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Cornelli L, Van Paemel R, Ferro Dos Santos MR, Roelandt S, Willems L, Vandersteene J, Baert E, Mus LM, Van Roy N, De Wilde B, De Preter K. Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid. Clin Epigenetics 2024; 16:87. [PMID: 38970137 PMCID: PMC11225235 DOI: 10.1186/s13148-024-01696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/17/2024] [Indexed: 07/07/2024] Open
Abstract
Pediatric central nervous system tumors remain challenging to diagnose. Imaging approaches do not provide sufficient detail to discriminate between different tumor types, while the histopathological examination of tumor tissue shows high inter-observer variability. Recent studies have demonstrated the accurate classification of central nervous system tumors based on the DNA methylation profile of a tumor biopsy. However, a brain biopsy holds significant risk of bleeding and damaging the surrounding tissues. Liquid biopsy approaches analyzing circulating tumor DNA show high potential as an alternative and less invasive tool to study the DNA methylation pattern of tumors. Here, we explore the potential of classifying pediatric brain tumors based on methylation profiling of the circulating cell-free DNA (cfDNA) in cerebrospinal fluid (CSF). For this proof-of-concept study, we collected cerebrospinal fluid samples from 19 pediatric brain cancer patients via a ventricular drain placed for reasons of increased intracranial pressure. Analyses on the cfDNA showed high variability of cfDNA quantities across patients ranging from levels below the limit of quantification to 40 ng cfDNA per milliliter of CSF. Classification based on methylation profiling of cfDNA from CSF was correct for 7 out of 20 samples in our cohort. Accurate results were mostly observed in samples of high quality, more specifically those with limited high molecular weight DNA contamination. Interestingly, we show that centrifugation of the CSF prior to processing increases the fraction of fragmented cfDNA to high molecular weight DNA. In addition, classification was mostly correct for samples with high tumoral cfDNA fraction as estimated by computational deconvolution (> 40%). In summary, analysis of cfDNA in the CSF shows potential as a tool for diagnosing pediatric nervous system tumors especially in patients with high levels of tumoral cfDNA in the CSF. Further optimization of the collection procedure, experimental workflow and bioinformatic approach is required to also allow classification for patients with low tumoral fractions in the CSF.
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Affiliation(s)
- Lotte Cornelli
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Ruben Van Paemel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Maísa R Ferro Dos Santos
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Sofie Roelandt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Leen Willems
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | - Edward Baert
- Department of Neurosurgery, Ghent University Hospital, Ghent, Belgium
| | - Liselot M Mus
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Nadine Van Roy
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
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2
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Baranová I, Samec M, Dvorská D, Šťastný I, Janíková K, Kašubová I, Hornáková A, Lukáčová E, Kapinová A, Biringer K, Halašová E, Danková Z. Droplet digital PCR analysis of CDH13 methylation status in Slovak women with invasive ductal breast cancer. Sci Rep 2024; 14:14700. [PMID: 38926485 PMCID: PMC11208553 DOI: 10.1038/s41598-024-65580-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
Identifying novel epigenetic biomarkers is a promising way to improve the clinical management of patients with breast cancer. Our study aimed to determine the methylation pattern of 25 tumor suppressor genes (TSG) and select the best methylation biomarker associated with clinicopathological features in the cohort of Slovak patients diagnosed with invasive ductal carcinoma (IDC). Overall, 166 formalin-fixed, paraffin-embedded (FFPE) tissues obtained from patients with IDC were included in the study. The methylation status of the promoter regions of 25 TSG was analyzed using semiquantitative methylation-specific MLPA (MS-MLPA). We identified CDH13 as the most frequently methylated gene in our cohort of patients. Further analysis by ddPCR confirmed an increased level of methylation in the promoter region of CDH13. A significant difference in CDH13 methylation levels was observed between IDC molecular subtypes LUM A versus HER2 (P = 0.0116) and HER2 versus TNBC (P = 0.0234). In addition, significantly higher methylation was detected in HER2+ versus HER2- tumors (P = 0.0004) and PR- versus PR+ tumors (P = 0.0421). Our results provide evidence that alteration in CDH13 methylation is associated with clinicopathological features in the cohort of Slovak patients with IDC. In addition, using ddPCR as a methylation-sensitive method represents a promising approach characterized by higher precision and technical simplicity to measure the methylation of target CpGs in CDH13 compared to other conventional methods such as MS-MLPA.
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Affiliation(s)
- Ivana Baranová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
- Department of Pathological Physiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
- Biobank for Cancer and Rare Diseases, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Marek Samec
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia.
- Department of Medical Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia.
| | - Dana Dvorská
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Igor Šťastný
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin and Martin University Hospital, Comenius University in Bratislava, Martin, Slovakia
| | - Katarína Janíková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ivana Kašubová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Hornáková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Lukáčová
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Kapinová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Kamil Biringer
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin and Martin University Hospital, Comenius University in Bratislava, Martin, Slovakia
| | - Erika Halašová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Danková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
- Biobank for Cancer and Rare Diseases, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
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3
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Wang Q, Zhang S, Li Y. Efficient DNA Coding Algorithm for Polymerase Chain Reaction Amplification Information Retrieval. Int J Mol Sci 2024; 25:6449. [PMID: 38928155 PMCID: PMC11204281 DOI: 10.3390/ijms25126449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Polymerase Chain Reaction (PCR) amplification is widely used for retrieving information from DNA storage. During the PCR amplification process, nonspecific pairing between the 3' end of the primer and the DNA sequence can cause cross-talk in the amplification reaction, leading to the generation of interfering sequences and reduced amplification accuracy. To address this issue, we propose an efficient coding algorithm for PCR amplification information retrieval (ECA-PCRAIR). This algorithm employs variable-length scanning and pruning optimization to construct a codebook that maximizes storage density while satisfying traditional biological constraints. Subsequently, a codeword search tree is constructed based on the primer library to optimize the codebook, and a variable-length interleaver is used for constraint detection and correction, thereby minimizing the likelihood of nonspecific pairing. Experimental results demonstrate that ECA-PCRAIR can reduce the probability of nonspecific pairing between the 3' end of the primer and the DNA sequence to 2-25%, enhancing the robustness of the DNA sequences. Additionally, ECA-PCRAIR achieves a storage density of 2.14-3.67 bits per nucleotide (bits/nt), significantly improving storage capacity.
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Affiliation(s)
| | - Shufang Zhang
- School of Electrical Automation and Information Engineering, Tianjin University, Tianjin 300072, China
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Ronsley R, Karvonen KA, Cole B, Paulson V, Stevens J, Crotty EE, Hauptman J, Lee A, Stasi SM, Lockwood CM, Leary SES. Detection of tumor-derived cell-free DNA in cerebrospinal fluid using a clinically validated targeted sequencing panel for pediatric brain tumors. J Neurooncol 2024; 168:215-224. [PMID: 38755519 DOI: 10.1007/s11060-024-04645-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/12/2024] [Indexed: 05/18/2024]
Abstract
PURPOSE Clinical sequencing of tumor DNA is necessary to render an integrated diagnosis and select therapy for children with primary central nervous system (CNS) tumors, but neurosurgical biopsy is not without risk. In this study, we describe cell-free DNA (cfDNA) in blood and cerebrospinal fluid (CSF) as sources for "liquid biopsy" in pediatric brain tumors. METHODS CSF samples were collected by lumbar puncture, ventriculostomy, or surgery from pediatric patients with CNS tumors. Following extraction, CSF-derived cfDNA was sequenced using UW-OncoPlex™, a clinically validated next-generation sequencing platform. CSF-derived cfDNA results and paired plasma and tumor samples concordance was also evaluated. RESULTS Seventeen CSF samples were obtained from 15 pediatric patients with primary CNS tumors. Tumor types included medulloblastoma (n = 7), atypical teratoid/rhabdoid tumor (n = 2), diffuse midline glioma with H3 K27 alteration (n = 4), pilocytic astrocytoma (n = 1), and pleomorphic xanthoastrocytoma (n = 1). CSF-derived cfDNA was detected in 9/17 (53%) of samples, and sufficient for sequencing in 8/10 (80%) of extracted samples. All somatic mutations and copy-number variants were also detected in matched tumor tissue, and tumor-derived cfDNA was absent in plasma samples and controls. Tumor-derived cfDNA alterations were detected in the absence of cytological evidence of malignant cells in as little as 200 µl of CSF. Several clinically relevant alterations, including a KIAA1549::BRAF fusion were detected. CONCLUSIONS Clinically relevant genomic alterations are detectable using CSF-derived cfDNA across a range of pediatric brain tumors. Next-generation sequencing platforms are capable of producing a high yield of DNA alterations with 100% concordance rate with tissue analysis.
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Affiliation(s)
- Rebecca Ronsley
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US.
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US.
- Fred Hutchinson Cancer Research Center, Seattle, WA, US.
- Seattle Children's Hospital, Mail Stop MB.8.501, 4800 Sand Point Way NE, Seattle, WA, 98105, USA.
| | - Kristine A Karvonen
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
- Fred Hutchinson Cancer Research Center, Seattle, WA, US
| | - Bonnie Cole
- Department of Laboratories, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US
| | - Vera Paulson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US
- Genetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jeff Stevens
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
| | - Erin E Crotty
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
- Fred Hutchinson Cancer Research Center, Seattle, WA, US
| | - Jason Hauptman
- Division of Neurosurgery, Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA, US
| | - Amy Lee
- Division of Neurosurgery, Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA, US
| | - Shannon M Stasi
- Department of Laboratories, Seattle Children's Hospital, University of Washington, Seattle, WA, US
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US
- Genetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Sarah E S Leary
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
- Fred Hutchinson Cancer Research Center, Seattle, WA, US
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5
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Mueller S, Kline C, Franson A, van der Lugt J, Prados M, Waszak SM, Plasschaert SLA, Molinaro AM, Koschmann C, Nazarian J. Rational combination platform trial design for children and young adults with diffuse midline glioma: A report from PNOC. Neuro Oncol 2024; 26:S125-S135. [PMID: 38124481 PMCID: PMC11066905 DOI: 10.1093/neuonc/noad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Indexed: 12/23/2023] Open
Abstract
Background Diffuse midline glioma (DMG) is a devastating pediatric brain tumor unresponsive to hundreds of clinical trials. Approximately 80% of DMGs harbor H3K27M oncohistones, which reprogram the epigenome to increase the metabolic profile of the tumor cells. Methods We have previously shown preclinical efficacy of targeting both oxidative phosphorylation and glycolysis through treatment with ONC201, which activates the mitochondrial protease ClpP, and paxalisib, which inhibits PI3K/mTOR, respectively. Results ONC201 and paxalisib combination treatment aimed at inducing metabolic distress led to the design of the first DMG-specific platform trial PNOC022 (NCT05009992). Conclusions Here, we expand on the PNOC022 rationale and discuss various considerations, including liquid biome, microbiome, and genomic biomarkers, quality-of-life endpoints, and novel imaging modalities, such that we offer direction on future clinical trials in DMG.
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Affiliation(s)
- Sabine Mueller
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, California, USA
| | - Cassie Kline
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Andrea Franson
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Michael Prados
- Department of Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Sebastian M Waszak
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
- Laboratory of Computational Neuro-Oncology, Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Annette M Molinaro
- Division of Biomedical Statistics and Informatics, Department of Neurosurgery, University of California, San Francisco, San Francisco, California, USA
| | - Carl Koschmann
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children’s National Health System, Washington, District of Columbia, USA
- Brain Tumor Institute, Children’s National Health System, Washington, District of Columbia, USA
- DMG Research Center, Department of Pediatrics, University Children’s Hospital, University of Zurich, Zürich, Switzerland
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6
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Szmyd B, Stanisławska P, Podstawka M, Zaczkowski K, Izbiński PM, Kulczycka-Wojdala D, Stawski R, Wiśniewski K, Janczar K, Braun M, Białasiewicz P, Jaskólski DJ, Bobeff EJ. D-Loop Mutations as Prognostic Markers in Glioblastoma-A Pilot Study. Int J Mol Sci 2024; 25:4334. [PMID: 38673919 PMCID: PMC11050196 DOI: 10.3390/ijms25084334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Glioblastoma, a highly aggressive brain tumor, poses significant treatment challenges. A deeper investigation into its molecular complexity is essential for the identification of novel prognostic biomarkers and therapeutic strategies, potentially improving patient outcomes in terms of survival and quality of life. While nuclear DNA mutations have been extensively studied, the role of mitochondrial DNA (mtDNA) mutations, specifically in the D-loop region, remains poorly understood. This prospective case-control study aimed to assess the prognostic significance of the mtDNA D-loop m.16126T>C variant in glioblastoma patients. Immunohistochemistry and droplet digital PCR (ddPCR) were employed for mutation analysis, complemented by statistical analyses and a literature review. The study cohort comprised 22 glioblastoma patients (mean age 59.36 ± 14.17, 12 (54.55%) females), and 25 controls (59.48 ± 13.22, 12 (80%) females). The D-loop m.16126T>C variant was observed in four (18%) of the glioblastoma samples and was associated with shorter median survival (9.5 vs. 18 months; p = 0.016, log-rank test). This study underscores the importance of investigating mtDNA, especially D-loop variants, in glioblastoma, suggesting its potential as a prognostic biomarker and, therefore, its possible therapeutic targets, warranting further exploration.
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Affiliation(s)
- Bartosz Szmyd
- Department of Neurosurgery and Neuro-Oncology, Barlicki University Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (B.S.); (P.S.); (M.P.); (K.Z.); (P.M.I.); (K.W.); (D.J.J.)
| | - Patrycja Stanisławska
- Department of Neurosurgery and Neuro-Oncology, Barlicki University Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (B.S.); (P.S.); (M.P.); (K.Z.); (P.M.I.); (K.W.); (D.J.J.)
| | - Małgorzata Podstawka
- Department of Neurosurgery and Neuro-Oncology, Barlicki University Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (B.S.); (P.S.); (M.P.); (K.Z.); (P.M.I.); (K.W.); (D.J.J.)
| | - Karol Zaczkowski
- Department of Neurosurgery and Neuro-Oncology, Barlicki University Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (B.S.); (P.S.); (M.P.); (K.Z.); (P.M.I.); (K.W.); (D.J.J.)
| | - Patryk M. Izbiński
- Department of Neurosurgery and Neuro-Oncology, Barlicki University Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (B.S.); (P.S.); (M.P.); (K.Z.); (P.M.I.); (K.W.); (D.J.J.)
| | | | - Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Karol Wiśniewski
- Department of Neurosurgery and Neuro-Oncology, Barlicki University Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (B.S.); (P.S.); (M.P.); (K.Z.); (P.M.I.); (K.W.); (D.J.J.)
| | - Karolina Janczar
- Department of Pathology, Medical University of Lodz, 92-213 Lodz, Poland; (K.J.); (M.B.)
| | - Marcin Braun
- Department of Pathology, Medical University of Lodz, 92-213 Lodz, Poland; (K.J.); (M.B.)
| | - Piotr Białasiewicz
- Department of Sleep Medicine and Metabolic Disorders, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Dariusz J. Jaskólski
- Department of Neurosurgery and Neuro-Oncology, Barlicki University Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (B.S.); (P.S.); (M.P.); (K.Z.); (P.M.I.); (K.W.); (D.J.J.)
| | - Ernest J. Bobeff
- Department of Neurosurgery and Neuro-Oncology, Barlicki University Hospital, Medical University of Lodz, 90-153 Lodz, Poland; (B.S.); (P.S.); (M.P.); (K.Z.); (P.M.I.); (K.W.); (D.J.J.)
- Department of Sleep Medicine and Metabolic Disorders, Medical University of Lodz, 92-215 Lodz, Poland;
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Otsuji R, Fujioka Y, Hata N, Kuga D, Hatae R, Sangatsuda Y, Nakamizo A, Mizoguchi M, Yoshimoto K. Liquid Biopsy for Glioma Using Cell-Free DNA in Cerebrospinal Fluid. Cancers (Basel) 2024; 16:1009. [PMID: 38473369 DOI: 10.3390/cancers16051009] [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: 12/25/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Glioma is one of the most common primary central nervous system (CNS) tumors, and its molecular diagnosis is crucial. However, surgical resection or biopsy is risky when the tumor is located deep in the brain or brainstem. In such cases, a minimally invasive approach to liquid biopsy is beneficial. Cell-free DNA (cfDNA), which directly reflects tumor-specific genetic changes, has attracted attention as a target for liquid biopsy, and blood-based cfDNA monitoring has been demonstrated for other extra-cranial cancers. However, it is still challenging to fully detect CNS tumors derived from cfDNA in the blood, including gliomas, because of the unique structure of the blood-brain barrier. Alternatively, cerebrospinal fluid (CSF) is an ideal source of cfDNA and is expected to contribute significantly to the liquid biopsy of gliomas. Several successful studies have been conducted to detect tumor-specific genetic alterations in cfDNA from CSF using digital PCR and/or next-generation sequencing. This review summarizes the current status of CSF-based cfDNA-targeted liquid biopsy for gliomas. It highlights how the approaches differ from liquid biopsies of other extra-cranial cancers and discusses the current issues and prospects.
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Affiliation(s)
- Ryosuke Otsuji
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yutaka Fujioka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Oita University Faculty of Medicine, Yufu 879-5593, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Nakamizo
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Neurosurgery, National Hospital Organization Kyushu Medical Center, Clinical Research Institute, Fukuoka 810-8563, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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8
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Zhang Y, Du H, Wang N, Wang L, Huang Y. An update of clinical value of circulating tumor DNA in esophageal cancer: a systematic review and meta-analysis. BMC Cancer 2024; 24:129. [PMID: 38267901 PMCID: PMC10809487 DOI: 10.1186/s12885-024-11879-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/13/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Esophageal cancer (EC) is a deadly disease with limited therapeutic options. Although circulating tumor DNA (ctDNA) could be a promising tool in this regard, the availiable evidence is limited. We performed a systematic review and meta-analysis to summarize the clinical applicability of the next-generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR) technology on the ctDNA detection of the EC and listed the current challenges. METHODS We systematically searched MEDLINE (via PubMed), Embase (via OVID), ISI Web of Science database and Cochrane Library from January, 2000 to April, 2023. Progression-free survival (PFS) and overall survival (OS) were set as primary outcome endpoints. Pathologic response was evaluated by tumor regression grade (TRG), according to the eighth edition of the American Joint Committee on Cancer (AJCC). Major pathologic regression (MPR) was defined as TRG 1 and 2. The MPR was set as secondary endpoint. Hazard rate (HR) and associated 95% CI were used as the effect indicators the association between ctDNA and prognosis of EC. MPR rates were also calculated. Fixed-effect model (Inverse Variance) or random-effect model (Mantel-Haenszel method) was performed depending on the statistically heterogeneity. RESULTS Twenty-two studies, containing 1144 patients with EC, were included in this meta-analysis. The results showed that OS (HR = 3.87; 95% CI, 2.86-5.23) and PFS (HR = 4.28; 95% CI, 3.34-5.48) were shorter in ctDNA-positive patients. In the neoadjuvant therapy, the sensitivity analysis showed the clarified HR of ctDNA-positive was 1.13(95% CI, 1.01-1.28). We also found that TP53, NOTCH1, CCND1 and CNKN2A are the most frequent mutation genes. CONCLUSIONS Positive ctDNA is associated with poor prognosis, which demonstrated clinical value of ctDNA. Longitudinal ctDNA monitoring showed potential prognostic value in the neoadjuvant therapy. In an era of precision medicine, ctDNA could be a promising tool to individualize treatment planning and to improve outcomes in EC. PROSPERO REGISTRATION NUMBER CRD42023412465.
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Affiliation(s)
- Yaozhong Zhang
- Department of Infectious diseases, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huazhen Du
- Department of Emergency, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Na Wang
- Department of Molecular Biology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lei Wang
- Department of Thoracic Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yajie Huang
- Department of Medical oncology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China.
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9
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On J, Natsumeda M, Takahashi H, Koyama A, Shibuma S, Shibata N, Watanabe J, Saito S, Kanemaru Y, Tsukamoto Y, Okada M, Ogura R, Eda T, Tada M, Shimizu H, Adachi JI, Mishima K, Nishikawa R, Kakita A, Oishi M. Reliable detection of genetic alterations in cyst fluid DNA for the diagnosis of brain tumors. J Neurooncol 2024; 166:273-282. [PMID: 38227143 DOI: 10.1007/s11060-023-04555-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/26/2023] [Indexed: 01/17/2024]
Abstract
PURPOSE Liquid biopsy of cyst fluid in brain tumors has not been extensively studied to date. The present study was performed to see whether diagnostic genetic alterations found in brain tumor tissue DNA could also be detected in cell-free DNA (cfDNA) of cyst fluid in cystic brain tumors. METHODS Cyst fluid was obtained from 22 patients undergoing surgery for a cystic brain tumor with confirmed genetic alterations in tumor DNA. Pathological diagnoses based on WHO 2021 classification and diagnostic alterations in the tumor DNA, such as IDH1 R132H and TERT promoter mutation for oligodendrogliomas, were detected by Sanger sequencing. The same alterations were analyzed by both droplet digital PCR (ddPCR) and Sanger sequencing in cyst fluid cfDNA. Additionally, multiplex ligation-dependent probe amplification (MLPA) assays were performed to assess 1p/19q status, presence of CDKN2A loss, PTEN loss and EGFR amplification, to assess whether differentiating between astrocytomas and oligodendrogliomas and grading is possible from cyst fluid cfDNA. RESULTS Twenty-five genetic alterations were found in 22 tumor samples. All (100%) alterations were detected in cyst fluid cfDNA by ddPCR. Twenty of the 25 (80%) alterations were also detected by Sanger sequencing of cyst fluid cfDNA. Variant allele frequency (VAF) in cyst fluid cfDNA was comparable to that of tumor DNA (R = 0.62, Pearson's correlation). MLPA was feasible in 11 out of 17 (65%) diffuse gliomas, with close correlation of results between tumor DNA and cyst fluid cfDNA. CONCLUSION Cell-free DNA obtained from cyst fluid in cystic brain tumors is a reliable alternative to tumor DNA when diagnosing brain tumors.
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Affiliation(s)
- Jotaro On
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Manabu Natsumeda
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan.
- Advanced Treatment of Neurological Diseases Branch, Brain Research Institute, Niigata University, Niigata, Japan.
| | - Haruhiko Takahashi
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akihide Koyama
- Department of Legal Medicine, Niigata University Graduate School of Medical and Dental Science, Niigata, Japan
| | - Satoshi Shibuma
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Nao Shibata
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jun Watanabe
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Shoji Saito
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yu Kanemaru
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yoshihiro Tsukamoto
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masayasu Okada
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Ryosuke Ogura
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Takeyoshi Eda
- Division of Pharmacy, Medical and Dental Hospital, Niigata University, Niigata, Japan
| | - Mari Tada
- Department of Pathology, Brain Research Institute, Niigata, Japan
| | - Hiroshi Shimizu
- Department of Pathology, Brain Research Institute, Niigata, Japan
| | - Jun-Ichi Adachi
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Kazuhiko Mishima
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Ryo Nishikawa
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata, Japan
| | - Makoto Oishi
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
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10
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Foster JB, Koptyra MP, Bagley SJ. Recent Developments in Blood Biomarkers in Neuro-oncology. Curr Neurol Neurosci Rep 2023; 23:857-867. [PMID: 37943477 DOI: 10.1007/s11910-023-01321-y] [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] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
PURPOSE OF REVIEW Given the invasive and high-risk nature of brain surgery, the need for non-invasive biomarkers obtained from the peripheral blood is greatest in tumors of the central nervous system (CNS). In this comprehensive review, we highlight recent advances in blood biomarker development for adult and pediatric brain tumors. RECENT FINDINGS We summarize recent blood biomarker development for CNS tumors across multiple key analytes, including peripheral blood mononuclear cells, cell-free DNA, cell-free RNA, proteomics, circulating tumor cells, and tumor-educated platelets. We also discuss methods for enhancing blood biomarker detection through transient opening of the blood-brain barrier. Although blood-based biomarkers are not yet used in routine neuro-oncology practice, this field is advancing rapidly and holds great promise for improved and non-invasive management of patients with brain tumors. Prospective and adequately powered studies are needed to confirm the clinical utility of any blood biomarker prior to widespread clinical implementation.
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Affiliation(s)
- Jessica B Foster
- Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mateusz P Koptyra
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stephen J Bagley
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, 10th Floor Perelman Center, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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11
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Erez N, Furth N, Fedyuk V, Wadden J, Aittaleb R, Schwark K, Niculcea M, Miclea M, Mody R, Franson A, Eze A, Nourmohammadi N, Nazarian J, Venneti S, Koschmann C, Shema E. Single-molecule systems for detection and monitoring of plasma circulating nucleosomes and oncoproteins in Diffuse Midline Glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568019. [PMID: 38045418 PMCID: PMC10690213 DOI: 10.1101/2023.11.21.568019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The analysis of cell-free tumor DNA (ctDNA) and proteins in the blood of cancer patients potentiates a new generation of non-invasive diagnostics and treatment monitoring approaches. However, confident detection of these tumor-originating markers is challenging, especially in the context of brain tumors, in which extremely low amounts of these analytes circulate in the patient's plasma. Here, we applied a sensitive single-molecule technology to profile multiple histone modifications on millions of individual nucleosomes from the plasma of Diffuse Midline Glioma (DMG) patients. The system reveals epigenetic patterns that are unique to DMG, significantly differentiating this group of patients from healthy subjects or individuals diagnosed with other cancer types. We further develop a method to directly capture and quantify the tumor-originating oncoproteins, H3-K27M and mutant p53, from the plasma of children diagnosed with DMG. This single-molecule system allows for accurate molecular classification of patients, utilizing less than 1ml of liquid-biopsy material. Furthermore, we show that our simple and rapid detection strategy correlates with MRI measurements and droplet-digital PCR (ddPCR) measurements of ctDNA, highlighting the utility of this approach for non-invasive treatment monitoring of DMG patients. This work underscores the clinical potential of single-molecule-based, multi-parametric assays for DMG diagnosis and treatment monitoring.
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12
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Khalili N, Shooli H, Hosseini N, Fathi Kazerooni A, Familiar A, Bagheri S, Anderson H, Bagley SJ, Nabavizadeh A. Adding Value to Liquid Biopsy for Brain Tumors: The Role of Imaging. Cancers (Basel) 2023; 15:5198. [PMID: 37958372 PMCID: PMC10650848 DOI: 10.3390/cancers15215198] [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: 09/18/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Clinical management in neuro-oncology has changed to an integrative approach that incorporates molecular profiles alongside histopathology and imaging findings. While the World Health Organization (WHO) guideline recommends the genotyping of informative alterations as a routine clinical practice for central nervous system (CNS) tumors, the acquisition of tumor tissue in the CNS is invasive and not always possible. Liquid biopsy is a non-invasive approach that provides the opportunity to capture the complex molecular heterogeneity of the whole tumor through the detection of circulating tumor biomarkers in body fluids, such as blood or cerebrospinal fluid (CSF). Despite all of the advantages, the low abundance of tumor-derived biomarkers, particularly in CNS tumors, as well as their short half-life has limited the application of liquid biopsy in clinical practice. Thus, it is crucial to identify the factors associated with the presence of these biomarkers and explore possible strategies that can increase the shedding of these tumoral components into biological fluids. In this review, we first describe the clinical applications of liquid biopsy in CNS tumors, including its roles in the early detection of recurrence and monitoring of treatment response. We then discuss the utilization of imaging in identifying the factors that affect the detection of circulating biomarkers as well as how image-guided interventions such as focused ultrasound can help enhance the presence of tumor biomarkers through blood-brain barrier (BBB) disruption.
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Affiliation(s)
- Nastaran Khalili
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (N.K.); (A.F.K.); (A.F.)
| | - Hossein Shooli
- Department of Radiology, Bushehr University of Medical Sciences, Bushehr 75146-33196, Iran
| | - Nastaran Hosseini
- School of Medicine, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran;
| | - Anahita Fathi Kazerooni
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (N.K.); (A.F.K.); (A.F.)
- AI2D Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ariana Familiar
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (N.K.); (A.F.K.); (A.F.)
| | - Sina Bagheri
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.B.); (H.A.)
| | - Hannah Anderson
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.B.); (H.A.)
| | - Stephen J. Bagley
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Ali Nabavizadeh
- Center for Data-Driven Discovery in Biomedicine (D3b), Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (N.K.); (A.F.K.); (A.F.)
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.B.); (H.A.)
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13
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Chicard M, Iddir Y, Masliah Planchon J, Combaret V, Attignon V, Saint-Charles A, Frappaz D, Faure-Conter C, Beccaria K, Varlet P, Geoerger B, Baulande S, Pierron G, Bouchoucha Y, Doz F, Delattre O, Waterfall JJ, Bourdeaut F, Schleiermacher G. Cell-Free DNA Extracted from CSF for the Molecular Diagnosis of Pediatric Embryonal Brain Tumors. Cancers (Basel) 2023; 15:3532. [PMID: 37444642 DOI: 10.3390/cancers15133532] [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: 06/03/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Liquid biopsies are revolutionary tools used to detect tumor-specific genetic alterations in body fluids, including the use of cell-free DNA (cfDNA) for molecular diagnosis in cancer patients. In brain tumors, cerebrospinal fluid (CSF) cfDNA might be more informative than plasma cfDNA. Here, we assess the use of CSF cfDNA in pediatric embryonal brain tumors (EBT) for molecular diagnosis. METHODS The CSF cfDNA of pediatric patients with medulloblastoma (n = 18), ATRT (n = 3), ETMR (n = 1), CNS NB FOXR2 (n = 2) and pediatric EBT NOS (n = 1) (mean cfDNA concentration 48 ng/mL; range 4-442 ng/mL) and matched tumor genomic DNA were sequenced by WES and/or a targeted sequencing approach to determine single-nucleotide variations (SNVs) and copy number alterations (CNA). A specific capture covering transcription start sites (TSS) of genes of interest was also used for nucleosome footprinting in CSF cfDNA. RESULTS 15/25 CSF cfDNA samples yielded informative results, with informative CNA and SNVs in 11 and 15 cases, respectively. For cases with paired tumor and CSF cfDNA WES (n = 15), a mean of 83 (range 1-160) shared SNVs were observed, including SNVs in classical medulloblastoma genes such as SMO and KMT2D. Interestingly, tumor-specific SNVs (mean 18; range 1-62) or CSF-specific SNVs (mean 5; range 0-25) were also observed, suggesting clonal heterogeneity. The TSS panel resulted in differential coverage profiles across all 112 studied genes in 7 cases, indicating distinct promoter accessibility. CONCLUSION CSF cfDNA sequencing yielded informative results in 60% (15/25) of all cases, with informative results in 83% (15/18) of all cases analyzed by WES. These results pave the way for the implementation of these novel approaches for molecular diagnosis and minimal residual disease monitoring.
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Affiliation(s)
- Mathieu Chicard
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Yasmine Iddir
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Julien Masliah Planchon
- Unité de Génétique Somatique, Service de Génétique, Institut Curie Hospital Group, 75005 Paris, France
| | - Valérie Combaret
- Plateforme de Génomique des Cancers, Centre Léon Bérard, 69008 Lyon, France
- Laboratoire de Recherche Translationnelle, Centre Léon-Bérard, 69373 Lyon, France
| | - Valéry Attignon
- Plateforme de Génomique des Cancers, Centre Léon Bérard, 69008 Lyon, France
- Laboratoire de Recherche Translationnelle, Centre Léon-Bérard, 69373 Lyon, France
| | - Alexandra Saint-Charles
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Didier Frappaz
- Department of Pediatric Clinical Trials and Department of Pediatric Neuro-Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, 69008 Lyon, France
| | - Cécile Faure-Conter
- Department of Pediatric Clinical Trials and Department of Pediatric Neuro-Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, 69008 Lyon, France
| | - Kévin Beccaria
- Department of Pediatric Neurosurgery, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris-Université Paris Cité, 75015 Paris, France
| | - Pascale Varlet
- GHU Psychiatrie et Neurosciences, Site Sainte-Anne, 75014 Paris, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, 94805 Villejuif, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, 75005 Paris, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service de Génétique, Institut Curie Hospital Group, 75005 Paris, France
| | - Yassine Bouchoucha
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
| | - François Doz
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
- Faculty of Medicine, Université Paris Cité, 75005 Paris, France
| | - Olivier Delattre
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
- Diversity and Plasticity of Childhood Tumors Laboratory, INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Joshua J Waterfall
- Integrative Functional Genomics of Cancer Laboratory, INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, PSL Research University, 75005 Paris, France
- Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Franck Bourdeaut
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
| | - Gudrun Schleiermacher
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
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14
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Gaitsch H, Franklin RJM, Reich DS. Cell-free DNA-based liquid biopsies in neurology. Brain 2023; 146:1758-1774. [PMID: 36408894 PMCID: PMC10151188 DOI: 10.1093/brain/awac438] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
This article reviews recent developments in the application of cell-free DNA-based liquid biopsies to neurological diseases. Over the past few decades, an explosion of interest in the use of accessible biofluids to identify and track molecular disease has revolutionized the fields of oncology, prenatal medicine and others. More recently, technological advances in signal detection have allowed for informative analysis of biofluids that are typically sparse in cells and other circulating components, such as CSF. In parallel, advancements in epigenetic profiling have allowed for novel applications of liquid biopsies to diseases without characteristic mutational profiles, including many degenerative, autoimmune, inflammatory, ischaemic and infectious disorders. These events have paved the way for a wide array of neurological conditions to benefit from enhanced diagnostic, prognostic, and treatment abilities through the use of liquid biomarkers: a 'liquid biopsy' approach. This review includes an overview of types of liquid biopsy targets with a focus on circulating cell-free DNA, methods used to identify and probe potential liquid biomarkers, and recent applications of such biomarkers to a variety of complex neurological conditions including CNS tumours, stroke, traumatic brain injury, Alzheimer's disease, epilepsy, multiple sclerosis and neuroinfectious disease. Finally, the challenges of translating liquid biopsies to use in clinical neurology settings-and the opportunities for improvement in disease management that such translation may provide-are discussed.
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Affiliation(s)
- Hallie Gaitsch
- NIH-Oxford-Cambridge Scholars Program, Wellcome-MRC Cambridge Stem Cell Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Wijetunga NA, Goglia AG, Weinhold N, Berger MF, Cislo M, Higginson DS, Chabot K, Osman AM, Schaff L, Pentsova E, Miller AM, Powell SN, Boire A, Yang JT. Dynamic Mutational Landscape of Cerebrospinal Fluid Circulating Tumor DNA and Predictors of Survival after Proton Craniospinal Irradiation for Leptomeningeal Metastases. Clin Cancer Res 2023; 29:775-783. [PMID: 36449664 PMCID: PMC9957915 DOI: 10.1158/1078-0432.ccr-22-2434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/05/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022]
Abstract
PURPOSE Proton craniospinal irradiation (pCSI) is a promising treatment for patients with solid tumor leptomeningeal metastasis (LM). We hypothesize that genetic characteristics before and changes resulting after pCSI will reflect clinical response to pCSI. We analyzed the cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) from patients receiving pCSI for LM and explored genetic variations associated with response. EXPERIMENTAL DESIGN We subjected CSF from 14 patients with LM before and after pCSI to cell-free DNA sequencing using a targeted-sequencing panel. In parallel, plasma ctDNA and primary tumors were subjected to targeted sequencing. Variant allele frequency (VAF) and cancer cell fraction (CCF) were calculated; clonality of observed mutations was determined. Kaplan-Meier analysis was used to associate genomic changes with survival. RESULTS The median overall survival (OS) for the cohort was 9 months [interquartile range (IQR), 5-21 months]. We showed clonal evolution between tumor and ctDNA of the CSF and plasma with unique mutations identified by compartment. Higher CSF ctDNA mean VAF before pCSI (VAFpre) had worse OS (6 months for VAFpre ≥ 0.32 vs. 9 months for VAFpre < 0.32; P = 0.05). Similarly, increased VAF after pCSI portended worse survival (6 vs. 18 months; P = 0.008). Higher mean CCF of subclonal mutations appearing after pCSI was associated with worse OS (8 vs. 17 months; P = 0.05). CONCLUSIONS In patients with solid tumor LM undergoing pCSI, we found unique genomic profiles associated with pCSI through CSF ctDNA analyses. Patients with reduced genomic diversity within the leptomeningeal compartment demonstrated improved OS after pCSI suggesting that CSF ctDNA analysis may have use in predicting pCSI response.
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Affiliation(s)
- N. Ari Wijetunga
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
| | | | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
| | | | - Michael Cislo
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
| | | | - Kiana Chabot
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | - Ahmed M. Osman
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
| | - Lauren Schaff
- Department of Neurology, Memorial Sloan Kettering Cancer Center
| | - Elena Pentsova
- Department of Neurology, Memorial Sloan Kettering Cancer Center
| | | | - Simon N. Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
| | - Adrienne Boire
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
- Department of Neurology, Memorial Sloan Kettering Cancer Center
| | - Jonathan T. Yang
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center
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16
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Tripathy A, John V, Wadden J, Kong S, Sharba S, Koschmann C. Liquid biopsy in pediatric brain tumors. Front Genet 2023; 13:1114762. [PMID: 36685825 PMCID: PMC9853427 DOI: 10.3389/fgene.2022.1114762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/23/2022] [Indexed: 01/09/2023] Open
Abstract
Malignant primary brain tumors are the most common cancer in children aged 0-14 years, and are the most common cause of death among pediatric cancer patients. Compared to other cancers, pediatric brain tumors have been difficult to diagnose and study given the high risk of intracranial biopsy penetrating through vital midline structures, where the majority of pediatric brain tumors originate (Ostrom et al., 2015). Furthermore, the vast majority of these tumors recur. With limitations in the ability to monitor using clinical and radiographic methods alone, minimally invasive methods such as liquid biopsy will be crucial to our understanding and treatment. Liquid biopsy of blood, urine, and cerebrospinal fluid (CSF) can be used to sample cfDNA, ctDNA, RNA, extracellular vesicles, and tumor-associated proteins. In the past year, four seminal papers have made significant advances in the use of liquid biopsy in pediatric brain tumor patients (Liu et al., 2021; Cantor et al., 2022; Miller et al., 2022; Pagès et al., 2022). In this review, we integrate the results of these studies and others to discuss how the newest technologies in liquid biopsy are being developed for molecular diagnosis and treatment response in pediatric brain tumors.
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Affiliation(s)
- Arushi Tripathy
- Department of Neurosurgery, Michigan Medicine, Ann Arbor, MI, United States
| | - Vishal John
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | - Jack Wadden
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | - Seongbae Kong
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | - Sana Sharba
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
| | - Carl Koschmann
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, United States
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17
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O’Halloran K, Yellapantula V, Christodoulou E, Ostrow D, Bootwalla M, Ji J, Cotter J, Chapman N, Chu J, Margol A, Krieger MD, Chiarelli PA, Gai X, Biegel JA. Low-pass whole-genome and targeted sequencing of cell-free DNA from cerebrospinal fluid in pediatric patients with central nervous system tumors. Neurooncol Adv 2023; 5:vdad077. [PMID: 37461402 PMCID: PMC10349915 DOI: 10.1093/noajnl/vdad077] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Background Central nervous system tumors are the most common pediatric solid tumors and the most frequent cause of cancer-related morbidity in childhood. Significant advances in understanding the molecular features of these tumors have facilitated the development of liquid biopsy assays that may aid in diagnosis and monitoring response to therapy. In this report, we describe our comprehensive liquid biopsy platform for detection of genome-wide copy number aberrations, sequence variants, and gene fusions using cerebrospinal fluid (CSF) from pediatric patients with brain, spinal cord, and peripheral nervous system tumors. Methods Cell-free DNA was isolated from the CSF from 55 patients, including 47 patients with tumors and 8 controls. Results Abnormalities in cell-free DNA were detected in 24 (51%) patients including 11 with copy number alterations, 9 with sequence variants, and 7 with KIAA1549::BRAF fusions. Positive findings were obtained in patients spanning histologic subtypes, tumor grades, and anatomic locations. Conclusions This study demonstrates the feasibility of employing this platform in routine clinical care in upfront diagnostic and monitoring settings. Future studies are required to determine the utility of this approach for assessing response to therapy and long-term surveillance.
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Affiliation(s)
- Katrina O’Halloran
- Corresponding Author: Katrina O’Halloran, Children’s Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA 90027, USA ()
| | - Venkata Yellapantula
- Division of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eirini Christodoulou
- Division of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, CA, USA
| | - Dejerianne Ostrow
- Division of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, CA, USA
| | - Moiz Bootwalla
- Division of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, CA, USA
| | - Jianling Ji
- Division of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jennifer Cotter
- Division of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nicholas Chapman
- Division of Neurosurgery, Children’s Hospital Los Angeles, CA, USA
| | - Jason Chu
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Neurosurgery, Children’s Hospital Los Angeles, CA, USA
| | - Ashley Margol
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mark D Krieger
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Neurosurgery, Children’s Hospital Los Angeles, CA, USA
| | - Peter A Chiarelli
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Neurosurgery, Children’s Hospital Los Angeles, CA, USA
| | - Xiaowu Gai
- Division of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jaclyn A Biegel
- Division of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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18
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Lehner KR, Jiang K, Rincon-Torroella J, Perera R, Bettegowda C. Cerebrospinal Fluid biomarkers in pediatric brain tumors: A systematic review. Neoplasia 2022; 35:100852. [PMID: 36516487 PMCID: PMC9764249 DOI: 10.1016/j.neo.2022.100852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/14/2022] Open
Abstract
Central nervous system (CNS) tumors are the leading cause of cancer death in pediatric patients. Though these tumors typically require invasive surgical procedures to diagnose, cerebrospinal fluid (CSF) liquid biopsy presents a potential method for rapid and noninvasive detection of markers of CNS malignancy. To characterize molecular biomarkers that can be used in the diagnosis, prognosis, and monitoring of pediatric cancer patients, a literature review was conducted in accordance with PRISMA guidelines. PubMed and EMBASE were searched for the terms biomarkers, liquid biopsy, cerebrospinal fluid, pediatric central nervous system tumor, and their synonyms. Studies including pediatric patients with CSF sampling for tumor evaluation were included. Studies were excluded if they did not have full text or if they were case studies, methodology reports, in languages other than English, or animal studies. Our search revealed 163 articles of which 42 were included. Proteomic, genomic, and small molecule markers associated with CNS tumors were identified for further analysis and development of detection tools.
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Affiliation(s)
- Kurt R. Lehner
- Department of Neurosurgery, Johns Hopkins School of Medicine, 1800 Orleans St, Baltimore, MD 21287, USA
| | - Kelly Jiang
- Department of Neurosurgery, Johns Hopkins School of Medicine, 1800 Orleans St, Baltimore, MD 21287, USA
| | - Jordina Rincon-Torroella
- Department of Neurosurgery, Johns Hopkins School of Medicine, 1800 Orleans St, Baltimore, MD 21287, USA
| | - Ranjan Perera
- Johns Hopkins All Children's Hospital, 600 5th St. South, St.Petersburg, FL 33701, USA
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins School of Medicine, 1800 Orleans St, Baltimore, MD 21287, USA,Corresponding author.
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19
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Miller AM, Karajannis MA. Current Role and Future Potential of CSF ctDNA for the Diagnosis and Clinical Management of Pediatric Central Nervous System Tumors. J Natl Compr Canc Netw 2022; 20:1363-1369. [PMID: 36509077 PMCID: PMC10050207 DOI: 10.6004/jnccn.2022.7093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/28/2022] [Indexed: 12/15/2022]
Abstract
Most pediatric central nervous system (CNS) tumors are located in eloquent anatomic areas, making surgical resection and, in some cases, even biopsy risky or impossible. This diagnostic predicament coupled with the move toward molecular classification for diagnosis has exposed an urgent need to develop a minimally invasive means to obtain diagnostic information. In non-CNS solid tumors, the detection of circulating tumor DNA (ctDNA) in plasma and other bodily fluids has been incorporated into routine practice and clinical trial design for selection of molecular targeted therapy and longitudinal monitoring. For primary CNS tumors, however, detection of ctDNA in plasma has been challenging. This is likely related at least in part to anatomic factors such as the blood-brain barrier. Due to the proximity of primary CNS tumors to the cerebrospinal fluid (CSF) space, our group and others have turned to CSF as a rich alternative source of ctDNA. Although multiple studies at this time have demonstrated the feasibility of CSF ctDNA detection across multiple types of pediatric CNS tumors, the optimal role and utility of CSF ctDNA in the clinical setting has not been established. This review discusses the work-to-date on CSF ctDNA liquid biopsy in pediatric CNS tumors and the associated technical challenges, and reviews the promising opportunities that lie ahead for integration of CSF ctDNA liquid biopsy into clinical care and clinical trial design.
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Affiliation(s)
- Alexandra M. Miller
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
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20
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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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21
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Abstract
Noninvasive molecular profiling of tumors using plasma-based next-generation sequencing (NGS) is increasingly used to aid in diagnosis, treatment selection, and disease monitoring in oncology. In patients with glioma, however, the plasma cell-free DNA (cfDNA) tumor fraction, defined as the fractional proportion of circulating tumor-derived DNA (ctDNA) relative to total cfDNA, is especially low, in large part due to the blood-brain barrier. As a result, commercial plasma-based NGS assays, designed to screen for a small number of actionable genomic alterations, are not sensitive enough to guide the management of patients with glioma. As this has been long recognized in neuro-oncology, significant research efforts have been undertaken to improve the sensitivity of plasma ctDNA detection in patients with glioma and to understand the biology and clinical relevance of non-tumor-derived cfDNA, which makes up most of the total cfDNA pool. Here, we review key recent advances in the field of plasma cfDNA analysis in patients with glioma, including (1) the prognostic impact of pre-treatment and on-treatment total plasma cfDNA concentrations, (2) use of tumor-guided sequencing approaches to improve the sensitivity of ctDNA detection in the plasma, and (3) the emergence of plasma cfDNA methylomics for detection and discrimination of glioma from other primary intracranial tumors.
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Affiliation(s)
- Erica L Carpenter
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen J Bagley
- Corresponding Author: Stephen J. Bagley, MD, MSCE, Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA ()
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22
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Abstract
Over the last decade, molecular markers have become an integral part in the management of Central Nervous System (CNS) tumors. Somatic mutations that identify and prognosticate tumors are also detected in the bio-fluids especially the serum and CSF; the sampling of which is known as liquid biopsy (LB). These tumor-derived biomarkers include plasma circulating tumor cells (CTCs), cell-free DNA (cf/ctDNAs), circulating cell-free microRNAs (cfmiRNAs), circulating extracellular vesicles, or exosomes (EVs), proteins, and tumor educated platelets. Established in the management of other malignancies, liquid biopsy is becoming an important tool in the management of CNS tumors as well. This review presents a snapshot of the current state of LB research its potential and the possible pitfalls.
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Affiliation(s)
- Amitava Ray
- Senior Consultant Neurosurgeon, Department of Neurosciences, Apollo Health City and Apollo Secunderabad, Hyderabad 500089, Telangana, India
| | - Tarang K Vohra
- Consultant Neurosurgeon, Department of Neurosciences, Apollo Health City, Hyderabad 500089, Telangana, India
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23
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Cahn F, Revon-Riviere G, Min V, Rome A, Filaine P, Pelletier A, Abed S, Gentet JC, Verschuur A, André N. Blood-Derived Liquid Biopsies Using Foundation One ® Liquid CDx for Children and Adolescents with High-Risk Malignancies: A Monocentric Experience. Cancers (Basel) 2022; 14:cancers14112774. [PMID: 35681754 PMCID: PMC9179410 DOI: 10.3390/cancers14112774] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/15/2022] [Accepted: 05/22/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Precision oncology requires tumor molecular profiling to identify actionable targets. Blood-derived liquid biopsy (LB) is a potential alternative that is not yet documented in real-world settings, especially in pediatric oncology. Analyzing, retrospectively, the use of LB in children with refractory relapsing diseases, we were able to show that this is a feasible alternative to tissue biopsy, resulting in successful analysis in a subset of patients. Abstract Precision oncology requires tumor molecular profiling to identify actionable targets. Tumor biopsies are considered as the gold standard, but their indications are limited by the burden of procedures in children. Blood-derived liquid biopsy (LB) is a potential alternative that is not yet documented in real-world settings, especially in pediatric oncology. We performed a retrospective analysis of children and teenagers with a relapsing or refractory disease, upon whom LB was performed using the Foundation One® liquid CDx from 1 January 2020 to 31 December 2021 in a single center. Forty-five patients (27 boys) were included, with a median age of 9 years of age (range: 1.5–17 years old). Underlying malignancies were neuroblastoma (12 patients), bone sarcoma (12), soft tissue sarcoma (9), brain tumors (7), and miscellaneous tumors (5). Forty-three patients had metastatic disease. Six patients had more than one biopsy because of a failure in first LB. Median time to obtain results was 13 days. Overall, analysis was successful for 33/45 patients. Eight patients did not present any molecular abnormalities. Molecular alterations were identified in 25 samples with a mean of 2.1 alterations per sample. The most common alterations concerned TP53 (7 pts), EWS-FLI1 (5), ALK (3), MYC (3), and CREBBP (2). TMB was low in all cases. Six patients received treatment based on the results from LB analysis and all were treated off-trial. Three additional patients were included in early phase clinical trials. Mean duration of treatment was 85 days, with one patient with stable disease after eight months. Molecular profiling using Foundation One® Liquid CDx was feasible in pediatric patients with high-risk solid tumors and lead to identification of targetable mutations in a subset of patients.
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Affiliation(s)
- Fanny Cahn
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Gabriel Revon-Riviere
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
- Centre d’essais Précoces en Cancérologie de Marseille (CEPCM), CLIPP2, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France;
| | - Victoria Min
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Angélique Rome
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Pauline Filaine
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
- Centre d’essais Précoces en Cancérologie de Marseille (CEPCM), CLIPP2, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France;
| | - Annick Pelletier
- Centre d’essais Précoces en Cancérologie de Marseille (CEPCM), CLIPP2, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France;
| | - Sylvie Abed
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Jean-Claude Gentet
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Arnauld Verschuur
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
| | - Nicolas André
- Department of Pediatric Oncology, La Timone University Hospital of Marseille, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France; (F.C.); (G.R.-R.); (V.M.); (A.R.); (P.F.); (S.A.); (J.-C.G.); (A.V.)
- Centre d’essais Précoces en Cancérologie de Marseille (CEPCM), CLIPP2, Assistance Publique-Hôpitaux de Marseille, 13005 Marseille, France;
- SMARTc Unit, CRCM Inserm 1068, CNRS UMR 7258, Aix-Marseille University, 13005 Marseille, France
- Correspondence:
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24
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Greuter L, Frank N, Guzman R, Soleman J. The Clinical Applications of Liquid Biopsies in Pediatric Brain Tumors: A Systematic Literature Review. Cancers (Basel) 2022; 14:cancers14112683. [PMID: 35681663 PMCID: PMC9179879 DOI: 10.3390/cancers14112683] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/03/2022] [Accepted: 05/25/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Brain tumors are the most common solid cancer in children and are traditionally diagnosed via a tissue biopsy or resection. Liquid biopsy offers the possibility to characterize brain tumors based on their circulating DNA in blood, cerebrospinal fluid or even urine. Moreover, disease progress can be monitored accurately and sometimes even detected before radiographic progression. More trials are needed to standardize the use of liquid biopsy in pediatric brain tumors. Abstract Background: Pediatric brain tumors are the most common solid tumor in children. Traditionally, tumor diagnosis and molecular analysis were carried out on tumor tissue harvested either via biopsy or resection. However, liquid biopsy allows analysis of circulating tumor DNA in corporeal fluids such as cerebrospinal fluid or blood. Methods: We performed a systematic review in Pubmed and Embase regarding the role of liquid biopsy in pediatric brain tumors. Results: Nine studies with a total of 570 patients were included. The preferred corporeal fluid for analysis with a relatively high yield of ct-DNA was cerebrospinal fluid (CSF). For high-grade glioma, liquid biopsy can successfully characterize H3K27mutations and predict tumor progression before it is radiographically detected. Moreover, liquid biopsy has the potential to distinguish between pseudo-progression and actual progression. In medulloblastoma, ct-DNA in the CSF can be used as a surrogate marker of measurable residual disease and correlates with response to therapy and progression of the tumor up to three months before radiographic detection. Conclusion: Liquid biopsy is primarily useful in high-grade pediatric brain tumors such as diffuse midline glioma or medulloblastoma. Disease detection and monitoring is feasible for both tumor entities. More trials to standardize its use for pediatric brain tumors are necessary.
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Affiliation(s)
- Ladina Greuter
- Department of Neurosurgery, University Hospital of Basel, 4031 Basel, Switzerland; (N.F.); (R.G.); (J.S.)
- Correspondence:
| | - Nicole Frank
- Department of Neurosurgery, University Hospital of Basel, 4031 Basel, Switzerland; (N.F.); (R.G.); (J.S.)
| | - Raphael Guzman
- Department of Neurosurgery, University Hospital of Basel, 4031 Basel, Switzerland; (N.F.); (R.G.); (J.S.)
- Department of Neurosurgery and Pediatric Neurosurgery, University Hospital of Basel and Children’s Hospital, 4056 Basel, Switzerland
- Faculty of Medicine, University of Basel, 4056 Basel, Switzerland
| | - Jehuda Soleman
- Department of Neurosurgery, University Hospital of Basel, 4031 Basel, Switzerland; (N.F.); (R.G.); (J.S.)
- Department of Neurosurgery and Pediatric Neurosurgery, University Hospital of Basel and Children’s Hospital, 4056 Basel, Switzerland
- Faculty of Medicine, University of Basel, 4056 Basel, Switzerland
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25
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Doculara L, Trahair TN, Bayat N, Lock RB. Circulating Tumor DNA in Pediatric Cancer. Front Mol Biosci 2022; 9:885597. [PMID: 35647029 PMCID: PMC9133724 DOI: 10.3389/fmolb.2022.885597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
The measurement of circulating tumor DNA (ctDNA) has gained increasing prominence as a minimally invasive tool for the detection of cancer-specific markers in plasma. In adult cancers, ctDNA detection has shown value for disease-monitoring applications including tumor mutation profiling, risk stratification, relapse prediction, and treatment response evaluation. To date, there are ctDNA tests used as companion diagnostics for adult cancers and it is not understood why the same cannot be said about childhood cancer, despite the marked differences between adult and pediatric oncology. In this review, we discuss the current understanding of ctDNA as a disease monitoring biomarker in the context of pediatric malignancies, including the challenges associated with ctDNA detection in liquid biopsies. The data and conclusions from pediatric cancer studies of ctDNA are summarized, highlighting treatment response, disease monitoring and the detection of subclonal disease as applications of ctDNA. While the data from retrospective studies highlight the potential of ctDNA, large clinical trials are required for ctDNA analysis for routine clinical use in pediatric cancers. We outline the requirements for the standardization of ctDNA detection in pediatric cancers, including sample handling and reproducibility of results. With better understanding of the advantages and limitations of ctDNA and improved detection methods, ctDNA analysis may become the standard of care for patient monitoring in childhood cancers.
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Affiliation(s)
- Louise Doculara
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Toby N. Trahair
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Narges Bayat
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B. Lock
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
- *Correspondence: Richard B. Lock,
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26
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Wadden J, Ravi K, John V, Babila CM, Koschmann C. Cell-Free Tumor DNA (cf-tDNA) Liquid Biopsy: Current Methods and Use in Brain Tumor Immunotherapy. Front Immunol 2022; 13:882452. [PMID: 35464472 PMCID: PMC9018987 DOI: 10.3389/fimmu.2022.882452] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022] Open
Abstract
Gliomas are tumors derived from mutations in glial brain cells. Gliomas cause significant morbidity and mortality and development of precision diagnostics and novel targeted immunotherapies are critically important. Radiographic imaging is the most common technique to diagnose and track response to treatment, but is an imperfect tool. Imaging does not provide molecular information, which is becoming critically important for identifying targeted immunotherapies and monitoring tumor evolution. Furthermore, immunotherapy induced inflammation can masquerade as tumor progression in images (pseudoprogression) and confound clinical decision making. More recently, circulating cell free tumor DNA (cf-tDNA) has been investigated as a promising biomarker for minimally invasive glioma diagnosis and disease monitoring. cf-tDNA is shed by gliomas into surrounding biofluids (e.g. cerebrospinal fluid and plasma) and, if precisely quantified, might provide a quantitative measure of tumor burden to help resolve pseudoprogression. cf-tDNA can also identify tumor genetic mutations to help guide targeted therapies. However, due to low concentrations of cf-tDNA, recovery and analysis remains challenging. Plasma cf-tDNA typically represents <1% of total cf-DNA due to the blood-brain barrier, limiting their usefulness in practice and motivating the development and use of highly sensitive and specific detection methods. This mini review summarizes the current and future trends of various approaches for cf-tDNA detection and analysis, including new methods that promise more rapid, lower-cost, and accessible diagnostics. We also review the most recent clinical case studies for longitudinal disease monitoring and highlight focus areas, such as novel accurate detection methodologies, as critical research priorities to enable translation to clinic.
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Affiliation(s)
- Jack Wadden
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
| | | | | | | | - Carl Koschmann
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
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27
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Liu APY, Northcott PA, Robinson GW, Gajjar A. Circulating tumor DNA profiling for childhood brain tumors: Technical challenges and evidence for utility. J Transl Med 2022; 102:134-142. [PMID: 34934181 DOI: 10.1038/s41374-021-00719-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 11/09/2022] Open
Abstract
Cell-free DNA (cfDNA) profiling as liquid biopsy has proven value in adult-onset malignancies, serving as a patient-specific surrogate for residual disease and providing a non-invasive tool for serial interrogation of tumor genomics. However, its application in neoplasms of the central nervous system (CNS) has not been as extensively studied. Unique considerations and methodological challenges exist, which need to be addressed before cfDNA studies can be incorporated as a clinical assay for primary CNS diseases. Here, we review the current status of applying cfDNA analysis in patients with CNS tumors, with special attention to diagnosis in pediatric patients. Technical concerns, evidence for utility, and potential developments are discussed.
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Affiliation(s)
- Anthony Pak-Yin Liu
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, SAR, China.
| | - Paul A Northcott
- Division of Brain Tumor Research, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Giles W Robinson
- Division of Neuro-Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Amar Gajjar
- Division of Neuro-Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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28
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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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