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Mangum R, Lin FY, Parsons DW. Recent Advancements and Innovations in Pediatric Precision Oncology. J Pediatr Hematol Oncol 2024; 46:262-271. [PMID: 38857189 DOI: 10.1097/mph.0000000000002871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/29/2024] [Indexed: 06/12/2024]
Abstract
Precision oncology incorporates comprehensive genomic profiling into the individualized clinical care of pediatric cancer patients. In recent years, comprehensive pan-cancer analyses have led to the successful implementation of genomics-based pediatric trials and accelerated approval of novel targeted agents. In addition, disease-specific studies have resulted in molecular subclassification of myriad cancer types with subsequent tailoring of treatment intensity based on the patient's prognostic factors. This review discusses the progress of the field and highlights developments that are leading to more personalized cancer care and improved patient outcomes. Increased understanding of the evolution of precision oncology over recent decades emphasizes the tremendous impact of improved genomic applications. New technologies and improved diagnostic modalities offer further promise for future advancements within the field.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ
| | - Frank Y Lin
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
| | - D Williams Parsons
- Department of Pediatrics, Texas Children's Cancer Center
- The Dan L. Duncan Cancer Center
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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2
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El Hayek T, Alnaser-Almusa OA, Alsalameh SM, Alhalabi MT, Sabbah AN, Alshehri EA, Mir TA, Mani NK, Al-Kattan K, Chinnappan R, Yaqinuddin A. Emerging role of exosomal microRNA in liver cancer in the era of precision medicine; potential and challenges. Front Mol Biosci 2024; 11:1381789. [PMID: 38993840 PMCID: PMC11236732 DOI: 10.3389/fmolb.2024.1381789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 06/05/2024] [Indexed: 07/13/2024] Open
Abstract
Exosomal microRNAs (miRNAs) have great potential in the fight against hepatocellular carcinoma (HCC), the fourth most common cause of cancer-related death worldwide. In this study, we explored the various applications of these small molecules while analyzing their complex roles in tumor development, metastasis, and changes in the tumor microenvironment. We also discussed the complex interactions that exist between exosomal miRNAs and other non-coding RNAs such as circular RNAs, and show how these interactions coordinate important biochemical pathways that propel the development of HCC. The possibility of targeting exosomal miRNAs for therapeutic intervention is paramount, even beyond their mechanistic significance. We also highlighted their growing potential as cutting-edge biomarkers that could lead to tailored treatment plans by enabling early identification, precise prognosis, and real-time treatment response monitoring. This thorough analysis revealed an intricate network of exosomal miRNAs lead to HCC progression. Finally, strategies for purification and isolation of exosomes and advanced biosensing techniques for detection of exosomal miRNAs are also discussed. Overall, this comprehensive review sheds light on the complex web of exosomal miRNAs in HCC, offering valuable insights for future advancements in diagnosis, prognosis, and ultimately, improved outcomes for patients battling this deadly disease.
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Affiliation(s)
- Tarek El Hayek
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | | | | | | | - Eman Abdullah Alshehri
- Tissue/Organ Bioengineering and BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Tanveer Ahmad Mir
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Tissue/Organ Bioengineering and BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Naresh Kumar Mani
- Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Khaled Al-Kattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Lung Health Center Department, Organ Transplant Centre of Excellence, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Raja Chinnappan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Tissue/Organ Bioengineering and BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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3
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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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4
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Bajin IY, Levine A, Dewan MC, Bennett J, Tabori U, Hawkins C, Bouffet E. Understanding diffuse leptomeningeal glioneuronal tumors. Childs Nerv Syst 2024:10.1007/s00381-024-06432-6. [PMID: 38795167 DOI: 10.1007/s00381-024-06432-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 04/27/2024] [Indexed: 05/27/2024]
Abstract
INTODUCTION Diffuse leptomeningeal glioneuronal tumors (DLGNTs) pose a rare and challenging entity within pediatric central nervous system neoplasms. Despite their rarity, DLGNTs exhibit complex clinical presentations and unique molecular characteristics, necessitating a deeper understanding of their diagnostic and therapeutic nuances. METHODS This review synthesizes contemporary literature on DLGNT, encompassing epidemiology, clinical manifestations, pathological features, treatment strategies, prognostic markers, and future research directions. To compile the existing body of knowledge on DLGNT, a comprehensive search of relevant databases was conducted. RESULTS DLGNT primarily affects pediatric populations but can manifest across all age groups. Its diagnosis is confounded by nonspecific clinical presentations and overlapping radiological features with other CNS neoplasms. Magnetic resonance imaging (MRI) serves as a cornerstone for DLGNT diagnosis, revealing characteristic leptomeningeal enhancement and intraparenchymal involvement. Histologically, DLGNT presents with low to moderate cellularity and exhibits molecular alterations in the MAPK/ERK signalling pathway. Optimal management of DLGNT necessitates a multidisciplinary approach encompassing surgical resection, chemotherapy, radiotherapy, and emerging targeted therapies directed against specific genetic alterations. Prognostication remains challenging, with factors such as age at diagnosis, histological subtypes, and genetic alterations influencing disease progression and treatment response. Long-term survival data are limited, underscoring the need for collaborative research efforts. CONCLUSION Advancements in molecular profiling, targeted therapies, and international collaborations hold promise for improving DLGNT outcomes. Harnessing the collective expertise of clinicians, researchers, and patient advocates, can advance the field of DLGNT research and optimize patient care paradigms.
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Affiliation(s)
- Inci Yaman Bajin
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ONT, Canada.
| | - Adrian Levine
- Department of Pathology, The Hospital for Sick Children, Toronto, ONT, Canada
| | - Michael C Dewan
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julie Bennett
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ONT, Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ONT, Canada
| | - Uri Tabori
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ONT, Canada
| | - Cynthia Hawkins
- Department of Pathology, The Hospital for Sick Children, Toronto, ONT, Canada
| | - Eric Bouffet
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ONT, Canada.
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Bennett J, Yeo KK, Tabori U, Hawkins C, Lim-Fat MJ. Pediatric-type low-grade gliomas in adolescents and young adults-challenges and emerging paradigms. Childs Nerv Syst 2024:10.1007/s00381-024-06449-x. [PMID: 38761264 DOI: 10.1007/s00381-024-06449-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/09/2024] [Indexed: 05/20/2024]
Abstract
Pediatric-type low-grade glioma (PLGG) encompasses a heterogeneous group of WHO grade 1 or 2 tumors and is the most common central nervous system tumor found in children. PLGG extends beyond pediatrics, into adolescents and young adults (AYA, ages 15-40). PLGG represents 25% of all gliomas diagnosed in AYA with differences in tumor location and molecular alterations compared to children, resulting in improved outcome for AYAs. Long-term outcome is excellent, though patients may suffer significant morbidity depending on tumor location. There are differences in treatment practices with radiation used to treat PLGG in AYAs more often than in children. Most PLGG in AYA harbor an alteration in the RAS/MAPK pathway, with limited insight into response to targeted therapy in this age group. This review discusses the epidemiology, current therapeutic approaches, and challenges in the management of PLGG in AYA.
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Affiliation(s)
- Julie Bennett
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada.
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada.
- Arthur and Sonia Labbatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Kee Kiat Yeo
- Department of Pediatric Oncology, Dana-Farber / Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | - Uri Tabori
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labbatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Cynthia Hawkins
- Arthur and Sonia Labbatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mary Jane Lim-Fat
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
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O’Halloran K, Margol A, Davidson TB, Estrine D, Tamrazi B, Cotter JA, Ji J, Biegel JA. Disease Evolution Monitored by Serial Cerebrospinal Fluid Liquid Biopsies in Two Cases of Recurrent Medulloblastoma. Int J Mol Sci 2024; 25:4882. [PMID: 38732099 PMCID: PMC11084520 DOI: 10.3390/ijms25094882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Medulloblastoma is the most common malignant brain tumor in childhood. Initial treatment generally includes surgery, irradiation, and chemotherapy. Approximately 20-30% of patients will experience a recurrence, which portends a very poor prognosis. The current standard of care for evaluation for relapse includes radiographic surveillance with magnetic resonance imaging at regular intervals. The presence of circulating tumor DNA in the cerebrospinal fluid has been demonstrated to be a predictor of a higher risk of progression in a research setting for patients with medulloblastoma treated on a prospective single institution clinical trial. We have previously published and clinically validated a liquid-biopsy-based genetic assay utilizing low-pass whole genome sequencing to detect copy number alterations in circulating tumor DNA. Here, we present two teenage patients with posterior fossa medulloblastoma with recurrent disease who have been monitored with serial liquid biopsies showing tumor evolution over time, demonstrating the clinical utility of these approaches.
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Affiliation(s)
- Katrina O’Halloran
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (K.O.); (A.M.); (T.B.D.)
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (B.T.); (J.A.C.); (J.J.)
| | - Ashley Margol
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (K.O.); (A.M.); (T.B.D.)
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (B.T.); (J.A.C.); (J.J.)
| | - Tom B. Davidson
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (K.O.); (A.M.); (T.B.D.)
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (B.T.); (J.A.C.); (J.J.)
| | - Dolores Estrine
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
| | - Benita Tamrazi
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (B.T.); (J.A.C.); (J.J.)
- Department of Radiology, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Jennifer A. Cotter
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (B.T.); (J.A.C.); (J.J.)
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
| | - Jianling Ji
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (B.T.); (J.A.C.); (J.J.)
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
| | - Jaclyn A. Biegel
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (B.T.); (J.A.C.); (J.J.)
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
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7
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Neil AJ, Chukwueke UN, Hoover N, Marris SRN, Rojas-Rudilla V, Manning DK, Mito JK, Cibas ES, Sholl LM. Validation of targeted next-generation sequencing of cell-free DNA from archival cerebrospinal fluid specimens for the detection of somatic variants in cancer involving the leptomeninges: Cytopathologic and radiographic correlation. Cancer Cytopathol 2024; 132:214-223. [PMID: 37812603 DOI: 10.1002/cncy.22768] [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: 05/24/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Leptomeningeal metastases occur across multiple solid and lymphoid cancers, and patients typically undergo cytopathologic assessment of cerebrospinal fluid (CSF) in this setting. For patients diagnosed with metastatic cancer, the detection of actionable somatic mutations in CSF can provide clinically valuable information for treatment without the need for additional tissue collection. METHODS The authors validated a targeted next-generation sequencing assay for the detection of somatic variants in cancer (OncoPanel) on cell-free DNA (cfDNA) isolated from archival CSF specimens in a cohort of 25 patients who had undergone molecular testing of a prior tumor specimen. RESULTS CSF storage time and volume had no impact on cfDNA concentration or mean target coverage of the assay. Previously identified somatic variants in CSF cfDNA were detected in 88%, 50%, and 27% of specimens diagnosed cytologically as positive, suspicious/atypical, and negative for malignancy, respectively. Somatic variants were identified in 81% of CSF specimens from patients who had leptomeningeal enhancement on magnetic resonance imaging compared with 31% from patients without such enhancement. CONCLUSIONS These data highlight the stability of cfDNA in CSF, which allows for cytopathologic evaluation before triage for next-generation sequencing assays. For a subset of cases in which clinical suspicion is high but cytologic or radiographic studies are inconclusive, the detection of pathogenic somatic variants in CSF cfDNA may aid in the diagnosis of leptomeningeal metastases.
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Affiliation(s)
- Alexander J Neil
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ugonma N Chukwueke
- Center for Neuro-Oncology, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Hoover
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sean R N Marris
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vanesa Rojas-Rudilla
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Danielle K Manning
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey K Mito
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edmund S Cibas
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Valerius AR, Webb MJ, Hammad N, Sener U, Malani R. Cerebrospinal Fluid Liquid Biopsies in the Evaluation of Adult Gliomas. Curr Oncol Rep 2024; 26:377-390. [PMID: 38488990 DOI: 10.1007/s11912-024-01517-6] [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] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
PURPOSE OF REVIEW This review aims to discuss recent research regarding the biomolecules explored in liquid biopsies and their potential clinical uses for adult-type diffuse gliomas. RECENT FINDINGS Evaluation of tumor biomolecules via cerebrospinal fluid (CSF) is an emerging technology in neuro-oncology. Studies to date have already identified various circulating tumor DNA, extracellular vesicle, micro-messenger RNA and protein biomarkers of interest. These biomarkers show potential to assist in multiple avenues of central nervous system (CNS) tumor evaluation, including tumor differentiation and diagnosis, treatment selection, response assessment, detection of tumor progression, and prognosis. In addition, CSF liquid biopsies have the potential to better characterize tumor heterogeneity compared to conventional tissue collection and CNS imaging. Current imaging modalities are not sufficient to establish a definitive glioma diagnosis and repeated tissue sampling via conventional biopsy is risky, therefore, there is a great need to improve non-invasive and minimally invasive sampling methods. CSF liquid biopsies represent a promising, minimally invasive adjunct to current approaches which can provide diagnostic and prognostic information as well as aid in response assessment.
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Affiliation(s)
| | - Mason J Webb
- Department of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Nouran Hammad
- Jordan University of Science and Technology School of Medicine, Irbid, Jordan
| | - Ugur Sener
- Department of Neurology, Department of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Rachna Malani
- University of UT - Huntsman Cancer Institute (Department of Neurosurgery), Salt Lake City, UT, USA
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Diaz M, Chudsky S, Pentsova E, Miller AM. Clinical applications of cerebrospinal fluid liquid biopsies in central nervous system tumors. Transl Oncol 2024; 41:101881. [PMID: 38218027 PMCID: PMC10825768 DOI: 10.1016/j.tranon.2024.101881] [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: 10/20/2022] [Revised: 11/28/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024] Open
Abstract
For patients with central nervous system (CNS) malignancies, liquid biopsies of the cerebrospinal fluid (CSF) may offer an unparalleled source of information about the tumor, with much less risk than traditional biopsies. Two techniques have been adapted to CSF in clinical settings: circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). CTCs have been employed mostly as a diagnostic tool for leptomeningeal metastases in epithelial tumors, although they may also have value in the prognostication and monitoring of this disease. The ctDNA technology has been studied in a variety of primary and metastatic brain and spinal cord tumors, where it can be used for diagnosis and molecular classification, with some work suggesting that it may also be useful for longitudinal tracking of tumor evolution or as a marker of residual disease. This review summarizes recent publications on the use of these two tests in CSF, focusing on their established and potential clinical applications.
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Affiliation(s)
- Maria Diaz
- Department of Neurology, Division of Neuro-Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sofia Chudsky
- Office of Professional Development, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Hunter College, New York, NY, USA
| | - Elena Pentsova
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra M Miller
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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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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Arthur C, Carlson LM, Svoboda J, Sandvik U, Jylhä C, Nordenskjöld M, Holm S, Tham E. Liquid biopsy guides successful molecular targeted therapy of an inoperable pediatric brainstem neoplasm. NPJ Precis Oncol 2024; 8:44. [PMID: 38388693 PMCID: PMC10884019 DOI: 10.1038/s41698-024-00535-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Midline CNS tumors are occasionally inaccessible for surgical biopsies. In these instances, cell-free DNA (cfDNA) may serve as a viable alternative for molecular analysis and identification of targetable mutations. Here, we report a young child with an inoperable brainstem tumor in whom a stereotactic biopsy was deemed unsafe. The tumor progressed on steroids and after radiotherapy the patient developed hydrocephalus and received a ventriculoperitoneal shunt. Droplet digital PCR analysis of cfDNA from an intraoperative cerebrospinal fluid liquid biopsy revealed a BRAF V600 mutation enabling targeted treatment with MEK and BRAF inhibitors. The patient, now on trametinib and dabrafenib for 1 year, has had substantial tumor volume regression and reduction of contrast enhancement on MRIs and is making remarkable clinical progress. This case highlights that in a subset of CNS tumors, access to liquid biopsy analysis may be crucial to identify actionable therapeutic targets that would otherwise go undiscovered.
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Affiliation(s)
- Cecilia Arthur
- Clinical Genetics, Karolinska University Hospital, 171 76, Stockholm, Sweden.
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden.
| | - Lena-Maria Carlson
- Pediatric Oncology, Karolinska University Hospital, 171 77, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Jan Svoboda
- Department of Pediatric Radiology, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Ulrika Sandvik
- Department of Clinical Neuroscience, Division of Neurosurgery, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Cecilia Jylhä
- Clinical Genetics, Karolinska University Hospital, 171 76, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Clinical Genetics, Karolinska University Hospital, 171 76, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden
| | - Stefan Holm
- Pediatric Oncology, Karolinska University Hospital, 171 77, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Emma Tham
- Clinical Genetics, Karolinska University Hospital, 171 76, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden
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12
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Fangusaro J, Jones DT, Packer RJ, Gutmann DH, Milde T, Witt O, Mueller S, Fisher MJ, Hansford JR, Tabori U, Hargrave D, Bandopadhayay P. Pediatric low-grade glioma: State-of-the-art and ongoing challenges. Neuro Oncol 2024; 26:25-37. [PMID: 37944912 PMCID: PMC10768984 DOI: 10.1093/neuonc/noad195] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
The most common childhood central nervous system (CNS) tumor is pediatric low-grade glioma (pLGG), representing 30%-40% of all CNS tumors in children. Although there is high associated morbidity, tumor-related mortality is relatively rare. pLGG is now conceptualized as a chronic disease, underscoring the importance of functional outcomes and quality-of-life measures. A wealth of data has emerged about these tumors, including a better understanding of their natural history and their molecular drivers, paving the way for the use of targeted inhibitors. While these treatments have heralded tremendous promise, challenges remain about how to best optimize their use, and the long-term toxicities associated with these inhibitors remain unknown. The International Pediatric Low-Grade Glioma Coalition (iPLGGc) is a global group of physicians and scientists with expertise in pLGG focused on addressing key pLGG issues. Here, the iPLGGc provides an overview of the current state-of-the-art in pLGG, including epidemiology, histology, molecular landscape, treatment paradigms, survival outcomes, functional outcomes, imaging response, and ongoing challenges. This paper also serves as an introduction to 3 other pLGG manuscripts on (1) pLGG preclinical models, (2) consensus framework for conducting early-phase clinical trials in pLGG, and (3) pLGG resistance, rebound, and recurrence.
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Affiliation(s)
- Jason Fangusaro
- Department of Hematology and Oncology, Children’s Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA
| | - David T Jones
- Translational Program, Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), University Hospital Heidelberg, Heidelberg, Germany
| | - Roger J Packer
- Brain Tumor Institute, Daniel and Jennifer Gilbert Neurofibromatosis Institute, Neuroscience and Behavioral Medicine, Children’s National Medical Center, Washington, District of Columbia, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Till Milde
- Translational Program, Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Olaf Witt
- Translational Program, Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Sabine Mueller
- Department of Neurological Surgery, University of California, San Francisco, California, USA
- Department of Pediatrics, University of California, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, California, USA
- Department of Oncology, University Children’s Hospital Zürich, Zürich, Switzerland
| | - Michael J Fisher
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jordan R Hansford
- Michael Rice Centre for Hematology and Oncology, Women’s and Children’s Hospital, Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australia ImmunoGENomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Uri Tabori
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Darren Hargrave
- University College London Great Ormond Street Institute of Child Health, London, UK
| | - Pratiti Bandopadhayay
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
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13
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Tosi U, Souweidane M. Diffuse Midline Gliomas: Challenges and New Strategies in a Changing Clinical Landscape. Cancers (Basel) 2024; 16:219. [PMID: 38201646 PMCID: PMC10778507 DOI: 10.3390/cancers16010219] [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: 12/14/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) was first described by Harvey Cushing, the father of modern neurosurgery, a century ago. Since then, the classification of this tumor changed significantly, as it is now part of the broader family of diffuse midline gliomas (DMGs), a heterogeneous group of tumors of midline structures encompassing the entire rostro-caudal space, from the thalamus to the spinal cord. DMGs are characterized by various epigenetic events that lead to chromatin remodeling similarities, as two decades of studies made possible by increased tissue availability showed. This new understanding of tumor (epi)biology is now driving novel clinical trials that rely on targeted agents, with finally real hopes for a change in an otherwise unforgiving prognosis. This biological discovery is being paralleled with equally exciting work in therapeutic drug delivery. Invasive and noninvasive platforms have been central to early phase clinical trials with a promising safety track record and anecdotal benefits in outcome.
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Affiliation(s)
- Umberto Tosi
- Department of Neurological Surgery, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Neurological Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark Souweidane
- Department of Neurological Surgery, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Neurological Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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14
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Krynina O, de Ståhl TD, Jylhä C, Arthur C, Giraud G, Nyman P, Fritzberg A, Sandgren J, Tham E, Sandvik U. The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma. Neurooncol Adv 2024; 6:vdae008. [PMID: 38371226 PMCID: PMC10874216 DOI: 10.1093/noajnl/vdae008] [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] [Indexed: 02/20/2024] Open
Abstract
Background Low-grade gliomas (LGGs) represent children's most prevalent central nervous system tumor, necessitating molecular profiling to diagnose and determine the most suitable treatment. Developing highly sensitive screening techniques for liquid biopsy samples is particularly beneficial, as it enables the early detection and molecular characterization of tumors with minimally invasive samples. Methods We examined CSF and plasma samples from patients with pilocytic astrocytoma (PA) using custom multiplexed droplet digital polymerase chain reaction (ddPCR) assays based on whole genome sequencing data. These assays included a screening test to analyze BRAF duplication and a targeted assay for the detection of patient-specific KIAA1549::BRAF fusion junction sequences or single nucleotide variants. Results Our findings revealed that 5 out of 13 individual cerebrospinal fluid (CSF) samples tested positive for circulating tumor DNA (ctDNA). Among these cases, 3 exhibited the KIAA1549::BRAF fusion, which was detected through copy number variation (CNV) analysis (n = 1) or a fusion-specific probe (n = 2), while 1 case each displayed the BRAF V600E mutation and the FGFR1 N577K mutation. Additionally, a quantitative analysis of cell-free DNA (cfDNA) concentrations in PA CSF samples showed that most cases had low cfDNA levels, below the limit of detection of our assay (<1.9 ng). Conclusions While CNV analysis of CSF samples from LGGs still has some limitations, it has the potential to serve as a valuable complementary tool. Furthermore, it can also be multiplexed with other aberrations, for example, to the BRAF V600 test, to provide important insights into the molecular characteristics of LGGs.
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Affiliation(s)
- Olha Krynina
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Cecilia Jylhä
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Arthur
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Geraldine Giraud
- Department of Immunology, Genetic and Pathology, Neuro-oncology, and Neurodegeneration Program Rudbeck Laboratory, Uppsala, Sweden
- Department of Women and Children’s Health, Akademiska University Hospital, Uppsala, Sweden
| | - Per Nyman
- Department of Health, Crown Princess Victoria Children´s Hospital, Linköping University Hospital, Linköping, Sweden
- Department of Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Centre for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Anders Fritzberg
- Daycare Unit of Oncology and Hematology, Clinic of Pediatrics Falun Hospital, Dalarna Region, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrika Sandvik
- Department of Clinical Neuroscience, Division of Neurosurgery, Karolinska Institutet, Stockholm, Sweden
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15
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Yang C, Gan X, Zeng Y, Xu Z, Xu L, Hu C, Ma H, Chai B, Hu S, Chai Y. Advanced design and applications of digital microfluidics in biomedical fields: An update of recent progress. Biosens Bioelectron 2023; 242:115723. [PMID: 37832347 DOI: 10.1016/j.bios.2023.115723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
Significant breakthroughs have been made in digital microfluidic (DMF)-based technologies over the past decades. DMF technology has attracted great interest in bioassays depending on automatic microscale liquid manipulations and complicated multi-step processing. In this review, the recent advances of DMF platforms in the biomedical field were summarized, focusing on the integrated design and applications of the DMF system. Firstly, the electrowetting-on-dielectric principle, fabrication of DMF chips, and commercialization of the DMF system were elaborated. Then, the updated droplets and magnetic beads manipulation strategies with DMF were explored. DMF-based biomedical applications were comprehensively discussed, including automated sample preparation strategies, immunoassays, molecular diagnosis, blood processing/testing, and microbe analysis. Emerging applications such as enzyme activity assessment and DNA storage were also explored. The performance of each bioassay was compared and discussed, providing insight into the novel design and applications of the DMF technology. Finally, the advantages, challenges, and future trends of DMF systems were systematically summarized, demonstrating new perspectives on the extensive applications of DMF in basic research and commercialization.
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Affiliation(s)
- Chengbin Yang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Xiangyu Gan
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Yuping Zeng
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Zhourui Xu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Longqian Xu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Chenxuan Hu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Hanbin Ma
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China; Guangdong ACXEL Micro & Nano Tech Co., Ltd, Foshan, China.
| | - Bao Chai
- Department of Dermatology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China; Department of Dermatology, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China.
| | - Siyi Hu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Yujuan Chai
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
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16
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Shuai Y, Ma Z, Ju J, Wei T, Gao S, Kang Y, Yang Z, Wang X, Yue J, Yuan P. Liquid-based biomarkers in breast cancer: looking beyond the blood. J Transl Med 2023; 21:809. [PMID: 37957623 PMCID: PMC10644618 DOI: 10.1186/s12967-023-04660-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
In recent decades, using circulating tumor cell (CTC), circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), exosomes and etc. as liquid biomarkers has received enormous attention in various tumors, including breast cancer (BC). To date, efforts in the area of liquid biopsy predominantly focus on the analysis of blood-based markers. It is worth noting that the identifications of markers from non-blood sources provide unique advantages beyond the blood and these alternative sources may be of great significance in offering supplementary information in certain settings. Here, we outline the latest advances in the analysis of non-blood biomarkers, predominantly including urine, saliva, cerebrospinal fluid, pleural fluid, stool and etc. The unique advantages of such testings, their current limitations and the appropriate use of non-blood assays and blood assays in different settings are further discussed. Finally, we propose to highlight the challenges of these alternative assays from basic to clinical implementation and explore the areas where more investigations are warranted to elucidate its potential utility.
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Affiliation(s)
- You Shuai
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhonghua Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Endoscopy, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jie Ju
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tong Wei
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Songlin Gao
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yikun Kang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zixuan Yang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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17
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Battini S, Gokden M, Palys V, Santos Horta E. Diffuse Leptomeningeal Glioneuronal Tumor: First Description of Metastasis to the Lung and Bone Marrow. Cureus 2023; 15:e48185. [PMID: 38050500 PMCID: PMC10693495 DOI: 10.7759/cureus.48185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
Diffuse leptomeningeal glioneuronal tumor (DLGNT) is a rare neoplasm of the central nervous system (CNS) that primarily affects the leptomeninges. However, it can also involve the brain parenchyma and spinal cord. We report the first case of metastasis of this primary CNS tumor to the lung and bone marrow. An 18-year-old male was diagnosed with DLGNT through meningeal biopsy after multiple events of transient neurologic signs and symptoms that included recurrent episodes of encephalopathy, seizures, cerebral vasospasms, cranial nerve palsy, and urinary dysfunction. Five months after diagnosis, the patient presented with pancytopenia and pulmonary effusion. At that time, he was being treated with temozolomide, after radiation treatment to the brain and spinal cord. Bone marrow biopsy and pleural cytology revealed systemic metastases from the primary CNS tumor. He was then treated with chemotherapy with carboplatin and vincristine which improved his condition for two and a half months. Unfortunately, the patient died of a high systemic metastatic burden. Primary CNS tumors rarely produce systemic metastases, and this is the first report of DLGNT with bone marrow and pulmonary metastases. Chemotherapy with carboplatin and vincristine should be considered as a treatment for patients with DLGNT, as the patient presented a systemic response with clinical and radiological improvement.
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Affiliation(s)
- Sahithi Battini
- Department of Neurology, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Viktoras Palys
- Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Erika Santos Horta
- Department of Neurology, University of Arkansas for Medical Sciences, Little Rock, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, USA
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18
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Berzero G, Pieri V, Mortini P, Filippi M, Finocchiaro G. The coming of age of liquid biopsy in neuro-oncology. Brain 2023; 146:4015-4024. [PMID: 37289981 PMCID: PMC10545511 DOI: 10.1093/brain/awad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 04/05/2023] [Accepted: 05/16/2023] [Indexed: 06/10/2023] Open
Abstract
The clinical role of liquid biopsy in oncology is growing significantly. In gliomas and other brain tumours, targeted sequencing of cell-free DNA (cfDNA) from CSF may help differential diagnosis when surgery is not recommended and be more representative of tumour heterogeneity than surgical specimens, unveiling targetable genetic alterations. Given the invasive nature of lumbar puncture to obtain CSF, the quantitative analysis of cfDNA in plasma is a lively option for patient follow-up. Confounding factors may be represented by cfDNA variations due to concomitant pathologies (inflammatory diseases, seizures) or clonal haematopoiesis. Pilot studies suggest that methylome analysis of cfDNA from plasma and temporary opening of the blood-brain barrier by ultrasound have the potential to overcome some of these limitations. Together with this, an increased understanding of mechanisms modulating the shedding of cfDNA by the tumour may help to decrypt the meaning of cfDNA kinetics in blood or CSF.
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Affiliation(s)
- Giulia Berzero
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Valentina Pieri
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Pietro Mortini
- Vita-Salute San Raffaele University, 20132 Milan, Italy
- Department of Neurosurgery and Gamma Knife Radiosurgery, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Massimo Filippi
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
- Neurorehabilitation Unit; Neurophysiology Unit; Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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19
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Wang Q, Liang Q, Wei W, Niu W, Liang C, Wang X, Wang X, Pan H. Concordance analysis of cerebrospinal fluid with the tumor tissue for integrated diagnosis in gliomas based on next-generation sequencing. Pathol Oncol Res 2023; 29:1611391. [PMID: 37822669 PMCID: PMC10562547 DOI: 10.3389/pore.2023.1611391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Purpose: The driver mutations of gliomas have been identified in cerebrospinal fluid (CSF). Here we compared the concordance between CSF and tumor tissue for integrated diagnosis in gliomas using next-generation sequencing (NGS) to evaluate the feasibility of CSF detection in gliomas. Patients and methods: 27 paired CSF/tumor tissues of glioma patients were sequenced by a customized gene panel based on NGS. All CSF samples were collected through lumbar puncture before surgery. Integrated diagnosis was made by analysis of histology and tumor DNA molecular pathology according to the 2021 WHO classification of the central nervous system tumors. Results: A total of 24 patients had detectable circulating tumor DNA (ctDNA) and 22 had at least one somatic mutation or chromosome alteration in CSF. The ctDNA levels varied significantly across different ages, Ki-67 index, magnetic resonance imaging signal and glioma subtypes (p < 0.05). The concordance between integrated ctDNA diagnosis and the final diagnosis came up to 91.6% (Kappa, 0.800). We reclassified the clinical diagnosis of 3 patients based on the results of CSF ctDNA sequencing, and 4 patients were reassessed depending on tumor DNA. Interestingly, a rare IDH1 R132C was identified in CSF ctDNA, but not in the corresponding tumor sample. Conclusion: This study demonstrates a high concordance between integrated ctDNA diagnosis and the final diagnosis of gliomas, highlighting the practicability of NGS based detection of mutations of CSF in assisting integrated diagnosis of gliomas, especially glioblastoma.
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Affiliation(s)
- Qiang Wang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Qiujin Liang
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Wuting Wei
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Wenhao Niu
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Chong Liang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Xiaoliang Wang
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
| | - Xiaoxuan Wang
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Hao Pan
- Department of Neurosurgery, Jinling Hospital, Nanjing, China
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20
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Miller AM, Karajannis MA. Cerebrospinal fluid: The new frontier for methylome-based diagnostic classification of brain tumors. Neuro Oncol 2023; 25:1461-1462. [PMID: 37078878 PMCID: PMC10398800 DOI: 10.1093/neuonc/noad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Indexed: 04/21/2023] Open
Affiliation(s)
- Alexandra M Miller
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, USA
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, USA
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21
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Mangum R, Reuther J, Baksi KS, Gandhi I, Zabriskie RC, Recinos A, Raesz-Martinez R, Lin FY, Potter SL, Sher AC, Kralik SF, Mohila CA, Chintagumpala MM, Muzny D, Hu J, Gibbs RA, Fisher KE, Bernini JC, Gill J, Griffin TC, Tomlinson GE, Vallance KL, Plon SE, Roy A, Parsons DW. Circulating tumor DNA sequencing of pediatric solid and brain tumor patients: An institutional feasibility study. Pediatr Hematol Oncol 2023; 40:719-738. [PMID: 37366551 PMCID: PMC10592361 DOI: 10.1080/08880018.2023.2228837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023]
Abstract
The potential of circulating tumor DNA (ctDNA) analysis to serve as a real-time "liquid biopsy" for children with central nervous system (CNS) and non-CNS solid tumors remains to be fully elucidated. We conducted a study to investigate the feasibility and potential clinical utility of ctDNA sequencing in pediatric patients enrolled on an institutional clinical genomics trial. A total of 240 patients had tumor DNA profiling performed during the study period. Plasma samples were collected at study enrollment from 217 patients and then longitudinally from a subset of patients. Successful cell-free DNA extraction and quantification occurred in 216 of 217 (99.5%) of these initial samples. Twenty-four patients were identified whose tumors harbored 30 unique variants that were potentially detectable on a commercially-available ctDNA panel. Twenty of these 30 mutations (67%) were successfully detected by next-generation sequencing in the ctDNA from at least one plasma sample. The rate of ctDNA mutation detection was higher in patients with non-CNS solid tumors (7/9, 78%) compared to those with CNS tumors (9/15, 60%). A higher ctDNA mutation detection rate was also observed in patients with metastatic disease (9/10, 90%) compared to non-metastatic disease (7/14, 50%), although tumor-specific variants were detected in a few patients in the absence of radiographic evidence of disease. This study illustrates the feasibility of incorporating longitudinal ctDNA analysis into the management of relapsed or refractory patients with childhood CNS or non-CNS solid tumors.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children’s Hospital, Phoenix, Arizona
| | - Jacquelyn Reuther
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Koel Sen Baksi
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ilavarasi Gandhi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Ryan C. Zabriskie
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Alva Recinos
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Robin Raesz-Martinez
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Frank Y. Lin
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Samara L. Potter
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio
- Department of Pediatrics, The Ohio State University, Columbus, Ohio
| | - Andrew C. Sher
- Department of Radiology, Texas Children’s Hospital, Houston, Texas
| | | | - Carrie A. Mohila
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Murali M. Chintagumpala
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Kevin E. Fisher
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Juan Carlos Bernini
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Jonathan Gill
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy C. Griffin
- Department of Hematology Oncology, The Children’s Hospital of San Antonio, Baylor College of Medicine, San Antonio, Texas
| | - Gail E Tomlinson
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | - Kelly L. Vallance
- Hematology and Oncology, Cook Children’s Medical Center, Fort Worth, Texas
| | - Sharon E. Plon
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Angshumoy Roy
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - D. Williams Parsons
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
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22
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Foster JB, Alonso MM, Sayour E, Davidson TB, Persson ML, Dun MD, Kline C, Mueller S, Vitanza NA, van der Lugt J. Translational considerations for immunotherapy clinical trials in pediatric neuro-oncology. Neoplasia 2023; 42:100909. [PMID: 37244226 DOI: 10.1016/j.neo.2023.100909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/20/2023] [Accepted: 05/11/2023] [Indexed: 05/29/2023]
Abstract
While immunotherapy for pediatric cancer has made great strides in recent decades, including the FDA approval of agents such as dinutuximab and tisgenlecleucel, these successes have rarely impacted children with pediatric central nervous system (CNS) tumors. As our understanding of the biological underpinnings of these tumors evolves, new immunotherapeutics are undergoing rapid clinical translation specifically designed for children with CNS tumors. Most recently, there have been notable clinical successes with oncolytic viruses, vaccines, adoptive cellular therapy, and immune checkpoint inhibition. In this article, the immunotherapy working group of the Pacific Pediatric Neuro-Oncology Consortium (PNOC) reviews the current and future state of immunotherapeutic CNS clinical trials with a focus on clinical trial development. Based on recent therapeutic trials, we discuss unique immunotherapy clinical trial challenges, including toxicity considerations, disease assessment, and correlative studies. Combinatorial strategies and future directions will be addressed. Through internationally collaborative efforts and consortia, we aim to direct this promising field of immuno-oncology to the next frontier of successful application against pediatric CNS tumors.
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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.
| | - Marta M Alonso
- Department of Pediatrics, Program of Solid Tumors, University Clinic of Navarra, Center for the Applied Medical Research (CIMA), Pamplona, Spain
| | - Elias Sayour
- Lillian S. Wells Department of Neurosurgery, Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, FL USA
| | - Tom B Davidson
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, United States
| | - Mika L Persson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Matthew D Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia; Mark Hughes Foundation Centre for Brain Cancer Research, Paediatric Program, College of Health, Medicine & Wellbeing, University of Newcastle, Callaghan, NSW, Australia
| | - Cassie Kline
- Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Sabine Mueller
- Department of Neurology, Department of Neurosurgery and Department of Pediatrics, UCSF, San Francisco, California, USA
| | - Nicholas A Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
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23
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Hickman RA, Miller AM, Arcila ME. Cerebrospinal fluid: A unique source of circulating tumor DNA with broad clinical applications. Transl Oncol 2023; 33:101688. [PMID: 37196447 DOI: 10.1016/j.tranon.2023.101688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
Malignancies involving the central nervous system present unique challenges for diagnosis and monitoring due to the difficulties and risks of direct biopsies and the low specificity and/or sensitivity of other techniques for assessment. In recent years, liquid biopsy of the cerebrospinal fluid (CSF) has emerged as a convenient alternative that combines minimal invasiveness with the ability to detect disease-defining or therapeutically actionable genetic alterations from circulating tumor DNA (ctDNA). Since CSF can be obtained by lumbar puncture, or an established ventricular access device at multiple time points, ctDNA analysis enables initial molecular characterization and longitudinal monitoring throughout a patient's disease course, promoting optimization of treatment regimens. This review outlines some of the key aspects of ctDNA from CSF as a highly suitable approach for clinical assessment, the benefits and drawbacks, testing methods, as well as potential future advancements in this field. We anticipate wider adoption of this practice as technologies and pipelines improve and envisage significant improvements for cancer care.
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Affiliation(s)
- Richard A Hickman
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, New York, NY, United States; Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Alexandra M Miller
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, New York, NY, United States; Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, United States.
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24
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Lovibond S, Gewirtz AN, Pasquini L, Krebs S, Graham MS. The promise of metabolic imaging in diffuse midline glioma. Neoplasia 2023; 39:100896. [PMID: 36944297 PMCID: PMC10036941 DOI: 10.1016/j.neo.2023.100896] [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: 10/14/2022] [Revised: 02/10/2023] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
Recent insights into histopathological and molecular subgroups of glioma have revolutionized the field of neuro-oncology by refining diagnostic categories. An emblematic example in pediatric neuro-oncology is the newly defined diffuse midline glioma (DMG), H3 K27-altered. DMG represents a rare tumor with a dismal prognosis. The diagnosis of DMG is largely based on clinical presentation and characteristic features on conventional magnetic resonance imaging (MRI), with biopsy limited by its delicate neuroanatomic location. Standard MRI remains limited in its ability to characterize tumor biology. Advanced MRI and positron emission tomography (PET) imaging offer additional value as they enable non-invasive evaluation of molecular and metabolic features of brain tumors. These techniques have been widely used for tumor detection, metabolic characterization and treatment response monitoring of brain tumors. However, their role in the realm of pediatric DMG is nascent. By summarizing DMG metabolic pathways in conjunction with their imaging surrogates, we aim to elucidate the untapped potential of such imaging techniques in this devastating disease.
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Affiliation(s)
- Samantha Lovibond
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra N Gewirtz
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luca Pasquini
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Krebs
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Radiochemistry and Imaging Sciences Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Radiology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Maya S Graham
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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25
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Stepien N, Senfter D, Furtner J, Haberler C, Dorfer C, Czech T, Lötsch-Gojo D, Mayr L, Hedrich C, Baumgartner A, Aliotti-Lippolis M, Schned H, Holler J, Bruckner K, Slavc I, Azizi AA, Peyrl A, Müllauer L, Madlener S, Gojo J. Proof-of-Concept for Liquid Biopsy Disease Monitoring of MYC-Amplified Group 3 Medulloblastoma by Droplet Digital PCR. Cancers (Basel) 2023; 15:2525. [PMID: 37173990 PMCID: PMC10177279 DOI: 10.3390/cancers15092525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Liquid biopsy diagnostic methods are an emerging complementary tool to imaging and pathology techniques across various cancer types. However, there is still no established method for the detection of molecular alterations and disease monitoring in MB, the most common malignant CNS tumor in the pediatric population. In the presented study, we investigated droplet digital polymerase chain reaction (ddPCR) as a highly sensitive method for the detection of MYC amplification in bodily fluids of group 3 MB patients. METHODS We identified a cohort of five MYC-amplified MBs by methylation array and FISH. Predesigned and wet-lab validated probes for ddPCR were used to establish the detection method and were validated in two MYC-amplified MB cell lines as well as tumor tissue of the MYC-amplified cohort. Finally, a total of 49 longitudinal CSF samples were analyzed at multiple timepoints during the course of the disease. RESULTS Detection of MYC amplification by ddPCR in CSF showed a sensitivity and specificity of 90% and 100%, respectively. We observed a steep increase in amplification rate (AR) at disease progression in 3/5 cases. ddPCR was proven to be more sensitive than cytology for the detection of residual disease. In contrast to CSF, MYC amplification was not detectable by ddPCR in blood samples. CONCLUSIONS ddPCR proves to be a sensitive and specific method for the detection of MYC amplification in the CSF of MB patients. These results warrant implementation of liquid biopsy in future prospective clinical trials to validate the potential for improved diagnosis, disease staging and monitoring.
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Affiliation(s)
- Natalia Stepien
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Daniel Senfter
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Julia Furtner
- Division of Neuroradiology and Musculoskeletal Radiology, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
- Research Center for Medical Image Analysis and Artificial Intelligence (MIAAI), Faculty of Medicine and Dentistry, Danube Private University, 3500 Krems-Stein, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniela Lötsch-Gojo
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Cora Hedrich
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Alicia Baumgartner
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Maria Aliotti-Lippolis
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Hannah Schned
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Johannes Holler
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Katharina Bruckner
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Amedeo A. Azizi
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
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26
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Das A, Nobre L. Genomics in pediatric high-grade gliomas: Hope or hype practical implications for resource limited settings. PEDIATRIC HEMATOLOGY ONCOLOGY JOURNAL 2023. [DOI: 10.1016/j.phoj.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
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Arthur C, Jylhä C, de Ståhl TD, Shamikh A, Sandgren J, Rosenquist R, Nordenskjöld M, Harila A, Barbany G, Sandvik U, Tham E. Simultaneous Ultra-Sensitive Detection of Structural and Single Nucleotide Variants Using Multiplex Droplet Digital PCR in Liquid Biopsies from Children with Medulloblastoma. Cancers (Basel) 2023; 15:cancers15071972. [PMID: 37046633 PMCID: PMC10092983 DOI: 10.3390/cancers15071972] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/10/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Medulloblastoma is a malignant embryonal tumor of the central nervous system (CNS) that mainly affects infants and children. Prognosis is highly variable, and molecular biomarkers for measurable residual disease (MRD) detection are lacking. Analysis of cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) using broad genomic approaches, such as low-coverage whole-genome sequencing, has shown promising prognostic value. However, more sensitive methods are needed for MRD analysis. Here, we show the technical feasibility of capturing medulloblastoma-associated structural variants and point mutations simultaneously in cfDNA using multiplexed droplet digital PCR (ddPCR). Assay sensitivity was assessed with a dilution series of tumor in normal genomic DNA, and the limit of detection was below 100 pg of input DNA for all assays. False positive rates were zero for structural variant assays. Liquid biopsies (CSF and plasma, n = 47) were analyzed from 12 children with medulloblastoma, all with negative CSF cytology. MRD was detected in 75% (9/12) of patients overall. In CSF samples taken before or within 21 days of surgery, MRD was detected in 88% (7/8) of patients with localized disease and in one patient with the metastasized disease. Our results suggest that this approach could expand the utility of ddPCR and complement broader analyses of cfDNA for MRD detection.
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28
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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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Diaz M, Rana S, Silva Correia CE, Reiner AS, Lin AL, Miller AM, Graham MS, Chudsky S, Bale TA, Rosenblum M, Karajannis MA, Pentsova E. Leptomeningeal disease in histone-mutant gliomas. Neurooncol Adv 2023; 5:vdad068. [PMID: 37346983 PMCID: PMC10281361 DOI: 10.1093/noajnl/vdad068] [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] [Indexed: 06/23/2023] Open
Abstract
Background The 2016 WHO classification described a subtype of midline gliomas harboring histone 3 (H3) K27M alterations, and the 2021 edition added a new subtype of hemispheric diffuse gliomas with H3 G34R/V mutations. The incidence and clinical behavior of leptomeningeal disease (LMD) in these patients is not well defined. Methods Retrospective study of patients with H3-altered gliomas diagnosed from 01/2012 to 08/2021; histone mutations were identified through next-generation sequencing (NGS) of tumor biopsy and/or cerebrospinal fluid (CSF). Results We identified 42 patients harboring H3 mutations (K27M mutations in 33 patients, G34R/V in 8, and both in one). Median age was 21 (4-70); 27 were male. LMD was diagnosed in 21/42 (50%) patients, corresponding to a 3-year cumulative incidence of 44.7% (95% confidence interval (CI): 26.1%-63.4%) for the K27-mutant group and a 1-year cumulative incidence of 37.5% in the G34-mutant group (95% CI: 0.01%-74.4%; no events after 1 year). Median time from tumor diagnosis to LMD was 12.9 months for H3-K27 patients and 5.6 months for H3-G34 patients. H3 mutation was detected in CSF in all patients with LMD who had NGS (8 H3-K27-mutant patients). In the H3-K27-mutant group, modeled risk of death was increased in patients who developed LMD (hazard ratio: 7.37, 95% CI: 2.98-18.23, P < .0001). Conclusions In our cohort, 50% of patients developed LMD. Although further studies are needed, CSF ctDNA characterization may aid in identifying molecular tumor profiles in glioma patients with LMD, and neuroaxis imaging and CSF NGS should be considered for early LMD detection.
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Affiliation(s)
- Maria Diaz
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Satshil Rana
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Anne S Reiner
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew L Lin
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra M Miller
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maya S Graham
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sofia Chudsky
- Office of Professional Development, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hunter College, New York, NY, USA
| | - Tejus A Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Elena Pentsova
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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30
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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: 0] [Impact Index Per Article: 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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31
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Short SC. EV packing allows meningioma tracking in blood. Neuro Oncol 2022; 24:2091-2092. [PMID: 36268772 PMCID: PMC9713496 DOI: 10.1093/neuonc/noac230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Susan C Short
- Leeds Institute of Medical Research, University of Leeds, LeedsUK
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32
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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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33
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Rosenberg T, Bandopadhayay P. Molecular genetics of paediatric brain tumours and opportunities for precision medicine - a focus on infant tumours. Curr Opin Neurol 2022; 35:772-778. [PMID: 36226704 DOI: 10.1097/wco.0000000000001110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW The last few decades have seen an explosion in our understanding of the molecular drivers of childhood brain tumours. These insights have opened the possibility for precision medicine approaches for some tumour types. However, a different spectrum of tumours is more likely to occur in infants and young children, who face additional therapeutic challenges. This review focuses on recent advances in molecular genetics of common infant brain tumours and their implication for diagnosis, prognostication and utilization of precision oncology approaches. RECENT FINDINGS Infant tumours have different biology and outcomes than similar tumours in older children and adults. For low-grade gliomas, targeted MAPK inhibition is well tolerated and likely efficacious. In high-grade gliomas, common tyrosine kinase alterations offer compelling targets for inhibition that are currently being evaluated. Paediatric-specific sequencing and methylation analysis offer insights into the driving biology of infant medulloblastoma, atypical teratoid rhabdoid tumours, embryonal tumours with multilayered rosettes, ependymoma and choroid plexus tumours, with molecular subgrouping shedding insights into distinct driving biology and clinical outcomes. SUMMARY Infant brain tumours are rare and heterogenous, with overall poor outcomes. Advances in molecular genetics have been incorporated into their diagnostic criteria and allow for accurate subgrouping and improved prognostication. The utilization of targeted agents appears beneficial for many low-grade gliomas and a subset of high-grade gliomas, but further research is urgently needed to improve outcomes for other tumour entities.
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Affiliation(s)
- Tom Rosenberg
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center
- Department of Pediatrics, Harvard Medical School
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center
- Department of Pediatrics, Harvard Medical School
- Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
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34
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Friedman JS, Hertz CAJ, Karajannis MA, Miller AM. Tapping into the genome: the role of CSF ctDNA liquid biopsy in glioma. Neurooncol Adv 2022; 4:ii33-ii40. [PMID: 36380863 PMCID: PMC9650472 DOI: 10.1093/noajnl/vdac034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Liquid biopsy has emerged as a novel noninvasive tool in cancer diagnostics. While significant strides have been made in other malignancies using liquid biopsy for diagnosis, disease monitoring, and treatment selection, development of these assays has been more challenging for brain tumors. Recently, research in primary and metastatic brain tumors has begun to harness the potential utility of liquid biopsy-particularly using circulating tumor DNA (ctDNA). Initial studies to identify ctDNA in plasma of brain tumor patients have shown feasibility, but the yield of ctDNA is far below that for other malignancies. Attention has therefore turned to the cerebrospinal fluid (CSF) as a more robust source of ctDNA. This review discusses the unique considerations in liquid biopsy for glioma and places them in the context of the work to date. We address the utility of CSF liquid biopsy for diagnosis, longitudinal monitoring, tracking tumor evolution, clinical trial eligibility, and prognostication. We discuss the differences in assay requirements for each clinical application to best optimize factors such as efficacy, cost, and speed. Ultimately, CSF liquid biopsy has the potential to transform how we manage primary brain tumor patients.
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Affiliation(s)
- Joshua S Friedman
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Charli Ann J Hertz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexandra M Miller
- Corresponding Author: Alexandra M. Miller, MD, PhD, Department of Neurology and Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York NY 10065, USA ()
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35
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Xu D, Di K, Fan B, Wu J, Gu X, Sun Y, Khan A, Li P, Li Z. MicroRNAs in extracellular vesicles: Sorting mechanisms, diagnostic value, isolation, and detection technology. Front Bioeng Biotechnol 2022; 10:948959. [PMID: 36324901 PMCID: PMC9618890 DOI: 10.3389/fbioe.2022.948959] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of short, single-stranded, noncoding RNAs, with a length of about 18–22 nucleotides. Extracellular vesicles (EVs) are derived from cells and play a vital role in the development of diseases and can be used as biomarkers for liquid biopsy, as they are the carriers of miRNA. Existing studies have found that most of the functions of miRNA are mainly realized through intercellular transmission of EVs, which can protect and sort miRNAs. Meanwhile, detection sensitivity and specificity of EV-derived miRNA are higher than those of conventional serum biomarkers. In recent years, EVs have been expected to become a new marker for liquid biopsy. This review summarizes recent progress in several aspects of EVs, including sorting mechanisms, diagnostic value, and technology for isolation of EVs and detection of EV-derived miRNAs. In addition, the study reviews challenges and future research avenues in the field of EVs, providing a basis for the application of EV-derived miRNAs as a disease marker to be used in clinical diagnosis and even for the development of point-of-care testing (POCT) platforms.
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Affiliation(s)
- Dongjie Xu
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Kaili Di
- Department of Laboratory Medicine, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Boyue Fan
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jie Wu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xinrui Gu
- Department of Laboratory Medicine, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yifan Sun
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Adeel Khan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), Southeast University, Nanjing, China
| | - Peng Li
- College of Animal Science, Yangtze University, Jingzhou, China
- *Correspondence: Peng Li, ; Zhiyang Li,
| | - Zhiyang Li
- Department of Laboratory Medicine, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
- *Correspondence: Peng Li, ; Zhiyang Li,
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Lazow MA, Palmer JD, Fouladi M, Salloum R. Medulloblastoma in the Modern Era: Review of Contemporary Trials, Molecular Advances, and Updates in Management. Neurotherapeutics 2022; 19:1733-1751. [PMID: 35859223 PMCID: PMC9723091 DOI: 10.1007/s13311-022-01273-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2022] [Indexed: 12/13/2022] Open
Abstract
Critical discoveries over the past two decades have transformed our understanding of medulloblastoma from a single entity into a clinically and biologically heterogeneous disease composed of at least four molecularly distinct subgroups with prognostically and therapeutically relevant genomic signatures. Contemporary clinical trials also have provided valuable insight guiding appropriate treatment strategies. Despite therapeutic and biological advances, medulloblastoma patients across the age spectrum experience tumor- and treatment-related morbidity and mortality. Using an updated risk stratification approach integrating both clinical and molecular features, ongoing research seeks to (1) cautiously reduce therapy and mitigate toxicity in low-average risk patients, and (2) thoughtfully intensify treatment with incorporation of novel, biologically guided agents for patients with high-risk disease. Herein, we review important historical and contemporary studies, discuss management updates, and summarize current knowledge of the biological landscape across unique pediatric, infant, young adult, and relapsed medulloblastoma populations.
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Affiliation(s)
- Margot A Lazow
- Pediatric Brain Tumor Program, Division of Hematology, Oncology, and Bone Marrow Transplant, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
- The Ohio State University College of Medicine, Columbus, OH, USA
| | - Joshua D Palmer
- The Ohio State University College of Medicine, Columbus, OH, USA
- The James Cancer Centre, Ohio State University, Columbus, OH, USA
| | - Maryam Fouladi
- Pediatric Brain Tumor Program, Division of Hematology, Oncology, and Bone Marrow Transplant, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
- The Ohio State University College of Medicine, Columbus, OH, USA
| | - Ralph Salloum
- Pediatric Brain Tumor Program, Division of Hematology, Oncology, and Bone Marrow Transplant, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA.
- The Ohio State University College of Medicine, Columbus, OH, USA.
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Lim-Fat MJ, Macdonald M, Lapointe S, Climans SA, Cacciotti C, Chahal M, Perreault S, Tsang DS, Gao A, Yip S, Keith J, Bennett J, Ramaswamy V, Detsky J, Tabori U, Das S, Hawkins C. Molecular testing for adolescent and young adult central nervous system tumors: A Canadian guideline. Front Oncol 2022; 12:960509. [PMID: 36249063 PMCID: PMC9559579 DOI: 10.3389/fonc.2022.960509] [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: 06/03/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022] Open
Abstract
The 2021 World Health Organization (WHO) classification of CNS tumors incorporates molecular signatures with histology and has highlighted differences across pediatric vs adult-type CNS tumors. However, adolescent and young adults (AYA; aged 15–39), can suffer from tumors across this spectrum and is a recognized orphan population that requires multidisciplinary, specialized care, and often through a transition phase. To advocate for a uniform testing strategy in AYAs, pediatric and adult specialists from neuro-oncology, radiation oncology, neuropathology, and neurosurgery helped develop this review and testing framework through the Canadian AYA Neuro-Oncology Consortium. We propose a comprehensive approach to molecular testing in this unique population, based on the recent tumor classification and within the clinical framework of the provincial health care systems in Canada.
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Affiliation(s)
- Mary Jane Lim-Fat
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mary Jane Lim-Fat,
| | - Maria Macdonald
- Department of Oncology, London Health Sciences Centre, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Sarah Lapointe
- Division of Neurology, Department of Medicine, Centre Hospitalier de l'Universite de Montreal, Montreal, QC, Canada
| | - Seth Andrew Climans
- Department of Oncology, London Health Sciences Centre, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Chantel Cacciotti
- Department of Paediatrics, Division of Pediatric Hematology/Oncology, London Health Sciences Centre, London, ON, Canada
| | - Manik Chahal
- Department of Medical Oncology, BC Cancer Vancouver Centre, Vancouver, BC, Canada
| | - Sebastien Perreault
- Department of Pediatrics, Division of Child Neurology, CHU Sainte-Justine, Montreal, QC, Canada
| | - Derek S. Tsang
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Andrew Gao
- Department of Laboratory Medicine and Pathobiology, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of British Columbia, BC, Canada
| | - Julia Keith
- Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Center, University of Toronto, Toronto, ON, Canada
| | - Julie Bennett
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto ON, Canada
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto ON, Canada
| | - Jay Detsky
- Department of Radiation Oncology, Sunnybrook Health Sciences Center, University of Toronto, Toronto, ON, Canada
| | - Uri Tabori
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto ON, Canada
| | - Sunit Das
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Cynthia Hawkins
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto ON, Canada
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Detection of mutation profiles and tumor mutation burden of cerebrospinal fluid circulating DNA by a cancer genomic panel sequencing in glioma patients. Clin Chim Acta 2022; 534:81-92. [PMID: 35810802 DOI: 10.1016/j.cca.2022.07.001] [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: 06/09/2022] [Accepted: 07/03/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND AIMS Circulating tumor DNA (ctDNA) has been recognized as a reliable source to reflect the molecular and genetic landscape of corresponding tumors in recent years. In this study, we tested the application of a cancer genomic panel sequencing on the cerebrospinal fluid (CSF)-derived ctDNA for the less invasive detection and diagnosis of glioma. MATERIALS AND METHODS CtDNA was extracted from 26 CSF samples and subject to a cancer genomic panel sequencing of 520 genes to analyze the mutation profiles and tumor mutation burden (TMB), which were compared with their corresponding tumor DNA samples. Associations between mutations or TMB and clinical characteristics were also evaluated. RESULTS A high detection rate of ctDNA (24/26, 92.3%) was observed in CSF. CtDNA mutations had high concordance rates with tumor DNA, especially in non-copy number variations and in glioblastoma. CSF ctDNA TMB also exhibited a strong correlation with tumor DNA TMB (R2 = 0.879, P < 0.001), particularly in glioblastoma (R2 = 0.992, P < 0.001). Age was significantly associated with CSF ctDNA TMB in glioma patients. CONCLUSION We established a less invasive but effective molecular diagnostic approach using a cancer genomic panel sequencing system targeting CSF ctDNA for glioma, especially in glioblastoma.
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