Medicine (Neurology), Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Tantip Arigul
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Wichayapat Thongrattana
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Azemat Jamshidi‐Parsian
- Department of Radiation OncologyUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Gunnar Boysen
- Department of Environmental and Occupational HealthUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Prapat Suriyaphol
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Bhoom Suktitipat
- Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
- Department of Biochemistry, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Prajak Srirabheebhat
- Department of Surgery (Neurosurgery), Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Pornsuk Cheunsuchon
- Department of Pathology, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Jantima Tanboon
- Department of Pathology, Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Sith Sathornsumetee
- Department of Medicine (Neurology), Faculty of Medicine Siriraj HospitalMahidol UniversityBangkokThailand
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18
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Krynina O, de Ståhl TD, Jylhä C, Arthur C, Giraud G, Nyman P, Fritzberg A, Sandgren J, Tham E, Sandvik U. The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma. Neurooncol Adv 2024; 6:vdae008. [PMID: 38371226 PMCID: PMC10874216 DOI: 10.1093/noajnl/vdae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
Background Low-grade gliomas (LGGs) represent children's most prevalent central nervous system tumor, necessitating molecular profiling to diagnose and determine the most suitable treatment. Developing highly sensitive screening techniques for liquid biopsy samples is particularly beneficial, as it enables the early detection and molecular characterization of tumors with minimally invasive samples. Methods We examined CSF and plasma samples from patients with pilocytic astrocytoma (PA) using custom multiplexed droplet digital polymerase chain reaction (ddPCR) assays based on whole genome sequencing data. These assays included a screening test to analyze BRAF duplication and a targeted assay for the detection of patient-specific KIAA1549::BRAF fusion junction sequences or single nucleotide variants. Results Our findings revealed that 5 out of 13 individual cerebrospinal fluid (CSF) samples tested positive for circulating tumor DNA (ctDNA). Among these cases, 3 exhibited the KIAA1549::BRAF fusion, which was detected through copy number variation (CNV) analysis (n = 1) or a fusion-specific probe (n = 2), while 1 case each displayed the BRAF V600E mutation and the FGFR1 N577K mutation. Additionally, a quantitative analysis of cell-free DNA (cfDNA) concentrations in PA CSF samples showed that most cases had low cfDNA levels, below the limit of detection of our assay (<1.9 ng). Conclusions While CNV analysis of CSF samples from LGGs still has some limitations, it has the potential to serve as a valuable complementary tool. Furthermore, it can also be multiplexed with other aberrations, for example, to the BRAF V600 test, to provide important insights into the molecular characteristics of LGGs.
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Affiliation(s)
- Olha Krynina
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Cecilia Jylhä
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Arthur
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Geraldine Giraud
- Department of Immunology, Genetic and Pathology, Neuro-oncology, and Neurodegeneration Program Rudbeck Laboratory, Uppsala, Sweden
- Department of Women and Children’s Health, Akademiska University Hospital, Uppsala, Sweden
| | - Per Nyman
- Department of Health, Crown Princess Victoria Children´s Hospital, Linköping University Hospital, Linköping, Sweden
- Department of Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Centre for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Anders Fritzberg
- Daycare Unit of Oncology and Hematology, Clinic of Pediatrics Falun Hospital, Dalarna Region, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrika Sandvik
- Department of Clinical Neuroscience, Division of Neurosurgery, Karolinska Institutet, Stockholm, Sweden
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19
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Barros Guinle MI, Nirschl JJ, Xing YL, Nettnin EA, Arana S, Feng ZP, Nasajpour E, Pronina A, Garcia CA, Grant GA, Vogel H, Yeom KW, Prolo LM, Petritsch CK. CDC42BPA::BRAF represents a novel fusion in desmoplastic infantile ganglioglioma/desmoplastic infantile astrocytoma. Neurooncol Adv 2024; 6:vdae050. [PMID: 38741773 PMCID: PMC11089409 DOI: 10.1093/noajnl/vdae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Affiliation(s)
| | - Jeffrey J Nirschl
- Division of Neuropathology, Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Yao Lulu Xing
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Ella A Nettnin
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Sophia Arana
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Zhi-Ping Feng
- The Australian National University Bioinformatics Consultancy, John Curtin School of Medical Research, The Australian National University, ACT 2600, Australia
| | - Emon Nasajpour
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Anna Pronina
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Cesar A Garcia
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Gerald A Grant
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hannes Vogel
- Division of Neuropathology, Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Kristen W Yeom
- Department of Radiology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Laura M Prolo
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, California, USA
- Division of Pediatric Neurosurgery, Lucile Packard Children’s Hospital, Palo Alto, California, USA
| | - Claudia K Petritsch
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, California, USA
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20
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Cipri S, Fabozzi F, Del Baldo G, Milano GM, Boccuto L, Carai A, Mastronuzzi A. Targeted therapy for pediatric central nervous system tumors harboring mutagenic tropomyosin receptor kinases. Front Oncol 2023; 13:1235794. [PMID: 38144536 PMCID: PMC10748602 DOI: 10.3389/fonc.2023.1235794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
The family of the neurotrophic tyrosine kinase receptor (NTRK) gene encodes for members of the tropomyosin receptor kinase (TRK) family. Rearrangements involving NTRK1/2/3 are rare oncogenic factors reported with variable frequencies in an extensive range of cancers in pediatrics and adult populations, although they are more common in the former than in the latter. The alterations in these genes are causative of the constitutive activation of TRKs that drive carcinogenesis. In 2017, first-generation TRK inhibitor (TRKi) larotrectinib was granted accelerated approval from the FDA, having demonstrated histologic-agnostic activity against NTRKs fusions tumors. Since this new era has begun, resistance to first-generation TRKi has been described and has opened the development of second-generation molecules, such as selitrectinib and repotrectinib. In this review, we provide a brief overview of the studies on NTRK alterations found in pediatric central nervous system tumors and first and second-generation TRKi useful in clinical practice.
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Affiliation(s)
- Selene Cipri
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Francesco Fabozzi
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Giada Del Baldo
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Maria Milano
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Luigi Boccuto
- Healthcare Genetics Program, School of Nursing, College of Behavioral, Social and Health Sciences, Clemson University, Clemson, SC, United States
| | - Andrea Carai
- Department of Neurosciences, Neurosurgery Unit, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Angela Mastronuzzi
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
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21
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Apostolides M, Li M, Arnoldo A, Ku M, Husić M, Ramani AK, Brudno M, Turinsky A, Hawkins C, Siddaway R. Clinical Implementation of MetaFusion for Accurate Cancer-Driving Fusion Detection from RNA Sequencing. J Mol Diagn 2023; 25:921-931. [PMID: 37748705 DOI: 10.1016/j.jmoldx.2023.09.002] [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: 11/23/2022] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023] Open
Abstract
Oncogenic fusion genes may be identified from next-generation sequencing data, typically RNA-sequencing. However, in a clinical setting, identifying these alterations is challenging against a background of nonrelevant fusion calls that reduce workflow precision and specificity. Furthermore, although numerous algorithms have been developed to detect fusions in RNA-sequencing, there are variations in their individual sensitivities. Here this problem was addressed by introducing MetaFusion into clinical use. Its utility was illustrated when applied to both whole-transcriptome and targeted sequencing data sets. MetaFusion combines ensemble fusion calls from eight individual fusion-calling algorithms with practice-informed identification of gene fusions that are known to be clinically relevant. In doing so, it allows oncogenic fusions to be identified with near-perfect sensitivity and high precision and specificity, significantly outperforming the individual fusion callers it uses as well as existing clinical-grade software. MetaFusion enhances clinical yield over existing methods and is able to identify fusions that have patient relevance for the purposes of diagnosis, prognosis, and treatment.
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Affiliation(s)
- Michael Apostolides
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Li
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anthony Arnoldo
- Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Ku
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mia Husić
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Arun K Ramani
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Brudno
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; University Health Network, Toronto, Ontario, Canada
| | - Andrei Turinsky
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Robert Siddaway
- Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.
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22
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Meredith DM, Pisapia DJ. 2021 World Health Organization Classification of Brain Tumors. Continuum (Minneap Minn) 2023; 29:1638-1661. [PMID: 38085892 DOI: 10.1212/con.0000000000001355] [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: 12/18/2023]
Abstract
OBJECTIVE The classification of brain tumors is a rapidly evolving field that requires extensive integration of molecular diagnostic findings from an expanding set of platforms and assays. This article summarizes the schema presented in the 5th edition of the World Health Organization (WHO) classification of central nervous system (CNS) tumors while highlighting diagnostic molecular findings and discussing the strengths and weaknesses of commonly available testing modalities. LATEST DEVELOPMENTS Several major changes in practice were introduced with the 5th edition of the CNS WHO classification, including molecular grading of adult diffuse gliomas, the introduction of many new entities within the spectrum of pediatric gliomas and glioneuronal tumors, and the widespread adoption of methylation classes as useful or even necessary diagnostic criteria. Additionally, several revisions to nomenclature (eg, IDH-mutant gliomas) were introduced for simplicity and to disambiguate from other tumor types. ESSENTIAL POINTS The classification of brain tumors continues to grow in complexity alongside our improved understanding of their nuanced molecular underpinnings.
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23
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Hardin EC, Schmid S, Sommerkamp A, Bodden C, Heipertz AE, Sievers P, Wittmann A, Milde T, Pfister SM, von Deimling A, Horn S, Herz NA, Simon M, Perera AA, Azizi A, Cruz O, Curry S, Van Damme A, Garami M, Hargrave D, Kattamis A, Kotnik BF, Lähteenmäki P, Scheinemann K, Schouten-van Meeteren AYN, Sehested A, Viscardi E, Wormdal OM, Zapotocky M, Ziegler DS, Koch A, Hernáiz Driever P, Witt O, Capper D, Sahm F, Jones DTW, van Tilburg CM. LOGGIC Core BioClinical Data Bank: Added clinical value of RNA-Seq in an international molecular diagnostic registry for pediatric low-grade glioma patients. Neuro Oncol 2023; 25:2087-2097. [PMID: 37075810 PMCID: PMC10628936 DOI: 10.1093/neuonc/noad078] [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: 01/01/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The international, multicenter registry LOGGIC Core BioClinical Data Bank aims to enhance the understanding of tumor biology in pediatric low-grade glioma (pLGG) and provide clinical and molecular data to support treatment decisions and interventional trial participation. Hence, the question arises whether implementation of RNA sequencing (RNA-Seq) using fresh frozen (FrFr) tumor tissue in addition to gene panel and DNA methylation analysis improves diagnostic accuracy and provides additional clinical benefit. METHODS Analysis of patients aged 0 to 21 years, enrolled in Germany between April 2019 and February 2021, and for whom FrFr tissue was available. Central reference histopathology, immunohistochemistry, 850k DNA methylation analysis, gene panel sequencing, and RNA-Seq were performed. RESULTS FrFr tissue was available in 178/379 enrolled cases. RNA-Seq was performed on 125 of these samples. We confirmed KIAA1549::BRAF-fusion (n = 71), BRAF V600E-mutation (n = 12), and alterations in FGFR1 (n = 14) as the most frequent alterations, among other common molecular drivers (n = 12). N = 16 cases (13%) presented rare gene fusions (eg, TPM3::NTRK1, EWSR1::VGLL1, SH3PXD2A::HTRA1, PDGFB::LRP1, GOPC::ROS1). In n = 27 cases (22%), RNA-Seq detected a driver alteration not otherwise identified (22/27 actionable). The rate of driver alteration detection was hereby increased from 75% to 97%. Furthermore, FGFR1 internal tandem duplications (n = 6) were only detected by RNA-Seq using current bioinformatics pipelines, leading to a change in analysis protocols. CONCLUSIONS The addition of RNA-Seq to current diagnostic methods improves diagnostic accuracy, making precision oncology treatments (MEKi/RAFi/ERKi/NTRKi/FGFRi/ROSi) more accessible. We propose to include RNA-Seq as part of routine diagnostics for all pLGG patients, especially when no common pLGG alteration was identified.
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Affiliation(s)
- Emily C Hardin
- 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)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- Heidelberg Medical Faculty, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Simone Schmid
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alexander Sommerkamp
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Paediatrics and Adolescent Medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Carina Bodden
- 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)
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Anna-Elisa Heipertz
- 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)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- Heidelberg Medical Faculty, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andrea Wittmann
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Till Milde
- 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)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Saint Luc University Hospital, Brussels, Belgium
| | - Svea Horn
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, HIT-LOGGIC German Registry for children and adolescents with low-grade glioma, Berlin, Germany
| | - Nina A Herz
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, HIT-LOGGIC German Registry for children and adolescents with low-grade glioma, Berlin, Germany
| | - Michèle Simon
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, HIT-LOGGIC German Registry for children and adolescents with low-grade glioma, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ashwyn A Perera
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Heidelberg Medical Faculty, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amedeo Azizi
- Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Ofelia Cruz
- Neuro-Oncology Unit, Pediatric Cancer Center, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Sarah Curry
- Department of Haematology and Oncology, Children’s Health Ireland at Crumlin, Dublin, Ireland
| | - An Van Damme
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Saint Luc University Hospital, Brussels, Belgium
| | - Miklos Garami
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Darren Hargrave
- Great Ormond Street Hospital for Children NHS Trust London, London, UK
| | - Antonis Kattamis
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- First Department of Paediatrics, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Barbara Faganel Kotnik
- Department of Haematology and Oncology, University Children’s Hospital, University Medical Centre Ljubljana (UMC), Ljubljana, Slovenia
| | - Päivi Lähteenmäki
- Turku University and University Hospital, Turku, Finland
- Swedish Childhood Cancer Registry, Karolinska Institutet, Stockholm, Sweden
| | - Katrin Scheinemann
- Division of Pediatric Oncology – Hematology, Department of Pediatrics, Kantonsspital Aarau, Aarau, Switzerland
- Department of Health Sciences and Medicine, University of Lucerne, Lucerne, Switzerland
- Department of Paediatrics, McMaster Children’s Hospital and McMaster University, Hamilton, Canada
| | | | - Astrid Sehested
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Paediatrics and Adolescent Medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | | | - Ole Mikal Wormdal
- Section of Pediatric Oncology, UNN University Hospital of Northern Norway, Tromsø, Norway
| | - Michal Zapotocky
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, University Hospital Motol, Charles University, Prague, Czech Republic
| | - David S Ziegler
- Kids Cancer Centre, Sydney Children’s Hospital, High St, Randwick, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Arend Koch
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- First Department of Paediatrics, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Pablo Hernáiz Driever
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, HIT-LOGGIC German Registry for children and adolescents with low-grade glioma, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Olaf Witt
- 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)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - 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)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
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24
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Apfelbaum A, Bandopadhayay P. "LOGGIC" of RNA-sequencing in enhancing diagnoses of pediatric low-grade gliomas. Neuro Oncol 2023; 25:2098-2099. [PMID: 37531270 PMCID: PMC10628933 DOI: 10.1093/neuonc/noad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 08/04/2023] Open
Affiliation(s)
- April Apfelbaum
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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25
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Cockle JV, Corley EA, Zebian B, Hettige S, Vaidya SJ, Angelini P, Stone J, Leitch RJ, Albanese A, Mandeville HC, Carceller F, Marshall LV. Novel therapeutic approaches for pediatric diencephalic tumors: improving functional outcomes. Front Oncol 2023; 13:1178553. [PMID: 37886179 PMCID: PMC10598386 DOI: 10.3389/fonc.2023.1178553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/06/2023] [Indexed: 10/28/2023] Open
Abstract
Pediatric diencephalic tumors represent a histopathologically and molecularly diverse group of neoplasms arising in the central part of the brain and involving eloquent structures, including the hypothalamic-pituitary axis (HPA), optic pathway, thalamus, and pineal gland. Presenting symptoms can include significant neurological, endocrine, or visual manifestations which may be exacerbated by injudicious intervention. Upfront multidisciplinary assessment and coordinated management is crucial from the outset to ensure best short- and long-term functional outcomes. In this review we discuss the clinical and pathological features of the neoplastic entities arising in this location, and their management. We emphasize a clear move towards 'function preserving' diagnostic and therapeutic approaches with novel toxicity-sparing strategies, including targeted therapies.
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Affiliation(s)
- Julia V. Cockle
- Department of Neuro-oncology, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Elizabeth A. Corley
- Pediatric and Adolescent Oncology Drug Development Team, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Bassel Zebian
- Department of Neurosurgery, Kings College Hospital National Health Service (NHS) Trust, London, United Kingdom
| | - Samantha Hettige
- Atkinson Morley Neurosurgery Centre, St George’s University Hospital National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Sucheta J. Vaidya
- Department of Neuro-oncology, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Paola Angelini
- Department of Neuro-oncology, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Joanna Stone
- Department of Neuro-oncology, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - R Jane Leitch
- Department of Ophthalmology, Epsom and St Hellier University Hospitals Trust, Carshalton, United Kingdom
| | - Assunta Albanese
- Department of Neuro-oncology, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
- Department of Pediatric Endocrinology, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Henry C. Mandeville
- Department of Neuro-oncology, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Department of Radiotherapy, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Fernando Carceller
- Department of Neuro-oncology, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Pediatric and Adolescent Oncology Drug Development Team, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Lynley V. Marshall
- Department of Neuro-oncology, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Pediatric and Adolescent Oncology Drug Development Team, Children and Young People’s Unit, The Royal Marsden National Health Service (NHS) Foundation Trust, London, United Kingdom
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26
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Bouffet E, Hansford JR, Garrè ML, Hara J, Plant-Fox A, Aerts I, Locatelli F, van der Lugt J, Papusha L, Sahm F, Tabori U, Cohen KJ, Packer RJ, Witt O, Sandalic L, Bento Pereira da Silva A, Russo M, Hargrave DR. Dabrafenib plus Trametinib in Pediatric Glioma with BRAF V600 Mutations. N Engl J Med 2023; 389:1108-1120. [PMID: 37733309 DOI: 10.1056/nejmoa2303815] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
BACKGROUND Detection of the BRAF V600E mutation in pediatric low-grade glioma has been associated with a lower response to standard chemotherapy. In previous trials, dabrafenib (both as monotherapy and in combination with trametinib) has shown efficacy in recurrent pediatric low-grade glioma with BRAF V600 mutations, findings that warrant further evaluation of this combination as first-line therapy. METHODS In this phase 2 trial, patients with pediatric low-grade glioma with BRAF V600 mutations who were scheduled to receive first-line therapy were randomly assigned in a 2:1 ratio to receive dabrafenib plus trametinib or standard chemotherapy (carboplatin plus vincristine). The primary outcome was the independently assessed overall response (complete or partial response) according to the Response Assessment in Neuro-Oncology criteria. Also assessed were the clinical benefit (complete or partial response or stable disease for ≥24 weeks) and progression-free survival. RESULTS A total of 110 patients underwent randomization (73 to receive dabrafenib plus trametinib and 37 to receive standard chemotherapy). At a median follow-up of 18.9 months, an overall response occurred in 47% of the patients treated with dabrafenib plus trametinib and in 11% of those treated with chemotherapy (risk ratio, 4.31; 95% confidence interval [CI], 1.7 to 11.2; P<0.001). Clinical benefit was observed in 86% of the patients receiving dabrafenib plus trametinib and in 46% receiving chemotherapy (risk ratio, 1.88; 95% CI, 1.3 to 2.7). The median progression-free survival was significantly longer with dabrafenib plus trametinib than with chemotherapy (20.1 months vs. 7.4 months; hazard ratio, 0.31; 95% CI, 0.17 to 0.55; P<0.001). Grade 3 or higher adverse events occurred in 47% of the patients receiving dabrafenib plus trametinib and in 94% of those receiving chemotherapy. CONCLUSIONS Among pediatric patients with low-grade glioma with BRAF V600 mutations, dabrafenib plus trametinib resulted in significantly more responses, longer progression-free survival, and a better safety profile than standard chemotherapy as first-line therapy. (Funded by Novartis; ClinicalTrials.gov number, NCT02684058.).
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Affiliation(s)
- Eric Bouffet
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Jordan R Hansford
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Maria Luisa Garrè
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Junichi Hara
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Ashley Plant-Fox
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Isabelle Aerts
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Franco Locatelli
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Jasper van der Lugt
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Ludmila Papusha
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Felix Sahm
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Uri Tabori
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Kenneth J Cohen
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Roger J Packer
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Olaf Witt
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Larissa Sandalic
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Ana Bento Pereira da Silva
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Mark Russo
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
| | - Darren R Hargrave
- From the Hospital for Sick Children, University of Toronto, Toronto (E.B., U.T.); the Royal Children's Hospital, University of Melbourne, Murdoch Children's Research Institute, Melbourne, VIC, and the Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australian immunoGENomics Cancer Institute, and the University of Adelaide, Adelaide - all in Australia (J.R.H.); IRCCS Giannina Gaslini Institute, Genoa (M.L.G.), and IRCCS Bambino Gesù Children's Hospital, Catholic University of the Sacred Heart, Rome (F.L.) - both in Italy; Osaka City General Hospital, Osaka, Japan (J.H.); the Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago (A.P.-F.); Institut Curie, SIREDO Oncology Center, Paris Sciences et Lettres Research University, Paris (I.A.); the Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (J.L.); Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow (L.P.); the Department of Neuropathology and Clinical Cooperation Unit Neuropathology (F.S.) and the Hopp Children's Cancer Center, German Consortium for Translational Cancer Research, and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany (F.S., O.W.); the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore (K.J.C.); Children's National Hospital, Washington, D.C. (R.J.P.); Novartis Pharma, Basel, Switzerland (L.S., A.B.P.S.); Novartis Pharmaceuticals, East Hanover, NJ (M.R.); and the University College London Great Ormond Street Institute of Child Health, London (D.R.H.)
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27
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Liu Z, Hong X, Wang L, Ma Z, Guan F, Wang W, Qiu Y, Zhang X, Duan W, Wang M, Sun C, Zhao Y, Duan J, Sun Q, Liu L, Ding L, Ji Y, Yan D, Liu X, Cheng J, Zhang Z, Li ZC, Yan J. Radiomic features from multiparametric magnetic resonance imaging predict molecular subgroups of pediatric low-grade gliomas. BMC Cancer 2023; 23:848. [PMID: 37697238 PMCID: PMC10496393 DOI: 10.1186/s12885-023-11338-8] [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: 10/25/2022] [Accepted: 08/25/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND We aimed to develop machine learning models for prediction of molecular subgroups (low-risk group and intermediate/high-risk group) and molecular marker (KIAA1549-BRAF fusion) of pediatric low-grade gliomas (PLGGs) based on radiomic features extracted from multiparametric MRI. METHODS 61 patients with PLGGs were included in this retrospective study, which were divided into a training set and an internal validation set at a ratio of 2:1 based on the molecular subgroups or the molecular marker. The patients were classified into low-risk and intermediate/high-risk groups, BRAF fusion positive and negative groups, respectively. We extracted 5929 radiomic features from multiparametric MRI. Thereafter, we removed redundant features, trained random forest models on the training set for predicting the molecular subgroups or the molecular marker, and validated their performance on the internal validation set. The performance of the prediction model was verified by 3-fold cross-validation. RESULTS We constructed the classification model differentiating low-risk PLGGs from intermediate/high-risk PLGGs using 4 relevant features, with an AUC of 0.833 and an accuracy of 76.2% in the internal validation set. In the prediction model for predicting KIAA1549-BRAF fusion using 4 relevant features, an AUC of 0.818 and an accuracy of 81.0% were achieved in the internal validation set. CONCLUSIONS The current study demonstrates that MRI radiomics is able to predict molecular subgroups of PLGGs and KIAA1549-BRAF fusion with satisfying sensitivity. TRIAL REGISTRATION This study was retrospectively registered at clinicaltrials.gov (NCT04217018).
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Grants
- 2019YFC0117704 the National Key R&D Program of China
- 202102310136, 202102310138, 202102310113, 202102310083 the Science and Technology Program of Henan Province
- 202102310136, 202102310138, 202102310113, 202102310083 the Science and Technology Program of Henan Province
- 202102310136, 202102310138, 202102310113, 202102310083 the Science and Technology Program of Henan Province
- 82102149, U20A20171, 61901458, 61571432, 81702465, 8217111948, U1804172, U1904148 the National Natural Science Foundation of China
- 82102149, U20A20171, 61901458, 61571432, 81702465, 8217111948, U1804172, U1904148 the National Natural Science Foundation of China
- 82102149, U20A20171, 61901458, 61571432, 81702465, 8217111948, U1804172, U1904148 the National Natural Science Foundation of China
- 82102149, U20A20171, 61901458, 61571432, 81702465, 8217111948, U1804172, U1904148 the National Natural Science Foundation of China
- 2021B0101420006 the Key-Area Research and Development Program of Guangdong Province
- YXKC2022061 the Excellent Youth Talent Cultivation Program of Innovation in Health Science and Technology of Henan Province
- SBGJ202002062 the Key Program of Medical Science and Technique Foundation of Henan Province
- the National Key R&D Program of China
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Affiliation(s)
- Zhen Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Xuanke Hong
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Linglong Wang
- Yanjing Medical College of Capital Medical University, Beijing, China
| | - Zeyu Ma
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Fangzhan Guan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Weiwei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuning Qiu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Xueping Zhang
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Wenchao Duan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Minkai Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Chen Sun
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Yuanshen Zhao
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingxian Duan
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuchang Sun
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Liu
- China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Lei Ding
- China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yuchen Ji
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Dongming Yan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Xianzhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Jingliang Cheng
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China.
| | - Zhi-Cheng Li
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Shenzhen United Imaging Research Institute of Innovative Medical Equipment, Shenzhen, 518045, China.
| | - Jing Yan
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Jian she Dong Road 1, Zhengzhou, 450052, Henan province, China.
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28
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Schieffer KM, Moccia A, Bucknor BA, Stonerock E, Jayaraman V, Jenkins H, McKinney A, Koo SC, Mathew MT, Mardis ER, Lee K, Reshmi SC, Cottrell CE. Expanding the Clinical Utility of Targeted RNA Sequencing Panels beyond Gene Fusions to Complex, Intragenic Structural Rearrangements. Cancers (Basel) 2023; 15:4394. [PMID: 37686670 PMCID: PMC10486946 DOI: 10.3390/cancers15174394] [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: 07/31/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Gene fusions are a form of structural rearrangement well established as driver events in pediatric and adult cancers. The identification of such events holds clinical significance in the refinement, prognostication, and provision of treatment in cancer. Structural rearrangements also extend beyond fusions to include intragenic rearrangements, such as internal tandem duplications (ITDs) or exon-level deletions. These intragenic events have been increasingly implicated as cancer-promoting events. However, the detection of intragenic rearrangements may be challenging to resolve bioinformatically with short-read sequencing technologies and therefore may not be routinely assessed in panel-based testing. Within an academic clinical laboratory, over three years, a total of 608 disease-involved samples (522 hematologic malignancy, 86 solid tumors) underwent clinical testing using Anchored Multiplex PCR (AMP)-based RNA sequencing. Hematologic malignancies were evaluated using a custom Pan-Heme 154 gene panel, while solid tumors were assessed using a custom Pan-Solid 115 gene panel. Gene fusions, ITDs, and intragenic deletions were assessed for diagnostic, prognostic, or therapeutic significance. When considering gene fusions alone, we report an overall diagnostic yield of 36% (37% hematologic malignancy, 41% solid tumors). When including intragenic structural rearrangements, the overall diagnostic yield increased to 48% (48% hematologic malignancy, 45% solid tumor). We demonstrate the clinical utility of reporting structural rearrangements, including gene fusions and intragenic structural rearrangements, using an AMP-based RNA sequencing panel.
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Affiliation(s)
- Kathleen M. Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Amanda Moccia
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Brianna A. Bucknor
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Heather Jenkins
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Selene C. Koo
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Mariam T. Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Shalini C. Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Catherine E. Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
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29
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Zhang L, Bordey A. Advances in glioma models using in vivo electroporation to highjack neurodevelopmental processes. Biochim Biophys Acta Rev Cancer 2023; 1878:188951. [PMID: 37433417 DOI: 10.1016/j.bbcan.2023.188951] [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: 01/29/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023]
Abstract
Glioma is the most prevalent type of neurological malignancies. Despite decades of efforts in neurosurgery, chemotherapy and radiation therapy, glioma remains one of the most treatment-resistant brain tumors with unfavorable outcomes. Recent progresses in genomic and epigenetic profiling have revealed new concepts of genetic events involved in the etiology of gliomas in humans, meanwhile, revolutionary technologies in gene editing and delivery allows to code these genetic "events" in animals to genetically engineer glioma models. This approach models the initiation and progression of gliomas in a natural microenvironment with an intact immune system and facilitates probing therapeutic strategies. In this review, we focus on recent advances in in vivo electroporation-based glioma modeling and outline the established genetically engineered glioma models (GEGMs).
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Affiliation(s)
- Longbo Zhang
- Departments of Neurosurgery, Changde hospital, Xiangya School of Medicine, Central South University, 818 Renmin Street, Wuling District, Changde, Hunan 415003, China; Departments of Neurosurgery, and National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China; Departments of Neurosurgery, and Cellular & Molecular Physiology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520-8082, USA.
| | - Angelique Bordey
- Departments of Neurosurgery, and Cellular & Molecular Physiology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520-8082, USA
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30
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Benhamida JK, Harmsen HJ, Ma D, William CM, Li BK, Villafania L, Sukhadia P, Mullaney KA, Dewan MC, Vakiani E, Karajannis MA, Snuderl M, Zagzag D, Ladanyi M, Rosenblum MK, Bale TA. Recurrent TRAK1::RAF1 Fusions in pediatric low-grade gliomas. Brain Pathol 2023; 33:e13185. [PMID: 37399073 PMCID: PMC10467040 DOI: 10.1111/bpa.13185] [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: 03/30/2023] [Accepted: 06/16/2023] [Indexed: 07/05/2023] Open
Abstract
Fusions involving CRAF (RAF1) are infrequent oncogenic drivers in pediatric low-grade gliomas, rarely identified in tumors bearing features of pilocytic astrocytoma, and involving a limited number of known fusion partners. We describe recurrent TRAK1::RAF1 fusions, previously unreported in brain tumors, in three pediatric patients with low-grade glial-glioneuronal tumors. We present the associated clinical, histopathologic and molecular features. Patients were all female, aged 8 years, 15 months, and 10 months at diagnosis. All tumors were located in the cerebral hemispheres and predominantly cortical, with leptomeningeal involvement in 2/3 patients. Similar to previously described activating RAF1 fusions, the breakpoints in RAF1 all occurred 5' of the kinase domain, while the breakpoints in the 3' partner preserved the N-terminal kinesin-interacting domain and coiled-coil motifs of TRAK1. Two of the three cases demonstrated methylation profiles (v12.5) compatible with desmoplastic infantile ganglioglioma (DIG)/desmoplastic infantile astrocytoma (DIA) and have remained clinically stable and without disease progression/recurrence after resection. The remaining tumor was non-classifiable; with focal recurrence 14 months after initial resection; the patient remains symptom free and without further recurrence/progression (5 months post re-resection and 19 months from initial diagnosis). Our report expands the landscape of oncogenic RAF1 fusions in pediatric gliomas, which will help to further refine tumor classification and guide management of patients with these alterations.
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Affiliation(s)
- Jamal K. Benhamida
- Department of Pathology and Laboratory MedicineMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Hannah J. Harmsen
- Department of Pathology, Microbiology and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Deqin Ma
- Department of PathologyUniversity of Iowa Hospitals and ClinicsIowa CityIowaUSA
| | | | - Bryan K. Li
- Department of PediatricsMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Present address:
Division of Pediatric Hematology/OncologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Liliana Villafania
- Department of Pathology and Laboratory MedicineMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Purvil Sukhadia
- Department of Pathology and Laboratory MedicineMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Kerry A. Mullaney
- Department of Pathology and Laboratory MedicineMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Michael C. Dewan
- Department of Neurological SurgeryVanderbilt University Medical Center
| | - Efsevia Vakiani
- Department of Pathology and Laboratory MedicineMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | | | - Matija Snuderl
- Department of PathologyNYU Langone HealthNew YorkNew YorkUSA
| | - David Zagzag
- Department of PathologyNYU Langone HealthNew YorkNew YorkUSA
- Department of NeurosurgeryNYU Langone HealthNew YorkNew YorkUSA
| | - Marc Ladanyi
- Department of Pathology and Laboratory MedicineMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Human Oncology and Pathogenesis ProgramMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Marc K. Rosenblum
- Department of Pathology and Laboratory MedicineMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Tejus A. Bale
- Department of Pathology and Laboratory MedicineMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
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31
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Kinnunen M, Liu X, Niemelä E, Öhman T, Gawriyski L, Salokas K, Keskitalo S, Varjosalo M. The Impact of ETV6-NTRK3 Oncogenic Gene Fusions on Molecular and Signaling Pathway Alterations. Cancers (Basel) 2023; 15:4246. [PMID: 37686522 PMCID: PMC10486691 DOI: 10.3390/cancers15174246] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Chromosomal translocations creating fusion genes are common cancer drivers. The oncogenic ETV6-NTRK3 (EN) gene fusion joins the sterile alpha domain of the ETV6 transcription factor with the tyrosine kinase domain of the neurotrophin-3 receptor NTRK3. Four EN variants with alternating break points have since been detected in a wide range of human cancers. To provide molecular level insight into EN oncogenesis, we employed a proximity labeling mass spectrometry approach to define the molecular context of the fusions. We identify in total 237 high-confidence interactors, which link EN fusions to several key signaling pathways, including ERBB, insulin and JAK/STAT. We then assessed the effects of EN variants on these pathways, and showed that the pan NTRK inhibitor Selitrectinib (LOXO-195) inhibits the oncogenic activity of EN2, the most common variant. This systems-level analysis defines the molecular framework in which EN oncofusions operate to promote cancer and provides some mechanisms for therapeutics.
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Affiliation(s)
- Matias Kinnunen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Elina Niemelä
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Tiina Öhman
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Lisa Gawriyski
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
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32
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Liu H, Tsai H, Yang M, Li G, Bian Q, Ding G, Wu D, Dai J. Three-dimensional genome structure and function. MedComm (Beijing) 2023; 4:e326. [PMID: 37426677 PMCID: PMC10329473 DOI: 10.1002/mco2.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.
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Affiliation(s)
- Hao Liu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Hsiangyu Tsai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Maoquan Yang
- School of Clinical MedicineWeifang Medical UniversityWeifangChina
| | - Guozhi Li
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Qian Bian
- Shanghai Institute of Precision MedicineShanghaiChina
| | - Gang Ding
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Dandan Wu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Jiewen Dai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
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Rajagopal R, Khan M, Lethbridge R, Lee G, Lee S, Dyke J, Fabian V, McGrath A, Taylor M, Jacoby P, Endersby R, Nagabushan S, Gottardo NG. Long-term outcomes of symptomatic optic pathway glioma: 32-year experience at a single Western Australian tertiary pediatric oncology center. Front Oncol 2023; 13:1157909. [PMID: 37519788 PMCID: PMC10379632 DOI: 10.3389/fonc.2023.1157909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Optic pathway gliomas (OPGs) are associated with significant risk of visual and endocrine morbidity, but data on long-term outcomes in symptomatic patients is sparse. This study reviews the clinical course, disease progression, survival outcomes and long-term sequelae in pediatric patients with symptomatic OPGs in our institution over three decades. Methods Retrospective review of patients with symptomatic OPG treated in a single tertiary pediatric oncology center from 1984 to 2016. Results A total of 37 patients were diagnosed with symptomatic OPG. Decreased visual acuity was the commonest presenting symptom (75.7%). Surgical intervention was performed in 62.2%; 56.5% underwent biopsy, 26.1% surgical debulking and 17.4% had orbital decompression with cystic fenestration and cosmetic optic nerve excision at different treatment intervals. CSF diversion was performed in 47.8% patients. Histopathologic examination confirmed 86% to be pilocytic astrocytoma and 1 ganglioglioma. 46% received chemotherapy and 48% had radiotherapy, at different intervals. Median follow-up was 13.74 years. In NF1 patients, overall survival (OS) was 100% at 5 years and 55.6 ± 24.8% at 25 years while progression-free-survival (PFS) was 50 ± 15.8% at 5 and 20 years. In non-NF1 patients, OS was 96.2 ± 3.8% at 5 years and 87.4 ± 9% at 25-years. 5-year PFS was 53.8 ± 9.8% and 25-year PFS was 49.0 ± 10%. Cumulative PFS was 53 ± 8.3% at 5 years and 49.7 ± 8.4% at 20 years while cumulative OS was 97.2 ± 2.7% at 5 years and 77.5 ± 10.8% at 25 years. 59.5% patients developed post-operative endocrinopathy. Long-term vision was normal in 8.1%, improved in 13.5%, stabilized in 40.5% but worsened in 37.8% patients. Three patients treated with radiotherapy developed second brain tumors. Conclusion 25-year OS in this cohort was 77.5% but survivorship carried significant long-term morbidities including radiation-induced second malignant brain tumors.
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Affiliation(s)
- Revathi Rajagopal
- Department of Global Pediatric Medicine, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Mumtaz Khan
- Department of Anesthesia, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Robert Lethbridge
- School of Pediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - Gabriel Lee
- Department of Neurosurgery, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Sharon Lee
- Department of Neurosurgery, Perth Children’s Hospital, Perth, WA, Australia
| | - Jason Dyke
- Department of Neuropathology, Royal Perth Hospital, Perth, WA, Australia
| | - Vicki Fabian
- Department of Neuropathology, Royal Perth Hospital, Perth, WA, Australia
| | - Alycea McGrath
- Department of Radiation Oncology, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Mandy Taylor
- Department of Radiation Oncology, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Peter Jacoby
- Department of Biostatistics, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Raelene Endersby
- Brain Tumor Research Program, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Sumanth Nagabushan
- Kids Cancer Centre, Sydney Children’s Hospital, Sydney, NSW, Australia
- School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW, Australia
| | - Nicholas G. Gottardo
- Brain Tumor Research Program, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
- Department of Pediatric and Adolescent Oncology and Hematology, Perth Children’s Hospital, Perth, WA, Australia
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Sansone G, Pini L, Salvalaggio A, Gaiola M, Volpin F, Baro V, Padovan M, Anglani M, Facchini S, Chioffi F, Zagonel V, D’Avella D, Denaro L, Lombardi G, Corbetta M. Patterns of gray and white matter functional networks involvement in glioblastoma patients: indirect mapping from clinical MRI scans. Front Neurol 2023; 14:1175576. [PMID: 37409023 PMCID: PMC10318144 DOI: 10.3389/fneur.2023.1175576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023] Open
Abstract
Background Resting-state functional-MRI studies identified several cortical gray matter functional networks (GMNs) and white matter functional networks (WMNs) with precise anatomical localization. Here, we aimed at describing the relationships between brain's functional topological organization and glioblastoma (GBM) location. Furthermore, we assessed whether GBM distribution across these networks was associated with overall survival (OS). Materials and methods We included patients with histopathological diagnosis of IDH-wildtype GBM, presurgical MRI and survival data. For each patient, we recorded clinical-prognostic variables. GBM core and edema were segmented and normalized to a standard space. Pre-existing functional connectivity-based atlases were used to define network parcellations: 17 GMNs and 12 WMNs were considered in particular. We computed the percentage of lesion overlap with GMNs and WMNs, both for core and edema. Differences between overlap percentages were assessed through descriptive statistics, ANOVA, post-hoc tests, Pearson's correlation tests and canonical correlations. Multiple linear and non-linear regression tests were employed to explore relationships with OS. Results 99 patients were included (70 males, mean age 62 years). The most involved GMNs included ventral somatomotor, salient ventral attention and default-mode networks; the most involved WMNs were ventral frontoparietal tracts, deep frontal white matter, and superior longitudinal fasciculus system. Superior longitudinal fasciculus system and dorsal frontoparietal tracts were significantly more included in the edema (p < 0.001). 5 main patterns of GBM core distribution across functional networks were found, while edema localization was less classifiable. ANOVA showed significant differences between mean overlap percentages, separately for GMNs and WMNs (p-values<0.0001). Core-N12 overlap predicts higher OS, although its inclusion does not increase the explained OS variance. Discussion and conclusion Both GBM core and edema preferentially overlap with specific GMNs and WMNs, especially associative networks, and GBM core follows five main distribution patterns. Some inter-related GMNs and WMNs were co-lesioned by GBM, suggesting that GBM distribution is not independent of the brain's structural and functional organization. Although the involvement of ventral frontoparietal tracts (N12) seems to have some role in predicting survival, network-topology information is overall scarcely informative about OS. fMRI-based approaches may more effectively demonstrate the effects of GBM on brain networks and survival.
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Affiliation(s)
- Giulio Sansone
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Lorenzo Pini
- Padova Neuroscience Center (PNC), University of Padova, Padova, Italy
| | - Alessandro Salvalaggio
- Department of Neuroscience, University of Padova, Padova, Italy
- Padova Neuroscience Center (PNC), University of Padova, Padova, Italy
| | - Matteo Gaiola
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Francesco Volpin
- Division of Neurosurgery, Azienda Ospedaliera Università di Padova, Padova, Italy
| | - Valentina Baro
- Academic Neurosurgery, Department of Neurosciences, University of Padova, Padova, Italy
| | - Marta Padovan
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | | | - Silvia Facchini
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Franco Chioffi
- Division of Neurosurgery, Azienda Ospedaliera Università di Padova, Padova, Italy
| | - Vittorina Zagonel
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Domenico D’Avella
- Academic Neurosurgery, Department of Neurosciences, University of Padova, Padova, Italy
| | - Luca Denaro
- Academic Neurosurgery, Department of Neurosciences, University of Padova, Padova, Italy
| | - Giuseppe Lombardi
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Maurizio Corbetta
- Department of Neuroscience, University of Padova, Padova, Italy
- Padova Neuroscience Center (PNC), University of Padova, Padova, Italy
- Venetian Institute of Molecular Medicine (VIMM), Fondazione Biomedica, Padova, Italy
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Warren KE, Vezina G, Krailo M, Springer L, Buxton A, Peer CJ, Figg WD, William-Hughes C, Kessel S, Fouladi M, Gajjar A, Bowers D. Phase II Randomized Trial of Lenalidomide in Children With Pilocytic Astrocytomas and Optic Pathway Gliomas: A Report From the Children's Oncology Group. J Clin Oncol 2023; 41:3374-3383. [PMID: 37126770 PMCID: PMC10414716 DOI: 10.1200/jco.22.01777] [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: 08/03/2022] [Revised: 03/06/2023] [Accepted: 03/15/2023] [Indexed: 05/03/2023] Open
Abstract
PURPOSE Children with low-grade glioma often require long-term therapy and suffer from treatment morbidity. Although targeted agents are promising, tumor targets often encompass normal developmental pathways and long-term effects of inhibition are unknown. Lenalidomide is an immunomodulatory agent with wide-ranging properties. Phase I studies indicated greater tolerability of lenalidomide in children compared with adults and a potential dose-response effect. PATIENTS AND METHODS We performed a phase II trial of lenalidomide in children with pilocytic astrocytomas and optic pathway gliomas who failed initial therapy. Primary objectives included determination of objective response rate of children randomly assigned to regimen A, low-dose (20 mg/m2/dose), or regimen B, high-dose (115 mg/m2/dose) lenalidomide, and assessment for early progression. Secondary objectives included estimation of event-free survival, overall survival, incidence of toxic events, and assessment of plasma lenalidomide concentrations. Lenalidomide was administered once daily × 21 days of each 28-day cycle for each regimen. RESULTS Seventy-four eligible patients were enrolled (n = 37, each arm). The predefined activity level of interest was achieved for both arms. Four objective responses were observed in each arm, and the number of early progressors was low. Eighteen patients completed 26 cycles of therapy (regimen A, n = 12; regimen B, n = 6). The median number of cycles was 14 (range, 2-26) for regimen A and 11 for regimen B (range, 1-26). Of 74 eligible patients who received study drug, 30 required dose reduction for toxicity (regimen A, n = 6; regimen B, n = 24) and 16 discontinued because of toxicity (regimen A, n = 2; regimen B, n = 14). CONCLUSION Lenalidomide demonstrates a sufficient level of activity in children with low-grade glioma to warrant further exploration. Low-dose (20 mg/m2/dose administered once daily × 21 days of each 28-day cycle) lenalidomide appears to have better tolerability with comparable activity.
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Affiliation(s)
| | | | - Mark Krailo
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | | | - Allen Buxton
- Statistics and Data Center, Children's Oncology Group, Monrovia, CA
| | - Cody J. Peer
- Clinical Pharmacology Program, National Cancer Institute, Bethesda, MD
| | - William D. Figg
- Clinical Pharmacology Program, National Cancer Institute, Bethesda, MD
| | | | - Sandy Kessel
- Imaging and Radiation Oncology Core Rhode Island (IROC RI), Lincoln, RI
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Cipri S, Del Baldo G, Fabozzi F, Boccuto L, Carai A, Mastronuzzi A. Unlocking the power of precision medicine for pediatric low-grade gliomas: molecular characterization for targeted therapies with enhanced safety and efficacy. Front Oncol 2023; 13:1204829. [PMID: 37397394 PMCID: PMC10311254 DOI: 10.3389/fonc.2023.1204829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
In the past decade significant advancements have been made in the discovery of targetable lesions in pediatric low-grade gliomas (pLGGs). These tumors account for 30-50% of all pediatric brain tumors with generally a favorable prognosis. The latest 2021 WHO classification of pLGGs places a strong emphasis on molecular characterization for significant implications on prognosis, diagnosis, management, and the potential target treatment. With the technological advances and new applications in molecular diagnostics, the molecular characterization of pLGGs has revealed that tumors that appear similar under a microscope can have different genetic and molecular characteristics. Therefore, the new classification system divides pLGGs into several distinct subtypes based on these characteristics, enabling a more accurate strategy for diagnosis and personalized therapy based on the specific genetic and molecular abnormalities present in each tumor. This approach holds great promise for improving outcomes for patients with pLGGs, highlighting the importance of the recent breakthroughs in the discovery of targetable lesions.
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Affiliation(s)
- Selene Cipri
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Giada Del Baldo
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesco Fabozzi
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Luigi Boccuto
- Healthcare Genetics Program, School of Nursing, College of Behavioral, Social and Health Sciences, Clemson University, Clemson, SC, United States
| | - Andrea Carai
- Department of Neurosciences, Neurosurgery Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Hematology/Oncology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Nguyen MA, Colebatch AJ, Van Beek D, Tierney G, Gupta R, Cooper WA. NTRK fusions in solid tumours: what every pathologist needs to know. Pathology 2023:S0031-3025(23)00128-9. [PMID: 37330338 DOI: 10.1016/j.pathol.2023.05.002] [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: 01/17/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 06/19/2023]
Abstract
Fusions involving the Neurotrophic tropomyosin receptor kinase (NTRK) gene family (NTRK1, NTRK2 and NTRK3) are targetable oncogenic alterations that are found in a diverse range of tumours. There is an increasing demand to identify tumours which harbour these fusions to enable treatment with selective tyrosine kinase inhibitors such as larotrectinib and entrectinib. NTRK fusions occur in a wide range of tumours including rare tumours such as infantile fibrosarcoma and secretory carcinomas of the salivary gland and breast, as well as at low frequencies in more common tumours including melanoma, colorectal, thyroid and lung carcinomas. Identifying NTRK fusions is a challenging task given the different genetic mechanisms underlying NTRK fusions, their varying frequency across different tumour types, complicated by other factors such as tissue availability, optimal detection methods, accessibility and costs of testing methods. Pathologists play a key role in navigating through these complexities by determining optimal approaches to NTRK testing which has important therapeutic and prognostic implications. This review provides an overview of tumours harbouring NTRK fusions, the importance of identifying these fusions, available testing methods including advantages and limitations, and generalised and tumour-specific approaches to testing.
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Affiliation(s)
- Minh Anh Nguyen
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Andrew J Colebatch
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Diana Van Beek
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Geraldine Tierney
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Ruta Gupta
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Wendy A Cooper
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; School of Medicine, Western Sydney University, Sydney, NSW, Australia.
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Díaz de Ståhl T, Shamikh A, Mayrhofer M, Juhos S, Basmaci E, Prochazka G, Garcia M, Somarajan PR, Zielinska-Chomej K, Illies C, Øra I, Siesjö P, Sandström PE, Stenman J, Sabel M, Gustavsson B, Kogner P, Pfeifer S, Ljungman G, Sandgren J, Nistér M. The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden. J Transl Med 2023; 21:342. [PMID: 37221626 DOI: 10.1186/s12967-023-04178-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023] Open
Abstract
The Swedish Childhood Tumor Biobank (BTB) is a nonprofit national infrastructure for collecting tissue samples and genomic data from pediatric patients diagnosed with central nervous system (CNS) and other solid tumors. The BTB is built on a multidisciplinary network established to provide the scientific community with standardized biospecimens and genomic data, thereby improving knowledge of the biology, treatment and outcome of childhood tumors. As of 2022, over 1100 fresh-frozen tumor samples are available for researchers. We present the workflow of the BTB from sample collection and processing to the generation of genomic data and services offered. To determine the research and clinical utility of the data, we performed bioinformatics analyses on next-generation sequencing (NGS) data obtained from a subset of 82 brain tumors and patient blood-derived DNA combined with methylation profiling to enhance the diagnostic accuracy and identified germline and somatic alterations with potential biological or clinical significance. The BTB procedures for collection, processing, sequencing, and bioinformatics deliver high-quality data. We observed that the findings could impact patient management by confirming or clarifying the diagnosis in 79 of the 82 tumors and detecting known or likely driver mutations in 68 of 79 patients. In addition to revealing known mutations in a broad spectrum of genes implicated in pediatric cancer, we discovered numerous alterations that may represent novel driver events and specific tumor entities. In summary, these examples reveal the power of NGS to identify a wide number of actionable gene alterations. Making the power of NGS available in healthcare is a challenging task requiring the integration of the work of clinical specialists and cancer biologists; this approach requires a dedicated infrastructure, as exemplified here by the BTB.
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Affiliation(s)
- Teresita Díaz de Ståhl
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden.
| | - Alia Shamikh
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Markus Mayrhofer
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Szilvester Juhos
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Elisa Basmaci
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gabriela Prochazka
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Maxime Garcia
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Christopher Illies
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid Øra
- Department of Paediatric Haematology Oncology and Immunology, Skåne University Hospital Lund, Lund, Sweden
| | - Peter Siesjö
- Department of Clinical Sciences Lund, Department of Neurosurgery, Lund University, Skåne University Hospital, Lund, Sweden
| | - Per-Erik Sandström
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Jakob Stenman
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Sabel
- Childhood Cancer Centre, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bengt Gustavsson
- Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Susan Pfeifer
- Pediatric Hematology/Oncology, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Gustaf Ljungman
- Pediatric Hematology/Oncology, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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Foss A, Pathania M. Pediatric Glioma Models Provide Insights into Tumor Development and Future Therapeutic Strategies. Dev Neurosci 2023; 46:22-43. [PMID: 37231843 DOI: 10.1159/000531040] [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: 02/20/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023] Open
Abstract
In depth study of pediatric gliomas has been hampered due to difficulties in accessing patient tissue and a lack of clinically representative tumor models. Over the last decade, however, profiling of carefully curated cohorts of pediatric tumors has identified genetic drivers that molecularly segregate pediatric gliomas from adult gliomas. This information has inspired the development of a new set of powerful in vitro and in vivo tumor models that can aid in identifying pediatric-specific oncogenic mechanisms and tumor microenvironment interactions. Single-cell analyses of both human tumors and these newly developed models have revealed that pediatric gliomas arise from spatiotemporally discrete neural progenitor populations in which developmental programs have become dysregulated. Pediatric high-grade gliomas also harbor distinct sets of co-segregating genetic and epigenetic alterations, often accompanied by unique features within the tumor microenvironment. The development of these novel tools and data resources has led to insights into the biology and heterogeneity of these tumors, including identification of distinctive sets of driver mutations, developmentally restricted cells of origin, recognizable patterns of tumor progression, characteristic immune environments, and tumor hijacking of normal microenvironmental and neural programs. As concerted efforts have broadened our understanding of these tumors, new therapeutic vulnerabilities have been identified, and for the first time, promising new strategies are being evaluated in the preclinical and clinical settings. Even so, dedicated and sustained collaborative efforts are necessary to refine our knowledge and bring these new strategies into general clinical use. In this review, we will discuss the range of currently available glioma models, the way in which they have each contributed to recent developments in the field, their benefits and drawbacks for addressing specific research questions, and their future utility in advancing biological understanding and treatment of pediatric glioma.
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Affiliation(s)
- Amelia Foss
- Department of Oncology and the Milner Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- CRUK Children's Brain Tumour Centre of Excellence, University of Cambridge, Cambridge, UK
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Manav Pathania
- Department of Oncology and the Milner Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- CRUK Children's Brain Tumour Centre of Excellence, University of Cambridge, Cambridge, UK
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Brown LM, Ekert PG, Fleuren EDG. Biological and clinical implications of FGFR aberrations in paediatric and young adult cancers. Oncogene 2023:10.1038/s41388-023-02705-7. [PMID: 37130917 DOI: 10.1038/s41388-023-02705-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/04/2023]
Abstract
Rare but recurrent mutations in the fibroblast growth factor receptor (FGFR) pathways, most commonly in one of the four FGFR receptor tyrosine kinase genes, can potentially be targeted with broad-spectrum multi-kinase or FGFR selective inhibitors. The complete spectrum of these mutations in paediatric cancers is emerging as precision medicine programs perform comprehensive sequencing of individual tumours. Identification of patients most likely to benefit from FGFR inhibition currently rests on identifying activating FGFR mutations, gene fusions, or gene amplification events. However, the expanding use of transcriptome sequencing (RNAseq) has identified that many tumours overexpress FGFRs, in the absence of any genomic aberration. The challenge now presented is to determine when this indicates true FGFR oncogenic activity. Under-appreciated mechanisms of FGFR pathway activation, including alternate FGFR transcript expression and concomitant FGFR and FGF ligand expression, may mark those tumours where FGFR overexpression is indicative of a dependence on FGFR signalling. In this review, we provide a comprehensive and mechanistic overview of FGFR pathway aberrations and their functional consequences in paediatric cancer. We explore how FGFR over expression might be associated with true receptor activation. Further, we discuss the therapeutic implications of these aberrations in the paediatric setting and outline current and emerging therapeutic strategies to treat paediatric patients with FGFR-driven cancers.
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Affiliation(s)
- Lauren M Brown
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Paul G Ekert
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia.
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia.
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC, Australia.
| | - Emmy D G Fleuren
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
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Pang Y, Chen X, Ji T, Cheng M, Wang R, Zhang C, Liu M, Zhang J, Zhong C. The Chromatin Remodeler ATRX: Role and Mechanism in Biology and Cancer. Cancers (Basel) 2023; 15:cancers15082228. [PMID: 37190157 DOI: 10.3390/cancers15082228] [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: 03/06/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
The alpha-thalassemia mental retardation X-linked (ATRX) syndrome protein is a chromatin remodeling protein that primarily promotes the deposit of H3.3 histone variants in the telomere area. ATRX mutations not only cause ATRX syndrome but also influence development and promote cancer. The primary molecular characteristics of ATRX, including its molecular structures and normal and malignant biological roles, are reviewed in this article. We discuss the role of ATRX in its interactions with the histone variant H3.3, chromatin remodeling, DNA damage response, replication stress, and cancers, particularly gliomas, neuroblastomas, and pancreatic neuroendocrine tumors. ATRX is implicated in several important cellular processes and serves a crucial function in regulating gene expression and genomic integrity throughout embryogenesis. However, the nature of its involvement in the growth and development of cancer remains unknown. As mechanistic and molecular investigations on ATRX disclose its essential functions in cancer, customized therapies targeting ATRX will become accessible.
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Affiliation(s)
- Ying Pang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Xu Chen
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Tongjie Ji
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Meng Cheng
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Rui Wang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Chunyu Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Min Liu
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
- Institute for Advanced Study, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
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42
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Liu Y, Klein J, Bajpai R, Dong L, Tran Q, Kolekar P, Smith JL, Ries RE, Huang BJ, Wang YC, Alonzo TA, Tian L, Mulder HL, Shaw TI, Ma J, Walsh MP, Song G, Westover T, Autry RJ, Gout AM, Wheeler DA, Wan S, Wu G, Yang JJ, Evans WE, Loh M, Easton J, Zhang J, Klco JM, Meshinchi S, Brown PA, Pruett-Miller SM, Ma X. Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication. Nat Commun 2023; 14:1739. [PMID: 37019972 PMCID: PMC10076316 DOI: 10.1038/s41467-023-37438-4] [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: 04/14/2022] [Accepted: 03/16/2023] [Indexed: 04/07/2023] Open
Abstract
Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define cancer subtype, predict outcome, persist through treatment, and can be ideal therapeutic targets. However, mechanistic understanding of the etiology of oncogenic fusions remains elusive. Here we report a comprehensive detection of 272 oncogenic fusion gene pairs by using tumor transcriptome sequencing data from 5190 childhood cancer patients. We identify diverse factors, including translation frame, protein domain, splicing, and gene length, that shape the formation of oncogenic fusions. Our mathematical modeling reveals a strong link between differential selection pressure and clinical outcome in CBFB-MYH11. We discover 4 oncogenic fusions, including RUNX1-RUNX1T1, TCF3-PBX1, CBFA2T3-GLIS2, and KMT2A-AFDN, with promoter-hijacking-like features that may offer alternative strategies for therapeutic targeting. We uncover extensive alternative splicing in oncogenic fusions including KMT2A-MLLT3, KMT2A-MLLT10, C11orf95-RELA, NUP98-NSD1, KMT2A-AFDN and ETV6-RUNX1. We discover neo splice sites in 18 oncogenic fusion gene pairs and demonstrate that such splice sites confer therapeutic vulnerability for etiology-based genome editing. Our study reveals general principles on the etiology of oncogenic fusions in childhood cancer and suggests profound clinical implications including etiology-based risk stratification and genome-editing-based therapeutics.
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Affiliation(s)
- Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathon Klein
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richa Bajpai
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Dong
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Quang Tran
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jenny L Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Benjamin J Huang
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Todd A Alonzo
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather L Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Timothy I Shaw
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Autry
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David A Wheeler
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon Loh
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute and the Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | | | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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43
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Sait SF, Giantini-Larsen AM, Tringale KR, Souweidane MM, Karajannis MA. Treatment of Pediatric Low-Grade Gliomas. Curr Neurol Neurosci Rep 2023; 23:185-199. [PMID: 36881254 PMCID: PMC10121885 DOI: 10.1007/s11910-023-01257-3] [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] [Accepted: 02/13/2023] [Indexed: 03/08/2023]
Abstract
PURPOSE OF REVIEW Pediatric low-grade gliomas and glioneuronal tumors (pLGG) account for approximately 30% of pediatric CNS neoplasms, encompassing a heterogeneous group of tumors of primarily glial or mixed neuronal-glial histology. This article reviews the treatment of pLGG with emphasis on an individualized approach incorporating multidisciplinary input from surgery, radiation oncology, neuroradiology, neuropathology, and pediatric oncology to carefully weigh the risks and benefits of specific interventions against tumor-related morbidity. Complete surgical resection can be curative for cerebellar and hemispheric lesions, while use of radiotherapy is restricted to older patients or those refractory to medical therapy. Chemotherapy remains the preferred first-line therapy for adjuvant treatment of the majority of recurrent or progressive pLGG. RECENT FINDINGS Technologic advances offer the potential to limit volume of normal brain exposed to low doses of radiation when treating pLGG with either conformal photon or proton RT. Recent neurosurgical techniques such as laser interstitial thermal therapy offer a "dual" diagnostic and therapeutic treatment modality for pLGG in specific surgically inaccessible anatomical locations. The emergence of novel molecular diagnostic tools has enabled scientific discoveries elucidating driver alterations in mitogen-activated protein kinase (MAPK) pathway components and enhanced our understanding of the natural history (oncogenic senescence). Molecular characterization strongly supplements the clinical risk stratification (age, extent of resection, histological grade) to improve diagnostic precision and accuracy, prognostication, and can lead to the identification of patients who stand to benefit from precision medicine treatment approaches. The success of molecular targeted therapy (BRAF inhibitors and/or MEK inhibitors) in the recurrent setting has led to a gradual and yet significant paradigm shift in the treatment of pLGG. Ongoing randomized trials comparing targeted therapy to standard of care chemotherapy are anticipated to further inform the approach to upfront management of pLGG patients.
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Affiliation(s)
- Sameer Farouk Sait
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| | - Alexandra M Giantini-Larsen
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
| | - Kathryn R Tringale
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Mark M Souweidane
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
| | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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44
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Phuong C, Qiu B, Mueller S, Braunstein SE. Precision based approach to tailoring radiotherapy in the multidisciplinary management of pediatric central nervous system tumors. JOURNAL OF THE NATIONAL CANCER CENTER 2023. [DOI: 10.1016/j.jncc.2023.03.001] [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
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45
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Leblond P, Tresch-Bruneel E, Probst A, Néant N, Solas C, Sterin A, Boulanger T, Aerts I, Faure-Conter C, Bertozzi AI, Chastagner P, Entz-Werlé N, De Carli E, Deley MCL, Bouche G, André N. Phase I Study of a Combination of Fluvastatin and Celecoxib in Children with Relapsing/Refractory Low-Grade or High-Grade Glioma (FLUVABREX). Cancers (Basel) 2023; 15:cancers15072020. [PMID: 37046681 PMCID: PMC10093481 DOI: 10.3390/cancers15072020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Preclinical data support the activity of celecoxib and fluvastatin in high-grade (HGG) and low-grade gliomas (LGG). A phase I trial (NCT02115074) was designed to evaluate the safety of this combination in children with refractory/relapsed HGG and LGG using four dose levels of fluvastatin with a fixed daily dose of celecoxib. A Continual Reassessment Method was used for fluvastatin dose escalation. Dose-limiting toxicities (DLT) were determined on the first treatment cycle. Twenty patients were included. Ten LGG and ten HGG patients received a median of 3.5 treatment cycles. Two DLTs were reported: one grade 3 maculopapular rash (4 mg/kg dose level) and one grade 4 increase of Creatine Phospho-Kinase (6 mg/kg dose level). We identified the dose of 6 mg/kg/day as the recommended phase II dose (RP2D) of fluvastatin with celecoxib. Four patients with LGG continued treatment beyond 12 cycles because of stable disease, including one patient who received 23 treatment cycles. In children with refractory/relapsed glioma, the RP2D of fluvastatin with celecoxib is 6 mg/kg/day. The long-term stable diseases observed in LGG suggest a possible role of the combination in a maintenance setting, given its good tolerance and low cost for children living in low- and middle-income countries.
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46
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Tamura R, Iwanami A, Ohara K, Nishimoto M, Pareira ES, Miwa T, Tsuzaki N, Kuranari Y, Morimoto Y, Toda M, Okano H, Nakamura M, Yoshida K, Sasaki H. Clinical, histopathological and molecular risk factors for recurrence of pilocytic astrocytomas: brainstem/spinal location, nestin expression and gain of 7q and 19 are associated with early tumor recurrence. Brain Tumor Pathol 2023; 40:109-123. [PMID: 36892668 DOI: 10.1007/s10014-023-00453-w] [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: 11/16/2022] [Accepted: 02/26/2023] [Indexed: 03/10/2023]
Abstract
Pilocytic astrocytomas (PAs) are benign tumors. However, clinically aggressive PAs despite benign histology have been reported, and histological and molecular risk factors for prognosis have not been elucidated. 38 PAs were studied for clinical, histological, and molecular factors, including tumor location, extent of resection, post-operative treatment, glioma-associated molecules (IDH1/2, ATRX, BRAF, FGFR1, PIK3CA, H3F3A, p53, VEGF, Nestin, PD-1/PD-L1), CDKN2A/B deletion, and chromosomal number aberrations, to see if there is any correlation with patient's progression-free survival (PFS). Brainstem/spinal location, extent of resection and post-operative treatment, and VEGF-A, Nestin and PD-L1 expression, copy number gain of chromosome 7q or 19, TP53 mutation were significantly associated with shorter PFS. None of the histological parameters was associated with PFS. Multivariate analyses demonstrated that high Nestin expression, gain of 7q or 19, and extent of removal were independently predictive for early tumor recurrence. The brainstem/spinal PAs appeared distinct from those in the other sites in terms of molecular characteristics. Clinically aggressive PAs despite benign histology exhibited high Nestin expression. Brainstem/spinal location, extent of resection and some molecular factors including Nestin expression and gains of 7q and 19, rather than histological parameters, may be associated with early tumor recurrence in PAs.
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Affiliation(s)
- Ryota Tamura
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Akio Iwanami
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan.,Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan.,Department of Orthopaedic Surgery, Spine Center, Koga General Hospital, 1555 Koga, Ibaraki, 306-0041, Japan
| | - Kentaro Ohara
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Masaaki Nishimoto
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Eriel Sandika Pareira
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Tomoru Miwa
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Naoko Tsuzaki
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Yuki Kuranari
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Yukina Morimoto
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Masahiro Toda
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Hideyuki Okano
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Masaya Nakamura
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Kazunari Yoshida
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Hikaru Sasaki
- Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan. .,Division of Neurosurgery, Tokyo Dental College Ichikawa General Hospital, 5-11-13, Sugano, Ichikawa, Chiba, 272-8513, Japan.
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47
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Chan PP, Sabus A, Hemenway MS, Chatfield KC, White CJ, Mirsky DM, Foreman NK, Dahl NA. Thromboembolic toxicity observed with concurrent trametinib and lenalidomide therapy. Pediatr Blood Cancer 2023; 70:e30190. [PMID: 36602034 PMCID: PMC10519171 DOI: 10.1002/pbc.30190] [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: 05/18/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023]
Abstract
The event-free survival of pediatric low-grade gliomas is poor, and patients often require multiple treatment strategies. While MEK and RAF inhibitors are efficacious in early-phase trials, not all patients respond, and many experience progression following completion of therapy. Evaluating combination therapies that may enhance efficacy or prolong disease stabilization is warranted. We report our institutional experience using concurrent trametinib and lenalidomide in the treatment of primary pediatric central and peripheral nervous system tumors. Two of four patients using this combination therapy experienced severe thromboembolic events, necessitating discontinuation of therapy. This combination requires further investigation, and we urge caution if used.
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Affiliation(s)
- Priya P Chan
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Ashley Sabus
- Department of Pharmacy, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Molly S Hemenway
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kathryn C Chatfield
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Christina J White
- Department of Radiology, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - David M Mirsky
- Department of Radiology, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Nicholas K Foreman
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Nathan A Dahl
- Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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48
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Suh YY, Lee K, Shim YM, Phi JH, Park CK, Kim SK, Choi SH, Yun H, Park SH. MYB/MYBL1::QKI fusion-positive diffuse glioma. J Neuropathol Exp Neurol 2023; 82:250-260. [PMID: 36592415 PMCID: PMC9941827 DOI: 10.1093/jnen/nlac123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The MYB/MYBL1::QKI fusion induces the protooncogene, MYB, and deletes the tumor suppressor gene, QKI. MYB/MYBL1::QKI rearrangement was previously reported only in angiocentric glioma (AG) and diffuse low-grade glioma. This report compares 2 tumors containing the MYB/MYBL1::QKI fusion: a diffuse pediatric-type high-grade glioma (DPedHGG) in an 11-year-old boy and an AG in a 46-year-old woman. We used immunohistochemistry, next-generation sequencing, and methylation profiling to characterize each tumor and compare our findings to the literature on AG and tumors with the MYB/MYBL1::QKI rearrangement. Both tumors were astrocytic with angiocentric patterns. The MYB::QKI fusion-positive DPedHGG, which recurred once, was accompanied by TP53 mutation and amplification of CDK6 and KRAS, suggesting malignant transformation secondary to additional genetic aberrations. The second case was the adult AG with MYBL1::QKI fusion, which mimicked ependymoma based on histopathology and its dot- and ring-like epithelial membrane antigen positivity. Combined with a literature review, our results suggest that MYB/MYBL1 alterations are not limited to low-grade gliomas, including AG. AG is most common in the cerebra of children and adolescents but exceptional cases occur in adults and the acquisition of additional genetic mutations may contribute to high-grade glioma. These cases further demonstrate that molecular characteristics, morphologic features, and clinical context are essential for diagnosis.
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Affiliation(s)
- Ye Yoon Suh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kwanghoon Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yu-Mi Shim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Hoon Phi
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung-Ki Kim
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Hong Choi
- Department of Radiology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea.,N euroscience Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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49
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Diencephalic syndrome-like presentation of brainstem tumor: a series case-based review. Childs Nerv Syst 2023; 39:1115-1122. [PMID: 36752912 DOI: 10.1007/s00381-023-05869-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/28/2023] [Indexed: 02/09/2023]
Abstract
PURPOSE Russel described a rare clinical entity known as diencephalic syndrome (DS) in 1951, which was traditionally caused by a neoplasm in the hypothalamic-optic chiasmatic region. DS is characterized by severe emaciation despite adequate or slightly reduced caloric intake, locomotor hyperactivity, euphoria and other minor features. Current evidence suggests that a rare population of children with a similar phenotype may have their tumor located in the posterior fossa instead, defining the DS-like presentation, a rare entity with few cases reported in the literature. METHODS A thorough search of three databases (PubMed, Ovid Medline, and Ovid Embase) was conducted to identify relevant papers reporting children with DS associated with brainstem tumors. To our knowledge, only seven cases have been documented in the literature. Moreover, we present four of our own cases, focusing on the unusual clinical presentation, the diagnosis process, and the lag time between the initial symptoms and the definitive diagnosis. RESULTS In this review, the mean lag time between the onset of symptoms and diagnosis was 20.9 months (median: 16 months; range: 1.5-72 months), whereas in our series of cases, the time was 32.5 months (median: 33 months; range: 7-57 months). CONCLUSION Despite recent significant advances in neuro-oncology diagnostic tools, this mean lag time did not improve when compared with the previous literature review from 1976. Throughout these data, we aim to raise awareness in the hopes of detecting intracranial neoplasms earlier in cases of children with profound emaciation of unknown cause.
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50
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Genomic analysis as a tool to infer disparate phylogenetic origins of dysembryoplastic neuroepithelial tumors and their satellite lesions. Sci Rep 2023; 13:682. [PMID: 36639714 PMCID: PMC9839671 DOI: 10.1038/s41598-022-26636-7] [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] [Received: 07/22/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
Dysembryoplastic neuroepithelial tumor (DNET) is a low-grade brain tumor commonly associated with drug-resistant epilepsy. About half of DNETs are accompanied by tiny nodular lesions separated from the main mass. The existence of these satellite lesions (SLs) has shown a strong association with tumor recurrence, suggesting that they are true tumors. However, it is not known whether SLs represent multiple foci of progenitor tumor cell extension and migration or a multifocal development of the main DNET. This study was designed to elucidate the histopathology and pathogenesis of SLs in DNETs. Separate biopsies from the main masses and SLs with DNET were analyzed. We performed comparative lesion sequencing and phylogenetic analysis. FGFR1 K656E and K655I mutations or duplication of the tyrosine kinase domain was found in all 3 DNET patients and the main masses and their SLs shared the same FGFR1 alterations. The phylogenic analysis revealed that the SLs developed independently from their main masses. It is possible that the main mass and its SLs were separated at an early stage in oncogenesis with shared FGFR1 alterations, and then they further expanded in different places. SLs of DNET are true tumors sharing pathogenic mutations with the main masses. It is plausible that multifocal tumor development takes place in the dysplastic cortex containing cells with a pathogenic genetic alteration.
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