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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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2
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Runkel A, Braig D, Bogner B, Schmid A, Lausch U, Boneberg A, Brugger Z, Eisenhardt A, Kiefer J, Pauli T, Boerries M, Fuellgraf H, Kurowski K, Bronsert P, Scholber J, Grosu AL, Rovedo P, Bamberg F, Eisenhardt SU, Jung M. Non-invasive monitoring of neoadjuvant radiation therapy response in soft tissue sarcomas by multiparametric MRI and quantification of circulating tumor DNA-A study protocol. PLoS One 2023; 18:e0285580. [PMID: 37910565 PMCID: PMC10619790 DOI: 10.1371/journal.pone.0285580] [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: 11/18/2022] [Accepted: 04/03/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Wide resection remains the cornerstone of localized soft-tissue sarcomas (STS) treatment. Neoadjuvant radiation therapy (NRT) may decrease the risk of local recurrences; however, its effectiveness for different histological STS subtypes has not been systematically investigated. The proposed prospective study evaluates the NRT response in STS using liquid biopsies and the correlation of multiparametric magnetic resonance imaging (mpMRI) with histopathology and immunohistochemistry. METHODS Patients with localized high-grade STS, who qualify for NRT, are included in this study. LIQUID BIOPSIES Quantification of circulating tumor DNA (ctDNA) in patient blood samples is performed by targeted next-generation sequencing. Soft-tissue sarcoma subtype-specific panel sequencing in combination with patient-specific exome sequencing allows the detection of individual structural variants and point mutations. Circulating free DNA is isolated from peritherapeutically collected patient plasma samples and ctDNA quantified therein. Identification of breakpoints is carried out using FACTERA. Bioinformatic analysis is performed using samtools, picard, fgbio, and the MIRACUM Pipeline. MPMRI Combination of conventional MRI sequences with diffusion-weighted imaging, intravoxel-incoherent motion, and dynamic contrast enhancement. Multiparametric MRI is performed before, during, and after NRT. We aim to correlate mpMRI data with the resected specimen's macroscopical, histological, and immunohistochemical findings. RESULTS Preliminary data support the notion that quantification of ctDNA in combination with tumor mass characterization through co-registration of mpMRI and histopathology can predict NRT response of STS. CLINICAL RELEVANCE The methods presented in this prospective study are necessary to assess therapy response in heterogeneous tumors and lay the foundation of future patient- and tumor-specific therapy concepts. These methods can be applied to various tumor entities. Thus, the participation and support of a wider group of oncologic surgeons are needed to validate these findings on a larger patient cohort.
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Affiliation(s)
- Alexander Runkel
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Berta-Ottenstein-Programme, University of Freiburg, Freiburg, Germany
| | - David Braig
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Balazs Bogner
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Adrian Schmid
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Ute Lausch
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anika Boneberg
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Zacharias Brugger
- Faculty of Medicine, Department of Medicine I, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anja Eisenhardt
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Jurij Kiefer
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Thomas Pauli
- Faculty of Medicine, Institute of Medical Bioinformatics, Medical Center—University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Faculty of Medicine, Institute of Medical Bioinformatics, Medical Center—University of Freiburg, Freiburg, Germany
| | - Hannah Fuellgraf
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Konrad Kurowski
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center—University of Freiburg, Freiburg, Germany
- Core Facility for Histopathology and Digital Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Jutta Scholber
- Faculty of Medicine, Department of Radiation Oncology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anca-Ligia Grosu
- Faculty of Medicine, Department of Radiation Oncology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Philipp Rovedo
- Faculty of Medicine, Department of Radiology, Medical Physics, Medical Center-University of Freiburg, Freiburg, Germany
| | - Fabian Bamberg
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Steffen Ulrich Eisenhardt
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Matthias Jung
- Faculty of Medicine, Berta-Ottenstein-Programme, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
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Meng Y, Yang Y, Hu M, Zhang Z, Zhou X. Artificial intelligence-based radiomics in bone tumors: Technical advances and clinical application. Semin Cancer Biol 2023; 95:75-87. [PMID: 37499847 DOI: 10.1016/j.semcancer.2023.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 07/29/2023]
Abstract
Radiomics is the extraction of predefined mathematic features from medical images for predicting variables of clinical interest. Recent research has demonstrated that radiomics can be processed by artificial intelligence algorithms to reveal complex patterns and trends for diagnosis, and prediction of prognosis and response to treatment modalities in various types of cancer. Artificial intelligence tools can utilize radiological images to solve next-generation issues in clinical decision making. Bone tumors can be classified as primary and secondary (metastatic) tumors. Osteosarcoma, Ewing sarcoma, and chondrosarcoma are the dominating primary tumors of bone. The development of bone tumor model systems and relevant research, and the assessment of novel treatment methods are ongoing to improve clinical outcomes, notably for patients with metastases. Artificial intelligence and radiomics have been utilized in almost full spectrum of clinical care of bone tumors. Radiomics models have achieved excellent performance in the diagnosis and grading of bone tumors. Furthermore, the models enable to predict overall survival, metastases, and recurrence. Radiomics features have exhibited promise in assisting therapeutic planning and evaluation, especially neoadjuvant chemotherapy. This review provides an overview of the evolution and opportunities for artificial intelligence in imaging, with a focus on hand-crafted features and deep learning-based radiomics approaches. We summarize the current application of artificial intelligence-based radiomics both in primary and metastatic bone tumors, and discuss the limitations and future opportunities of artificial intelligence-based radiomics in this field. In the era of personalized medicine, our in-depth understanding of emerging artificial intelligence-based radiomics approaches will bring innovative solutions to bone tumors and achieve clinical application.
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Affiliation(s)
- Yichen Meng
- Department of Orthopedics, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, PR China
| | - Yue Yang
- Department of Orthopedics, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, PR China
| | - Miao Hu
- Department of Orthopedics, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, PR China
| | - Zheng Zhang
- Department of Orthopedics, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, PR China.
| | - Xuhui Zhou
- Department of Orthopedics, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, PR China.
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4
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Shulman DS, Merriam P, Choy E, Guenther LM, Cavanaugh KL, Kao P, Posner A, Bhushan K, Fairchild G, Barker E, Klega K, Stegmaier K, Crompton BD, London WB, DuBois SG. Phase 2 trial of palbociclib and ganitumab in patients with relapsed Ewing sarcoma. Cancer Med 2023; 12:15207-15216. [PMID: 37306107 PMCID: PMC10417097 DOI: 10.1002/cam4.6208] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/08/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023] Open
Abstract
BACKGROUND Ewing sarcoma (EWS) is an aggressive sarcoma with few treatment options for patients with relapsed disease. Cyclin-dependent kinase 4 (CDK4) is a genomic vulnerability in EWS that is synergistic with IGF-1R inhibition in preclinical studies. We present the results of a phase 2 study combining palbociclib (CDK4/6 inhibitor) with ganitumab (IGF-1R monoclonal antibody) for patients with relapsed EWS. PATIENTS AND METHODS This open-label, non-randomized, phase 2 trial enrolled patients ≥12 years with relapsed EWS. All patients had molecular confirmation of EWS and RECIST measurable disease. Patients initially received palbociclib 125 mg orally on Days 1-21 and ganitumab 18 mg/kg intravenously on Days 1 and 15 of a 28-day cycle. The primary endpoints were objective response (complete or partial) per RECIST and toxicity by CTCAE. An exact one-stage design required ≥4 responders out of 15 to evaluate an alternative hypothesis of 40% response rate against a null of 10%. The study was closed following enrollment of the 10th patient due to discontinuation of ganitumab supply. RESULTS Ten evaluable patients enrolled [median age 25.7 years (range 12.3-40.1)]. The median duration of therapy was 2.5 months (range 0.9-10.8). There were no complete or partial responders. Three of 10 patients had stable disease for >4 cycles and 2 had stable disease at completion of planned therapy or study closure. Six-month progression-free survival was 30% (95% CI 1.6%-58.4%). Two patients had cycle 1 hematologic dose-limiting toxicities (DLTs) triggering palbociclib dose reduction to 100 mg daily for 21 days. Two subsequent patients had cycle 1 hematologic DLTs at the reduced dose. Eighty percent of patients had grade 3/4 AEs, including neutropenia (n = 8), white blood cell decreased (n = 7), and thrombocytopenia (n = 5). Serum total IGF-1 significantly increased (p = 0.013) and ctDNA decreased during the first cycle. CONCLUSIONS This combination lacks adequate therapeutic activity for further study, though a subset of patients had prolonged stable disease.
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Affiliation(s)
- David S. Shulman
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Priscilla Merriam
- Dana‐Farber Cancer Institute and Harvard Medical SchoolBostonMassachusettsUSA
| | - Edwin Choy
- Massachusetts General HospitalMassachusetts General Hospital Cancer CenterBostonMassachusettsUSA
| | | | - Kerri L. Cavanaugh
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Pei‐Chi Kao
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Andrew Posner
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Ketki Bhushan
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Grace Fairchild
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Emma Barker
- Dana‐Farber Cancer Institute and Harvard Medical SchoolBostonMassachusettsUSA
| | - Kelly Klega
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Kimberly Stegmaier
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Brian D. Crompton
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Wendy B. London
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - Steven G. DuBois
- Dana‐Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical SchoolBostonMassachusettsUSA
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5
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Kjær EKR, Vase CB, Rossing M, Ahlborn LB, Hjalgrim LL. Detection of circulating tumor-derived material in peripheral blood of pediatric sarcoma patients: A systematic review. Transl Oncol 2023; 34:101690. [PMID: 37201250 DOI: 10.1016/j.tranon.2023.101690] [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: 11/01/2022] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Detection of circulating tumor-derived material (cTM) in the peripheral blood (PB) of cancer patients has been shown to be useful in early diagnosis, prediction of prognosis, and disease monitoring. However, it has not yet been thoroughly evaluated for pediatric sarcoma patients. METHODS We searched the PubMed and EMBASE databases for studies reporting the detection of circulating tumor cells, circulating tumor DNA, and circulating RNA in PB of pediatric sarcoma patients. Data on performance in identifying cTM and its applicability in diagnosis, and evaluation of tumor characteristics, prognostic factors, and treatment response was extracted from publications. RESULTS A total of 79 studies were assigned for the present systematic review, including detection of circulating tumor cells (116 patients), circulating tumor DNA (716 patients), and circulating RNA (2887 patients). Circulating tumor cells were detected in 76% of patients. Circulating DNA was detected in 63% by targeted NGS, 66% by shallow WGS, and 79% by digital droplet PCR. Circulating RNA was detected in 37% of patients. CONCLUSION Of the cTM from Ewing's sarcoma and rhabdomyosarcoma ctDNA proved to be the best target for clinical application including diagnosis, tumor characterization, prognosis, and monitoring of disease progression and treatment response. For osteosarcoma the most promising targets are copy number alterations or patient specific micro RNAs, however, further investigations are needed to obtain consensus on clinical utility.
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Affiliation(s)
- Eva Kristine Ruud Kjær
- Department of Paediatrics and Adolescent Medicine, Paediatric Oncology Research Laboratory (Bonkolab), Copenhagen University Hospital Rigshospitalet, 5704, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Christian Bach Vase
- Department of Paediatrics and Adolescent Medicine, Paediatric Oncology Research Laboratory (Bonkolab), Copenhagen University Hospital Rigshospitalet, 5704, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Maria Rossing
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark; Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Lise Barlebo Ahlborn
- Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Lisa Lyngsie Hjalgrim
- Department of Paediatrics and Adolescent Medicine, Paediatric Oncology Research Laboratory (Bonkolab), Copenhagen University Hospital Rigshospitalet, 5704, Blegdamsvej 9, Copenhagen DK-2100, Denmark.
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Abbou S, Klega K, Tsuji J, Tanhaemami M, Hall D, Barkauskas DA, Krailo MD, Cibulskis C, Nag A, Thorner AR, Pollock S, Imamovic-Tuco A, Shern JF, DuBois SG, Venkatramani R, Hawkins DS, Crompton BD. Circulating Tumor DNA Is Prognostic in Intermediate-Risk Rhabdomyosarcoma: A Report From the Children's Oncology Group. J Clin Oncol 2023; 41:2382-2393. [PMID: 36724417 PMCID: PMC10150913 DOI: 10.1200/jco.22.00409] [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: 02/18/2022] [Revised: 12/12/2022] [Accepted: 12/29/2022] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Novel biomarkers are needed to differentiate outcomes in intermediate-risk rhabdomyosarcoma (IR RMS). We sought to evaluate strategies for identifying circulating tumor DNA (ctDNA) in IR RMS and to determine whether ctDNA detection before therapy is associated with outcome. PATIENTS AND METHODS Pretreatment serum and tumor samples were available from 124 patients with newly diagnosed IR RMS from the Children's Oncology Group biorepository, including 75 patients with fusion-negative rhabdomyosarcoma (FN-RMS) and 49 with fusion-positive rhabdomyosarcoma (FP-RMS) disease. We used ultralow passage whole-genome sequencing to detect copy number alterations and a new custom sequencing assay, Rhabdo-Seq, to detect rearrangements and single-nucleotide variants. RESULTS We found that ultralow passage whole-genome sequencing was a method applicable to ctDNA detection in all patients with FN-RMS and that ctDNA was detectable in 13 of 75 serum samples (17%). However, the use of Rhabdo-Seq in FN-RMS samples also identified single-nucleotide variants, such as MYOD1L122R, previously associated with prognosis. Identification of pathognomonic translocations between PAX3 or PAX7 and FOXO1 by Rhabdo-Seq was the best method for measuring ctDNA in FP-RMS and detected ctDNA in 27 of 49 cases (55%). Patients with FN-RMS with detectable ctDNA at diagnosis had significantly worse outcomes than patients without detectable ctDNA (event-free survival, 33.3% v 68.9%; P = .0028; overall survival, 33.3% v 83.2%; P < .0001) as did patients with FP-RMS (event-free survival, 37% v 70%; P = .045; overall survival, 39.2% v 75%; P = .023). In multivariable analysis, ctDNA was independently associated with worse prognosis in FN-RMS but not in the smaller FP-RMS cohort. CONCLUSION Our study demonstrates that baseline ctDNA detection is feasible and is prognostic in IR RMS.
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Affiliation(s)
- Samuel Abbou
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Children and Adolescent Oncology Department, INSERM U1015, Paris-Saclay University, Villejuif, France
| | - Kelly Klega
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Junko Tsuji
- Broad Institute of Harvard and MIT, Cambridge, MA
| | | | - David Hall
- QuadW-COG Childhood Sarcoma Biostatistics and Annotation Office, Children's Oncology Group, Monrovia, CA
| | - Donald A. Barkauskas
- QuadW-COG Childhood Sarcoma Biostatistics and Annotation Office, Children's Oncology Group, Monrovia, CA
- Department of Population and Public Health Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | - Mark D. Krailo
- QuadW-COG Childhood Sarcoma Biostatistics and Annotation Office, Children's Oncology Group, Monrovia, CA
- Department of Population and Public Health Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | | | - Anwesha Nag
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Aaron R. Thorner
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Alma Imamovic-Tuco
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Jack F. Shern
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Steven G. DuBois
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Rajkumar Venkatramani
- Division of Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | | | - Brian D. Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
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Anderson P, Ghisoli M, Crompton BD, Klega KS, Wexler LH, Slotkin EK, Stanbery L, Manning L, Wallraven G, Manley M, Horvath S, Bognar E, Nemunaitis J. Pilot Study of Recurrent Ewing's Sarcoma Management with Vigil/Temozolomide/Irinotecan and Assessment of Circulating Tumor (ct) DNA. Clin Cancer Res 2023; 29:1689-1697. [PMID: 36780200 PMCID: PMC10150239 DOI: 10.1158/1078-0432.ccr-22-2292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/08/2022] [Accepted: 02/08/2023] [Indexed: 02/14/2023]
Abstract
PURPOSE Treatment options for recurrent or refractory Ewing's sarcoma (ES) are limited. Vigil is a novel autologous tumor cell therapy expressing bi-shRNA furin/GMCSF plasmid, which previously demonstrated monotherapy activity in advanced ES. Herein we report safety and evidence of benefit to Vigil for ES as potential treatment. PATIENTS AND METHODS In this pilot trial, eligible patients with recurrent or refractory ES who failed initial standard-of-care therapy received treatment with temozolomide (TEM) 100 mg/m2/day oral and irinotecan (IRI) 50 mg/m2/day oral, Days 1 to 5, in combination with Vigil (1 × 106-107 cells/mL/day intradermal, Day 15), every 21 days (Vigil/TEM/IRI). Objective response rate (ORR) by RECIST v1.1, progression-free survival (PFS), and overall survival (OS) were assessed. Circulating tumor (ct) DNA analysis was done by patient-specific droplet digital PCR on baseline and serially collected on-treatment samples. RESULTS Eight of 10 enrolled patients were evaluable for safety and efficacy (mean age 24.6; 12.6-46.1 years old); 2 did not receive Vigil. Seven of 8 patients previously received TEM/IRI. No Vigil-related adverse events were reported. Common ≥Grade 3 chemotherapy-related toxicity included neutropenia (50%) and thrombocytopenia (38%). We observed two partial response patients by RECIST; both showed histologic complete response without additional cancer therapy. Median PFS was 8.2 months (95% confidence interval, 4.3-NA). Five patients showed stable disease or better for ≥6 months. Patient-specific EWS/FLI1 ctDNA was detectable in all 8 evaluable patients at baseline. Changes in ctDNA levels corresponded to changes in disease burden. CONCLUSIONS Results demonstrated safety of combination Vigil/TEM/IRI.
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Affiliation(s)
| | | | | | | | - Leonard H. Wexler
- MSK KIDS, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily K. Slotkin
- MSK KIDS, Memorial Sloan Kettering Cancer Center, New York, New York
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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: 0] [Impact Index Per Article: 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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9
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Frederico SC, Darling C, Zhang X, Huq S, Agnihotri S, Gardner PA, Snyderman CH, Wang EW, Zenonos GA. Circulating tumor DNA – A potential aid in the management of chordomas. Front Oncol 2022; 12:1016385. [PMID: 36338734 PMCID: PMC9632974 DOI: 10.3389/fonc.2022.1016385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/30/2022] [Indexed: 11/18/2022] Open
Abstract
Chordomas are a locally invasive, low-grade, CNS malignancy that are primarily found in the skull base, spine, and sacrum. They are thought to be derived from notochordal remnants and remain a significant clinical challenge due to their local invasiveness, resistance to chemoradiation, and difficulty in achieving a complete resection. Adjuvant therapy such as proton beam therapy is critical in preventing recurrence in patients who are at high risk, however this treatment is associated with increased risk of complication. Currently, intraoperative observation and imaging findings are used to determine recurrence and success of gross total resection. These methods can be unreliable due to limited operative view, bony and soft tissue involvement, and complex post-operative changes on MRI. Earlier detection of incomplete resection or recurrence will allow for earlier ability to intervene and potentially improve patient outcomes. Circulating-tumor DNA (ctDNA) is cell-free DNA that is released by tumor cells as they undergo cellular turn-over. Monitoring ctDNA has been shown to be more sensitive at predicting residual tumor than imaging in numerous solid malignancies. Furthermore, ctDNA could be detected earlier in peripheral blood as opposed to imaging changes, allowing for earlier intervention. In this review, we intend to give a brief overview of the current state of molecular diagnosis for skull base chordomas. We will then discuss current advances in the utilization of ctDNA for the management of CNS pathologies such as glioblastoma (GBM) and brain metastases. We will also discuss the role ctDNA has in the management of non-CNS pathologies such as osteosarcoma and Ewing sarcoma (EWS). Finally, we will discuss potential implications of ctDNA monitoring for chordoma management.
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Affiliation(s)
- Stephen C. Frederico
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Corbin Darling
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Xiaoran Zhang
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sakibul Huq
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Paul A. Gardner
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Carl H. Snyderman
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Eric W. Wang
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Georgios A. Zenonos
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Georgios A. Zenonos,
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10
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An international working group consensus report for the prioritization of molecular biomarkers for Ewing sarcoma. NPJ Precis Oncol 2022; 6:65. [PMID: 36115869 PMCID: PMC9482616 DOI: 10.1038/s41698-022-00307-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/19/2022] [Indexed: 12/11/2022] Open
Abstract
The advent of dose intensified interval compressed therapy has improved event-free survival for patients with localized Ewing sarcoma (EwS) to 78% at 5 years. However, nearly a quarter of patients with localized tumors and 60–80% of patients with metastatic tumors suffer relapse and die of disease. In addition, those who survive are often left with debilitating late effects. Clinical features aside from stage have proven inadequate to meaningfully classify patients for risk-stratified therapy. Therefore, there is a critical need to develop approaches to risk stratify patients with EwS based on molecular features. Over the past decade, new technology has enabled the study of multiple molecular biomarkers in EwS. Preliminary evidence requiring validation supports copy number changes, and loss of function mutations in tumor suppressor genes as biomarkers of outcome in EwS. Initial studies of circulating tumor DNA demonstrated that diagnostic ctDNA burden and ctDNA clearance during induction are also associated with outcome. In addition, fusion partner should be a pre-requisite for enrollment on EwS clinical trials, and the fusion type and structure require further study to determine prognostic impact. These emerging biomarkers represent a new horizon in our understanding of disease risk and will enable future efforts to develop risk-adapted treatment.
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11
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Madanat-Harjuoja LM, Renfro LA, Klega K, Tornwall B, Thorner AR, Nag A, Dix D, Dome JS, Diller LR, Fernandez CV, Mullen EA, Crompton BD. Circulating Tumor DNA as a Biomarker in Patients With Stage III and IV Wilms Tumor: Analysis From a Children's Oncology Group Trial, AREN0533. J Clin Oncol 2022; 40:3047-3056. [PMID: 35580298 PMCID: PMC9462535 DOI: 10.1200/jco.22.00098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/09/2022] [Accepted: 04/01/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The utility of circulating tumor DNA (ctDNA) analyses has not been established in the risk stratification of Wilms tumor (WT). We evaluated the detection of ctDNA and selected risk markers in the serum and urine of patients with WT and compared findings with those of matched diagnostic tumor samples. PATIENTS AND METHODS Fifty of 395 children with stage III or IV WT enrolled on Children's Oncology Group trial AREN0533 had banked pretreatment serum, urine, and tumor available. Next-generation sequencing was used to detect ctDNA. Copy-number changes in 1q, 16q, and 1p, and single-nucleotide variants in serum and urine were compared with tumor biopsy data. Event-free survival (EFS) was compared between patients with and without ctDNA detection. RESULTS ctDNA was detected in the serum of 41/50 (82%) and in the urine in 13/50 (26%) patients. Agreement between serum ctDNA detection and tumor sequencing results was as follows: 77% for 1q gain, 88% for 16q deletions, and 70% for 1p deletions, with ĸ-coefficients of 0.56, 0.74, and 0.29, respectively. Sequencing also demonstrated that single-nucleotide variants detected in tumors could be identified in the ctDNA. There was a trend toward worse EFS in patients with ctDNA detected in the serum (4-year EFS 80% v 100%, P = .14). CONCLUSION ctDNA demonstrates promise as an easily accessible prognostic biomarker with potential to detect tumor heterogeneity. The observed trend toward more favorable outcome in patients with undetectable ctDNA requires validation. ctDNA profiling should be further explored as a noninvasive diagnostic and prognostic tool in the risk-adapted treatment of patients with WT.
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Affiliation(s)
| | | | - Kelly Klega
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Brett Tornwall
- Children's Oncology Group Statistics and Data Center, Monrovia, CA
| | - Aaron R. Thorner
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA
| | - Anwesha Nag
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA
| | - David Dix
- BC Children's Hospital, Vancouver, BC, Canada
| | - Jeffrey S. Dome
- Children's National Hospital and the George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Lisa R. Diller
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | | | - Brian D. Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
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12
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Braig D, Runkel A, Eisenhardt AE, Schmid A, Zeller J, Pauli T, Lausch U, Wehrle J, Bronsert P, Jung M, Kiefer J, Boerries M, Eisenhardt SU. Individualized Mini-Panel Sequencing of ctDNA Allows Tumor Monitoring in Complex Karyotype Sarcomas. Int J Mol Sci 2022; 23:ijms231810215. [PMID: 36142126 PMCID: PMC9499617 DOI: 10.3390/ijms231810215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/31/2022] [Accepted: 09/04/2022] [Indexed: 11/28/2022] Open
Abstract
Soft tissue sarcomas (STS) are rare tumors of mesenchymal origin with high mortality. After curative resection, about one third of patients suffer from distant metastases. Tumor follow-up only covers a portion of recurrences and is associated with high cost and radiation burden. For metastasized STS, only limited inferences can be drawn from imaging data regarding therapy response. To date there are no established and evidence-based diagnostic biomarkers for STS due to their rarity and diversity. In a proof-of-concept study, circulating tumor DNA (ctDNA) was quantified in (n = 25) plasma samples obtained from (n = 3) patients with complex karyotype STS collected over three years. Genotyping of tumor tissue was performed by exome sequencing. Patient-individual mini-panels for targeted next-generation sequencing were designed encompassing up to 30 mutated regions of interest. Circulating free DNA (cfDNA) was purified from plasma and ctDNA quantified therein. ctDNA values were correlated with clinical parameters. ctDNA concentrations correlated with the tumor burden. In case of full remission, no ctDNA was detectable. Patients with a recurrence at a later stage showed low levels of ctDNA during clinical remission, indicating minimal residual disease. In active disease (primary tumor or metastatic disease), ctDNA was highly elevated. We observed direct response to treatment, with a ctDNA decline after tumor resections, radiotherapy, and chemotherapy. Quantification of ctDNA allows for the early detection of recurrence or metastases and can be used to monitor treatment response in STS. Therapeutic decisions can be made earlier, such as the continuation of a targeted adjuvant therapy or the implementation of extended imaging to detect recurrences. In metastatic disease, therapy can be adjusted promptly in case of no response. These advantages may lead to a survival benefit for patients in the future.
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Affiliation(s)
- David Braig
- Department of Plastic and Hand Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, Ludwig Maximilian University of Munich, 80336 Munich, Germany
- Correspondence:
| | - Alexander Runkel
- Department of Plastic and Hand Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Anja E. Eisenhardt
- Department of Plastic and Hand Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Adrian Schmid
- Department of Plastic and Hand Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Johannes Zeller
- Department of Plastic and Hand Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Thomas Pauli
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Ute Lausch
- Department of Plastic and Hand Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Julius Wehrle
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Matthias Jung
- Department of Diagnostic and Interventional Radiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Jurij Kiefer
- Department of Plastic and Hand Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Steffen U. Eisenhardt
- Department of Plastic and Hand Surgery, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
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13
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Eisenhardt AE, Brugger Z, Lausch U, Kiefer J, Zeller J, Runkel A, Schmid A, Bronsert P, Wehrle J, Leithner A, Liegl-Atzwanger B, Giunta RE, Eisenhardt SU, Braig D. Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas. Cancers (Basel) 2022; 14:cancers14092078. [PMID: 35565213 PMCID: PMC9105697 DOI: 10.3390/cancers14092078] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Synovial sarcomas (SS) are rare soft tissue tumors of mesenchymal origin. Following resection of the primary tumor, about one third to half of the patients suffer from recurrence. Detection of local and distant recurrence during follow-up is commonly accomplished by imaging. There are no biomarkers available for routine diagnostics. We employ a highly sensitive targeted next-generation sequencing approach to monitor tumor dynamics by genotyping of circulating free DNA (cfDNA) in SS patients. cfDNA which harbors tumor-specific mutations (circulating tumor-DNA; ctDNA) correlated with the presence of viable tumor tissue. This enables timely and non-invasive detection of tumor recurrence and monitoring of treatment response independent of the anatomic location. Abstract Background: Synovial sarcoma (SS) is a malignant soft tissue tumor of mesenchymal origin that frequently occurs in young adults. Translocation of the SYT gene on chromosome 18 to the SSX genes on chromosome X leads to the formation of oncogenic fusion genes, which lead to initiation and proliferation of tumor cells. The detection and quantification of circulating tumor DNA (ctDNA) can serve as a non-invasive method for diagnostics of local or distant tumor recurrence, which could improve survival rates due to early detection. Methods: We developed a subtype-specific targeted next-generation sequencing (NGS) approach specifically targeting SS t(X;18)(p11;q11), which fuses SS18 (SYT) in chromosome 18 to SSX1 or SSX2 in chromosome x, and recurrent point mutations. In addition, patient-specific panels were designed from tumor exome sequencing. Both approaches were used to quantify ctDNA in patients’ plasma. Results: The subtype-specific assay allowed detection of somatic mutations from 25/25 tumors with a mean of 1.68 targetable mutations. The minimal limit of detection was determined at a variant allele frequency of 0.05%. Analysis of 29 plasma samples from 15 tumor patients identified breakpoint ctDNA in 6 patients (sensitivity: 40%, specificity 100%). The addition of more mutations further increased assay sensitivity. Quantification of ctDNA in plasma samples (n = 11) from one patient collected over 3 years, with a patient-specific panel based on tumor exome sequencing, correlated with the clinical course, response to treatment and tumor volume. Conclusions: Targeted NGS allows for highly sensitive tumor profiling and non-invasive detection of ctDNA in SS patients, enabling non-invasive monitoring of tumor dynamics.
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Affiliation(s)
- Anja E. Eisenhardt
- Department of Plastic and Hand Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (A.E.E.); (Z.B.); (U.L.); (J.K.); (J.Z.); (A.R.); (A.S.); (S.U.E.)
| | - Zacharias Brugger
- Department of Plastic and Hand Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (A.E.E.); (Z.B.); (U.L.); (J.K.); (J.Z.); (A.R.); (A.S.); (S.U.E.)
| | - Ute Lausch
- Department of Plastic and Hand Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (A.E.E.); (Z.B.); (U.L.); (J.K.); (J.Z.); (A.R.); (A.S.); (S.U.E.)
| | - Jurij Kiefer
- Department of Plastic and Hand Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (A.E.E.); (Z.B.); (U.L.); (J.K.); (J.Z.); (A.R.); (A.S.); (S.U.E.)
| | - Johannes Zeller
- Department of Plastic and Hand Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (A.E.E.); (Z.B.); (U.L.); (J.K.); (J.Z.); (A.R.); (A.S.); (S.U.E.)
| | - Alexander Runkel
- Department of Plastic and Hand Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (A.E.E.); (Z.B.); (U.L.); (J.K.); (J.Z.); (A.R.); (A.S.); (S.U.E.)
| | - Adrian Schmid
- Department of Plastic and Hand Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (A.E.E.); (Z.B.); (U.L.); (J.K.); (J.Z.); (A.R.); (A.S.); (S.U.E.)
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany;
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Julius Wehrle
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany;
| | - Andreas Leithner
- Department of Orthopedics and Trauma, Medical University of Graz, 8036 Graz, Austria;
| | | | - Riccardo E. Giunta
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, Ludwig Maximilian University of Munich, 80336 Munich, Germany;
| | - Steffen U. Eisenhardt
- Department of Plastic and Hand Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (A.E.E.); (Z.B.); (U.L.); (J.K.); (J.Z.); (A.R.); (A.S.); (S.U.E.)
| | - David Braig
- Department of Plastic and Hand Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (A.E.E.); (Z.B.); (U.L.); (J.K.); (J.Z.); (A.R.); (A.S.); (S.U.E.)
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, Ludwig Maximilian University of Munich, 80336 Munich, Germany;
- Correspondence:
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14
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Seidel MG, Kashofer K, Moser T, Thueringer A, Liegl-Atzwanger B, Leithner A, Szkandera J, Benesch M, El-Heliebi A, Heitzer E. Clinical implementation of plasma cell-free circulating tumor DNA quantification by digital droplet PCR for the monitoring of Ewing sarcoma in children and adolescents. Front Pediatr 2022; 10:926405. [PMID: 36046479 PMCID: PMC9420963 DOI: 10.3389/fped.2022.926405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Treatment stratification and response assessment in pediatric sarcomas has relied on imaging studies and surgical/histopathological evidence of vital tumor cells. Such studies and evidence collection processes often involve radiation and/or general anesthesia in children. Cell-free circulating tumor DNA (ctDNA) detection in blood plasma is one available method of so-called liquid biopsies that has been shown to correlate qualitatively and quantitatively with the existence of vital tumor cells in the body. Our clinical observational study focused on the utility and feasibility of ctDNA detection in pediatric Ewing sarcoma (EWS) as a marker of minimal residual disease (MRD). PATIENTS AND METHODS We performed whole genome sequencing (WGS) to identify the exact breakpoints in tumors known to carry the EWS-FLI1 fusion gene. Patient-specific fusion breakpoints were tracked in peripheral blood plasma using digital droplet PCR (ddPCR) before, during, and after therapy in six children and young adults with EWS. Presence and levels of fusion breakpoints were correlated with clinical disease courses. RESULTS We show that the detection of ctDNA in the peripheral blood of EWS patients (i) is feasible in the clinical routine and (ii) allows for the longitudinal real-time monitoring of MRD activity in children and young adults. Although changing ctDNA levels correlated well with clinical outcome within patients, between patients, a high variability was observed (inter-individually). CONCLUSION ctDNA detection by ddPCR is a highly sensitive, specific, feasible, and highly accurate method that can be applied in EWS for follow-up assessments as an additional surrogate parameter for clinical MRD monitoring and, potentially, also for treatment stratification in the near future.
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Affiliation(s)
- Markus G Seidel
- Division for Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Tina Moser
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Andrea Thueringer
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Bernadette Liegl-Atzwanger
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Andreas Leithner
- Department of Orthopedics and Trauma, Medical University of Graz, Graz, Austria
| | - Joanna Szkandera
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Martin Benesch
- Division for Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Amin El-Heliebi
- BioTechMed-Graz, Graz, Austria.,Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria.,Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Ellen Heitzer
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
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