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Reed DR, Tulpule A, Metts J, Trucco M, Robertson-Tessi M, O'Donohue TJ, Iglesias-Cardenas F, Isakoff MS, Mauguen A, Shukla N, Dela Cruz FS, Tap W, Kentsis A, Morris CD, Hameed M, Honeyman JN, Behr GG, Sulis ML, Ortiz MV, Slotkin E. Pediatric Leukemia Roadmaps Are a Guide for Positive Metastatic Bone Sarcoma Trials. J Clin Oncol 2024; 42:2955-2960. [PMID: 38843482 DOI: 10.1200/jco.23.02717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 03/02/2024] [Accepted: 04/11/2024] [Indexed: 08/30/2024] Open
Abstract
ALL cures require many MRD therapies. This strategy should drive experiments and trials in metastatic bone sarcomas.
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Affiliation(s)
- Damon R Reed
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Asmin Tulpule
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jonathan Metts
- Johns Hopkins All Children's Hospital, St Petersburg, FL
| | | | | | - Tara J O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Filemon S Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - William Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alex Kentsis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Carol D Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joshua N Honeyman
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gerald G Behr
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Luisa Sulis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
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2
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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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Anderson CJ, Yang H, Parsons J, Ahrens WA, Jagosky MH, Hsu JH, Patt JC, Kneisl JS, Steuerwald NM. Can a Liquid Biopsy Detect Circulating Tumor DNA With Low-passage Whole-genome Sequencing in Patients With a Sarcoma? A Pilot Evaluation. Clin Orthop Relat Res 2024:00003086-990000000-01651. [PMID: 38905450 DOI: 10.1097/corr.0000000000003161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/30/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND A liquid biopsy is a test that evaluates the status of a disease by analyzing a sample of bodily fluid, most commonly blood. In recent years, there has been progress in the development and clinical application of liquid biopsy methods to identify blood-based, tumor-specific biomarkers for many cancer types. However, the implementation of these technologies to aid in the treatment of patients who have a sarcoma remains behind other fields of cancer medicine. For this study, we chose to evaluate a sarcoma liquid biopsy based on circulating tumor DNA (ctDNA). All human beings have normal cell-free DNA (cfDNA) circulating in the blood. In contrast with cfDNA, ctDNA is genetic material present in the blood stream that is derived from a tumor. ctDNA carries the unique genomic fingerprint of the tumor with changes that are not present in normal circulating cfDNA. A successful ctDNA liquid biopsy must be able to target these tumor-specific genetic alterations. For instance, epidermal growth factor receptor (EGFR) mutations are common in lung cancers, and ctDNA liquid biopsies are currently in clinical use to evaluate the status of disease in patients who have a lung cancer by detecting EGFR mutations in the blood. As opposed to many carcinomas, sarcomas do not have common recurrent mutations that could serve as the foundation to a ctDNA liquid biopsy. However, many sarcomas have structural changes to their chromosomes, including gains and losses of portions or entire chromosomes, known as copy number alterations (CNAs), that could serve as a target for a ctDNA liquid biopsy. Murine double minute 2 (MDM2) amplification in select lipomatous tumors or parosteal osteosarcoma is an example of a CNA due to the presence of extra copies of a segment of the long arm of chromosome 12. Since a majority of sarcomas demonstrate a complex karyotype with numerous CNAs, a blood-based liquid biopsy strategy that searches for these CNAs may be able to detect the presence of sarcoma ctDNA. Whole-genome sequencing (WGS) is a next-generation sequencing technique that evaluates the entire genome. The depth of coverage of WGS refers to how detailed the sequencing is, like higher versus lower power on a microscope. WGS can be performed with high-depth sequencing (that is, > 60×), which can detect individual point mutations, or low-depth sequencing (that is, 0.1× to 5×), referred to as low-passage whole-genome sequencing (LP-WGS), which may not detect individual mutations but can detect structural chromosomal changes including gains and losses (that is, CNAs). While similar strategies have shown favorable early results for specific sarcoma subtypes, LP-WGS has not been evaluated for applicability to the broader population of patients who have a sarcoma. QUESTIONS/PURPOSES Does an LP-WGS liquid biopsy evaluating for CNAs detect ctDNA in plasma samples from patients who have sarcomas representing a variety of histologic subtypes? METHODS This was a retrospective study conducted at a community-based, tertiary referral center. Nine paired (plasma and formalin-fixed paraffin-embedded [FFPE] tissue) and four unpaired (plasma) specimens from patients who had a sarcoma were obtained from a commercial biospecimen bank. Three control specimens from individuals who did not have cancer were also obtained. The paired and unpaired specimens from patients who had a sarcoma represented a variety of sarcoma histologic subtypes. cfDNA was extracted, amplified, and quantified. Libraries were prepared, and LP-WGS was performed using a NextSeq 500 next-generation sequencing machine at a low depth of sequencing coverage (∼1×). The ichorCNA bioinformatics algorithm, which was designed to detect CNAs from low-depth genomic sequencing data, was used to analyze the data. In contrast with the gold standard for diagnosis in the form of histopathologic analysis of a tissue sample, this test does not discriminate between sarcoma subtypes but detects the presence of tumor-derived CNAs within the ctDNA in the blood that should not be present in a patient who does not have cancer. The liquid biopsy was positive for the detection of cancer if the ichorCNA algorithm detected the presence of ctDNA. The algorithm was also used to quantitatively estimate the percent ctDNA within the cfDNA. The concentration of ctDNA was then calculated from the percent ctDNA relative to the total concentration of cfDNA. The CNAs of the paired FFPE tissue and plasma samples were graphically visualized using aCNViewer software. RESULTS This LP-WGS liquid biopsy detected ctDNA in 9 of 13 of the plasma specimens from patients with a sarcoma. The other four samples from patients with a sarcoma and all serum specimens from patients without cancer had no detectable ctDNA. Of those 9 patients with positive liquid biopsy results, the percent ctDNA ranged from 6% to 11%, and calculated ctDNA quantities were 0.04 to 5.6 ng/mL, which are levels to be expected when ctDNA is detectable. CONCLUSION In this small pilot study, we were able to detect sarcoma ctDNA with an LP-WGS liquid biopsy searching for CNAs in the plasma of most patients who had a sarcoma representing a variety of histologic subtypes. CLINICAL RELEVANCE These results suggest that an LP-WGS liquid biopsy evaluating for CNAs to identify ctDNA may be more broadly applicable to the population of patients who have a sarcoma than previously reported in studies focusing on specific subtypes. Large prospective clinical trials that gather samples at multiple time points during the process of diagnosis, treatment, and surveillance will be needed to further assess whether this technique can be clinically useful. At our institution, we are in the process of developing a large prospective clinical trial for this purpose.
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Affiliation(s)
- Colin J Anderson
- Musculoskeletal Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - HsihTe Yang
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Judy Parsons
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Will A Ahrens
- Carolina Pathology Group, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Megan H Jagosky
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Johann H Hsu
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Joshua C Patt
- Musculoskeletal Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Jeffrey S Kneisl
- Musculoskeletal Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
| | - Nury M Steuerwald
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
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Mohr A, Marques Da Costa ME, Fromigue O, Audinot B, Balde T, Droit R, Abbou S, Khneisser P, Berlanga P, Perez E, Marchais A, Gaspar N. From biology to personalized medicine: Recent knowledge in osteosarcoma. Eur J Med Genet 2024; 69:104941. [PMID: 38677541 DOI: 10.1016/j.ejmg.2024.104941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
High-grade osteosarcoma is the most common paediatric bone cancer. More than one third of patients relapse and die of osteosarcoma using current chemotherapeutic and surgical strategies. To improve outcomes in osteosarcoma, two crucial challenges need to be tackled: 1-the identification of hard-to-treat disease, ideally from diagnosis; 2- choosing the best combined or novel therapies to eradicate tumor cells which are resistant to current therapies leading to disease dissemination and metastasize as well as their favorable microenvironment. Genetic chaos, tumor complexity and heterogeneity render this task difficult. The development of new technologies like next generation sequencing has led to an improvement in osteosarcoma oncogenesis knownledge. This review summarizes recent biological and therapeutical advances in osteosarcoma, as well as the challenges that must be overcome in order to develop personalized medicine and new therapeutic strategies and ultimately improve patient survival.
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Affiliation(s)
- Audrey Mohr
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | | | - Olivia Fromigue
- National Institute for Health and Medical Research (INSERM) U981, Gustave Roussy Institute, Villejuif, France
| | - Baptiste Audinot
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | - Thierno Balde
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | - Robin Droit
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | - Samuel Abbou
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France; Department of Oncology for Children and Adolescents, Gustave Roussy Institute, Villejuif, France
| | - Pierre Khneisser
- Department of medical Biology and Pathology, Gustave Roussy Institute, Villejuif, France
| | - Pablo Berlanga
- Department of Oncology for Children and Adolescents, Gustave Roussy Institute, Villejuif, France
| | - Esperanza Perez
- Department of Oncology for Children and Adolescents, Gustave Roussy Institute, Villejuif, France
| | - Antonin Marchais
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | - Nathalie Gaspar
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France; Department of Oncology for Children and Adolescents, Gustave Roussy Institute, Villejuif, France.
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5
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Vayani OR, Kaufman ME, Moore K, Chennakesavalu M, TerHaar R, Chaves G, Chlenski A, He C, Cohn SL, Applebaum MA. Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma. Pediatr Blood Cancer 2024; 71:e30735. [PMID: 37859597 PMCID: PMC10842006 DOI: 10.1002/pbc.30735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Cell-free DNA (cfDNA) profiles of 5-hydroxymethylcytosine (5-hmC), an epigenetic marker of open chromatin and active gene expression, are correlated with metastatic disease burden in patients with neuroblastoma. Neuroblastoma tumors are comprised of adrenergic (ADRN) and mesenchymal (MES) cells, and the relative abundance of each in tumor biopsies has prognostic implications. We hypothesized that ADRN and MES-specific signatures could be quantified in cfDNA 5-hmC profiles and would augment the detection of metastatic burden in patients with neuroblastoma. METHODS We previously performed an integrative analysis to identify ADRN and MES-specific genes (n = 373 and n = 159, respectively). Purified DNA from cell lines was serial diluted with healthy donor cfDNA. Using Gene Set Variation Analysis (GSVA), ADRN and MES signatures were optimized. We then quantified signature scores, and our prior neuroblastoma signature, in cfDNA from 84 samples from 46 high-risk patients including 21 patients with serial samples. RESULTS Samples from patients with higher metastatic burden had increased GSVA scores for both ADRN and MES gene signatures (p < .001). While ADRN and MES signature scores tracked together in serially collected samples, we identified instances of patients with increases in either MES or ADRN score at relapse. CONCLUSIONS While it is feasible to identify ADRN and MES signatures using 5-hmC profiles of cfDNA from neuroblastoma patients and correlate these signatures to metastatic burden, additional data are needed to determine the optimal strategies for clinical implementation. Prospective evaluation in larger cohorts is ongoing.
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Affiliation(s)
- Omar R Vayani
- Pritzker School of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Maria E Kaufman
- Pritzker School of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Kelley Moore
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | | | - Rachel TerHaar
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Gepoliano Chaves
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Alexandre Chlenski
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
| | - Susan L Cohn
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Mark A Applebaum
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
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Prasanth BK, Alkhowaiter S, Sawarkar G, Dharshini BD, R Baskaran A. Unlocking Early Cancer Detection: Exploring Biomarkers, Circulating DNA, and Innovative Technological Approaches. Cureus 2023; 15:e51090. [PMID: 38274938 PMCID: PMC10808885 DOI: 10.7759/cureus.51090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/25/2023] [Indexed: 01/27/2024] Open
Abstract
Research and development improvements in early cancer diagnosis have had a significant positive impact on health. In the treatment and prevention of cancer, early detection is essential. In this context, biomarkers are essential because they offer important information on the state of cells at any particular time. Cells go through unique changes when they shift from a healthy condition to a malignant state, changes that appropriate biomarkers may pick up. Recent advancements have been made to identify and characterize circulating cancer-specific mutations in cell-free circulating DNA derived from tumors and tumor cells. A patient's delay between the time they first detect symptoms and the time they contact a doctor has been noted for many cancer forms. The tumor's location and features significantly impact the presentation of symptoms judged appropriate for early diagnosis. Lack of knowledge of the severity of the symptoms may be one cause for this delay. Our review is largely focused on the ongoing developments of early diagnosis in the study of biomarkers, circulating DNA for diagnosis, the biology of early challenges, early symptoms, liquid biopsies, detectable by imaging, established tumor markers, plasma DNA technologies, gender differences, and artificial intelligence (AI) in diagnosis. This review aims to determine and evaluate Indicators for detecting early cancer, assessing medical conditions, and evaluating potential risks. For Individuals with a heightened likelihood of developing cancer or who have already been diagnosed, early identification is crucial for enhancing prognosis and raising the likelihood of effective treatment.
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Affiliation(s)
- B Krishna Prasanth
- Department of Community Medicine, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research, Chennai, IND
| | - Saad Alkhowaiter
- Department of Gastroenterology, College of Medicine, King Khalid University Hospital, Riyadh, SAU
| | - Gaurav Sawarkar
- Rachana Sharir, Mahatma Gandhi Ayurveda College, Hospital and Research Centre, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - B Divya Dharshini
- Department of Biochemistry, Government Medical College, Khammam, Telangana, IND
| | - Ajay R Baskaran
- Department of Psychiatry, National Health Service, Shrewsbury, GBR
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7
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Vayani OR, Kaufman ME, Moore K, Chennakesavalu M, TerHaar R, Chaves G, Chlenski A, He C, Cohn SL, Applebaum MA. Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.554943. [PMID: 37693610 PMCID: PMC10491182 DOI: 10.1101/2023.08.30.554943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background Cell free DNA (cfDNA) profiles of 5-hydroxymethylcytosine (5-hmC), an epigenetic marker of open chromatin and active gene expression, are correlated with metastatic disease burden in patients with neuroblastoma. Neuroblastoma tumors are comprised of adrenergic (ADRN) and mesenchymal (MES) cells, and the relative abundance of each in tumor biopsies has prognostic implications. We hypothesized that ADRN and MES specific signatures could be quantified in cfDNA 5-hmC profiles and would augment the detection of metastatic burden in patients with neuroblastoma. Methods We previously performed an integrative analysis to identify ADRN and MES specific genes (n=373 and n=159, respectively). Purified DNA from cell lines was serial diluted with healthy donor cfDNA. Using Gene Set Variation Analysis (GSVA), ADRN and MES signatures were optimized. We then quantified signature scores, and our prior neuroblastoma signature, in cfDNA from 84 samples from 46 high-risk patients including 21 patients with serial samples. Results Samples from patients with higher metastatic burden had increased GSVA scores for both ADRN and MES gene signatures (p < 0.001). While ADRN and MES signature scores tracked together in serially collected samples, we identified instances of patients with increases in either MES or ADRN score at relapse. Conclusions While it is feasible to identify ADRN and MES signatures using 5-hmC profiles of cfDNA from neuroblastoma patients and correlate these signatures to metastatic burden, additional data are needed to determine the optimal strategies for clinical implementation. Prospective evaluation in larger cohorts is ongoing.
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8
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Silva FLT, Ruas JS, Euzébio MF, Hoffmann IL, Junqueira T, Tedeschi H, Pereira LH, Cassone AE, Cardinalli IA, Seidinger AL, Jotta PY, Maschietto M. 11p15 Epimutations in Pediatric Embryonic Tumors: Insights from a Methylome Analysis. Cancers (Basel) 2023; 15:4256. [PMID: 37686532 PMCID: PMC10486592 DOI: 10.3390/cancers15174256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023] Open
Abstract
Embryonic tumors share few recurrent mutations, suggesting that other mechanisms, such as aberrant DNA methylation, play a prominent role in their development. The loss of imprinting (LOI) at the chromosome region 11p15 is the germline alteration behind Beckwith-Wiedemann syndrome that results in an increased risk of developing several embryonic tumors. This study analyzed the methylome, using EPIC Beadchip arrays from 99 sporadic embryonic tumors. Among these tumors, 46.5% and 14.6% presented alterations at imprinted control regions (ICRs) 1 and 2, respectively. Based on the methylation levels of ICR1 and ICR2, four clusters formed with distinct methylation patterns, mostly for medulloblastomas (ICR1 loss of methylation (LOM)), Wilms tumors, and hepatoblastomas (ICR1 gain of methylation (GOM), with or without ICR2 LOM). To validate the results, the methylation status of 29 cases was assessed with MS-MLPA, and a high level of agreement was found between both methodologies: 93% for ICR1 and 79% for ICR2. The MS-MLPA results indicate that 15 (51.7%) had ICR1 GOM and 11 (37.9%) had ICR2 LOM. To further validate our findings, the ICR1 methylation status was characterized via digital PCR (dPCR) in cell-free DNA (cfDNA) extracted from peripheral blood. At diagnosis, we detected alterations in the methylation levels of ICR1 in 62% of the cases, with an agreement of 76% between the tumor tissue (MS-MLPA) and cfDNA methods. Among the disagreements, the dPCR was able to detect ICR1 methylation level changes presented at heterogeneous levels in the tumor tissue, which were detected only in the methylome analysis. This study highlights the prevalence of 11p15 methylation status in sporadic embryonic tumors, with differences relating to methylation levels (gain or loss), location (ICR1 or ICR2), and tumor types (medulloblastomas, Wilms tumors, and hepatoblastomas).
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Affiliation(s)
- Felipe Luz Torres Silva
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | - Juliana Silveira Ruas
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
| | - Mayara Ferreira Euzébio
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | | | - Thais Junqueira
- Boldrini Children’s Hospital, Campinas 13083-210, SP, Brazil
| | - Helder Tedeschi
- Boldrini Children’s Hospital, Campinas 13083-210, SP, Brazil
| | | | | | | | - Ana Luiza Seidinger
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
| | - Patricia Yoshioka Jotta
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
| | - Mariana Maschietto
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
- 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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Gelineau NU, van Barneveld A, Samim A, Van Zogchel L, Lak N, Tas ML, Matser Y, Mavinkurve-Groothuis AMC, van Grotel M, Zsiros J, van Eijkelenburg NKA, Knops RRG, van Ewijk R, Langenberg KPS, Krijger RD, Hiemcke-Jiwa LS, Van Paemel R, Cornelli L, De Preter K, De Wilde B, Van Der Schoot E, Tytgat G. Case series on clinical applications of liquid biopsy in pediatric solid tumors: towards improved diagnostics and disease monitoring. Front Oncol 2023; 13:1209150. [PMID: 37664065 PMCID: PMC10473251 DOI: 10.3389/fonc.2023.1209150] [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: 04/20/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Background and aims Solid tumors account for about 30% of all pediatric cancers. The diagnosis is typically based on histological and molecular analysis of a primary tumor biopsy. Liquid biopsies carry several advantages over conventional tissue biopsy. However, their use for genomic analysis and response monitoring of pediatric solid tumors is still in experimental stages and mostly performed retrospectively without direct impact on patient management. In this case series we discuss six clinical cases of children with a solid tumor for whom a liquid biopsy assay was performed and demonstrate the potential of liquid biopsy for future clinical decision making. Methods We performed quantitative real-time PCR (RT-qPCR), droplet digital PCR (ddPCR) or reduced representation bisulphite sequencing of cell-free DNA (cfRRBS) on liquid biopsies collected from six pediatric patients with a solid tumor treated between 2017 and 2023 at the Princess Máxima Center for Pediatric Oncology in the Netherlands. Results were used to aid in clinical decision making by contribution to establish a diagnosis, by prognostication and response to therapy monitoring. Results In three patients cfRRBS helped to establish the diagnosis of a rhabdomyosarcoma, an Ewing sarcoma and a neuroblastoma (case 1-3). In two patients, liquid biopsies were used for prognostication, by MYCN ddPCR in a patient with neuroblastoma and by RT-qPCR testing rhabdomyosarcoma-specific mRNA in bone marrow of a patient with a rhabdomyosarcoma (case 4 and 5). In case 6, mRNA testing demonstrated disease progression and assisted clinical decision making. Conclusion This case series illustrates the value of liquid biopsy. We further demonstrate and recommend the use of liquid biopsies to be used in conjunction with conventional methods for the determination of metastatic status, prognostication and monitoring of treatment response in patients with pediatric solid tumors.
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Affiliation(s)
- Nina U. Gelineau
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
| | | | - Atia Samim
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Lieke Van Zogchel
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
| | - Nathalie Lak
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
| | - Michelle L. Tas
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Yvette Matser
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Martine van Grotel
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Jószef Zsiros
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Rutger R. G. Knops
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Roelof van Ewijk
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Ronald De Krijger
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Laura S. Hiemcke-Jiwa
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ruben Van Paemel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University, Ghent, Belgium
- Research Institute, Ghent University, Ghent, East Flanders, Belgium
| | - Lotte Cornelli
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Gent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Research Institute, Ghent University, Ghent, East Flanders, Belgium
- VIB-UGent Center for Medical Biotechnology, Gent, Belgium
| | - Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University, Ghent, Belgium
- Research Institute, Ghent University, Ghent, East Flanders, Belgium
| | - Ellen Van Der Schoot
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
| | - Godelieve Tytgat
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
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10
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Cohen-Gogo S, Denburg AE, Villani A, Thacker N, Egan G, Simao Rafael M, Malkin D, Morgenstern DA. Precision oncology for children: A primer for paediatricians. Paediatr Child Health 2023; 28:278-284. [PMID: 37484033 PMCID: PMC10362955 DOI: 10.1093/pch/pxac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/09/2022] [Indexed: 07/25/2023] Open
Abstract
Cancer is the leading cause of disease-related death in children, adolescents, and young adults beyond the newborn period in North America. Improving survival rates for patients with hard-to-cure cancer remains a challenge. One approach that has gained particular traction is 'precision oncology', whereby next-generation sequencing is used to identify genomic or transcriptomic changes that can help clarify the diagnosis, refine prognosis, define an underlying genetic cause, or identify a unique treatment target for a patient's cancer. In this primer, we provide a brief overview of the evolution of precision paediatric oncology, its current application to clinical oncology practice, and its future potential as a foundational approach to paediatric oncology care in Canada and around the world. We also address the many challenges and limitations inherent to the implementation of precision oncology as the standard of care, including ethical and economic considerations.
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Affiliation(s)
- Sarah Cohen-Gogo
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Avram E Denburg
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Anita Villani
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Nirav Thacker
- Division of Hematology/Oncology, Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Grace Egan
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margarida Simao Rafael
- Department of Oncology, Solid Tumor Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - David Malkin
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel A Morgenstern
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
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11
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Zheng H, Liu J, Pan X, Cui X. Biomarkers for patients with Wilms tumor: a review. Front Oncol 2023; 13:1137346. [PMID: 37554168 PMCID: PMC10405734 DOI: 10.3389/fonc.2023.1137346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/27/2023] [Indexed: 08/10/2023] Open
Abstract
Wilms tumor, originating from aberrant fetal nephrogenesis, is the most common renal malignancy in childhood. The overall survival of children is approximately 90%. Although existing risk-stratification systems are helpful in identifying patients with poor prognosis, the recurrence rate of Wilms tumors remains as high as 15%. To resolve this clinical problem, diverse studies on the occurrence and progression of the disease have been conducted, and the results are encouraging. A series of molecular biomarkers have been identified with further studies on the mechanism of tumorigenesis. Some of these show prognostic value and have been introduced into clinical practice. Identification of these biomarkers can supplement the existing risk-stratification systems. In the future, more biomarkers will be discovered, and more studies are required to validate their roles in improving the detection rate of occurrence or recurrence of Wilms tumor and to enhance clinical outcomes.
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Affiliation(s)
| | | | - Xiuwu Pan
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xingang Cui
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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12
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Mangum R, Reuther J, Baksi KS, Gandhi I, Zabriskie RC, Recinos A, Raesz-Martinez R, Lin FY, Potter SL, Sher AC, Kralik SF, Mohila CA, Chintagumpala MM, Muzny D, Hu J, Gibbs RA, Fisher KE, Bernini JC, Gill J, Griffin TC, Tomlinson GE, Vallance KL, Plon SE, Roy A, Parsons DW. Circulating tumor DNA sequencing of pediatric solid and brain tumor patients: An institutional feasibility study. Pediatr Hematol Oncol 2023; 40:719-738. [PMID: 37366551 PMCID: PMC10592361 DOI: 10.1080/08880018.2023.2228837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023]
Abstract
The potential of circulating tumor DNA (ctDNA) analysis to serve as a real-time "liquid biopsy" for children with central nervous system (CNS) and non-CNS solid tumors remains to be fully elucidated. We conducted a study to investigate the feasibility and potential clinical utility of ctDNA sequencing in pediatric patients enrolled on an institutional clinical genomics trial. A total of 240 patients had tumor DNA profiling performed during the study period. Plasma samples were collected at study enrollment from 217 patients and then longitudinally from a subset of patients. Successful cell-free DNA extraction and quantification occurred in 216 of 217 (99.5%) of these initial samples. Twenty-four patients were identified whose tumors harbored 30 unique variants that were potentially detectable on a commercially-available ctDNA panel. Twenty of these 30 mutations (67%) were successfully detected by next-generation sequencing in the ctDNA from at least one plasma sample. The rate of ctDNA mutation detection was higher in patients with non-CNS solid tumors (7/9, 78%) compared to those with CNS tumors (9/15, 60%). A higher ctDNA mutation detection rate was also observed in patients with metastatic disease (9/10, 90%) compared to non-metastatic disease (7/14, 50%), although tumor-specific variants were detected in a few patients in the absence of radiographic evidence of disease. This study illustrates the feasibility of incorporating longitudinal ctDNA analysis into the management of relapsed or refractory patients with childhood CNS or non-CNS solid tumors.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children’s Hospital, Phoenix, Arizona
| | - Jacquelyn Reuther
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Koel Sen Baksi
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ilavarasi Gandhi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Ryan C. Zabriskie
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Alva Recinos
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Robin Raesz-Martinez
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Frank Y. Lin
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Samara L. Potter
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio
- Department of Pediatrics, The Ohio State University, Columbus, Ohio
| | - Andrew C. Sher
- Department of Radiology, Texas Children’s Hospital, Houston, Texas
| | | | - Carrie A. Mohila
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Murali M. Chintagumpala
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Kevin E. Fisher
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Juan Carlos Bernini
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Jonathan Gill
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy C. Griffin
- Department of Hematology Oncology, The Children’s Hospital of San Antonio, Baylor College of Medicine, San Antonio, Texas
| | - Gail E Tomlinson
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | - Kelly L. Vallance
- Hematology and Oncology, Cook Children’s Medical Center, Fort Worth, Texas
| | - Sharon E. Plon
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Angshumoy Roy
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - D. Williams Parsons
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
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13
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Lu B, Curtius K, Graham TA, Yang Z, Barnes CP. CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples. Genome Biol 2023; 24:144. [PMID: 37340508 DOI: 10.1186/s13059-023-02983-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation.
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Affiliation(s)
- Bingxin Lu
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| | - Kit Curtius
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Trevor A Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
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14
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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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15
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Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors. NPJ Precis Oncol 2023; 7:21. [PMID: 36805676 PMCID: PMC9941464 DOI: 10.1038/s41698-023-00357-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
We designed a liquid biopsy (LB) platform employing low-pass whole genome sequencing (LP-WGS) and targeted sequencing of cell-free (cf) DNA from plasma to detect genome-wide copy number alterations (CNAs) and gene fusions in pediatric solid tumors. A total of 143 plasma samples were analyzed from 19 controls and 73 patients, including 44 bone or soft-tissue sarcomas and 12 renal, 10 germ cell, five hepatic, and two thyroid tumors. cfDNA was isolated from plasma collected at diagnosis, during and after therapy, and/or at relapse. Twenty-six of 37 (70%) patients enrolled at diagnosis without prior therapy (radiation, surgery, or chemotherapy) had circulating tumor DNA (ctDNA), based on the detection of CNAs from LP-WGS, including 18 of 27 (67%) patients with localized disease and eight of 10 (80%) patients with metastatic disease. None of the controls had detectable somatic CNAs. There was a high concordance of CNAs identified by LP-WGS to CNAs detected by chromosomal microarray analysis in the matching tumors. Mutations identified in tumor samples with our next-generation sequencing (NGS) panel, OncoKids®, were also detected by LP-WGS of ctDNA in 14 of 26 plasma samples. Finally, we developed a hybridization-based capture panel to target EWSR1 and FOXO1 fusions from patients with Ewing sarcoma or alveolar rhabdomyosarcoma (ARMS), respectively. Fusions were detected in the plasma from 10 of 12 patients with Ewing sarcoma and in two of two patients with ARMS. Combined, these data demonstrate the clinical applicability of our LB platform to evaluate pediatric patients with a variety of solid tumors.
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16
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Walz AL, Maschietto M, Crompton B, Evageliou N, Dix D, Tytgat G, Gessler M, Gisselsson D, Daw NC, Wegert J. Tumor biology, biomarkers, and liquid biopsy in pediatric renal tumors. Pediatr Blood Cancer 2023; 70 Suppl 2:e30130. [PMID: 36592003 DOI: 10.1002/pbc.30130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 01/03/2023]
Abstract
The expansion of knowledge regarding driver mutations for Wilms tumor (WT) and malignant rhabdoid tumor of the kidney (MRT) and various translocations for other pediatric renal tumors opens up new possibilities for diagnosis and treatment. In addition, there are growing data surrounding prognostic factors that can be used to stratify WT treatment to improve outcomes. Here, we review the molecular landscape of WT and other pediatric renal tumors as well as WT prognostic factors. We also review incorporation of circulating tumor DNA/liquid biopsies to leverage this molecular landscape, with potential use in the future for distinguishing renal tumors at the time of diagnosis and elucidating intratumor heterogeneity, which is not well evaluated with standard biopsies. Incorporation of liquid biopsies will require longitudinal collection of multiple biospecimens. Further preclinical research, identification and validation of biomarkers, molecular studies, and data sharing among investigators are crucial to inform therapeutic strategies that improve patient outcomes.
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Affiliation(s)
- Amy L Walz
- Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Mariana Maschietto
- Research Center, Boldrini Children's Hospital, Campinas, São Paulo, Brazil
| | - Brian Crompton
- Department of Pediatric Oncology, Dana-Farber/Harvard Cancer Center, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Nicholas Evageliou
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - David Dix
- British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Godelieve Tytgat
- Princess Máxima Center for Pediatric Oncology, CS Utrecht, The Netherlands
| | - Manfred Gessler
- Comprehensive Cancer Center Mainfranken, Wuerzburg, Germany.,Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, University of Wuerzburg, Wuerzburg, Germany
| | - David Gisselsson
- Cancer Cell Evolution Unit, Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Najat C Daw
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, University of Wuerzburg, Wuerzburg, Germany
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17
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Stankunaite R, Marshall LV, Carceller F, Chesler L, Hubank M, George SL. Liquid biopsy for children with central nervous system tumours: Clinical integration and technical considerations. Front Pediatr 2022; 10:957944. [PMID: 36467471 PMCID: PMC9709284 DOI: 10.3389/fped.2022.957944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) analysis has the potential to revolutionise the care of patients with cancer and is already moving towards standard of care in some adult malignancies. Evidence for the utility of cfDNA analysis in paediatric cancer patients is also accumulating. In this review we discuss the limitations of blood-based assays in patients with brain tumours and describe the evidence supporting cerebrospinal fluid (CSF) cfDNA analysis. We make recommendations for CSF cfDNA processing to aid the standardisation and technical validation of future assays. We discuss the considerations for interpretation of cfDNA analysis and highlight promising future directions. Overall, cfDNA profiling shows great potential as an adjunct to the analysis of biopsy tissue in paediatric cancer patients, with the potential to provide a genetic molecular profile of the tumour when tissue biopsy is not feasible. However, to fully realise the potential of cfDNA analysis for children with brain tumours larger prospective studies incorporating serial CSF sampling are required.
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Affiliation(s)
- Reda Stankunaite
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Clinical Genomics, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Evolutionary Genomics and Modelling, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Lynley V. Marshall
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Fernando Carceller
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Michael Hubank
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Clinical Genomics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sally L. George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
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18
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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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19
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Stegmaier S, Sparber-Sauer M, Aakcha-Rudel E, Münch P, Reeh T, Feuchtgruber S, Hallmen E, Blattmann C, Bielack S, Klingebiel T, Koscielniak E. Fusion transcripts as liquid biopsy markers in alveolar rhabdomyosarcoma and synovial sarcoma: A report of the Cooperative Weichteilsarkom Studiengruppe (CWS). Pediatr Blood Cancer 2022; 69:e29652. [PMID: 35338758 DOI: 10.1002/pbc.29652] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND The possible application of gene fusion transcripts as tumor-specific noninvasive liquid biopsy biomarkers was investigated in blood plasma from patients with alveolar rhabdomyosarcoma (ARMS) and synovial sarcoma (SS). METHODS Patients entered in the CWS Soft-Tissue Sarcoma Registry (SoTiSaR) with tumors positive for fusion genes and available blood/plasma samples were included in our analysis. Cell-free exosomal RNA was extracted and used to detect PAX-FOXO1 or SYT-SSX fusion transcripts by reverse transcription quantitative PCR (RT-qPCR). RESULTS The analysis included 112 ethylene diamine tetraacetic acid blood samples from 80 patients (65 with ARMS, 15 with SS; 34 with localized, 46 with metastatic disease). For patients with metastatic ARMS, 62% (n = 18) of initial liquid biopsies were positive, and 16 (89%) of them showed initial bone marrow (BM) metastases. For all patients with primary localized ARMS, liquid biopsy was negative at diagnosis. Of the 48 plasma samples collected during therapy and follow-up, five were positive. None of the liquid biopsies from patients with SS were positive. CONCLUSIONS This liquid biopsy assay based on the detection of fusion transcripts in cell-free RNA from blood exosomes is suitable for analysis of patients with ARMS. Results showed good correlation with the initial tumor status; liquid biopsy was positive in 94% of patients with metastatic ARMS and initial BM involvement, whereas biopsies from all patients with localized tumors were negative. Prospective validation and optimization of the assay, as well as its application for other markers in diagnostics and monitoring of soft-tissue sarcoma, are ongoing.
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Affiliation(s)
- Sabine Stegmaier
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Monika Sparber-Sauer
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Esther Aakcha-Rudel
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Petra Münch
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Theresa Reeh
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Simone Feuchtgruber
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Erika Hallmen
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Claudia Blattmann
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Stefan Bielack
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany.,Department of Pediatric Hematology and Oncology, University of Muenster, Muenster, Germany
| | - Thomas Klingebiel
- Department for Children and Adolescents, University Hospital of Frankfurt, Frankfurt/M, Germany
| | - Ewa Koscielniak
- Olgahospital, Zentrum für Kinder- Jugend und Frauenmedizin, Klinikum Stuttgart, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
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20
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Gadd S, Huff V, Skol AD, Renfro LA, Fernandez CV, Mullen EA, Jones CD, Hoadley KA, Yap KL, Ramirez NC, Aris S, Phung QH, Perlman EJ. Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study. Cell Rep Med 2022; 3:100644. [PMID: 35617957 PMCID: PMC9244995 DOI: 10.1016/j.xcrm.2022.100644] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/23/2022] [Accepted: 05/04/2022] [Indexed: 12/15/2022]
Abstract
Over the last decade, sequencing of primary tumors has clarified the genetic underpinnings of Wilms tumor but has not affected therapy, outcome, or toxicity. We now sharpen our focus on relapse samples from the umbrella AREN03B2 study. We show that over 40% of relapse samples contain mutations in SIX1 or genes of the MYCN network, drivers of progenitor proliferation. Not previously seen in large studies of primary Wilms tumors, DIS3 and TERT are now identified as recurrently mutated. The analysis of primary-relapse tumor pairs suggests that 11p15 loss of heterozygosity (and other copy number changes) and mutations in WT1 and MLLT1 typically occur early, but mutations in SIX1, MYCN, and WTX are late developments in some individuals. Most strikingly, 75% of relapse samples had gain of 1q, providing strong conceptual support for studying circulating tumor DNA in clinical trials to better detect 1q gain earlier and monitor response.
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Affiliation(s)
- Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Robert H. Lurie Cancer Center, Northwestern University, 225 East Chicago Avenue, Box 17, Chicago, IL 60611, USA
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew D Skol
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Robert H. Lurie Cancer Center, Northwestern University, 225 East Chicago Avenue, Box 17, Chicago, IL 60611, USA
| | - Lindsay A Renfro
- Division of Biostatistics, University of Southern California, Los Angeles, CA 90007, USA
| | - Conrad V Fernandez
- Department of Pediatrics, IWK Health Centre and Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Elizabeth A Mullen
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, MA 02215, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kai Lee Yap
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Robert H. Lurie Cancer Center, Northwestern University, 225 East Chicago Avenue, Box 17, Chicago, IL 60611, USA
| | - Nilsa C Ramirez
- Institute for Genomic Medicine and Biopathology Center, Nationwide Children's Hospital, Departments of Pathology and Pediatrics, Ohio State University, Columbus, OH 43205, USA
| | - Sheena Aris
- Biospecimen Research Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Quy H Phung
- Biospecimen Research Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Robert H. Lurie Cancer Center, Northwestern University, 225 East Chicago Avenue, Box 17, Chicago, IL 60611, USA.
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21
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Madanat-Harjuoja LM, Klega K, Lu Y, Shulman DS, Thorner AR, Nag A, Tap WD, Reinke DK, Diller L, Ballman KV, George S, Crompton BD. Circulating Tumor DNA Is Associated with Response and Survival in Patients with Advanced Leiomyosarcoma. Clin Cancer Res 2022; 28:2579-2586. [PMID: 35561344 PMCID: PMC9359745 DOI: 10.1158/1078-0432.ccr-21-3951] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 02/17/2022] [Indexed: 01/26/2023]
Abstract
PURPOSE We sought to determine whether the detection of circulating tumor DNA (ctDNA) in samples of patients undergoing chemotherapy for advanced leiomyosarcoma (LMS) is associated with objective response or survival. EXPERIMENTAL DESIGN Using ultra-low-passage whole-genome sequencing (ULP-WGS) of plasma cell-free DNA from patients treated on a prospective clinical trial, we tested whether detection of ctDNA evaluated prior to the start of therapy and after two cycles of chemotherapy was associated with treatment response and outcome. Associations between detection of ctDNA and pathologic measures of disease burden were evaluated. RESULTS We found that ctDNA was detectable by ULP-WGS in 49% patients prior to treatment and in 24.6% patients after two cycles of chemotherapy. Detection of pretreatment ctDNA was significantly associated with a lower overall survival [HR, 1.55; 95% confidence interval (CI), 1.03-2.31; P = 0.03] and a significantly lower likelihood of objective response [odds ratio (OR), 0.21; 95% CI, 0.06-0.59; P = 0.005]. After two cycles of chemotherapy, patients who continued to have detectable levels of ctDNA experienced a significantly worse overall survival (HR, 1.77; 95% CI, 1-3.14; P = 0.05) and were unlikely to experience an objective response (OR, 0.05; 95% CI, 0-0.39; P = 0.001). CONCLUSIONS Our results demonstrate that detection of ctDNA is associated with outcome and objective response to chemotherapy in patients with advanced LMS. These results suggest that liquid biopsy assays could be used to inform treatment decisions by recognizing patients who are likely and unlikely to benefit from chemotherapy. See related commentary by Kasper and Wilky, p. 2480.
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Affiliation(s)
| | - Kelly Klega
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Yao Lu
- Weill Cornell Medicine, New York, New York
| | - David S. Shulman
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Aaron R. Thorner
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anwesha Nag
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William D. Tap
- Weill Cornell Medicine, New York, New York.,Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise K. Reinke
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan
| | - Lisa Diller
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | | | - Suzanne George
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Brian D. Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Corresponding Author: Brian D. Crompton, Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, 450 Brookline Avenue, Boston, MA 02215. E-mail:
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22
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Shirai R, Osumi T, Sato-Otsubo A, Nakabayashi K, Ishiwata K, Yamada Y, Yoshida M, Yoshida K, Shioda Y, Kiyotani C, Terashima K, Tomizawa D, Takasugi N, Takita J, Miyazaki O, Kiyokawa N, Yoneda A, Kanamori Y, Hishiki T, Matsumoto K, Hata K, Yoshioka T, Kato M. Quantitative assessment of copy number alterations by liquid biopsy for neuroblastoma. Genes Chromosomes Cancer 2022; 61:662-669. [PMID: 35655408 DOI: 10.1002/gcc.23073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/27/2022] [Accepted: 05/10/2022] [Indexed: 11/08/2022] Open
Abstract
Liquid biopsy, a method of detecting genomic alterations using blood specimens, has recently attracted attention as a non-invasive alternative to surgical tissue biopsy. We attempted quantitative analysis to detect amplification of MYCN (MYCNamp) and loss of heterozygosity at 11q (11qLOH), which are clinical requisites as prognostic factors of neuroblastoma. In this study, cell-free DNA (cfDNA) was extracted from plasma samples from 24 neuroblastoma patients at diagnosis. Copy numbers of MYCN and NAGK genes were quantitatively analyzed by droplet digital PCR (ddPCR). 11qLOH was also assessed by detecting allelic imbalances of heterozygous single nucleotide polymorphisms in the 11q region. The results obtained were compared to those of specimens from tumor tissues. The correlation coefficient of MYCN copy number of cfDNA and tumor DNA was 0.88 (P < 0.00001). 11qLOH was also accurately detected from cfDNA, except for one case with localized NB. Given the high accuracy of liquid biopsy, to investigate components of cfDNA, the proportion of tumor-derived DNA was estimated by examining the variant allele frequency of tumor-specific mutations in cfDNA. The proportion of tumor-derived DNA in cfDNA was 42.5% (range, 16.9%-55.9%), suggesting sufficient sensitivity of liquid biopsy for neuroblastoma. In conclusion, MYCN copy number and 11qLOH could be quantitatively analyzed in plasma cfDNA by ddPCR assay. These results suggest that plasma cfDNA can be substituted for tumor DNA and can also be applied for comprehensive genomic profiling analysis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ryota Shirai
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Tomoo Osumi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, University of Tokyo, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Keisuke Ishiwata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuji Yamada
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masanori Yoshida
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Kaoru Yoshida
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoko Shioda
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Chikako Kiyotani
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Keita Terashima
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Daisuke Tomizawa
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Nao Takasugi
- Department of Pediatrics, University of Tokyo, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Graduate School of Medicine Kyoto University, Kyoto City, Japan
| | - Osamu Miyazaki
- Department of Radiology, National Center for Child Health and Development, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akihiro Yoneda
- Division of Surgical Oncology, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yutaka Kanamori
- Division of Surgery, Department of Surgical Specialties, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoro Hishiki
- Division of Surgical Oncology, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Kimikazu Matsumoto
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takako Yoshioka
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, University of Tokyo, Tokyo, Japan
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23
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Abstract
PURPOSE OF REVIEW Liquid biopsies have emerged as a noninvasive alternative to tissue biopsy with potential applications during all stages of pediatric oncology care. The purpose of this review is to provide a survey of pediatric cell-free DNA (cfDNA) studies, illustrate their potential applications in pediatric oncology, and to discuss technological challenges and approaches to overcome these hurdles. RECENT FINDINGS Recent literature has demonstrated liquid biopsies' ability to inform treatment selection at diagnosis, monitor clonal evolution during treatment, sensitively detect minimum residual disease following local control, and provide sensitive posttherapy surveillance. Advantages include reduced procedural anesthesia, molecular profiling unbiased by tissue heterogeneity, and ability to track clonal evolution. Challenges to wider implementation in pediatric oncology, however, include blood volume restrictions and relatively low mutational burden in childhood cancers. Multiomic approaches address challenges presented by low-mutational burden, and novel bioinformatic analyses allow a single assay to yield increasing amounts of information, reducing blood volume requirements. SUMMARY Liquid biopsies hold tremendous promise in pediatric oncology, enabling noninvasive serial surveillance with adaptive care. Already integrated into adult care, recent advances in technologies and bioinformatics have improved applicability to the pediatric cancer landscape.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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24
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Stankunaite R, George SL, Gallagher L, Jamal S, Shaikh R, Yuan L, Hughes D, Proszek PZ, Carter P, Pietka G, Heide T, James C, Tari H, Lynn C, Jain N, Portela LR, Rogers T, Vaidya SJ, Chisholm JC, Carceller F, Szychot E, Mandeville H, Angelini P, Jesudason AB, Jackson M, Marshall LV, Gatz SA, Anderson J, Sottoriva A, Chesler L, Hubank M. Circulating tumour DNA sequencing to determine therapeutic response and identify tumour heterogeneity in patients with paediatric solid tumours. Eur J Cancer 2022; 162:209-220. [PMID: 34933802 DOI: 10.1016/j.ejca.2021.09.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/13/2021] [Accepted: 09/28/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Clinical diagnostic sequencing of circulating tumour DNA (ctDNA) is well advanced for adult patients, but application to paediatric cancer patients lags behind. METHODS To address this, we have developed a clinically relevant (67 gene) NGS capture panel and accompanying workflow that enables sensitive and reliable detection of low-frequency genetic variants in cell-free DNA (cfDNA) from children with solid tumours. We combined gene panel sequencing with low pass whole-genome sequencing of the same library to inform on genome-wide copy number changes in the blood. RESULTS Analytical validity was evaluated using control materials, and the method was found to be highly sensitive (0.96 for SNVs and 0.97 for INDEL), specific (0.82 for SNVs and 0.978 for INDEL), repeatable (>0.93 [95% CI: 0.89-0.95]) and reproducible (>0.87 [95% CI: 0.87-0.95]). Potential for clinical application was demonstrated in 39 childhood cancer patients with a spectrum of solid tumours in which the single nucleotide variants expected from tumour sequencing were detected in cfDNA in 94.4% (17/18) of cases with active extracranial disease. In 13 patients, where serial samples were available, we show a close correlation between events detected in cfDNA and treatment response, demonstrate that cfDNA analysis could be a useful tool to monitor disease progression, and show cfDNA sequencing has the potential to identify targetable variants that were not detected in tumour samples. CONCLUSIONS This is the first pan-cancer DNA sequencing panel that we know to be optimised for cfDNA in children for blood-based molecular diagnostics in paediatric solid tumours.
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Affiliation(s)
- Reda Stankunaite
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK; Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Sally L George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Lewis Gallagher
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Sabri Jamal
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Ridwan Shaikh
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Lina Yuan
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Debbie Hughes
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Paula Z Proszek
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Paul Carter
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Grzegorz Pietka
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Chela James
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Haider Tari
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Glioma Lab, The Institute of Cancer Research, London, UK.
| | - Claire Lynn
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Neha Jain
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Laura Rey Portela
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Tony Rogers
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK.
| | - Sucheta J Vaidya
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Julia C Chisholm
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Fernando Carceller
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Elwira Szychot
- Oak Centre for Children and Young People, Royal Marsden NHS Foundation Trust Hospital, Sutton, UK; Department of Paediatrics, Paediatric Oncology and Immunology, Pomeranian Medical University, Szczecin, Poland.
| | - Henry Mandeville
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Paola Angelini
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Angela B Jesudason
- Department of Paediatric Haematology and Oncology, Royal Hospital for Sick Children, Edinburgh, UK
| | - Michael Jackson
- Department of Paediatric Haematology and Oncology, Royal Hospital for Sick Children, Edinburgh, UK
| | - Lynley V Marshall
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Susanne A Gatz
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK; Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK.
| | - John Anderson
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Michael Hubank
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
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25
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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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26
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Varkey J, Nicolaides T. Tumor-Educated Platelets: A Review of Current and Potential Applications in Solid Tumors. Cureus 2021; 13:e19189. [PMID: 34873529 PMCID: PMC8635758 DOI: 10.7759/cureus.19189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 12/30/2022] Open
Abstract
In this current era of precision medicine, liquid biopsy poses a unique opportunity for an easily accessible, comprehensive molecular profile that would allow for the identification of therapeutic targets and sequential monitoring. Solid tumors are definitively diagnosed by analyzing primary tumor tissue, but surgical sampling is not always sufficient to generate a comprehensive genetic fingerprint at the time of diagnosis, or an appropriate means for continued monitoring. Platelets are known to have a dynamic, bidirectional relationship with tumors, acting beyond their role of hemostasis. Tumor-educated platelets (TEP) are modified by the tumor in multiple ways and act as a carrier and protector of metastasis. Data so far have shown that the mRNA in TEP can be harnessed for cancer diagnostics, with many potential applications.
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Affiliation(s)
- Joyce Varkey
- Pediatric Hematology Oncology, New York University Langone, New York, USA
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27
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Krumbholz M, Eiblwieser J, Ranft A, Zierk J, Schmidkonz C, Stütz AM, Peneder P, Tomazou EM, Agaimy A, Bäuerle T, Hartmann W, Dirksen U, Metzler M. Quantification of Translocation-Specific ctDNA Provides an Integrating Parameter for Early Assessment of Treatment Response and Risk Stratification in Ewing Sarcoma. Clin Cancer Res 2021; 27:5922-5930. [PMID: 34426444 DOI: 10.1158/1078-0432.ccr-21-1324] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/05/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE We evaluated the predictive and prognostic value of circulating tumor DNA (ctDNA) in patients with Ewing sarcoma (EWS) treated in the EWING2008 trial. EXPERIMENTAL DESIGN Plasma samples from 102 patients with EWS enrolled in the EWING2008 trial were obtained before and during induction chemotherapy. Genomic EWSR1 fusion sequence spanning primers and probes were used for highly specific and sensitive quantification of the levels of ctDNA by digital droplet PCR. ctDNA levels were correlated to established clinical risk factors and outcome parameters. RESULTS Pretreatment ctDNA copy numbers were correlated with event-free and overall survival. The reduction in ctDNA levels below the detection limit was observed in most cases after only two blocks of vincristine, ifosfamide, doxorubicin, and etoposide (VIDE) induction chemotherapy. The persistence of ctDNA after two VIDE blocks was a strong predictor of poor outcomes. ctDNA levels correlated well with most established clinical risk factors; an inverse correlation was found only for the histologic response to induction therapy. ctDNA levels did not provide simple representations of tumor volume, but integrated information from various tumor characteristics represented an independent EWS tumor marker with predictive and prognostic value. CONCLUSIONS ctDNA copy number in the plasma of patients with EWS is a quantifiable parameter for early risk stratification and can be used as a dynamic noninvasive biomarker for early prediction of treatment response and outcome of patients.
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Affiliation(s)
- Manuela Krumbholz
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany. .,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Johanna Eiblwieser
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Andreas Ranft
- Pediatrics III, West German Cancer Centre, University Hospital of Essen, Essen, Germany
| | - Jakob Zierk
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | | | - Adrian M Stütz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter Peneder
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eleni M Tomazou
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Abbas Agaimy
- Department of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Tobias Bäuerle
- Department of Radiology, University Hospital Erlangen, Erlangen, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, University Hospital Muenster, Gerhard Domagk Institute of Pathology, Muenster, Germany
| | - Uta Dirksen
- Pediatrics III, West German Cancer Centre, University Hospital of Essen, Essen, Germany
| | - Markus Metzler
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany.,Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
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28
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Irwin MS, Naranjo A, Zhang FF, Cohn SL, London WB, Gastier-Foster JM, Ramirez NC, Pfau R, Reshmi S, Wagner E, Nuchtern J, Asgharzadeh S, Shimada H, Maris JM, Bagatell R, Park JR, Hogarty MD. Revised Neuroblastoma Risk Classification System: A Report From the Children's Oncology Group. J Clin Oncol 2021; 39:3229-3241. [PMID: 34319759 PMCID: PMC8500606 DOI: 10.1200/jco.21.00278] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
PURPOSE Treatment planning for children with neuroblastoma requires accurate assessment of prognosis. The most recent Children's Oncology Group (COG) risk classification system used tumor stage as defined by the International Neuroblastoma Staging System. Here, we validate a revised classifier using the International Neuroblastoma Risk Group Staging System (INRGSS) and incorporate segmental chromosome aberrations (SCA) as an additional genomic biomarker. METHODS Newly diagnosed patients enrolled on the COG neuroblastoma biology study ANBL00B1 between 2007 and 2017 with known age, International Neuroblastoma Staging System, and INRGSS stage were identified (N = 4,832). Tumor MYCN status, ploidy, SCA status (1p and 11q), and International Neuroblastoma Pathology Classification histology were determined centrally. Survival analyses were performed for combinations of prognostic factors used in COG risk classification according to the prior version 1, and to validate a revised algorithm (version 2). RESULTS Most patients with locoregional tumors had excellent outcomes except for those with image-defined risk factors (INRGSS L2) with MYCN amplification (5-year event-free survival and overall survival: 76.3% ± 5.8% and 79.9% ± 5.5%, respectively) or patients age ≥ 18 months with L2 MYCN nonamplified tumors with unfavorable International Neuroblastoma Pathology Classification histology (72.7% ± 5.4% and 82.4% ± 4.6%), which includes the majority of L2 patients with SCA. For patients with stage M (metastatic) and MS (metastatic, special) disease, genomic biomarkers affected risk group assignment for those < 12 months (MYCN) or 12-18 months (MYCN, histology, ploidy, and SCA) of age. In a retrospective analysis of patient outcome, the 5-year event-free survival and overall survival using COG version 1 were low-risk: 89.4% ± 1.1% and 97.9% ± 0.5%; intermediate-risk: 86.1% ± 1.3% and 94.9% ± 0.8%; high-risk: 50.8% ± 1.4% and 61.9% ± 1.3%; and using COG version 2 were low-risk: 90.7% ± 1.1% and 97.9% ± 0.5%; intermediate-risk: 85.1% ± 1.4% and 95.8% ± 0.8%; high-risk: 51.2% ± 1.4% and 62.5% ± 1.3%, respectively. CONCLUSION A revised 2021 COG neuroblastoma risk classifier (version 2) that uses the INRGSS and incorporates SCAs has been adopted to prospectively define COG clinical trial eligibility and treatment assignment.
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Affiliation(s)
- Meredith S Irwin
- Department of Pediatrics, Hospital for Sick Children, Toronto, ON, Canada
| | - Arlene Naranjo
- Children's Oncology Group Statistics and Data Center, Department of Biostatistics, University of Florida, Gainesville, FL
| | - Fan F Zhang
- Children's Oncology Group Statistics and Data Center, Monrovia, CA
| | - Susan L Cohn
- Department of Pediatrics, The University of Chicago, Chicago, IL
| | - Wendy B London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Julie M Gastier-Foster
- Institute for Genomic Medicine and Biopathology Center, Nationwide Children's Hospital, Columbus, OH.,Departments of Pathology and Pediatrics, Ohio State University, Columbus, OH
| | - Nilsa C Ramirez
- Institute for Genomic Medicine and Biopathology Center, Nationwide Children's Hospital, Columbus, OH.,Departments of Pathology and Pediatrics, Ohio State University, Columbus, OH
| | - Ruthann Pfau
- Institute for Genomic Medicine and Biopathology Center, Nationwide Children's Hospital, Columbus, OH.,Departments of Pathology and Pediatrics, Ohio State University, Columbus, OH
| | - Shalini Reshmi
- Institute for Genomic Medicine and Biopathology Center, Nationwide Children's Hospital, Columbus, OH.,Departments of Pathology and Pediatrics, Ohio State University, Columbus, OH
| | - Elizabeth Wagner
- Institute for Genomic Medicine and Biopathology Center, Nationwide Children's Hospital, Columbus, OH
| | - Jed Nuchtern
- Division of Pediatric Surgery, Department of Surgery, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Shahab Asgharzadeh
- Division of Hematology/Oncology, Children's Hospital of Los Angeles, Los Angeles, CA
| | - Hiroyuki Shimada
- Departments of Pathology and Pediatrics, Stanford University, Stanford, CA
| | - John M Maris
- Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Rochelle Bagatell
- Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Julie R Park
- Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Michael D Hogarty
- Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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29
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Kahana-Edwin S, Cain LE, McCowage G, Darmanian A, Wright D, Mullins A, Saletta F, Karpelowsky J. Neuroblastoma Molecular Risk-Stratification of DNA Copy Number and ALK Genotyping via Cell-Free Circulating Tumor DNA Profiling. Cancers (Basel) 2021; 13:3365. [PMID: 34282791 PMCID: PMC8267662 DOI: 10.3390/cancers13133365] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND MYCN amplification (MNA), segmental chromosomal aberrations (SCA) and ALK activating mutations are biomarkers for risk-group stratification and for targeted therapeutics for neuroblastoma, both of which are currently assessed on tissue biopsy. Increase in demand for tumor genetic testing for neuroblastoma diagnosis is posing a challenge to current practice, as the small size of the core needle biopsies obtained are required for multiple molecular tests. We evaluated the utility of detecting these biomarkers in the circulation. METHODS Various pre-analytical conditions tested to optimize circulating-tumor DNA (ctDNA) copy number changes evaluations. Plasma samples from 10 patients diagnosed with neuroblastoma assessed for SCA and MNA using single nucleotide polymorphism (SNP) array approach currently used for neuroblastoma diagnosis, with MNA status assessed independently using digital-droplet PCR (ddPCR). Three patients (one in common with the previous 10) tested for ALK activating mutations p.F1174L and p.F1245I using ddPCR. RESULTS Copy number detection is highly affected by physical perturbations of the blood sample (mimicking suboptimal sample shipment), which could be overcome using specialized preservative collection tubes. Pre-analytical DNA repair procedures on ctDNA before SNP chromosome microarray processing improved the lower limit of detection for SCA and MNA, defined as 20% and 10%, respectively. We detected SCA in 10/10 (100%) patients using SNP array, 7 of which also presented MNA. Circulating-free DNA (cfDNA) and matched tumor DNA profiles were generally identical. MNA was detected using ddPCR in 7/7 (100%) of MNA and 0/12 (0%) non-MNA cases. MNA and ALK mutation dynamic change was assessed in longitudinal samples from 4 and 3 patients (one patient with both), respectively, accurately reflected response to treatment in 6/6 (100%) and disease recurrence in 5/6 (83%) of cases. Samples taken prior to targeted treatment with the ALK inhibitor Lorlatinib and 6-8 weeks on treatment showed reduction/increase in ALK variants according to response to treatment. CONCLUSIONS These results demonstrate the feasibility of ctDNA profiling for molecular risk-stratification, and treatment monitoring in a clinically relevant time frame and the potential to reduce fresh tissue requirements currently embedded in the management of neuroblastoma.
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Affiliation(s)
- Smadar Kahana-Edwin
- Advanced Molecular Diagnostics, Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (F.S.); (J.K.)
| | - Lucy E. Cain
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (L.E.C.); (G.M.); (A.M.)
| | - Geoffrey McCowage
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (L.E.C.); (G.M.); (A.M.)
| | - Artur Darmanian
- Cytogenetics Department, Sydney Genome Diagnostics, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (A.D.); (D.W.)
| | - Dale Wright
- Cytogenetics Department, Sydney Genome Diagnostics, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (A.D.); (D.W.)
- Division of Child and Adolescent Health, The University of Sydney, Sydney, NSW 2145, Australia
| | - Anna Mullins
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (L.E.C.); (G.M.); (A.M.)
| | - Federica Saletta
- Advanced Molecular Diagnostics, Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (F.S.); (J.K.)
| | - Jonathan Karpelowsky
- Advanced Molecular Diagnostics, Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia; (F.S.); (J.K.)
- Division of Child and Adolescent Health, The University of Sydney, Sydney, NSW 2145, Australia
- Paediatric Oncology and Thoracic Surgery, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
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30
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Liquid biomarkers for the management of paediatric neuroblastoma: an approach to personalised and targeted cancer therapy. JOURNAL OF RADIOTHERAPY IN PRACTICE 2021. [DOI: 10.1017/s1460396920000102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractBackground:Neuroblastoma is the most common extracranial solid tumour of infancy and accounts for about 6–10% of paediatric cancers. It has a biologically and clinically heterogeneous behaviour that ranges from spontaneous regression to cases of highly aggressive metastatic disease that could be unresponsive to standard therapy. In recent years, there have been several investigations into the development of various diagnostic, predictive and prognostic biomarkers towards personalised and targeted management of the disease.Materials and Methods:This paper reports on the review of current clinical and emerging biomarkers used in risk assessment, screening for early detection and diagnosis, prognostication and monitoring of the response of treatment of neuroblastoma in paediatric patients.Conclusions:Tumour markers can significantly improve diagnosis; however, the invasive, unpleasant and inconvenient nature of current tissue biopsies limits their applications, especially in paediatric patients. Therefore, the development of a non-invasive, reliable high accurate and personalised diagnostic tool capable of early detection and rapid response is the most promising step towards advanced cancer management from tumour diagnosis, therapy to patient monitoring and represents an important step towards the promise of precision, personalised and targeted medicine. Liquid biopsy assay with wide ranges of clinical applications is emerging to hold incredible potential for advancing cancer treatment and has greater promise for diagnostic purposes, identification and tracking of tumour-specific alterations during the course of the disease and to guide therapeutic decisions.
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31
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Peneder P, Stütz AM, Surdez D, Krumbholz M, Semper S, Chicard M, Sheffield NC, Pierron G, Lapouble E, Tötzl M, Ergüner B, Barreca D, Rendeiro AF, Agaimy A, Boztug H, Engstler G, Dworzak M, Bernkopf M, Taschner-Mandl S, Ambros IM, Myklebost O, Marec-Bérard P, Burchill SA, Brennan B, Strauss SJ, Whelan J, Schleiermacher G, Schaefer C, Dirksen U, Hutter C, Boye K, Ambros PF, Delattre O, Metzler M, Bock C, Tomazou EM. Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden. Nat Commun 2021; 12:3230. [PMID: 34050156 PMCID: PMC8163828 DOI: 10.1038/s41467-021-23445-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/29/2021] [Indexed: 12/19/2022] Open
Abstract
Sequencing of cell-free DNA in the blood of cancer patients (liquid biopsy) provides attractive opportunities for early diagnosis, assessment of treatment response, and minimally invasive disease monitoring. To unlock liquid biopsy analysis for pediatric tumors with few genetic aberrations, we introduce an integrated genetic/epigenetic analysis method and demonstrate its utility on 241 deep whole-genome sequencing profiles of 95 patients with Ewing sarcoma and 31 patients with other pediatric sarcomas. Our method achieves sensitive detection and classification of circulating tumor DNA in peripheral blood independent of any genetic alterations. Moreover, we benchmark different metrics for cell-free DNA fragmentation analysis, and we introduce the LIQUORICE algorithm for detecting circulating tumor DNA based on cancer-specific chromatin signatures. Finally, we combine several fragmentation-based metrics into an integrated machine learning classifier for liquid biopsy analysis that exploits widespread epigenetic deregulation and is tailored to cancers with low mutation rates. Clinical associations highlight the potential value of cfDNA fragmentation patterns as prognostic biomarkers in Ewing sarcoma. In summary, our study provides a comprehensive analysis of circulating tumor DNA beyond recurrent genetic aberrations, and it renders the benefits of liquid biopsy more readily accessible for childhood cancers.
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Affiliation(s)
- Peter Peneder
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Adrian M Stütz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Manuela Krumbholz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Sabine Semper
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Mathieu Chicard
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Eve Lapouble
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Marcus Tötzl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Heidrun Boztug
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Gernot Engstler
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Michael Dworzak
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | | | - Inge M Ambros
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Perrine Marec-Bérard
- Pediatric Department, Hematology and Oncology Pediatric Institute, Centre Léon Bérard, Lyon, France
| | - Susan Ann Burchill
- Children's Cancer Research Group, Leeds Institute of Medical Research, St. James's University Hospital, Leeds, UK
| | - Bernadette Brennan
- Department of Pediatric Oncology, Royal Manchester Children's Hospital, Manchester, UK
| | - Sandra J Strauss
- Department of Oncology, UCL Cancer Institute, London, UK
- Department of Oncology, University College London Hospital, London, UK
| | - Jeremy Whelan
- Department of Oncology, University College London Hospital, London, UK
| | - Gudrun Schleiermacher
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Christiane Schaefer
- University Hospital Essen, Pediatrics III, West German Cancer Centre, Essen, Germany
| | - Uta Dirksen
- University Hospital Essen, Pediatrics III, West German Cancer Centre, Essen, Germany
| | - Caroline Hutter
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Peter F Ambros
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Markus Metzler
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria.
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.
| | - Eleni M Tomazou
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
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32
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Cell-free DNA Oncogene Copy Number as a Surrogate Molecular Biomarker in ALK/MYCN-coamplified Neuroblastoma. J Pediatr Hematol Oncol 2021; 43:e165-e168. [PMID: 32032241 DOI: 10.1097/mph.0000000000001720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/28/2019] [Indexed: 12/28/2022]
Abstract
Secondary expansion and/or evolution of aggressive subclones are associated with the disease progression and resistance to chemotherapy in neuroblastoma, and it is important to track the clonal changes during the treatment period. Cell-free (cf) DNA analysis, namely liquid biopsy, can detect the genomic change of tumor cells without surgical procedures. In this report, we showed that serial polymerase chain reaction-based cf DNA neuroblastoma proto-oncogene quantification is sensitive enough to evaluate the aggressive cellular characteristics of ALK/MYCN-coamplified neuroblastoma and stressed the promise of cf DNA analyses as a reliable molecular marker in advanced neuroblastoma.
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33
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Keller L, Belloum Y, Wikman H, Pantel K. Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond. Br J Cancer 2021; 124:345-358. [PMID: 32968207 PMCID: PMC7852556 DOI: 10.1038/s41416-020-01047-5] [Citation(s) in RCA: 216] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/22/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Cell-free DNA (cfDNA) derived from tumours is present in the plasma of cancer patients. The majority of currently available studies on the use of this circulating tumour DNA (ctDNA) deal with the detection of mutations. The analysis of cfDNA is often discussed in the context of the noninvasive detection of mutations that lead to resistance mechanisms and therapeutic and disease monitoring in cancer patients. Indeed, substantial advances have been made in this area, with the development of methods that reach high sensitivity and can interrogate a large number of genes. Interestingly, however, cfDNA can also be used to analyse different features of DNA, such as methylation status, size fragment patterns, transcriptomics and viral load, which open new avenues for the analysis of liquid biopsy samples from cancer patients. This review will focus on the new perspectives and challenges of cfDNA analysis from mutation detection in patients with solid malignancies.
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Affiliation(s)
- Laura Keller
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany
| | - Yassine Belloum
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany
| | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany
| | - Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, Building N27, 20246, Hamburg, Germany.
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Cimmino F, Lasorsa VA, Vetrella S, Iolascon A, Capasso M. A Targeted Gene Panel for Circulating Tumor DNA Sequencing in Neuroblastoma. Front Oncol 2020; 10:596191. [PMID: 33381456 PMCID: PMC7769379 DOI: 10.3389/fonc.2020.596191] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background Liquid biopsies do not reflect the complete mutation profile of the tumor but have the potential to identify actionable mutations when tumor biopsies are not available as well as variants with low allele frequency. Most retrospective studies conducted in small cohorts of pediatric cancers have illustrated that the technology yield substantial potential in neuroblastoma. Aim The molecular landscape of neuroblastoma harbors potentially actionable genomic alterations. We aimed to study the utility of liquid biopsy to characterize the mutational landscape of primary neuroblastoma using a custom gene panel for ctDNA targeted sequencing. Methods Targeted next-generation sequencing (NGS) was performed on ctDNA of 11 patients with primary neuroblastoma stage 4. To avoid the detection of false variants, we used UMIs (unique molecular identifiers) for the library construction, increased the sequencing depth and developed ad hoc bioinformatic analyses including the hard filtering of the variant calls. Results We identified 9/11 (81.8%) patients who carry at least one pathogenic variation. The most frequently mutated genes were KMT2C (five cases), NOTCH1/2 (four cases), CREBBP (three cases), ARID1A/B (three cases), ALK (two cases), FGFR1 (two cases), FAT4 (two cases) and CARD11 (two cases). Conclusions We developed a targeted NGS approach to identify tumor-specific alterations in ctDNA of neuroblastoma patients. Our results show the reliability of our approach to generate genomic information which can be integrated with clinical and pathological data at diagnosis.
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Affiliation(s)
| | - Vito Alessandro Lasorsa
- CEINGE Biotecnologie Avanzate, Napoli, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Simona Vetrella
- Department of Pediatric Oncology, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Achille Iolascon
- CEINGE Biotecnologie Avanzate, Napoli, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Mario Capasso
- CEINGE Biotecnologie Avanzate, Napoli, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli, Italy
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35
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Paramathas S, Guha T, Pugh TJ, Malkin D, Villani A. Considerations for the use of circulating tumor DNA sequencing as a screening tool in cancer predisposition syndromes. Pediatr Blood Cancer 2020; 67:e28758. [PMID: 33047872 DOI: 10.1002/pbc.28758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022]
Abstract
Liquid biopsy, specifically circulating tumor DNA (ctDNA) detection, has started to revolutionize the clinical management of patients with cancer by surpassing many limitations of traditional tissue biopsies, particularly for serial testing. ctDNA sequencing has been successfully utilized for cancer detection, prognostication, and assessment of disease response and evolution. While the applications of ctDNA analysis are growing, the majority of studies to date have primarily evaluated its use as a tool for tracking a known cancer, and in most cases at advanced stage. Herein, we discuss the potential application of ctDNA for surveillance and early cancer detection in patients with a cancer predisposition syndrome.
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Affiliation(s)
- Sangeetha Paramathas
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Tanya Guha
- Institute of Medical Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Centre, Toronto, Canada.,Ontario Institute for Cancer Research, Toronto, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Institute of Medical Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Anita Villani
- Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
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Coombs CC, Dickherber T, Crompton BD. Chasing ctDNA in Patients With Sarcoma. Am Soc Clin Oncol Educ Book 2020; 40:e351-e360. [PMID: 32598183 DOI: 10.1200/edbk_280749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Liquid biopsies are new technologies that allow cancer profiling of tumor fragments found in body fluids, such as peripheral blood, collected noninvasively from patients with malignancies. These assays are increasingly valuable in clinical oncology practice as prognostic biomarkers, as guides for therapy selection, for treatment monitoring, and for early detection of disease progression and relapse. However, application of these assays to rare cancers, such as pediatric and adult sarcomas, have lagged. In this article, we review the technical challenges of applying liquid biopsy technologies to sarcomas, provide an update on progress in the field, describe common pitfalls in interpreting liquid biopsy data, and discuss the intersection of sarcoma clinical care and commercial assays emerging on the horizon.
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Affiliation(s)
| | | | - Brian D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
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Andersson D, Fagman H, Dalin MG, Ståhlberg A. Circulating cell-free tumor DNA analysis in pediatric cancers. Mol Aspects Med 2020; 72:100819. [DOI: 10.1016/j.mam.2019.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/06/2019] [Accepted: 09/12/2019] [Indexed: 12/18/2022]
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Reed DR, Metts J, Pressley M, Fridley BL, Hayashi M, Isakoff MS, Loeb DM, Makanji R, Roberts RD, Trucco M, Wagner LM, Alexandrow MG, Gatenby RA, Brown JS. An evolutionary framework for treating pediatric sarcomas. Cancer 2020; 126:2577-2587. [PMID: 32176331 PMCID: PMC7318114 DOI: 10.1002/cncr.32777] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 12/17/2022]
Abstract
Lessons from extinction can be used in trials designed to pursue a cure for cancer. When cancer cannot be cured, similar strategies may be unwise, and strategies that leverage the adaptations of cancer to therapy should be considered.
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Affiliation(s)
- Damon R Reed
- Department of Interdisciplinary Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Adolescent and Young Adult Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jonathan Metts
- Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St Petersburg, Florida
| | - Mariyah Pressley
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Integrative Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Brooke L Fridley
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Biostatistics and Bioinformatics Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Masanori Hayashi
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado
| | - Michael S Isakoff
- Center for Cancer and Blood Disorders, Connecticut Children's Medical Center, Hartford, Connecticut
| | - David M Loeb
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York
| | - Rikesh Makanji
- Diagnostic Imaging and Interventional Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ryan D Roberts
- Department of Pediatric Hematology, Oncology, and Bone Marrow Transplantation, Nationwide Children's Hospital, Columbus, Ohio
| | - Matteo Trucco
- Depatment of Pediatrics, University of Miami, Miami, Florida
| | - Lars M Wagner
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina
| | - Mark G Alexandrow
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert A Gatenby
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Integrative Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Diagnostic Imaging and Interventional Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Joel S Brown
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Integrative Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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Weiser DA, West-Szymanski DC, Fraint E, Weiner S, Rivas MA, Zhao CWT, He C, Applebaum MA. Progress toward liquid biopsies in pediatric solid tumors. Cancer Metastasis Rev 2020; 38:553-571. [PMID: 31836951 DOI: 10.1007/s10555-019-09825-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pediatric solid tumors have long been known to shed tumor cells, DNA, RNA, and proteins into the blood. Recent technological advances have allowed for improved capture and analysis of these typically scant circulating materials. Efforts are ongoing to develop "liquid biopsy" assays as minimally invasive tools to address diagnostic, prognostic, and disease monitoring needs in childhood cancer care. Applying these highly sensitive technologies to serial liquid biopsies is expected to advance understanding of tumor biology, heterogeneity, and evolution over the course of therapy, thus opening new avenues for personalized therapy. In this review, we outline the latest technologies available for liquid biopsies and describe the methods, pitfalls, and benefits of the assays that are being developed for children with extracranial solid tumors. We discuss what has been learned in several of the most common pediatric solid tumors including neuroblastoma, sarcoma, Wilms tumor, and hepatoblastoma and highlight promising future directions for the field.
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Affiliation(s)
- Daniel A Weiser
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | | | - Ellen Fraint
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | - Shoshana Weiner
- Department of Pediatrics, Weill Cornell Medical Center, New York, NY, USA
| | - Marco A Rivas
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Carolyn W T Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Mark A Applebaum
- Department of Pediatrics, The University of Chicago, 900 E. 57th St., KCBD 5116, Chicago, IL, 60637, USA.
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40
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Using Liquid Biopsy in the Treatment of Patient with OS. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1257:95-105. [PMID: 32483734 DOI: 10.1007/978-3-030-43032-0_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Liquid biopsies encompass a number of new technologies designed to derive tumor data through the minimally invasive sampling of an accessible body fluid. These technologies remain early in their clinical development, and applications for patients with osteosarcoma are actively under investigation. In this chapter, we outline the current state of liquid biopsy technologies as they apply to cancer generally and osteosarcoma specifically, focusing on assays that detect and profile circulating tumor DNA (ctDNA), microRNAs (miRNA), and circulating tumor cells (CTCs). At present, ctDNA assays are the most mature, with multiple assays demonstrating the feasibility of detecting and quantifying ctDNA from blood samples of patients with osteosarcoma. Initial studies show that ctDNA can be detected in the majority of patients with osteosarcoma and that the detection and level of ctDNA correlates with a worse prognosis. Profiling of ctDNA can also identify specific somatic events that may have prognostic relevance, such as 8q gain in osteosarcoma. miRNAs are stable RNAs that regulate gene expression and are known to be dysregulated in cancer, and patterns of miRNA expression have been evaluated in multiple studies of patients with osteosarcoma. While studies have identified differential expression of many miRNAs in osteosarcomas compared to healthy controls, a consensus set of prognostic miRNAs has yet to be definitively validated. Recent studies have also demonstrated the feasibility of capturing CTCs in patients with osteosarcoma. The development of assays that quantify and profile CTCs for use as prognostic biomarkers or tools for biologic discovery is still in development. However, CTC technology holds incredible promise given the potential to perform multi-omic approaches in single cancer cells to understand osteosarcoma heterogeneity and tumor evolution. The next step required to move liquid biopsy technologies closer to helping patients will be wide-scale collection of patient samples from large prospective studies.
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García-Romero N, Carrión-Navarro J, Areal-Hidalgo P, Ortiz de Mendivil A, Asensi-Puig A, Madurga R, Núñez-Torres R, González-Neira A, Belda-Iniesta C, González-Rumayor V, López-Ibor B, Ayuso-Sacido A. BRAF V600E Detection in Liquid Biopsies from Pediatric Central Nervous System Tumors. Cancers (Basel) 2019; 12:cancers12010066. [PMID: 31881643 PMCID: PMC7016762 DOI: 10.3390/cancers12010066] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/14/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Pediatric Central Nervous System (CNS) tumors are the most fatal cancer diseases in childhood. Due to their localization and infiltrative nature, some tumor resections or biopsies are not feasible. In those cases, the use of minimally invasive methods as diagnostic, molecular marker detection, prognostic or monitoring therapies are emerging. The analysis of liquid biopsies which contain genetic information from the tumor has been much more widely explored in adults than in children. We compare the detection of BRAF V600E targetable mutation by digital-PCR from cell-free-DNA and EV-derived DNA (ctDNA) in serum, plasma and cerebrospinal fluid (CSF) isolated from a cohort of 29 CNS pediatric patients. Here we demonstrate that ctDNA isolated from serum and plasma could be successfully analyzed to obtain tumor genetic information which could be used to guide critical treatment decisions.
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Affiliation(s)
- Noemi García-Romero
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain; (N.G.-R.); (J.C.-N.); (P.A.-H.); (A.O.d.M.); (R.M.); (C.B.-I.)
| | - Josefa Carrión-Navarro
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain; (N.G.-R.); (J.C.-N.); (P.A.-H.); (A.O.d.M.); (R.M.); (C.B.-I.)
| | - Pilar Areal-Hidalgo
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain; (N.G.-R.); (J.C.-N.); (P.A.-H.); (A.O.d.M.); (R.M.); (C.B.-I.)
- Pediatric Hematology and Oncology Unit, Madrid Montepríncipe Hospital, 28660 Madrid, Spain
| | - Ana Ortiz de Mendivil
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain; (N.G.-R.); (J.C.-N.); (P.A.-H.); (A.O.d.M.); (R.M.); (C.B.-I.)
| | | | - Rodrigo Madurga
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain; (N.G.-R.); (J.C.-N.); (P.A.-H.); (A.O.d.M.); (R.M.); (C.B.-I.)
| | - Rocio Núñez-Torres
- Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (R.N.-T.); (A.G.-N.)
| | - Anna González-Neira
- Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (R.N.-T.); (A.G.-N.)
| | - Cristobal Belda-Iniesta
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain; (N.G.-R.); (J.C.-N.); (P.A.-H.); (A.O.d.M.); (R.M.); (C.B.-I.)
| | | | - Blanca López-Ibor
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain; (N.G.-R.); (J.C.-N.); (P.A.-H.); (A.O.d.M.); (R.M.); (C.B.-I.)
- Pediatric Hematology and Oncology Unit, Madrid Montepríncipe Hospital, 28660 Madrid, Spain
- Correspondence: (B.L.-I.); (A.A.-S.); Tel.: +34-91372-4700 (A.A.-S.)
| | - Angel Ayuso-Sacido
- Fundación de Investigación HM Hospitales, HM Hospitales, 28015 Madrid, Spain; (N.G.-R.); (J.C.-N.); (P.A.-H.); (A.O.d.M.); (R.M.); (C.B.-I.)
- Facultad de Medicina (IMMA), Universidad San Pablo-CEU, 28668 Madrid, Spain
- Correspondence: (B.L.-I.); (A.A.-S.); Tel.: +34-91372-4700 (A.A.-S.)
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Cell-free DNA in blood as a noninvasive insight into the sarcoma genome. Mol Aspects Med 2019; 72:100827. [PMID: 31703948 DOI: 10.1016/j.mam.2019.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/02/2019] [Accepted: 10/18/2019] [Indexed: 12/26/2022]
Abstract
Sarcomas are malignant tumors of mesenchymal origin that arise mainly from connective and supportive tissue. Sarcomas include a wide range of histological subtypes, showing a large diversity at the molecular level, from simple to highly complex karyotypes but with few recurrent somatic changes. Therapeutic decisions increasingly rely on the molecular characteristics of the individual tumor. Circulating cell-free DNA (ctDNA) is released into peripheral blood and can be used for the genomic analysis of sarcomas. However, the diversity and heterogeneity of somatic changes observed in sarcomas pose a challenge when choosing an adequate assay for the detection of ctDNA in body fluids. In this review, we provide an overview of different studies on ctDNA from blood in bone and soft tissue sarcomas, including gastrointestinal stromal tumors. We will specifically address the technological challenges that must be considered to achieve the sensitive detection of ctDNA and discuss the clinical applications of ctDNA in the management and treatment of sarcomas.
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