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Kahana-Edwin S, Torpy J, Cain LE, Mullins A, McCowage G, Woodfield SE, Vasudevan SA, Shea DPT, Minoche AE, Espinoza AF, Kummerfeld S, Goldstein LD, Karpelowsky J. Quantitative ctDNA Detection in Hepatoblastoma: Implications for Precision Medicine. Cancers (Basel) 2023; 16:12. [PMID: 38201440 PMCID: PMC10778269 DOI: 10.3390/cancers16010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatoblastoma is characterized by driver mutations in CTNNB1, making it an attractive biomarker for a liquid biopsy approach utilizing circulating tumor DNA (ctDNA). This prospective observational study sought to ascertain the feasibility of ctDNA detection in patients with hepatoblastoma and explore its associations with established clinical indicators and biomarkers, including serum Alpha-fetoprotein (AFP). We obtained 38 plasma samples and 17 tumor samples from 20 patients with hepatoblastoma. These samples were collected at various stages: 10 at initial diagnosis, 17 during neoadjuvant chemotherapy, 6 post-operatively, and 5 at disease recurrence. Utilizing a bespoke sequencing assay we developed called QUENCH, we identified single nucleotide variants and deletions in CTNNB1 ctDNA. Our study demonstrated the capability to quantitate ctDNA down to a variant allele frequency of 0.3%, achieving a sensitivity of 90% for patients at initial diagnosis, and a specificity of 100% at the patient level. Notably, ctDNA positivity correlated with tumor burden, and ctDNA levels exhibited associations with macroscopic residual disease and treatment response. Our findings provide evidence for the utility of quantitative ctDNA detection in hepatoblastoma management. Given the distinct detection targets, ctDNA and AFP-based stratification and monitoring approaches could synergize to enhance clinical decision-making. Further research is needed to elucidate the interplay between ctDNA and AFP and determine the optimal clinical applications for both methods in risk stratification and residual disease detection.
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Affiliation(s)
- Smadar Kahana-Edwin
- Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - James Torpy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Lucy E. Cain
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Anna Mullins
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Geoffrey McCowage
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Sarah E. Woodfield
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sanjeev A. Vasudevan
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dan P. T. Shea
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Andre E. Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Andres F. Espinoza
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Kummerfeld
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, NSW 2217, Australia
| | - Leonard D. Goldstein
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, NSW 2217, Australia
| | - Jonathan Karpelowsky
- Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Paediatric Oncology and Thoracic Surgery, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Division of Child and Adolescent Health, The University of Sydney, Sydney, NSW 2050, Australia
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2
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Grebstad Tune B, Sareen H, Powter B, Kahana-Edwin S, Cooper A, Koh ES, Lee CS, Po JW, McCowage G, Dexter M, Cain L, O'Neill G, Prior V, Karpelowsky J, Tsoli M, Baumbusch LO, Ziegler D, Roberts TL, DeSouza P, Becker TM, Ma Y. From Pediatric to Adult Brain Cancer: Exploring Histone H3 Mutations in Australian Brain Cancer Patients. Biomedicines 2023; 11:2907. [PMID: 38001908 PMCID: PMC10669073 DOI: 10.3390/biomedicines11112907] [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: 09/29/2023] [Revised: 10/14/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
Genetic histone variants have been implicated in cancer development and progression. Mutations affecting the histone 3 (H3) family, H3.1 (encoded by HIST1H3B and HIST1H3C) and H3.3 (encoded by H3F3A), are mainly associated with pediatric brain cancers. While considered poor prognostic brain cancer biomarkers in children, more recent studies have reported H3 alterations in adult brain cancer as well. Here, we established reliable droplet digital PCR based assays to detect three histone mutations (H3.3-K27M, H3.3-G34R, and H3.1-K27M) primarily linked to childhood brain cancer. We demonstrate the utility of our assays for sensitively detecting these mutations in cell-free DNA released from cultured diffuse intrinsic pontine glioma (DIPG) cells and in the cerebral spinal fluid of a pediatric patient with DIPG. We further screened tumor tissue DNA from 89 adult patients with glioma and 1 with diffuse hemispheric glioma from Southwestern Sydney, Australia, an ethnically diverse region, for these three mutations. No histone mutations were detected in adult glioma tissue, while H3.3-G34R presence was confirmed in the diffuse hemispheric glioma patient.
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Affiliation(s)
- Benedicte Grebstad Tune
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
| | - Heena Sareen
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
| | - Branka Powter
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
| | - Smadar Kahana-Edwin
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Adam Cooper
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Eng-Siew Koh
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Cheok S Lee
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Joseph W Po
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
| | - Geoff McCowage
- Cancer Centre for Children, The Children Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Mark Dexter
- Neurosurgery, The Children Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Lucy Cain
- Cancer Centre for Children, The Children Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Geraldine O'Neill
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- The University of Sydney Children's Hospital Westmead Clinical School, Faculty of Medicine & Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Victoria Prior
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- The University of Sydney Children's Hospital Westmead Clinical School, Faculty of Medicine & Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Jonathan Karpelowsky
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- Paediatric Oncology and Thoracic Surgery, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- Division of Child and Adolescent Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Maria Tsoli
- Children's Cancer Institute, Randwick, NSW 2031, Australia
| | - Lars O Baumbusch
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
- Faculty of Health, Welfare and Organization, Østfold University College, 1757 Halden, Norway
| | - David Ziegler
- Children's Cancer Institute, Randwick, NSW 2031, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2052, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Tara L Roberts
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Paul DeSouza
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Therese M Becker
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Yafeng Ma
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
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3
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Horgan D, Čufer T, Gatto F, Lugowska I, Verbanac D, Carvalho Â, Lal JA, Kozaric M, Toomey S, Ivanov HY, Longshore J, Malapelle U, Hasenleithner S, Hofman P, Alix-Panabières C. Accelerating the Development and Validation of Liquid Biopsy for Early Cancer Screening and Treatment Tailoring. Healthcare (Basel) 2022; 10:1714. [PMID: 36141326 PMCID: PMC9498805 DOI: 10.3390/healthcare10091714] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 11/26/2022] Open
Abstract
Liquid biopsy (LB) is a minimally invasive method which aims to detect circulating tumor-derived components in body fluids. It provides an alternative to current cancer screening methods that use tissue biopsies for the confirmation of diagnosis. This paper attempts to determine how far the regulatory, policy, and governance framework provide support to LB implementation into healthcare systems and how the situation can be improved. For that reason, the European Alliance for Personalised Medicine (EAPM) organized series of expert panels including different key stakeholders to identify different steps, challenges, and opportunities that need to be taken to effectively implement LB technology at the country level across Europe. To accomplish a change of patient care with an LB approach, it is required to establish collaboration between multiple stakeholders, including payers, policymakers, the medical and scientific community, and patient organizations, both at the national and international level. Regulators, pharma companies, and payers could have a major impact in their own domain. Linking national efforts to EU efforts and vice versa could help in implementation of LB across Europe, while patients, scientists, physicians, and kit manufacturers can generate a pull by undertaking more research into biomarkers.
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Affiliation(s)
- Denis Horgan
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Faculty of Engineering and Technology, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India
| | - Tanja Čufer
- Medical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Francesco Gatto
- Department of Oncology-Pathology, Karolinska Institute, 171 64 Stockholm, Sweden
| | - Iwona Lugowska
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute and Oncology Centre (MSCI), 02781 Warsaw, Poland
| | - Donatella Verbanac
- Department of Medical Biochemistry and Hematology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Ângela Carvalho
- i3S—nstituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- INEB—Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Jonathan A. Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Faculty of Engineering and Technology, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India
- Institute for Public Health Genomics, Department of Genetics and Cell Biology, GROW School of Oncology and Developmental Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Marta Kozaric
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium
| | - Sinead Toomey
- Department of Molecular Medicine, RCSI University of Medicine and Health Sciences, Beaumont Hospital, Smurfit Building, D09 Dublin, Ireland
| | - Hristo Y. Ivanov
- Department of Paediatric and Medical Genetics, Medical University, 4000 Plovdiv, Bulgaria
| | - John Longshore
- Astra Zeneca, 1800 Concord Pike, Wilmington, DE 19803, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80137 Naples, Italy
| | - Samantha Hasenleithner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8036 Graz, Austria
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Pasteur Hospital, University Côte d’Azur, CEDEX 01, 06001 Nice, France
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, 641 Avenue du Doyen Gaston Giraud, CEDEX 5, 34093 Montpellier, France
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4
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Tozzi AE, Fabozzi F, Eckley M, Croci I, Dell’Anna VA, Colantonio E, Mastronuzzi A. Gaps and Opportunities of Artificial Intelligence Applications for Pediatric Oncology in European Research: A Systematic Review of Reviews and a Bibliometric Analysis. Front Oncol 2022; 12:905770. [PMID: 35712463 PMCID: PMC9194810 DOI: 10.3389/fonc.2022.905770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/04/2022] [Indexed: 12/23/2022] Open
Abstract
The application of artificial intelligence (AI) systems is emerging in many fields in recent years, due to the increased computing power available at lower cost. Although its applications in various branches of medicine, such as pediatric oncology, are many and promising, its use is still in an embryonic stage. The aim of this paper is to provide an overview of the state of the art regarding the AI application in pediatric oncology, through a systematic review of systematic reviews, and to analyze current trends in Europe, through a bibliometric analysis of publications written by European authors. Among 330 records found, 25 were included in the systematic review. All papers have been published since 2017, demonstrating only recent attention to this field. The total number of studies included in the selected reviews was 674, with a third including an author with a European affiliation. In bibliometric analysis, 304 out of the 978 records found were included. Similarly, the number of publications began to dramatically increase from 2017. Most explored AI applications regard the use of diagnostic images, particularly radiomics, as well as the group of neoplasms most involved are the central nervous system tumors. No evidence was found regarding the use of AI for process mining, clinical pathway modeling, or computer interpreted guidelines to improve the healthcare process. No robust evidence is yet available in any of the domains investigated by systematic reviews. However, the scientific production in Europe is significant and consistent with the topics covered in systematic reviews at the global level. The use of AI in pediatric oncology is developing rapidly with promising results, but numerous gaps and challenges persist to validate its utilization in clinical practice. An important limitation is the need for large datasets for training algorithms, calling for international collaborative studies.
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Affiliation(s)
- Alberto Eugenio Tozzi
- Multifactorial and Complex Diseases Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Francesco Fabozzi
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Pediatrics, University of Rome Tor Vergata, Rome, Italy
| | - Megan Eckley
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Ileana Croci
- Multifactorial and Complex Diseases Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Vito Andrea Dell’Anna
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Erica Colantonio
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Angela Mastronuzzi
- Department of Onco Hematology and Cell and Gene Therapy, Bambino Gesù Pediatric Hospital, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- *Correspondence: Angela Mastronuzzi,
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5
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Doculara L, Trahair TN, Bayat N, Lock RB. Circulating Tumor DNA in Pediatric Cancer. Front Mol Biosci 2022; 9:885597. [PMID: 35647029 PMCID: PMC9133724 DOI: 10.3389/fmolb.2022.885597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
The measurement of circulating tumor DNA (ctDNA) has gained increasing prominence as a minimally invasive tool for the detection of cancer-specific markers in plasma. In adult cancers, ctDNA detection has shown value for disease-monitoring applications including tumor mutation profiling, risk stratification, relapse prediction, and treatment response evaluation. To date, there are ctDNA tests used as companion diagnostics for adult cancers and it is not understood why the same cannot be said about childhood cancer, despite the marked differences between adult and pediatric oncology. In this review, we discuss the current understanding of ctDNA as a disease monitoring biomarker in the context of pediatric malignancies, including the challenges associated with ctDNA detection in liquid biopsies. The data and conclusions from pediatric cancer studies of ctDNA are summarized, highlighting treatment response, disease monitoring and the detection of subclonal disease as applications of ctDNA. While the data from retrospective studies highlight the potential of ctDNA, large clinical trials are required for ctDNA analysis for routine clinical use in pediatric cancers. We outline the requirements for the standardization of ctDNA detection in pediatric cancers, including sample handling and reproducibility of results. With better understanding of the advantages and limitations of ctDNA and improved detection methods, ctDNA analysis may become the standard of care for patient monitoring in childhood cancers.
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Affiliation(s)
- Louise Doculara
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Toby N. Trahair
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Narges Bayat
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B. Lock
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
- *Correspondence: Richard B. Lock,
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6
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Sundby RT, Pan A, Shern JF. Liquid biopsies in pediatric oncology: opportunities and obstacles. Curr Opin Pediatr 2022; 34:39-47. [PMID: 34840249 PMCID: PMC8727502 DOI: 10.1097/mop.0000000000001088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Liquid biopsies have emerged as a noninvasive alternative to tissue biopsy with potential applications during all stages of pediatric oncology care. The purpose of this review is to provide a survey of pediatric cell-free DNA (cfDNA) studies, illustrate their potential applications in pediatric oncology, and to discuss technological challenges and approaches to overcome these hurdles. RECENT FINDINGS Recent literature has demonstrated liquid biopsies' ability to inform treatment selection at diagnosis, monitor clonal evolution during treatment, sensitively detect minimum residual disease following local control, and provide sensitive posttherapy surveillance. Advantages include reduced procedural anesthesia, molecular profiling unbiased by tissue heterogeneity, and ability to track clonal evolution. Challenges to wider implementation in pediatric oncology, however, include blood volume restrictions and relatively low mutational burden in childhood cancers. Multiomic approaches address challenges presented by low-mutational burden, and novel bioinformatic analyses allow a single assay to yield increasing amounts of information, reducing blood volume requirements. SUMMARY Liquid biopsies hold tremendous promise in pediatric oncology, enabling noninvasive serial surveillance with adaptive care. Already integrated into adult care, recent advances in technologies and bioinformatics have improved applicability to the pediatric cancer landscape.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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7
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McEachron TA, Helman LJ. Recent Advances in Pediatric Cancer Research. Cancer Res 2021; 81:5783-5799. [PMID: 34561271 DOI: 10.1158/0008-5472.can-21-1191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/05/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022]
Abstract
Over the past few years, the field of pediatric cancer has experienced a shift in momentum, and this has led to new and exciting findings that have relevance beyond pediatric malignancies. Here we present the current status of key aspects of pediatric cancer research. We have focused on genetic and epigenetic drivers of disease, cellular origins of different pediatric cancers, disease models, the tumor microenvironment, and cellular immunotherapies.
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Affiliation(s)
| | - Lee J Helman
- Osteosarcoma Institute, Dallas, Texas
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California
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8
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Kahana-Edwin S, Cain LE, McCowage G, Darmanian A, Wright D, Mullins A, Saletta F, Karpelowsky J. Neuroblastoma Molecular Risk-Stratification of DNA Copy Number and ALK Genotyping via Cell-Free Circulating Tumor DNA Profiling. Cancers (Basel) 2021; 13:3365. [PMID: 34282791 PMCID: PMC8267662 DOI: 10.3390/cancers13133365] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND MYCN amplification (MNA), segmental chromosomal aberrations (SCA) and ALK activating mutations are biomarkers for risk-group stratification and for targeted therapeutics for neuroblastoma, both of which are currently assessed on tissue biopsy. Increase in demand for tumor genetic testing for neuroblastoma diagnosis is posing a challenge to current practice, as the small size of the core needle biopsies obtained are required for multiple molecular tests. We evaluated the utility of detecting these biomarkers in the circulation. METHODS Various pre-analytical conditions tested to optimize circulating-tumor DNA (ctDNA) copy number changes evaluations. Plasma samples from 10 patients diagnosed with neuroblastoma assessed for SCA and MNA using single nucleotide polymorphism (SNP) array approach currently used for neuroblastoma diagnosis, with MNA status assessed independently using digital-droplet PCR (ddPCR). Three patients (one in common with the previous 10) tested for ALK activating mutations p.F1174L and p.F1245I using ddPCR. RESULTS Copy number detection is highly affected by physical perturbations of the blood sample (mimicking suboptimal sample shipment), which could be overcome using specialized preservative collection tubes. Pre-analytical DNA repair procedures on ctDNA before SNP chromosome microarray processing improved the lower limit of detection for SCA and MNA, defined as 20% and 10%, respectively. We detected SCA in 10/10 (100%) patients using SNP array, 7 of which also presented MNA. Circulating-free DNA (cfDNA) and matched tumor DNA profiles were generally identical. MNA was detected using ddPCR in 7/7 (100%) of MNA and 0/12 (0%) non-MNA cases. MNA and ALK mutation dynamic change was assessed in longitudinal samples from 4 and 3 patients (one patient with both), respectively, accurately reflected response to treatment in 6/6 (100%) and disease recurrence in 5/6 (83%) of cases. Samples taken prior to targeted treatment with the ALK inhibitor Lorlatinib and 6-8 weeks on treatment showed reduction/increase in ALK variants according to response to treatment. CONCLUSIONS These results demonstrate the feasibility of ctDNA profiling for molecular risk-stratification, and treatment monitoring in a clinically relevant time frame and the potential to reduce fresh tissue requirements currently embedded in the management of neuroblastoma.
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Affiliation(s)
- Smadar Kahana-Edwin
- Advanced Molecular Diagnostics, Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (F.S.); (J.K.)
| | - Lucy E. Cain
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (L.E.C.); (G.M.); (A.M.)
| | - Geoffrey McCowage
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (L.E.C.); (G.M.); (A.M.)
| | - Artur Darmanian
- Cytogenetics Department, Sydney Genome Diagnostics, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (A.D.); (D.W.)
| | - Dale Wright
- Cytogenetics Department, Sydney Genome Diagnostics, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (A.D.); (D.W.)
- Division of Child and Adolescent Health, The University of Sydney, Sydney, NSW 2145, Australia
| | - Anna Mullins
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (L.E.C.); (G.M.); (A.M.)
| | - Federica Saletta
- Advanced Molecular Diagnostics, Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (F.S.); (J.K.)
| | - Jonathan Karpelowsky
- Advanced Molecular Diagnostics, Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (F.S.); (J.K.)
- Division of Child and Adolescent Health, The University of Sydney, Sydney, NSW 2145, Australia
- Paediatric Oncology and Thoracic Surgery, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
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