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Janssen FW, Lak NSM, Janda CY, Kester LA, Meister MT, Merks JHM, van den Heuvel-Eibrink MM, van Noesel MM, Zsiros J, Tytgat GAM, Looijenga LHJ. A comprehensive overview of liquid biopsy applications in pediatric solid tumors. NPJ Precis Oncol 2024; 8:172. [PMID: 39097671 PMCID: PMC11297996 DOI: 10.1038/s41698-024-00657-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/15/2024] [Indexed: 08/05/2024] Open
Abstract
Liquid biopsies are emerging as an alternative source for pediatric cancer biomarkers with potential applications during all stages of patient care, from diagnosis to long-term follow-up. While developments within this field are reported, these mainly focus on dedicated items such as a specific liquid biopsy matrix, analyte, and/or single tumor type. To the best of our knowledge, a comprehensive overview is lacking. Here, we review the current state of liquid biopsy research for the most common non-central nervous system pediatric solid tumors. These include neuroblastoma, renal tumors, germ cell tumors, osteosarcoma, Ewing sarcoma, rhabdomyosarcoma and other soft tissue sarcomas, and liver tumors. Within this selection, we discuss the most important or recent studies involving liquid biopsy-based biomarkers, anticipated clinical applications, and the current challenges for success. Furthermore, we provide an overview of liquid biopsy-based biomarker publication output for each tumor type based on a comprehensive literature search between 1989 and 2023. Per study identified, we list the relevant liquid biopsy-based biomarkers, matrices (e.g., peripheral blood, bone marrow, or cerebrospinal fluid), analytes (e.g., circulating cell-free and tumor DNA, microRNAs, and circulating tumor cells), methods (e.g., digital droplet PCR and next-generation sequencing), the involved pediatric patient cohort, and proposed applications. As such, we identified 344 unique publications. Taken together, while the liquid biopsy field in pediatric oncology is still behind adult oncology, potentially relevant publications have increased over the last decade. Importantly, steps towards clinical implementation are rapidly gaining ground, notably through validation of liquid biopsy-based biomarkers in pediatric clinical trials.
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Affiliation(s)
| | | | | | | | - Michael T Meister
- Princess Máxima Center, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Johannes H M Merks
- Princess Máxima Center, Utrecht, the Netherlands
- Division of Imaging and Oncology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Marry M van den Heuvel-Eibrink
- Princess Máxima Center, Utrecht, the Netherlands
- Wilhelmina Children's Hospital-Division of CHILDHEALTH, University Medical Center Utrech, University of Utrecht, Utrecht, the Netherlands
| | - Max M van Noesel
- Princess Máxima Center, Utrecht, the Netherlands
- Division of Imaging and Oncology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | | | - Godelieve A M Tytgat
- Princess Máxima Center, Utrecht, the Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Leendert H J Looijenga
- Princess Máxima Center, Utrecht, the Netherlands.
- Department of Pathology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands.
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2
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Ye S, Wang X, Chen R. A novel classification predicts prognosis and drug sensitivity in osteosarcoma based on alterations in gene sets. Aging (Albany NY) 2024; 16:4579-4590. [PMID: 38428404 PMCID: PMC10968677 DOI: 10.18632/aging.205614] [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: 10/23/2023] [Accepted: 01/23/2024] [Indexed: 03/03/2024]
Abstract
Osteosarcoma is a cancer originating in the bone cells, specifically in the osteoblasts. Previous studies mainly focused on particular molecules but the whole pathway network. We comprehensively analyzed the enrichment score of each signal pathway and identified a novel classification by 20 machine learning algorithms. Furthermore, differences in tumor immune infiltration cells and drug sensitivity were compared in low and high groups. We identified a model consisting of four signaling pathways that predict the prognosis and the immune status of the tumor microenvironment and drug sensitivity in osteosarcoma patients. The novel classification may be used in clinical applications to predict prognosis and drug sensitivity.
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Affiliation(s)
- Shuxi Ye
- Department of Spine Surgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, China
| | - Xiaopeng Wang
- Department of Spine Surgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, China
| | - Rongchun Chen
- Department of Spine Surgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, China
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3
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Audinot B, Drubay D, Gaspar N, Mohr A, Cordero C, Marec-Bérard P, Lervat C, Piperno-Neumann S, Jimenez M, Mansuy L, Castex MP, Revon-Riviere G, Marie-Cardine A, Berger C, Piguet C, Massau K, Job B, Moquin-Beaudry G, Le Deley MC, Tabone MD, Berlanga P, Brugières L, Crompton BD, Marchais A, Abbou S. ctDNA quantification improves estimation of outcomes in patients with high-grade osteosarcoma: a translational study from the OS2006 trial. Ann Oncol 2023:S0923-7534(23)05113-X. [PMID: 38142939 DOI: 10.1016/j.annonc.2023.12.006] [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: 10/13/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Osteosarcoma stratification relies on clinical parameters and histological response. We developed a new personalized stratification using less invasive circulating tumor DNA (ctDNA) quantification. PATIENTS AND METHODS Plasma from patients homogeneously treated in the prospective protocol OS2006, at diagnosis, before surgery and end of treatment, were sequenced using low-passage whole-genome sequencing (lpWGS) for copy number alteration detection. We developed a prediction tool including ctDNA quantification and known clinical parameters to estimate patients' individual risk of event. RESULTS ctDNA quantification at diagnosis (diagCPA) was evaluated for 183 patients of the protocol OS2006. diagCPA as a continuous variable was a major prognostic factor, independent of other clinical parameters, including metastatic status [diagCPA hazard ratio (HR) = 3.5, P = 0.002 and 3.51, P = 0.012, for progression-free survival (PFS) and overall survival (OS)]. At the time of surgery and until the end of treatment, diagCPA was also a major prognostic factor independent of histological response (diagCPA HR = 9.2, P < 0.001 and 11.6, P < 0.001, for PFS and OS). Therefore, the addition of diagCPA to metastatic status at diagnosis or poor histological response after surgery improved the prognostic stratification of patients with osteosarcoma. We developed the prediction tool PRONOS to generate individual risk estimations, showing great performance ctDNA quantification at the time of surgery and the end of treatment still required improvement to overcome the low sensitivity of lpWGS and to enable the follow-up of disease progression. CONCLUSIONS The addition of ctDNA quantification to known risk factors improves the estimation of prognosis calculated by our prediction tool PRONOS. To confirm its value, an external validation in the Sarcoma 13 trial is underway.
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Affiliation(s)
- B Audinot
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - D Drubay
- Gustave Roussy, Office of Biostatistics and Epidemiology, Université Paris-Saclay, Villejuif; Inserm, Université Paris-Saclay, CESP U1018, Oncostat, labeled Ligue Contre le Cancer, Villejuif
| | - N Gaspar
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif; Gustave Roussy Cancer Campus, Children and Adolescent Oncology Department, Villejuif; French Cancer Society (SFCE), Bordeaux
| | - A Mohr
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - C Cordero
- Pediatric Department, Institut Curie, Paris; French Cancer Society (SFCE), Bordeaux
| | - P Marec-Bérard
- Department of Oncology for Child and Adolescent, Centre Léon Bérard, Pediatric Oncology and Hematology Institute (IHOPe), Lyon; French Cancer Society (SFCE), Bordeaux
| | - C Lervat
- Department of Pediatric Oncology, Adolescents and Young Adults, Centre Oscar Lambret, Lille; French Cancer Society (SFCE), Bordeaux
| | | | - M Jimenez
- Research and Development Department, Unicancer, Paris
| | - L Mansuy
- Department of Pediatric Hematology and Oncology, Nancy University Hospital, Vandœuvre-lès-Nancy; French Cancer Society (SFCE), Bordeaux
| | - M-P Castex
- Pediatric Oncology Immunology Hematology Unit, Children's University Hospital, Toulouse; French Cancer Society (SFCE), Bordeaux
| | - G Revon-Riviere
- Department of Pediatric Hematology and Oncology, La Timone Children's Hospital, Marseille; French Cancer Society (SFCE), Bordeaux
| | - A Marie-Cardine
- Department of Pediatric Hematology and Oncology, Rouen University Hospital, Rouen; French Cancer Society (SFCE), Bordeaux
| | - C Berger
- Department of Pediatric Oncology, North Hospital, University Hospital of Saint Etienne, Saint Etienne; French Cancer Society (SFCE), Bordeaux
| | - C Piguet
- Pediatric Oncology Hematology Unit, Limoges University Hospital, Limoges; French Cancer Society (SFCE), Bordeaux
| | - K Massau
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - B Job
- National Institute for Health and Medical Research (INSERM) US23, Gustave Roussy, Villejuif
| | - G Moquin-Beaudry
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - M-C Le Deley
- Gustave Roussy, Office of Biostatistics and Epidemiology, Université Paris-Saclay, Villejuif; Clinical Research Department, Centre Oscar Lambret, Lille
| | - M-D Tabone
- Pediatric Hematology Department, Trousseau Hospital, Sorbonne Université, Paris, France; French Cancer Society (SFCE), Bordeaux
| | - P Berlanga
- Gustave Roussy Cancer Campus, Children and Adolescent Oncology Department, Villejuif; French Cancer Society (SFCE), Bordeaux
| | - L Brugières
- Gustave Roussy Cancer Campus, Children and Adolescent Oncology Department, Villejuif; French Cancer Society (SFCE), Bordeaux
| | - B D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston; Broad Institute of Harvard and MIT, Cambridge, USA
| | - A Marchais
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - S Abbou
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif; Gustave Roussy Cancer Campus, Children and Adolescent Oncology Department, Villejuif; French Cancer Society (SFCE), Bordeaux.
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4
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Akshintala S, Sundby RT, Bernstein D, Glod JW, Kaplan RN, Yohe ME, Gross AM, Derdak J, Lei H, Pan A, Dombi E, Palacio-Yance I, Herrera KR, Miettinen MM, Chen HX, Steinberg SM, Helman LJ, Mascarenhas L, Widemann BC, Navid F, Shern JF, Heske CM. Phase I trial of Ganitumab plus Dasatinib to Cotarget the Insulin-Like Growth Factor 1 Receptor and Src Family Kinase YES in Rhabdomyosarcoma. Clin Cancer Res 2023; 29:3329-3339. [PMID: 37398992 PMCID: PMC10529967 DOI: 10.1158/1078-0432.ccr-23-0709] [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: 03/24/2023] [Revised: 05/05/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
PURPOSE Antibodies against insulin-like growth factor (IGF) type 1 receptor have shown meaningful but transient tumor responses in patients with rhabdomyosarcoma (RMS). The SRC family member YES has been shown to mediate IGF type 1 receptor (IGF-1R) antibody acquired resistance, and cotargeting IGF-1R and YES resulted in sustained responses in murine RMS models. We conducted a phase I trial of the anti-IGF-1R antibody ganitumab combined with dasatinib, a multi-kinase inhibitor targeting YES, in patients with RMS (NCT03041701). PATIENTS AND METHODS Patients with relapsed/refractory alveolar or embryonal RMS and measurable disease were eligible. All patients received ganitumab 18 mg/kg intravenously every 2 weeks. Dasatinib dose was 60 mg/m2/dose (max 100 mg) oral once daily [dose level (DL)1] or 60 mg/m2/dose (max 70 mg) twice daily (DL2). A 3+3 dose escalation design was used, and maximum tolerated dose (MTD) was determined on the basis of cycle 1 dose-limiting toxicities (DLT). RESULTS Thirteen eligible patients, median age 18 years (range 8-29) enrolled. Median number of prior systemic therapies was 3; all had received prior radiation. Of 11 toxicity-evaluable patients, 1/6 had a DLT at DL1 (diarrhea) and 2/5 had a DLT at DL2 (pneumonitis, hematuria) confirming DL1 as MTD. Of nine response-evaluable patients, one had a confirmed partial response for four cycles, and one had stable disease for six cycles. Genomic studies from cell-free DNA correlated with disease response. CONCLUSIONS The combination of dasatinib 60 mg/m2/dose daily and ganitumab 18 mg/kg every 2 weeks was safe and tolerable. This combination had a disease control rate of 22% at 5 months.
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Affiliation(s)
- Srivandana Akshintala
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - R. Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Donna Bernstein
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - John W. Glod
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Rosandra N. Kaplan
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Marielle E. Yohe
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, Maryland
| | - Andrea M. Gross
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Joanne Derdak
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Haiyan Lei
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Alexander Pan
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Eva Dombi
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Isabel Palacio-Yance
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Kailey R. Herrera
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Markku M. Miettinen
- Laboratory of Pathology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Helen X. Chen
- Cancer Therapy Evaluation Program (CTEP), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Seth M. Steinberg
- Biostatistics and Data Management, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Lee J. Helman
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles (CHLA), Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California
- The Osteosarcoma Institute, Dallas, Texas
| | - Leo Mascarenhas
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles (CHLA), Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Brigitte C. Widemann
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Fariba Navid
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles (CHLA), Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jack F. Shern
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Christine M. Heske
- Pediatric Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
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Ruas JS, Silva FLT, Euzébio MF, Biazon TO, Daiggi CMM, Nava D, Franco MT, Cardinalli IA, Cassone AE, Pereira LH, Seidinger AL, Maschietto M, Jotta PY. Somatic Copy Number Alteration in Circulating Tumor DNA for Monitoring of Pediatric Patients with Cancer. Biomedicines 2023; 11:biomedicines11041082. [PMID: 37189699 DOI: 10.3390/biomedicines11041082] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 04/07/2023] Open
Abstract
Pediatric tumors share few recurrent mutations and are instead characterized by copy number alterations (CNAs). The cell-free DNA (cfDNA) is a prominent source for the detection of cancer-specific biomarkers in plasma. We profiled CNAs in the tumor tissues for further evaluation of alterations in 1q, MYCN and 17p in the circulating tumor DNA (ctDNA) in the peripheral blood at diagnosis and follow-up using digital PCR. We report that among the different kinds of tumors (neuroblastoma, Wilms tumor, Ewing sarcoma, rhabdomyosarcoma, leiomyosarcoma, osteosarcoma and benign teratoma), neuroblastoma presented the greatest amount of cfDNA, in correlation with tumor volume. Considering all tumors, cfDNA levels correlated with tumor stage, metastasis at diagnosis and metastasis developed during therapy. In the tumor tissue, at least one CNA (at CRABP2, TP53, surrogate markers for 1q and 17p, respectively, and MYCN) was observed in 89% of patients. At diagnosis, CNAs levels were concordant between tumor and ctDNA in 56% of the cases, and for the remaining 44%, 91.4% of the CNAs were present only in cfDNA and 8.6% only in the tumor. Within the cfDNA, we observed that 46% and 23% of the patients had MYCN and 1q gain, respectively. The use of specific CNAs as targets for liquid biopsy in pediatric patients with cancer can improve diagnosis and should be considered for monitoring of the disease response.
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Affiliation(s)
| | - Felipe Luz Torres Silva
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | - Mayara Ferreira Euzébio
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | - Tássia Oliveira Biazon
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | | | - Daniel Nava
- Boldrini Children’s Hospital, Campinas 13083-210, SP, Brazil
| | | | | | | | | | - Ana Luiza Seidinger
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
| | - Mariana Maschietto
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
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Prudowsky ZD, Yustein JT. Recent Insights into Therapy Resistance in Osteosarcoma. Cancers (Basel) 2020; 13:E83. [PMID: 33396725 PMCID: PMC7795058 DOI: 10.3390/cancers13010083] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 12/22/2022] Open
Abstract
Osteosarcoma, the most common bone malignancy of childhood, has been a challenge to treat and cure. Standard chemotherapy regimens work well for many patients, but there remain minimal options for patients with progressive or resistant disease, as clinical trials over recent decades have failed to significantly improve survival. A better understanding of therapy resistance is necessary to improve current treatments and design new strategies for future treatment options. In this review, we discuss known mechanisms and recent scientific advancements regarding osteosarcoma and its patterns of resistance against chemotherapy, radiation, and other newly-introduced therapeutics.
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Affiliation(s)
- Zachary D. Prudowsky
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Houston, TX 77030, USA;
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason T. Yustein
- Texas Children’s Cancer and Hematology Centers and The Faris D. Virani Ewing Sarcoma Center, Houston, TX 77030, USA;
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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