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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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The methylome and cell-free DNA: current applications in medicine and pediatric disease. Pediatr Res 2023:10.1038/s41390-022-02448-3. [PMID: 36646885 PMCID: PMC9842217 DOI: 10.1038/s41390-022-02448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 11/21/2022] [Accepted: 12/18/2022] [Indexed: 01/18/2023]
Abstract
DNA methylation is an epigenetic mechanism that contributes to cell regulation and development, and different methylation patterns allow for the identification of cell and tissue type. Cell-free DNA (cfDNA) is composed of small circulating fragments of DNA found in plasma and urine. Total cfDNA levels correlate with the presence of inflammation and tissue injury in a variety of disease states. Unfortunately, the utility of cfDNA is limited by its lack of tissue or cell-type specificity. However, methylome analysis of cfDNA allows the identification of the tissue or cell type from which cfDNA originated. Thus, methylation patterns in cfDNA from tissues isolated from direct study may provide windows into health and disease states, thereby serving as a "liquid biopsy". This review will discuss methylation and its role in establishing cellular identity, cfDNA as a biomarker and its pathophysiologic role in the inflammatory process, and the ways cfDNA and methylomics can be jointly applied in medicine. IMPACT: Cell-free DNA (cfDNA) is increasingly being used as a noninvasive diagnostic and disease-monitoring tool in pediatric medicine. However, the lack of specificity of cfDNA limits its utility. Identification of cell type-specific methylation signatures can help overcome the limited specificity of cfDNA. As knowledge of the cfDNA methylome improves, cfDNA will be more broadly applied in medicine, such that clinicians will need to understand the methods and applications of its use.
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van Zogchel LMJ, Lak NSM, Gelineau NU, Sergeeva I, Stelloo E, Swennenhuis J, Feitsma H, van Min M, Splinter E, Bleijs M, Groot Koerkamp M, Breunis W, Meister MT, Kholossy WH, Holstege FCP, Molenaar JJ, de Leng WWJ, Stutterheim J, van der Schoot CE, Tytgat GAM. Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors. Front Oncol 2023; 13:1124737. [PMID: 37152023 PMCID: PMC10157037 DOI: 10.3389/fonc.2023.1124737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Background Liquid biopsies combine minimally invasive sample collection with sensitive detection of residual disease. Pediatric malignancies harbor tumor-driving copy number alterations or fusion genes, rather than recurrent point mutations. These regions contain tumor-specific DNA breakpoint sequences. We investigated the feasibility to use these breakpoints to design patient-specific markers to detect tumor-derived cell-free DNA (cfDNA) in plasma from patients with pediatric solid tumors. Materials and methods Regions of interest (ROI) were identified through standard clinical diagnostic pipelines, using SNP array for CNAs, and FISH or RT-qPCR for fusion genes. Using targeted locus amplification (TLA) on tumor organoids grown from tumor material or targeted locus capture (TLC) on FFPE material, ROI-specific primers and probes were designed, which were used to design droplet digital PCR (ddPCR) assays. cfDNA from patient plasma at diagnosis and during therapy was analyzed. Results TLA was performed on material from 2 rhabdomyosarcoma, 1 Ewing sarcoma and 3 neuroblastoma. FFPE-TLC was performed on 8 neuroblastoma tumors. For all patients, at least one patient-specific ddPCR was successfully designed and in all diagnostic plasma samples the patient-specific markers were detected. In the rhabdomyosarcoma and Ewing sarcoma patients, all samples after start of therapy were negative. In neuroblastoma patients, presence of patient-specific markers in cfDNA tracked tumor burden, decreasing during induction therapy, disappearing at complete remission and re-appearing at relapse. Conclusion We demonstrate the feasibility to determine tumor-specific breakpoints using TLA/TLC in different pediatric solid tumors and use these for analysis of cfDNA from plasma. Considering the high prevalence of CNAs and fusion genes in pediatric solid tumors, this approach holds great promise and deserves further study in a larger cohort with standardized plasma sampling protocols.
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Affiliation(s)
- Lieke M. J. van Zogchel
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Nathalie S. M. Lak
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Nina U. Gelineau
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | | | | | | | | | | | | | - Margit Bleijs
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Willemijn Breunis
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- University Children’s Hospital Zürich, Zürich, Switzerland
| | - Michael Torsten Meister
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | | | - Frank C. P. Holstege
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center (UMC) Utrecht and Utrecht University, Utrecht, Netherlands
| | - Jan J. Molenaar
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Wendy W. J. de Leng
- Department of Pathology, University Medical Center (UMC) Utrecht, Utrecht, Netherlands
| | - Janine Stutterheim
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - C. Ellen van der Schoot
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Godelieve A. M. Tytgat
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- *Correspondence: Godelieve A. M. Tytgat,
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Borba FMSG, Almeida AD, Tomaz ES, Silva NSED, Louzada CF. Aspectos Clínicos e Fatores Prognósticos do Neuroblastoma: Relato de Caso. REVISTA BRASILEIRA DE CANCEROLOGIA 2022. [DOI: 10.32635/2176-9745.rbc.2022v68n3.2515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
Introdução: O neuroblastoma é um tumor extracraniano originado de falhas das células da crista neural. É a neoplasia maligna mais comum dos lactentes e apresenta perfil clínico bastante heterogêneo. O objetivo deste artigo é relatar o caso de um neuroblastoma em estádio avançado e sobrevida satisfatória, a despeito dos fatores prognósticos desfavoráveis. Relato do caso: Paciente feminina, 1 ano e 4 meses, iniciou quadro de irritabilidade, distensão abdominal e febre intermitente com três meses de evolução. Ao exame físico, apresentou alopecia sugestiva de tricotilomania, linfonodomegalia cervical, inguinal e axilar e distensão abdominal. A tomografia computadorizada de abdome evidenciou massa expansiva, medindo 6,8 x 5,8 x 4,0 cm, localizada no espaço pararrenal anterior esquerdo. À cintilografia óssea e ressonância nuclear magnética, foram visualizadas imagens sugestivas de implantes secundários a distância. Após exérese tumoral total, foi confirmado neuroblastoma pouco diferenciado, com gene MYCN não amplificado e histologia desfavorável. Biópsia da crista ilíaca bilateral revelou áreas compatíveis com infiltração medular. Por se tratar de neuroblastoma estádio IV, estabeleceu-se terapêutica multimodal, com quimioterapia adjuvante após cirurgia, seguida de transplante autólogo de medula óssea, radioterapia no sítio primário da lesão e nos locais de metástases ósseas e uso de ácido 13-cis-retinoico. Conclusão: Apesar de apresentar diversos indicadores de mau prognóstico (idade, metástases ósseas, estadiamento IV, infiltração medular), a paciente permanece em remissão completa da doença há 39 meses.
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Circulating Cell-Free DNA Profiling Predicts the Therapeutic Outcome in Advanced Hepatocellular Carcinoma Patients Treated with Combination Immunotherapy. Cancers (Basel) 2022; 14:cancers14143367. [PMID: 35884434 PMCID: PMC9320668 DOI: 10.3390/cancers14143367] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Atezolizumab/bevacizumab (Atezo/Bev) combination immunotherapy has become a front-line therapy for unresectable hepatocellular carcinoma (u-HCC), but some patients are initially nonresponders. We investigated the potential of cell-free DNA (cfDNA)/circulating tumor DNA (ctDNA) as biomarkers for predicting the therapeutic outcome of u-HCC patients treated with anti-programmed cell death1-ligand1 (PD-L1)/vascular endothelial growth factor (VEGF) therapy. Patients with high levels of cfDNA showed a significantly lower overall response rate and shorter progression-free survival and overall survival (OS) than those with low levels of cfDNA. Ultradeep sequencing of cfDNA showed that the telomerase reverse transcriptase (TERT) promoter, tumor protein 53 (TP53) and catenin beta 1 (CTNNB1) were the most frequently mutated genes in ctDNA. Lastly, a TERT ctDNA mutation and a high alpha-fetoprotein (AFP) level were independent predictors of shorter OS in u-HCC patients treated with Atezo/Bev therapy and could stratify their prognoses. Collectively, cfDNA/ctDNA profiling may be useful to predict therapeutic outcome in u-HCC patients treated with Atezo/Bev therapy. Abstract Combination immunotherapy with anti-programmed cell death1-ligand1 (PD-L1) and anti-vascular endothelial growth factor (VEGF) antibodies has become the standard treatment for patients with unresectable HCC (u-HCC). However, limited patients obtain clinical benefits. Cell-free DNA (cfDNA) in peripheral blood contains circulating tumor DNA (ctDNA) that reflects molecular abnormalities in tumor tissue. We investigated the potential of cfDNA/ctDNA as biomarkers for predicting the therapeutic outcome in u-HCC patients treated with anti-PD-L1/VEGF therapy. We enrolled a multicenter cohort of 85 HCC patients treated with atezolizumab and bevacizumab (Atezo/Bev) between 2020 and 2021. Pretreatment plasma was collected, and cfDNA levels were quantified. Ultradeep sequencing of cfDNA was performed with a custom-made panel for detecting mutations in 25 HCC-related cancer genes. We evaluated the association of cfDNA/ctDNA profiles and clinical outcomes. Patients with high plasma cfDNA levels showed a significantly lower response rate and shorter progression-free survival and overall survival (OS) than those with low cfDNA levels. ctDNA detected in 55% of HCC patients included the telomerase reverse transcriptase (TERT) promoter in 31% of these patients, tumor protein 53 (TP53) in 21%, catenin beta 1 (CTNNB1) in 13% and phosphatase and tensin homolog (PTEN) in 7%. The presence or absence of ctDNA did not predict the efficacy of Atezo/Bev therapy. Twenty-six patients with a TERT mutation had significantly shorter OS than those without. The presence of a TERT mutation and alpha-fetoprotein (AFP) ≥ 400 ng/mL were independent predictors of poor OS according to multivariate Cox proportional hazard analysis and could be used to stratify patients treated with Atezo/Bev therapy based on prognosis. In conclusion, pretreatment cfDNA/ctDNA profiling may be useful for predicting the therapeutic outcome in u-HCC patients treated with anti-PD-L1/VEGF therapy.
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Feng L, Qian L, Yang S, Ren Q, Zhang S, Qin H, Wang W, Wang C, Zhang H, Yang J. Clinical parameters combined with radiomics features of PET/CT can predict recurrence in patients with high-risk pediatric neuroblastoma. BMC Med Imaging 2022; 22:102. [PMID: 35643445 PMCID: PMC9148481 DOI: 10.1186/s12880-022-00828-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/17/2022] [Indexed: 02/03/2023] Open
Abstract
Background This retrospective study aimed to develop and validate a combined model based [18F]FDG PET/CT radiomics and clinical parameters for predicting recurrence in high-risk pediatric neuroblastoma patients. Methods Eighty-four high-risk neuroblastoma patients were retrospectively enrolled and divided into training and test sets according to the ratio of 3:2. [18F]FDG PET/CT images of the tumor were segmented by 3D Slicer software and the radiomics features were extracted. The effective features were selected by the least absolute shrinkage and selection operator to construct the radiomics score (Rad_score). And the radiomics model (R_model) was constructed based on Rad_score for prediction of recurrence. Then, univariate and multivariate analyses were used to screen out the independent clinical risk parameters and construct the clinical model (C_model). A combined model (RC_model) was developed based on the Rad_score and independent clinical risk parameters and presented as radiomics nomogram. The performance of the above three models was assessed by the area under the receiver operating characteristic curve (AUC) and decision curve analysis (DCA). Results Seven radiomics features were selected for building the R_model. The AUCs of the C_model in training and test sets were 0.744 (95% confidence interval [CI], 0.595–0.874) and 0.750 (95% CI, 0.577–0.904), respectively. The R_model yielded AUCs of 0.813 (95% CI, 0.685–0.916) and 0.869 (95% CI, 0.715–0.985) in the training and test sets, respectively. The RC_model demonstrated the largest AUCs of 0.889 (95% CI, 0.794–0.963) and 0.892 (95% CI, 0.758–0.992) in the training and test sets, respectively. DCA demonstrated that RC_model added more net benefits than either the C_model or the R_model for predicting recurrence in high-risk pediatric neuroblastoma. Conclusions The combined model performed well for predicting recurrence in high-risk pediatric neuroblastoma, which can facilitate disease follow-up and management in clinical practice.
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Abstract
Neuroblastomas are tumours of sympathetic origin, with a heterogeneous clinical course ranging from localized or spontaneously regressing to widely metastatic disease. Neuroblastomas recapitulate many of the features of sympathoadrenal development, which have been directly targeted to improve the survival outcomes in patients with high-risk disease. Over the past few decades, improvements in the 5-year survival of patients with metastatic neuroblastomas, from <20% to >50%, have resulted from clinical trials incorporating high-dose chemotherapy with autologous stem cell transplantation, differentiating agents and immunotherapy with anti-GD2 monoclonal antibodies. The next generation of trials are designed to improve the initial response rates in patients with high-risk neuroblastomas via the addition of immunotherapies, targeted therapies (such as ALK inhibitors) and radiopharmaceuticals to standard induction regimens. Other trials are focused on testing precision medicine strategies for patients with relapsed and/or refractory disease, enhancing the antitumour immune response and improving the effectiveness of maintenance regimens, in order to prolong disease remission. In this Review, we describe advances in delineating the pathogenesis of neuroblastoma and in identifying the drivers of high-risk disease. We then discuss how this knowledge has informed improvements in risk stratification, risk-adapted therapy and the development of novel therapies.
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Fan H, Xing T, Hong H, Duan C, Zhao W, Zhao Q, Wang X, Huang C, Zhu S, Jin M, Su Y, Gao C, Ma X. The expression of PHOX2B in bone marrow and peripheral blood predicts adverse clinical outcome in non-high-risk neuroblastoma. Pediatr Hematol Oncol 2022; 39:343-356. [PMID: 34752187 DOI: 10.1080/08880018.2021.1995090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Paired-like homeobox 2B (PHOX2B) is a highly sensitive and specific biomarker for diagnosing neuroblastoma, as well as detecting minimal residual disease in neuroblastoma. The clinical significance of PHOX2B expression in bone marrow (BM) and peripheral blood (PB) samples of newly diagnosed patients with very low-, low- and intermediate-risk neuroblastoma remains unknown, to the best of our knowledge. The expression level of PHOX2B in paired BM and PB samples of patients with newly diagnosed neuroblastoma was validated using reverse transcription-quantitative polymerase chain reaction (RTqPCR). Among the 132 patients, 26 exhibited a positive PHOX2B expression BM (19.7%) and 11 in PB (8.3%) samples. PHOX2B was highly expressed in BM and PB samples from patients aged <18 months, with International Neuroblastoma Risk Group Staging System stages M and MS, 1p loss of heterozygosity, and high levels of lactate dehydrogenase, serum ferritin and neuron-specific enolase (p < 0.05). In all eligible patients, the 2-year event-free survival (EFS) and overall survival (OS) rates were 94.7 ± 2.0% and 97.7 ± 1.3%, respectively. However, the 2-year EFS rates were significantly decreased to 76.9 ± 8.3% and 63.6 ± 14.5% in patients with a positive PHOX2B expression in BM and PB samples, respectively (p < 0.05). Similarly, the 2-year OS rates were also decreased to 88.5 ± 6.3% and 81.8 ± 11.6% in patients with a positive PHOX2B expression in BM and PB samples, respectively (p < 0.05). In conclusion, a positive PHOX2B expression in BM and PB samples at diagnosis had a strong adverse prognostic effect on patients with non-high-risk neuroblastoma.
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Affiliation(s)
- Hongjun Fan
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Tianyu Xing
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology; National Key Discipline of Pediatrics (Capital Medical University); Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Huimin Hong
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Chao Duan
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Wen Zhao
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Qian Zhao
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Xisi Wang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Cheng Huang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Shuai Zhu
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Mei Jin
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Yan Su
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
| | - Chao Gao
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology; National Key Discipline of Pediatrics (Capital Medical University); Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Xiaoli Ma
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Ocology, Key Laboratory of Major Diseases in Children, Ministry of Education, 56 Nan Lishi Road, Xicheng District, Beijing, China
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Circulating Cell-Free DNA Assessment in Biofluids from Children with Neuroblastoma Demonstrates Feasibility and Potential for Minimally Invasive Molecular Diagnostics. Cancers (Basel) 2022; 14:cancers14092080. [PMID: 35565208 PMCID: PMC9099910 DOI: 10.3390/cancers14092080] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary The invasive nature of surgical biopsies prevents their sequential application to monitor disease. Single biopsies fail to reflect cancer dynamics, intratumor heterogeneity, and drug sensitivities that change over time. Detection and characterization of cell-free circulating tumor DNA in biofluids from patients with solid tumors may better support disease monitoring and provide advanced molecular information for clinical decision-making toward personalized medicine. Here, we investigated the cell-free DNA characteristics in blood, bone marrow, cerebrospinal fluid, and urine provided from 84 infants and children with low-, intermediate-, or high-risk neuroblastoma. We report characteristic size distribution and concentration patterns for each biofluid to provide information to support the development of successful liquid biopsy biobanking strategies. We investigate potential correlations between disease activity and cfDNA concentration and provide strong evidence that markers specific for neuroblastoma can be detected in very small blood volumes from infants. Abstract Liquid biopsy strategies in pediatric patients are challenging due to low body weight. This study investigated cfDNA size distribution and concentration in blood, bone marrow, cerebrospinal fluid, and urine from 84 patients with neuroblastoma classified as low (n = 28), intermediate (n = 6), or high risk (n = 50) to provide key data for liquid biopsy biobanking strategies. The average volume of blood and bone marrow plasma provided ranged between 1 and 2 mL. Analysis of 637 DNA electropherograms obtained by Agilent TapeStation measurement revealed five different major profiles and characteristic DNA size distribution patterns for each of the biofluids. The proportion of samples containing primarily cfDNA was, at 85.5%, the highest for blood plasma. The median cfDNA concentration amounted to 6.28 ng/mL (blood plasma), 58.2 ng/mL (bone marrow plasma), 0.08 ng/mL (cerebrospinal fluid), and 0.49 ng/mL (urine) in samples. Meta-analysis of the dataset demonstrated that multiple cfDNA-based assays employing the same biofluid sample optimally require sampling volumes of 1 mL for blood and bone marrow plasma, 2 mL for cerebrospinal fluid, and as large as possible for urine samples. A favorable response to treatment was associated with a rapid decrease in blood-based cfDNA concentration in patients with high-risk neuroblastoma. Blood-based cfDNA concentration was not sufficient as a single parameter to indicate high-risk disease recurrence. We provide proof of concept that monitoring neuroblastoma-specific markers in very small blood volumes from infants is feasible.
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van Zogchel LMJ, Lak NSM, Verhagen OJHM, Tissoudali A, Gussmalla Nuru M, Gelineau NU, Zappeij-Kannengieter L, Javadi A, Zijtregtop EAM, Merks JHM, van den Heuvel-Eibrink M, Schouten-van Meeteren AYN, Stutterheim J, van der Schoot CE, Tytgat GAM. Novel Circulating Hypermethylated RASSF1A ddPCR for Liquid Biopsies in Patients With Pediatric Solid Tumors. JCO Precis Oncol 2021; 5:PO.21.00130. [PMID: 34820594 PMCID: PMC8608265 DOI: 10.1200/po.21.00130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/06/2021] [Accepted: 10/08/2021] [Indexed: 12/19/2022] Open
Abstract
Liquid biopsies can be used to investigate tumor-derived DNA, circulating in the cell-free DNA (cfDNA) pool in blood. We aimed to develop a droplet digital polymerase chain reaction (ddPCR) assay detecting hypermethylation of tumor suppressor gene RASSF1A as a simple standard test to detect various pediatric tumor types in small volume blood samples and to evaluate this test for monitoring treatment response of patients with high-risk neuroblastoma. The circulating tumor marker hypermethylated RASSF1A can be detected in the plasma of pediatric patients with solid tumors![]()
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Affiliation(s)
- Lieke M J van Zogchel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Nathalie S M Lak
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Onno J H M Verhagen
- Department of Immunocytology, Sanquin Diagnostic Services, Amsterdam, the Netherlands
| | - Ahmed Tissoudali
- Department of Immunohematology Diagnostics, Sanquin Diagnostic Services, Amsterdam, the Netherlands
| | - Mohammed Gussmalla Nuru
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Nina U Gelineau
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Lily Zappeij-Kannengieter
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands.,Department of Immunocytology, Sanquin Diagnostic Services, Amsterdam, the Netherlands
| | - Ahmad Javadi
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Eline A M Zijtregtop
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pediatric Oncology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, the Netherlands
| | | | | | | | | | - C Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
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11
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Liu T, Merguerian MD, Rowe SP, Pratilas CA, Chen AR, Ladle BH. Exceptional response to the ALK and ROS1 inhibitor lorlatinib and subsequent mechanism of resistance in relapsed ALK F1174L-mutated neuroblastoma. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006064. [PMID: 34210658 PMCID: PMC8327881 DOI: 10.1101/mcs.a006064] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/14/2021] [Indexed: 11/24/2022] Open
Abstract
Treatment of high-risk neuroblastoma typically incorporates multiagent chemotherapy, surgery, radiation therapy, autologous stem cell transplantation, immunotherapy, and differentiation therapy. The discovery of activating mutations in ALK receptor tyrosine kinase (ALK) in ∼8% of neuroblastomas opens the possibility of further improving outcomes for this subset of patients with the addition of ALK inhibitors. ALK inhibitors have shown efficacy in tumors such as non-small-cell lung cancer and anaplastic large cell lymphoma in which wild-type ALK overexpression is driven by translocation events. In contrast, ALK mutations driving neuroblastomas are missense mutations in the tyrosine kinase domain yielding constitutive activation and differing sensitivity to available ALK inhibitors. We describe a case of a patient with relapsed, refractory, metastatic ALK F1174L-mutated neuroblastoma who showed no response to the first-generation ALK inhibitor crizotinib but had a subsequent complete response to the ALK/ROS1 inhibitor lorlatinib. The patient's disease relapsed after 13 mo of treatment. Sequencing of cell-free DNA at the time of relapse pointed toward a potential mechanism of acquired lorlatinib resistance: amplification of CDK4 and FGFR1 and a NRAS Q61K mutation. We review the literature regarding differing sensitivity of ALK mutations found in neuroblastoma to current FDA-approved ALK inhibitors and known pathways of acquired resistance. Our report adds to the literature of important correlations between neuroblastoma ALK mutation status and clinical responsiveness to ALK inhibitors. It also highlights the importance of understanding acquired mechanisms of resistance.
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Affiliation(s)
- Tingting Liu
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Division of Pediatric Oncology, Baltimore, Maryland 21287, USA
| | - Matthew D Merguerian
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Division of Pediatric Oncology, Baltimore, Maryland 21287, USA
| | - Steven P Rowe
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, Maryland 21287, USA
| | - Christine A Pratilas
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Division of Pediatric Oncology, Baltimore, Maryland 21287, USA
| | - Allen R Chen
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Division of Pediatric Oncology, Baltimore, Maryland 21287, USA
| | - Brian H Ladle
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Division of Pediatric Oncology, Baltimore, Maryland 21287, USA
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12
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Retrieval of vector integration sites from cell-free DNA. Nat Med 2021; 27:1458-1470. [PMID: 34140705 DOI: 10.1038/s41591-021-01389-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 05/07/2021] [Indexed: 12/23/2022]
Abstract
Gene therapy (GT) has rapidly attracted renewed interest as a treatment for otherwise incurable diseases, with several GT products already on the market and many more entering clinical testing for selected indications. Clonal tracking techniques based on vector integration enable monitoring of the fate of engineered cells in the blood of patients receiving GT and allow assessment of the safety and efficacy of these procedures. However, owing to the limited number of cells that can be tested and the impracticality of studying cells residing in peripheral organs without performing invasive biopsies, this approach provides only a partial snapshot of the clonal repertoire and dynamics of genetically modified cells and reduces the predictive power as a safety readout. In this study, we developed liquid biopsy integration site sequencing, or LiBIS-seq, a polymerase chain reaction technique optimized to quantitatively retrieve vector integration sites from cell-free DNA released into the bloodstream by dying cells residing in several tissues. This approach enabled longitudinal monitoring of in vivo liver-directed GT and clonal tracking in patients receiving hematopoietic stem cell GT, improving our understanding of the clonal composition and turnover of genetically modified cells in solid tissues and, in contrast to conventional analyses based only on circulating blood cells, enabling earlier detection of vector-marked clones that are aberrantly expanding in peripheral tissues.
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13
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Liu J, Zhang M, Kan Y, Wang W, Liu J, Gong J, Yang J. Nuclear Factor-κB Activating Protein Plays an Oncogenic Role in Neuroblastoma Tumorigenesis and Recurrence Through the Phosphatidylinositol 3-Kinase/Protein Kinase B Signaling Pathway. Front Cell Dev Biol 2021; 8:622793. [PMID: 33553160 PMCID: PMC7859273 DOI: 10.3389/fcell.2020.622793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Nuclear factor-κB activating protein (NKAP) is a conserved nuclear protein that acts as an oncogene in various cancers and is associated with a poor prognosis. This study aimed to investigate the role of NKAP in neuroblastoma (NB) progression and recurrence. We compared NKAP gene expression between 89 recurrence and 134 non-recurrence patients with NB by utilizing the ArrayExpress database. The relationship between NKAP expression and clinicopathological features was evaluated by correlation analysis. We knocked down NKAP expression in NB1 and SK-N-SH cells by small interfering RNA transfection to verify its role in tumor proliferation, apoptosis, and the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway. NKAP gene expression in NB tissues was significantly overexpressed in the recurrence group compared with the non-recurrence group, and NKAP was enriched in the PI3K/AKT pathway. Correlation analysis revealed NKAP expression was correlated with chromosome 11q deletion in patients with NB. Knockdown of NKAP expression significantly inhibited the proliferation and promoted the apoptosis of NB1 and SK-N-SH cells. Moreover, we found that small interfering NKAP significantly reduced p-PI3K and p-AKT expression. NKAP knockdown played an oncogenic role in NB by inhibiting PI3K/AKT signaling pathway activations both in vitro and in vivo. Our research revealed that NKAP mediates NB cells by inhibited proliferation and promoted apoptosis through activating the PI3K/AKT signaling pathways, and the expression of NKAP may act as a novel biomarker for predicting recurrence and chromosome 11q deletion in patients with NB.
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Affiliation(s)
- Jun Liu
- Department of Nuclear Medicine, Beijing Friendship Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Mingyu Zhang
- Department of Nuclear Medicine, Beijing Friendship Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Ying Kan
- Department of Nuclear Medicine, Beijing Friendship Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Wei Wang
- Department of Nuclear Medicine, Beijing Friendship Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Jie Liu
- Department of Nuclear Medicine, Beijing Friendship Hospital, Affiliated to Capital Medical University, Beijing, China
| | - Jianhua Gong
- Oncology Department, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jigang Yang
- Department of Nuclear Medicine, Beijing Friendship Hospital, Affiliated to Capital Medical University, Beijing, China
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14
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Su Y, Wang L, Zhao Q, Yue Z, Zhao W, Wang X, Duan C, Jin M, Zhang D, Chen S, Yin J, Qiu L, Cheng X, Xu Z, Ma X. Implementation of the plasma MYCN/NAGK ratio to detect MYCN amplification in patients with neuroblastoma. Mol Oncol 2020; 14:2884-2893. [PMID: 32896084 PMCID: PMC7607162 DOI: 10.1002/1878-0261.12794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/28/2020] [Accepted: 09/01/2020] [Indexed: 01/26/2023] Open
Abstract
Detection of amplification of the MYCN gene is essential for determining optimal treatment and estimating prognosis of patients with neuroblastoma (NB). DNA FISH with neuroblastoma tissues or patient‐derived bone marrow cells is the standard clinical practice for the detection of MYCN amplification. As tumor cells may often be unavailable, we developed a method to detect MYCN amplification in the plasma of patients with neuroblastoma. Taking single‐copy NAGK DNA as reference, we used real‐time quantitative PCR (qPCR) to determine the MYCN/NAGK ratio in the plasma of 115 patients diagnosed with NB. An increased MYCN/NAGK ratio in the plasma was consistent with MYCN amplification as assessed by DNA FISH. The AUC for a MYCN/NAGK ratio equal to 6.965 was 0.943, with 86% sensitivity and 100% specificity. Beyond the threshold of 6.965, the MYCN/NAGK ratio correlated with a heavier tumor burden. Event‐free and overall survival of two years were significantly shortened in stage 4 patients with a MYCN/NAGK ratio higher than 6.965. Plasma MYCN/NAGK ratios increased in patients with progressive disease and relapse. Thus, we conclude that the determination of the plasma MYCN/NAGK ratio by qPCR is a noninvasive and reproducible method to measure MYCN amplification in patients with NB.
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Affiliation(s)
- Yan Su
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lijun Wang
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, China
| | - Qian Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhixia Yue
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wen Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xisi Wang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chao Duan
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Mei Jin
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Dawei Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Shenglan Chen
- Taizhou Genewill Medical Laboratory Company Limited, China
| | - Jianfeng Yin
- Taizhou Genewill Medical Laboratory Company Limited, China
| | - Lihua Qiu
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, China
| | - Xianfeng Cheng
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, China
| | - Zhong Xu
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, China
| | - Xiaoli Ma
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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