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Dirven I, Vounckx M, Kessels JI, Lauwyck J, Awada G, Vanbinst AM, Neyns B. Detection of cell-free tumor DNA in cerebrospinal fluid as a diagnostic biomarker for leptomeningeal melanoma metastasis: A case series. Pigment Cell Melanoma Res 2024. [PMID: 38990845 DOI: 10.1111/pcmr.13186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/19/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Leptomeningeal melanoma metastases (LMM) are associated with poor survival. Diagnosis is based on clinical presentation, brain MRI and cerebrospinal fluid (CSF) analysis. Inconclusive findings at initial presentation can delay treatment. In this single-center case series, detection of BRAFV600- and NRASQ61-mutant cell-free tumor DNA (cfDNA) in CSF was evaluated as a complementary diagnostic biomarker. In 12 patients with clinical suspicion of LMM, a retrospective analysis of MRI, CSF cytology and cfDNA analysis on 1 mL of CSF using the Idylla® platform was carried out. Nine patients displayed MRI abnormalities suggesting LMM. CSF analysis identified malignant cells in three patients (including one without MRI abnormalities). BRAFV600- or NRASQ61-mutant cfDNA was detected in CSF of nine patients (eight with and one without MRI abnormalities; all patients with positive CSF cytology). Subsequent follow-up confirmed LMM in all patients with positive and in one patient with a negative CSF cfDNA analysis (sensitivity 81.8%; specificity 100%). Our findings suggest that analyzing BRAFV600- and NRASQ61-mutant cfDNA in CSF using the Idylla® platform holds promise as a sensitive and specific complementary diagnostic biomarker for LMM, particularly in case of inconsistency between imaging and CSF cytology. The 110-min analysis can facilitate urgent treatment decisions.
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Affiliation(s)
- Iris Dirven
- Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel)/Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Manon Vounckx
- Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel)/Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Jolien I Kessels
- Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel)/Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Justine Lauwyck
- Department of Medical Oncology, Algemeen Ziekenhuis Sint-Lucas, Brugge, Belgium
| | - Gil Awada
- Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel)/Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Anne-Marie Vanbinst
- Department of Radiology, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Bart Neyns
- Department of Medical Oncology, Universitair Ziekenhuis Brussel (UZ Brussel)/Vrije Universiteit Brussel (VUB), Brussels, Belgium
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2
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Lai M, Mu T, Liu M, Hu Q, Li J, Huang T, Li Y, Chen S, Cai L. Personalized therapy guided by longitudinal liquid biopsies for treatment of leptomeningeal disease from lung adenocarcinoma: A case report. Oncol Lett 2024; 28:299. [PMID: 38751754 PMCID: PMC11094582 DOI: 10.3892/ol.2024.14432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/20/2024] [Indexed: 05/18/2024] Open
Abstract
Molecular-based targeted therapies have significantly benefited certain patients with cancer; however, those with leptomeningeal disease (LMD) persistently exhibit a poor prognosis and are often excluded from clinical trials. Tumor-derived cell-free (cf)DNA, found in the cerebrospinal fluid (CSF) of patients with LMD, can assist in diagnosis and tracking of disease progression. However, the utilization of CSF to direct targeted cancer therapy has yet to be extensively explored. The present study reported the case of a patient with lung adenocarcinoma and LMD who was monitored by performing a series of liquid biopsies of CSF and blood. Targeted sequencing was performed on cfDNA from the CSF and plasma, and the variant allele frequencies (VAFs) of BRAF and NRAS mutations were assessed and analyzed in conjunction with the clinical presentation of the patient. The patient then underwent serial chemotherapy, radiation therapy, immunotherapy and targeted treatment based on the results of the liquid biopsies. Upon the LMD diagnosis, a BRAF p.V600E mutation was detected in plasma cfDNA. Consequently, the patient was treated with vemurafenib and responded favorably to this consolidation treatment for 13 months. After a relapse in July 2018, both BRAF p.V600E and NRAS p.Q61K mutations were detected in CSF supernatant and sediment cell samples, suggesting drug resistance. Therefore, the treatment strategy for the patient changed to cobimetnib plus vemurafenib. Notably, the changes of VAF in the CSF supernatant samples were associated with the clinical status of the patient. The patient survived for 33 months post-LMD diagnosis. The present case report highlights the potential use of liquid biopsy in personalized therapy, as it was instrumental in informing the combinational treatment plan of the patient, which ultimately proved beneficial.
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Affiliation(s)
- Mingyao Lai
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, Guangdong 510510, P.R. China
| | - Tianhao Mu
- HaploX Biotechnology, Shenzhen, Guangdong 518057, P.R. China
- Department of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 440300, P.R. China
| | - Ming Liu
- HaploX Biotechnology, Shenzhen, Guangdong 518057, P.R. China
| | - Qingjun Hu
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, Guangdong 510510, P.R. China
| | - Juan Li
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, Guangdong 510510, P.R. China
| | - Tanxiao Huang
- HaploX Biotechnology, Shenzhen, Guangdong 518057, P.R. China
| | - Yingmei Li
- HaploX Biotechnology, Shenzhen, Guangdong 518057, P.R. China
| | - Shifu Chen
- HaploX Biotechnology, Shenzhen, Guangdong 518057, P.R. China
- Department of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 440300, P.R. China
| | - Linbo Cai
- Department of Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, Guangdong 510510, P.R. China
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3
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Azad TD, Nanjo S, Jin MC, Chabon JJ, Kurtz DM, Chaudhuri AA, Connolly ID, Hui ABY, Liu CL, Merriott D, Ko R, Yoo C, Carter J, Chen E, Bonilla R, Hata A, Katakami N, Irie K, Yano S, Okimoto R, Bivona TG, Newman AM, Iv M, Nagpal S, Gephart MH, Alizadeh AA, Diehn M. Quantification of cerebrospinal fluid tumor DNA in lung cancer patients with suspected leptomeningeal carcinomatosis. NPJ Precis Oncol 2024; 8:121. [PMID: 38806586 PMCID: PMC11133465 DOI: 10.1038/s41698-024-00582-1] [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: 07/03/2023] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
Cerebrospinal fluid tumor-derived DNA (CSF-tDNA) analysis is a promising approach for monitoring the neoplastic processes of the central nervous system. We applied a lung cancer-specific sequencing panel (CAPP-Seq) to 81 CSF, blood, and tissue samples from 24 lung cancer patients who underwent lumbar puncture (LP) for suspected leptomeningeal disease (LMD). A subset of the cohort (N = 12) participated in a prospective trial of osimertinib for refractory LMD in which serial LPs were performed before and during treatment. CSF-tDNA variant allele fractions (VAFs) were significantly higher than plasma circulating tumor DNA (ctDNA) VAFs (median CSF-tDNA, 32.7%; median plasma ctDNA, 1.8%; P < 0.0001). Concentrations of tumor DNA in CSF and plasma were positively correlated (Spearman's ρ, 0.45; P = 0.03). For LMD diagnosis, cytology was 81.8% sensitive and CSF-tDNA was 91.7% sensitive. CSF-tDNA was also strongly prognostic for overall survival (HR = 7.1; P = 0.02). Among patients with progression on targeted therapy, resistance mutations, such as EGFR T790M and MET amplification, were common in peripheral blood but were rare in time-matched CSF, indicating differences in resistance mechanisms based on the anatomic compartment. In the osimertinib cohort, patients with CNS progression had increased CSF-tDNA VAFs at follow-up LP. Post-osimertinib CSF-tDNA VAF was strongly prognostic for CNS progression (HR = 6.2, P = 0.009). Detection of CSF-tDNA in lung cancer patients with suspected LMD is feasible and may have clinical utility. CSF-tDNA improves the sensitivity of LMD diagnosis, enables improved prognostication, and drives therapeutic strategies that account for spatial heterogeneity in resistance mechanisms.
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Affiliation(s)
- Tej D Azad
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Shigeki Nanjo
- Department of Medicine, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Respiratory Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | - Michael C Jin
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - David M Kurtz
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Comprehensive Cancer Center, Rochester, MN, USA
| | - Ian D Connolly
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Angela Bik-Yu Hui
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David Merriott
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Ryan Ko
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Christopher Yoo
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Justin Carter
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Emily Chen
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Rene Bonilla
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Akito Hata
- Department of Medical Oncology, Kobe Minimally Invasive Cancer Center, Kobe, Japan
| | - Nobuyuki Katakami
- Department of Medical Oncology, Takarazuka City Hospital, Hyogo, Japan
| | - Kei Irie
- Department of Pharmaceutics, Faculty of Pharmaceutical Science, Kobe Gakuin University, Kobe, Japan
| | - Seiji Yano
- Department of Respiratory Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | - Ross Okimoto
- Department of Medicine, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Aaron M Newman
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Michael Iv
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Seema Nagpal
- Department of Neurology, Stanford University, Stanford, CA, USA
| | | | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
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4
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Yubin LI, Xiaoyan LI. [Advances in Clinical Application of Cerebrospinal Fluid Circulating Tumor DNA
in Leptomeningeal Metastasis of Non-small Cell Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2024; 27:376-382. [PMID: 38880925 PMCID: PMC11183312 DOI: 10.3779/j.issn.1009-3419.2024.102.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Indexed: 06/18/2024]
Abstract
Leptomeningeal metastasis (LM) is a lethal complication of malignant tumors, with an incidence rate of 3%-5% among patients with non-small cell lung cancer (NSCLC). LM poses significant challenges in diagnosis, has poor prognosis, limited treatment options, and lacks standardized criteria for evaluating therapeutic efficacy, making it a difficult aspect of NSCLC management. Circulating tumor DNA (ctDNA), shed from tumor cells and carrying cancer-related information, holds significant value in precision oncology. Cerebrospinal fluid (CSF), present in the subarachnoid space of the brain, the spinal cord, and the central canal, and in direct contact with meningeal tissues, serves as the fluid medium that best reflects the genetic characteristics of LM. In recent years, CSF ctDNA has become a focal point due to its multi-omics features, playing a crucial role in the management of central nervous system (CNS) metastatic tumors. Its applications span the entire continuum of care, including aiding in diagnosis, assessing treatment response, predicting prognosis, and analyzing resistance mechanisms. This article provides a concise overview of CSF ctDNA detection techniques and their clinical applications in patients with NSCLC-LM.
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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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6
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Jafari F, Nodeh MM, Hosseinjani H, Baharara H, Azad S, Arasteh O, Johnston TP, Sahebkar A. A Review on the Efficacy and Safety of Intrathecal Administration of Novel Medications for Leptomeningeal Metastases in Solid Cancers. Curr Med Chem 2024; 31:2732-2750. [PMID: 37157199 DOI: 10.2174/0929867330666230508142657] [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: 10/30/2022] [Revised: 02/27/2023] [Accepted: 03/31/2023] [Indexed: 05/10/2023]
Abstract
Leptomeningeal disease (LMD) is a rare and lethal manifestation that may occur in the advanced stages of solid tumors and hematological malignancies. With advances in diagnostic techniques, the detection and confirmation of the presence of LMD have increased. Although its optimal treatment remains a challenge, the use of the intrathecal route for the delivery of novel therapeutics is now considered a promising drug delivery strategy to complement radiation and systemic-based therapies. Although methotrexate, cytarabine, and thiotepa have a long history in the treatment of LMD, other medications have also been shown to be beneficial. In this article, we have reviewed the effects of novel medications administered via the intrathecal route for the treatment of solid tumors. We have searched PubMed, Scopus, and Google Scholar databases till the end of September 2021 using the following keywords: "leptomeningeal disease", "leptomeningeal carcinomatosis", "leptomeningeal metastases", "solid tumors", "solid cancers", and "intrathecal". Our literature findings have uncovered that most studies on LMD, which occurs secondary to solid cancers, are available as 'case reports', and few clinical trials have been conducted to date. Single-drug (monotherapy) or combination drug therapy, administered via the intrathecal route, especially in metastatic breast and lung cancer, has been shown to improve patients' symptoms and overall lifespan, while exhibiting a low and acceptable prevalence of side effects. However, judgments/conclusions about the effectiveness and safety of these drugs still require further clinical evaluation.
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Affiliation(s)
- Fatemeh Jafari
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Moeini Nodeh
- Division of Hematology and Oncology, Department of Internal Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hesamoddin Hosseinjani
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamed Baharara
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sajad Azad
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Omid Arasteh
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Thomas P Johnston
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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7
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Spiliopoulou P, Holanda Lopes CD, Spreafico A. Promising and Minimally Invasive Biomarkers: Targeting Melanoma. Cells 2023; 13:19. [PMID: 38201222 PMCID: PMC10777980 DOI: 10.3390/cells13010019] [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: 11/06/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
The therapeutic landscape of malignant melanoma has been radically reformed in recent years, with novel treatments emerging in both the field of cancer immunotherapy and signalling pathway inhibition. Large-scale tumour genomic characterization has accurately classified malignant melanoma into four different genomic subtypes so far. Despite this, only somatic mutations in BRAF oncogene, as assessed in tumour biopsies, has so far become a validated predictive biomarker of treatment with small molecule inhibitors. The biology of tumour evolution and heterogeneity has uncovered the current limitations associated with decoding genomic drivers based only on a single-site tumour biopsy. There is an urgent need to develop minimally invasive biomarkers that accurately reflect the real-time evolution of melanoma and that allow for streamlined collection, analysis, and interpretation. These will enable us to face challenges with tumour tissue attainment and process and will fulfil the vision of utilizing "liquid biopsy" to guide clinical decisions, in a manner akin to how it is used in the management of haematological malignancies. In this review, we will summarize the most recent published evidence on the role of minimally invasive biomarkers in melanoma, commenting on their future potential to lead to practice-changing discoveries.
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Affiliation(s)
- Pavlina Spiliopoulou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | | | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
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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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9
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Roy-O'Reilly MA, Lanman T, Ruiz A, Rogawski D, Stocksdale B, Nagpal S. Diagnostic and Therapeutic Updates in Leptomeningeal Disease. Curr Oncol Rep 2023; 25:937-950. [PMID: 37256537 PMCID: PMC10326117 DOI: 10.1007/s11912-023-01432-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2023] [Indexed: 06/01/2023]
Abstract
PURPOSE OF REVIEW Leptomeningeal disease (LMD) is a devastating complication of advanced metastatic cancer associated with a poor prognosis and limited treatment options. This study reviews the current understanding of the clinical presentation, pathogenesis, diagnosis, and treatment of LMD. We highlight opportunities for advances in this disease. RECENT FINDINGS In recent years, the use of soluble CSF biomarkers has expanded, suggesting improved sensitivity over traditional cytology, identification of targetable mutations, and potential utility for monitoring disease burden. Recent studies of targeted small molecules and intrathecal based therapies have demonstrated an increase in overall and progression-free survival. In addition, there are several ongoing trials evaluating immunotherapy in LMD. Though overall prognosis of LMD remains poor, studies suggest a potential role for soluble CSF biomarkers in diagnosis and management and demonstrate promising findings in patient outcomes with targeted therapies for specific solid tumors. Despite these advances, there continues to be a gap of knowledge in this disease, emphasizing the importance of inclusion of LMD patients in clinical trials.
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Affiliation(s)
| | - Tyler Lanman
- Department of Neurology, Stanford Medicine, Palo Alto, CA, 94305, USA
| | - Amber Ruiz
- Department of Neurology, Stanford Medicine, Palo Alto, CA, 94305, USA
| | - David Rogawski
- Department of Neurology, Stanford Medicine, Palo Alto, CA, 94305, USA
| | - Brian Stocksdale
- Department of Neurology, Stanford Medicine, Palo Alto, CA, 94305, USA
| | - Seema Nagpal
- Department of Neurology, Stanford Medicine, Palo Alto, CA, 94305, USA.
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10
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Jenkins S, Zhang W, Steinberg SM, Nousome D, Houston N, Wu X, Armstrong TS, Burton E, Smart DD, Shah R, Peer CJ, Mozarsky B, Arisa O, Figg WD, Mendoza TR, Vera E, Brastianos P, Carter S, Gilbert MR, Anders CK, Connolly RM, Tweed C, Smith KL, Khan I, Lipkowitz S, Steeg PS, Zimmer AS. Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases. Clin Cancer Res 2023; 29:1450-1459. [PMID: 36705597 PMCID: PMC10153633 DOI: 10.1158/1078-0432.ccr-22-0855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/22/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023]
Abstract
PURPOSE Preclinical data showed that prophylactic, low-dose temozolomide (TMZ) significantly prevented breast cancer brain metastasis. We present results of a phase I trial combining T-DM1 with TMZ for the prevention of additional brain metastases after previous occurrence and local treatment in patients with HER2+ breast cancer. PATIENTS AND METHODS Eligible patients had HER2+ breast cancer with brain metastases and were within 12 weeks of whole brain radiation therapy (WBRT), stereotactic radiosurgery, and/or surgery. Standard doses of T-DM1 were administered intravenously every 21 days (3.6 mg/kg) and TMZ was given orally daily in a 3+3 phase I dose escalation design at 30, 40, or 50 mg/m2, continuously. DLT period was one 21-day cycle. Primary endpoint was safety and recommended phase II dose. Symptom questionnaires, brain MRI, and systemic CT scans were performed every 6 weeks. Cell-free DNA sequencing was performed on patients' plasma and CSF. RESULTS Twelve women enrolled, nine (75%) with prior SRS therapy and three (25%) with prior WBRT. Grade 3 or 4 AEs included thrombocytopenia (1/12), neutropenia (1/12), lymphopenia (6/12), and decreased CD4 (6/12), requiring pentamidine for Pneumocystis jirovecii pneumonia prophylaxis. No DLT was observed. Four patients on the highest TMZ dose underwent dose reductions. At trial entry, 6 of 12 patients had tumor mutations in CSF, indicating ongoing metastatic colonization despite a clear MRI. Median follow-up on study was 9.6 m (2.8-33.9); only 2 patients developed new parenchymal brain metastases. Tumor mutations varied with patient outcome. CONCLUSIONS Metronomic TMZ in combination with standard dose T-DM1 shows low-grade toxicity and potential activity in secondary prevention of HER2+ brain metastases.
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Affiliation(s)
- Sarah Jenkins
- Women’s Malignancies Branch; Center for Cancer Research, NCI, NIH
| | - Wei Zhang
- Women’s Malignancies Branch; Center for Cancer Research, NCI, NIH
| | - Seth M. Steinberg
- Biostatistics and Data Management Section; Center for Cancer Research, NCI, NIH
| | - Darryl Nousome
- Center for Cancer Research Collaborative Bioinformatics Resource, NCI, NIH
| | - Nicole Houston
- Women’s Malignancies Branch; Center for Cancer Research, NCI, NIH
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Dee Dee Smart
- Radiation Oncology Branch, Center for Cancer Research, NCI NIH
| | - Ritu Shah
- Neuro-Radiology, Clinical Center Cancer Research, NIH
| | - Cody J. Peer
- Clinical Pharmacology Program, Center for Cancer Research, NCI NIH
| | - Brett Mozarsky
- Clinical Pharmacology Program, Center for Cancer Research, NCI NIH
| | - Oluwatobi Arisa
- Clinical Pharmacology Program, Center for Cancer Research, NCI NIH
| | - William D. Figg
- Clinical Pharmacology Program, Center for Cancer Research, NCI NIH
| | | | | | - Priscilla Brastianos
- Massachusetts General Hospital, Harvard Cancer Center, Harvard University, Boston, MA
| | - Scott Carter
- Division of Medical Sciences, Harvard University, Boston, MA
| | | | | | | | - Carol Tweed
- University of Maryland Oncology, Baltimore MD
| | - Karen L. Smith
- Johns Hopkins University School of Medicine, Baltimore, MD
| | - Imran Khan
- Women’s Malignancies Branch; Center for Cancer Research, NCI, NIH
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11
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Pingle SC, Lin F, Anekoji MS, Patro CK, Datta S, Jones LD, Kesari S, Ashili S. Exploring the role of cerebrospinal fluid as analyte in neurologic disorders. Future Sci OA 2023; 9:FSO851. [PMID: 37090492 PMCID: PMC10116372 DOI: 10.2144/fsoa-2023-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
The cerebrospinal fluid (CSF) is a clear ultrafiltrate of blood that envelopes and protects the central nervous system while regulating neuronal function through the maintenance of interstitial fluid homeostasis in the brain. Due to its anatomic location and physiological functions, the CSF can provide a reliable source of biomarkers for the diagnosis and treatment monitoring of different neurological diseases, including neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and primary and secondary brain malignancies. The incorporation of CSF biomarkers into the drug discovery and development can improve the efficiency of drug development and increase the chances of success. This review aims to consolidate the current use of CSF biomarkers in clinical practice and explore future perspectives for the field.
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Affiliation(s)
- Sandeep C Pingle
- CureScience Institute, 5820 Oberlin Drive #202, San Diego, CA 92121, USA
| | - Feng Lin
- CureScience Institute, 5820 Oberlin Drive #202, San Diego, CA 92121, USA
- Author for correspondence:
| | - Misa S Anekoji
- CureScience Institute, 5820 Oberlin Drive #202, San Diego, CA 92121, USA
| | - C Pawan K Patro
- CureScience Institute, 5820 Oberlin Drive #202, San Diego, CA 92121, USA
| | - Souvik Datta
- Rhenix Lifesciences, 237 Vengal Rao Nagar, Hyderabad, TG, 500038, India
| | - Lawrence D Jones
- CureScience Institute, 5820 Oberlin Drive #202, San Diego, CA 92121, USA
| | - Santosh Kesari
- Department of Translational Neurosciences, Saint John's Cancer Institute at Providence Saint John's Health Center & Pacific Neuroscience Institute, Santa Monica, CA 90404, USA
| | - Shashaanka Ashili
- CureScience Institute, 5820 Oberlin Drive #202, San Diego, CA 92121, USA
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12
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Benito-Martín A, Jasiulionis MG, García-Silva S. Extracellular vesicles and melanoma: New perspectives on tumor microenvironment and metastasis. Front Cell Dev Biol 2023; 10:1061982. [PMID: 36704194 PMCID: PMC9871288 DOI: 10.3389/fcell.2022.1061982] [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: 10/05/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Secreted extracellular vesicles (EVs) are lipid bilayer particles without functional nucleus naturally released from cells which constitute an intercellular communication system. There is a broad spectrum of vesicles shed by cells based on their physical properties such as size (small EVs and large EVs), biogenesis, cargo and functions, which provide an increasingly heterogenous landscape. In addition, they are involved in multiple physiological and pathological processes. In cancer, EV release is opted by tumor cells as a beneficial process for tumor progression. Cutaneous melanoma is a cancer that originates from the melanocyte lineage and shows a favorable prognosis at early stages. However, when melanoma cells acquire invasive capacity, it constitutes the most aggressive and deadly skin cancer. In this context, extracellular vesicles have been shown their relevance in facilitating melanoma progression through the modulation of the microenvironment and metastatic spreading. In agreement with the melanosome secretory capacity of melanocytes, melanoma cells display an enhanced EV shedding activity that has contributed to the utility of melanoma models for unravelling EV cargo and functions within a cancer scenario. In this review, we provide an in-depth overview of the characteristics of melanoma-derived EVs and their role in melanoma progression highlighting key advances and remaining open questions in the field.
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Affiliation(s)
- Alberto Benito-Martín
- Facultad de Medicina, Unidad de Investigación Biomédica, Universidad Alfonso X El Sabio (UAX), Villanueva de la Cañada, Spain,*Correspondence: Alberto Benito-Martín, ; Miriam Galvonas Jasiulionis, ; Susana García-Silva,
| | - Miriam Galvonas Jasiulionis
- Departamento de Farmacologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil,*Correspondence: Alberto Benito-Martín, ; Miriam Galvonas Jasiulionis, ; Susana García-Silva,
| | - Susana García-Silva
- Microenvironment and Metastasis Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain,*Correspondence: Alberto Benito-Martín, ; Miriam Galvonas Jasiulionis, ; Susana García-Silva,
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13
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Ma J, Teng Y, Youming H, Tao X, Fan Y. The Value of Cell-Free Circulating DNA Profiling in Patients with Skin Diseases. Methods Mol Biol 2023; 2695:247-262. [PMID: 37450124 DOI: 10.1007/978-1-0716-3346-5_17] [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] [Indexed: 07/18/2023]
Abstract
Liquid biopsy, also known as fluid biopsy or fluid-phase biopsy, is the sampling and analysis of the blood, cerebrospinal fluid, saliva, pleural fluid, ascites, and urine. Compared with tissue biopsy, liquid biopsy technology has the advantages of being noninvasive, having strong repeatability, enabling early diagnosis, dynamic monitoring, and overcoming tumor heterogeneity. However, interest in cfDNA and skin diseases has not expanded until recently. In this review, we present an overview of the literature related to the basic biology of cfDNA in the field of dermatology as a biomarker for early diagnosis, monitoring disease activity, predicting progression, and treatment response.
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Affiliation(s)
- Jingwen Ma
- Medical Cosmetic Center, Shanghai Skin Disease Hospital, Tongji University, Shanghai, People's Republic of China
| | - Yan Teng
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Huang Youming
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Xiaohua Tao
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Yibin Fan
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China.
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14
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Congur I, Koni E, Onat OE, Tokcaer Keskin Z. Meta-analysis of commonly mutated genes in leptomeningeal carcinomatosis. PeerJ 2023; 11:e15250. [PMID: 37096065 PMCID: PMC10122459 DOI: 10.7717/peerj.15250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/28/2023] [Indexed: 04/26/2023] Open
Abstract
Background Leptomeningeal carcinomatosis (LMC) is a rare type of cancer that settles at the meninges through metastasis of non-small cell lung cancer (NSCLC), breast cancer and melanoma. The molecular mechanism underlying LMC is not known, therefore molecular studies investigating the development of LMC are needed. Here, we aimed to identify commonly mutated genes in LMC caused by NSCLC, breast cancer, and melanoma using an in-slico approach and their interactions using integrated bioinformatic approaches/tools in this meta-analysis. Methods We conducted a meta-analysis using information from 16 studies that included different sequencing techniques of patients with LMC caused by three different primary cancers: breast cancer, NSCLC, and melanoma. All studies that assessed mutation information from patients with LMC were searched in PubMed, from their inception to February, 16 2022. Studies that performed NGS on LMC patients with NSCLC, breast cancer, or melanoma were included, while studies that did not apply NGS to CSF samples, did not provide information on altered genes, were reviews, editorials, or conference abstracts, or whose main goal was the detection of malignancies were all excluded. We identified commonly mutated genes in all three types of cancer. Next, we constructed a protein-protein interaction network, then performed pathway enrichment analysis. We searched National Institutes of Health (NIH) and Drug-Gene Interaction Database (DGIdb) to find candidate drugs. Results We found that TP53, PTEN, PIK3CA, IL7R, and KMT2D genes were commonly mutated genes in all three types of cancer via our meta-analysis that consisted out of 16 studies. Our pathway enrichment analysis showed that all five genes were primarily associated with regulation of cell communication and signaling, and cell proliferation. Other enriched pathways included regulation of apoptotic processes of leukocytes and fibroblasts, macroautophagy and growth. According to our drug search we found candidate drugs; Everolimus, Bevacizumab and Temozolomide, which interact with these five genes. Conclusion In conclusion, a total of 96 mutated genes in LMC were investigated via meta-analysis. Our findings suggested vital roles of TP53, PTEN, PIK3CA, KMT2D, and IL7R, which can provide insight into the molecular basis of LMC development and paving the door to the development of new targeted medicine and will encourage molecular biologists to seek biological evidence.
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Affiliation(s)
- Irem Congur
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Ekin Koni
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Onur Emre Onat
- Department of Genome Studies, Institute of Health Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
- Department of Molecular Biology, Institute of Life Sciences and Biotechnology, Bezmialem Foundation University, Istanbul, Turkey
| | - Zeynep Tokcaer Keskin
- Department of Molecular and Translational Biomedicine, Institute of Natural and Applied Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Engineering and Natural Sciences, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
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15
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Khaddour K, Zhou A, Butt OH, Budde G, Malashevich AK, Ansstas G. Case report: Real-world experience using a personalized cancer-specific circulating tumor DNA assay in different metastatic melanoma scenarios. Front Oncol 2022; 12:978996. [PMID: 36465349 PMCID: PMC9713015 DOI: 10.3389/fonc.2022.978996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Circulating-tumor DNA (ctDNA) has emerged as an important biomarker for monitoring disease status in cancer patients. Different ctDNA testing platforms have shown promising results in the early detection of disease, monitoring response to treatment, and prognostication in metastatic melanoma. However, several challenges exist, including the reduced shedding of ctDNA into the bloodstream in the metastatic setting, differences in sensitivity among various ctDNA assays, and the inherent inability to distinguish tumor-specific mutations from other mutations that are not related to the cancer of interest. Using a ctDNA assay that is designed to detect multiple single-nucleotide variants (SNVs) that are specific to the tumor itself may allow for more accurate monitoring of disease status in metastatic melanoma. In this case series, we describe a real-world experience using a personalized, tumor-informed ctDNA assay to monitor the clinical trajectories of four patients with metastatic melanoma. Our report highlights potential benefits and limitations using ctDNA in this setting to inform clinical decision-making. This report provides a proof of concept of the technique using an mPCR-NGS-based ctDNA assay (Signatera TM) in the clinical context and in adjunct with other radiological information. Large cohort prospective trials would be needed to validate the utility and validity of this approach.
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Affiliation(s)
- Karam Khaddour
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, United States
- Department of Medicine, Division of Hematology and Oncology, University of Illinois at Chicago, Chicago, IL, United States
| | - Alice Zhou
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, United States
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO, United States
| | | | | | - George Ansstas
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO, United States
- *Correspondence: George Ansstas,
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16
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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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17
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Tivey A, Church M, Rothwell D, Dive C, Cook N. Circulating tumour DNA - looking beyond the blood. Nat Rev Clin Oncol 2022; 19:600-612. [PMID: 35915225 PMCID: PMC9341152 DOI: 10.1038/s41571-022-00660-y] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 02/06/2023]
Abstract
Over the past decade, various liquid biopsy techniques have emerged as viable alternatives to the analysis of traditional tissue biopsy samples. Such surrogate 'biopsies' offer numerous advantages, including the relative ease of obtaining serial samples and overcoming the issues of interpreting one or more small tissue samples that might not reflect the entire tumour burden. To date, the majority of research in the area of liquid biopsies has focused on blood-based biomarkers, predominantly using plasma-derived circulating tumour DNA (ctDNA). However, ctDNA can also be obtained from various non-blood sources and these might offer unique advantages over plasma ctDNA. In this Review, we discuss advances in the analysis of ctDNA from non-blood sources, focusing on urine, cerebrospinal fluid, and pleural or peritoneal fluid, but also consider other sources of ctDNA. We discuss how these alternative sources can have a distinct yet complementary role to that of blood ctDNA analysis and consider various technical aspects of non-blood ctDNA assay development. We also reflect on the settings in which non-blood ctDNA can offer distinct advantages over plasma ctDNA and explore some of the challenges associated with translating these alternative assays from academia into clinical use.
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Affiliation(s)
- Ann Tivey
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Matt Church
- The Christie NHS Foundation Trust, Manchester, UK
| | - Dominic Rothwell
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, The University of Manchester, Manchester, UK
| | - Caroline Dive
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, The University of Manchester, Manchester, UK
| | - Natalie Cook
- Division of Cancer Sciences, The University of Manchester, Manchester, UK.
- The Christie NHS Foundation Trust, Manchester, UK.
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18
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Pott C, Kotrova M, Darzentas N, Brüggemann M, Khouja M. cfDNA-Based NGS IG Analysis in Lymphoma. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:101-117. [PMID: 35622323 DOI: 10.1007/978-1-0716-2115-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Liquid biopsy is a novel diagnostic approach at first developed to characterize the molecular profile of solid tumors by analyzing body fluids. For cancer patients, it represents a noninvasive way to monitor the status of the solid tumor with respect to representative biomarkers. There is growing interest in the utilization of circulating tumor DNA (ctDNA) analysis also in the diagnostic and prognostic fields of lymphomas. Clonal immunoglobulin (IG) gene rearrangements are fingerprints of the respective lymphoid malignancy and thus are highly suited as specific molecular targets for minimal residual disease (MRD) detection. Tracing of the clonal IG rearrangement patterns in ctDNA pool during treatment can be used for MRD assessment in B-cell lymphomas. Here, we describe a reproducible next-generation sequencing assay to identify and characterize clonal IG gene rearrangements for MRD detection in cell-free DNA.
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Affiliation(s)
- Christiane Pott
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany.
| | - Michaela Kotrova
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nikos Darzentas
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Monika Brüggemann
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Mouhamad Khouja
- Medical Department II, University Hospital Schleswig-Holstein, Kiel, Germany
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19
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Tivey A, Britton F, Scott JA, Rothwell D, Lorigan P, Lee R. Circulating Tumour DNA in Melanoma-Clinic Ready? Curr Oncol Rep 2022; 24:363-373. [PMID: 35133615 PMCID: PMC8885536 DOI: 10.1007/s11912-021-01151-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW Liquid biopsies, including circulating tumour DNA (ctDNA), can inform a variety of clinical questions. This review examines the potential role of ctDNA as a clinical tool to inform clinical decision-making from early to late stage cutaneous melanoma. RECENT FINDINGS In pre-clinical studies, ctDNA has been shown to detect minimal residual disease and molecular relapse; predict and monitor response to therapy; and identify key resistance mechanisms. Here, we examine the potential utility of ctDNA and discuss its limitations for use in patients with melanoma. We present novel clinical trials, which are testing its value as a tool to augment clinical decision-making. Finally, we discuss the steps that are needed to ensure that ctDNA is used optimally in order to improve outcomes for patients with melanoma. Preclinical studies have shown that ctDNA has huge potential to provide real-time information about disease status in patients with melanoma. It is now time to test it rigorously within clinical trials to assess how it can be optimally used to benefit patients in the clinic.
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Affiliation(s)
- Ann Tivey
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
- Division of Cancer Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Fiona Britton
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Julie-Ann Scott
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Dominic Rothwell
- Division of Cancer Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
- Nucleic Acids Biomarker Team, Cancer Research UK Manchester Institute, Cancer Biomarker Centre, The University of Manchester, Alderley Park, SK10 4TG, UK
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
- Division of Cancer Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Rebecca Lee
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK.
- Division of Cancer Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK.
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20
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Carvalho DM, Richardson PJ, Olaciregui N, Stankunaite R, Lavarino C, Molinari V, Corley EA, Smith DP, Ruddle R, Donovan A, Pal A, Raynaud FI, Temelso S, Mackay A, Overington JP, Phelan A, Sheppard D, Mackinnon A, Zebian B, Al-Sarraj S, Merve A, Pryce J, Grill J, Hubank M, Cruz O, Morales La Madrid A, Mueller S, Carcaboso AM, Carceller F, Jones C. Repurposing Vandetanib plus Everolimus for the Treatment of ACVR1-Mutant Diffuse Intrinsic Pontine Glioma. Cancer Discov 2022; 12:416-431. [PMID: 34551970 PMCID: PMC7612365 DOI: 10.1158/2159-8290.cd-20-1201] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/17/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022]
Abstract
Somatic mutations in ACVR1 are found in a quarter of children with diffuse intrinsic pontine glioma (DIPG), but there are no ACVR1 inhibitors licensed for the disease. Using an artificial intelligence-based platform to search for approved compounds for ACVR1-mutant DIPG, the combination of vandetanib and everolimus was identified as a possible therapeutic approach. Vandetanib, an inhibitor of VEGFR/RET/EGFR, was found to target ACVR1 (K d = 150 nmol/L) and reduce DIPG cell viability in vitro but has limited ability to cross the blood-brain barrier. In addition to mTOR, everolimus inhibited ABCG2 (BCRP) and ABCB1 (P-gp) transporters and was synergistic in DIPG cells when combined with vandetanib in vitro. This combination was well tolerated in vivo and significantly extended survival and reduced tumor burden in an orthotopic ACVR1-mutant patient-derived DIPG xenograft model. Four patients with ACVR1-mutant DIPG were treated with vandetanib plus an mTOR inhibitor, informing the dosing and toxicity profile of this combination for future clinical studies. SIGNIFICANCE: Twenty-five percent of patients with the incurable brainstem tumor DIPG harbor somatic activating mutations in ACVR1, but there are no approved drugs targeting the receptor. Using artificial intelligence, we identify and validate, both experimentally and clinically, the novel combination of vandetanib and everolimus in these children based on both signaling and pharmacokinetic synergies.This article is highlighted in the In This Issue feature, p. 275.
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Affiliation(s)
- Diana M Carvalho
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | | | - Nagore Olaciregui
- Laboratory of Molecular Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Reda Stankunaite
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Cinzia Lavarino
- Laboratory of Molecular Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Valeria Molinari
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Elizabeth A Corley
- Children & Young People's Unit, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | | | - Ruth Ruddle
- Division of Cancer Therapeutics, Institute of Cancer Research, London, United Kingdom
| | - Adam Donovan
- Division of Cancer Therapeutics, Institute of Cancer Research, London, United Kingdom
| | - Akos Pal
- Division of Cancer Therapeutics, Institute of Cancer Research, London, United Kingdom
| | - Florence I Raynaud
- Division of Cancer Therapeutics, Institute of Cancer Research, London, United Kingdom
| | - Sara Temelso
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Alan Mackay
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | | | | | | | - Andrew Mackinnon
- Children & Young People's Unit, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
- Atkinson Morley Regional Neuroscience Centre, St George's Hospital NHS Trust, London, United Kingdom
| | - Bassel Zebian
- Department of Neurosurgery, Kings College Hospital NHS Trust, London, United Kingdom
| | - Safa Al-Sarraj
- Department of Clinical Neuropathology, Kings College Hospital NHS Trust, London, United Kingdom
| | - Ashirwad Merve
- Institute of Neurology, University College London Hospitals, London, United Kingdom
| | - Jeremy Pryce
- South West London Pathology, St George's Hospital NHS Trust, London, United Kingdom
| | - Jacques Grill
- Department of Pediatric and Adolescent Oncology and INSERM Unit U891, Team "Genomics and Oncogenesis of Pediatric Brain Tumors," Gustave Roussy and University Paris-Saclay, Villejuif, France
| | - Michael Hubank
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Ofelia Cruz
- Paediatric Oncology, Neuro-Oncology Unit, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Sabine Mueller
- University Children's Hospital, Zurich, Switzerland
- University of California, San Francisco, San Francisco, California
| | - Angel M Carcaboso
- Laboratory of Molecular Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Fernando Carceller
- Children & Young People's Unit, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom.
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom.
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21
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Li Y, Polyak D, Lamsam L, Connolly ID, Johnson E, Khoeur LK, Andersen S, Granucci M, Stanley G, Liu B, Nagpal S, Hayden Gephart M. Comprehensive RNA analysis of CSF reveals a role for CEACAM6 in lung cancer leptomeningeal metastases. NPJ Precis Oncol 2021; 5:90. [PMID: 34625644 PMCID: PMC8501028 DOI: 10.1038/s41698-021-00228-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 08/26/2021] [Indexed: 12/02/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) metastatic to the brain leptomeninges is rapidly fatal, cannot be biopsied, and cancer cells in the cerebrospinal fluid (CSF) are few; therefore, available tissue samples to develop effective treatments are severely limited. This study aimed to converge single-cell RNA-seq and cell-free RNA (cfRNA) analyses to both diagnose NSCLC leptomeningeal metastases (LM), and to use gene expression profiles to understand progression mechanisms of NSCLC in the brain leptomeninges. NSCLC patients with suspected LM underwent withdrawal of CSF via lumbar puncture. Four cytology-positive CSF samples underwent single-cell capture (n = 197 cells) by microfluidic chip. Using robust principal component analyses, NSCLC LM cell gene expression was compared to immune cells. Massively parallel qPCR (9216 simultaneous reactions) on human CSF cfRNA samples compared the relative gene expression of patients with NSCLC LM (n = 14) to non-tumor controls (n = 7). The NSCLC-associated gene, CEACAM6, underwent in vitro validation in NSCLC cell lines for involvement in pathologic behaviors characteristic of LM. NSCLC LM gene expression revealed by single-cell RNA-seq was also reflected in CSF cfRNA of cytology-positive patients. Tumor-associated cfRNA (e.g., CEACAM6, MUC1) was present in NSCLC LM patients' CSF, but not in controls (CEACAM6 detection sensitivity 88.24% and specificity 100%). Cell migration in NSCLC cell lines was directly proportional to CEACAM6 expression, suggesting a role in disease progression. NSCLC-associated cfRNA is detectable in the CSF of patients with LM, and corresponds to the gene expression profile of NSCLC LM cells. CEACAM6 contributes significantly to NSCLC migration, a hallmark of LM pathophysiology.
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Affiliation(s)
- Yingmei Li
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Dina Polyak
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Layton Lamsam
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Ian David Connolly
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Eli Johnson
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Lina Khav Khoeur
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephanie Andersen
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Monica Granucci
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Geoff Stanley
- Department of Biophysics, Stanford University School of Medicine, Stanford, CA, USA
| | - Boxiang Liu
- Department of Biology, Stanford University School of Humanities & Sciences, Stanford, CA, USA
| | - Seema Nagpal
- Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
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22
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White MD, Klein RH, Shaw B, Kim A, Subramanian M, Mora JL, Giobbie-Hurder A, Nagabhushan D, Jain A, Singh M, Kuter BM, Nayyar N, Bertalan MS, Stocking JH, Markson SC, Lastrapes M, Alvarez-Breckenridge C, Cahill DP, Gydush G, Rhoades J, Rotem D, Adalsteinsson VA, Mahar M, Kaplan A, Oh K, Sullivan RJ, Gerstner E, Carter SL, Brastianos PK. Detection of Leptomeningeal Disease Using Cell-Free DNA From Cerebrospinal Fluid. JAMA Netw Open 2021; 4:e2120040. [PMID: 34369989 PMCID: PMC8353541 DOI: 10.1001/jamanetworkopen.2021.20040] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/05/2021] [Indexed: 12/27/2022] Open
Abstract
Importance Leptomeningeal disease (LMD) is a devastating complication of cancer that is frequently underdiagnosed owing to the low sensitivity of cerebrospinal fluid (CSF) cytologic assessment, the current benchmark diagnostic method. Improving diagnostic sensitivity may lead to improved treatment decisions. Objective To assess whether cell-free DNA (cfDNA) analysis of CSF may be used to diagnose LMD more accurately than cytologic analysis. Design, Setting, and Participants This diagnostic study conducted in a neuro-oncology clinic at 2 large, tertiary medical centers assessed the use of genomic sequencing of CSF samples obtained from 30 patients with suspected or confirmed LMD from 2015 through 2018 to identify tumor-derived cfDNA. From the same CSF samples, cytologic analyses were conducted, and the results of the 2 tests were compared. This study consisted of 2 patient populations: 22 patients with cytologically confirmed LMD without parenchymal tumors abutting their CSF and 8 patients with parenchymal brain metastases with no evidence of LMD. Patients were considered positive for the presence of LMD if previous CSF cytologic analysis was positive for malignant cells. The analysis was conducted from 2015 to 2018. Main Outcomes and Measures The primary outcome was the diagnostic accuracy of cfDNA analysis, defined as the number of tests that resulted in correct diagnoses out of the total number of tests assayed. Hypotheses were formed before data collection. Results In total, 30 patients (23 women [77%]; median age, 51 years [range, 28-81 years]), primarily presenting with metastatic solid malignant neoplasms, participated in this study. For 48 follow-up samples from patients previously diagnosed via cytologic analysis as having LMD with no parenchymal tumor abutting CSF, cfDNA findings were accurate in the assessment of LMD in 45 samples (94%; 95% CI, 83%-99%), whereas cytologic analysis was accurate in 36 samples (75%; 95% CI, 60%-86%), a significant difference (P = .02). Of 43 LMD-positive samples, CSF cfDNA analysis was sensitive to LMD in 40 samples (93%; 95% CI, 81%-99%), and cytologic analysis was sensitive to LMD in 31 samples (72%; 95% CI, 56%-85%), a significant difference (P = .02). For 3 patients with parenchymal brain metastases abutting the CSF and no suspicion of LMD, cytologic findings were negative for LMD in all 3 patients, whereas cfDNA findings were positive in all 3 patients. Conclusions and Relevance This diagnostic study found improved sensitivity and accuracy of cfDNA CSF testing vs cytologic assessment for diagnosing LMD with the exception of parenchymal tumors abutting CSF, suggesting improved ability to diagnosis LMD. Consideration of incorporating CSF cfDNA analysis into clinical care is warranted.
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Affiliation(s)
- Michael D. White
- Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
- Cancer Center, Massachusetts General Hospital, Boston
- Division of Comprehensive Neurology, Massachusetts General Hospital, Harvard Medical School, Boston
- Division of Neuro-Oncology, University of Rochester School of Medicine, Rochester, New York
| | - Robert H. Klein
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Brian Shaw
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Albert Kim
- Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
- Cancer Center, Massachusetts General Hospital, Boston
| | - Megha Subramanian
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- Alnylam Pharmaceuticals, Cambridge, Massachusetts
| | - Joana L. Mora
- Cancer Center, Massachusetts General Hospital, Boston
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Anita Giobbie-Hurder
- Division of Biostatistics, Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Deepika Nagabhushan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Aarushi Jain
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Mohini Singh
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Benjamin M. Kuter
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- Boston University, Boston, Massachusetts
| | - Naema Nayyar
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Mia S. Bertalan
- Cancer Center, Massachusetts General Hospital, Boston
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- Geisel School of Medicine, Dartmouth College, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Jackson H. Stocking
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- University of Colorado School of Medicine, Aurora
| | - Samuel C. Markson
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew Lastrapes
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- University of Texas Health Science Center at Houston, Houston
| | - Christopher Alvarez-Breckenridge
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston
- The University of Texas MD Anderson Cancer Center, Houston
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Gregory Gydush
- Broad Institute of MIT and Harvard, Boston, Massachusetts
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Boston, Massachusetts
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Tessera Therapeutics, Cambridge, Massachusetts
| | | | - Maura Mahar
- Division of Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School, Boston
- Cancer Center, Massachusetts General Hospital, Boston
| | - Alexander Kaplan
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
- University of Massachusetts, Boston, Massachusetts
| | - Kevin Oh
- Cancer Center, Massachusetts General Hospital, Boston
| | - Ryan J. Sullivan
- Cancer Center, Massachusetts General Hospital, Boston
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
| | - Elizabeth Gerstner
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston
- Department of Radiology, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Scott L. Carter
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Division of Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Priscilla K. Brastianos
- Cancer Center, Massachusetts General Hospital, Boston
- Broad Institute of MIT and Harvard, Boston, Massachusetts
- Department of Medicine, Harvard Medical School & Massachusetts General Hospital, Boston, Massachusetts
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23
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Bhambhvani HP, Rodrigues AJ, Umeh-Garcia MC, Hayden Gephart M. Leptomeningeal Carcinomatosis: Molecular Landscape, Current Management, and Emerging Therapies. Neurosurg Clin N Am 2021; 31:613-625. [PMID: 32921356 DOI: 10.1016/j.nec.2020.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Leptomeningeal carcinomatosis is a devastating consequence of late-stage cancer, and despite multimodal treatment, remains rapidly fatal. Definitive diagnosis requires identification of malignant cells in the cerebrospinal fluid (CSF), or frank disease on MRI. Therapy is generally palliative and consists primarily of radiotherapy and/or chemotherapy, which is administered intrathecally or systemically. Immunotherapies and novel experimental therapies have emerged as promising options for decreasing patient morbidity and mortality. In this review, the authors discuss a refined view of the molecular pathophysiology of leptomeningeal carcinomatosis, current approaches to disease management, and emerging therapies.
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Affiliation(s)
- Hriday P Bhambhvani
- Department of Neurosurgery, Stanford University Medical Center, 300 Pasteur Drive, Palo Alto, CA, 94305 USA
| | - Adrian J Rodrigues
- Department of Neurosurgery, Stanford University Medical Center, 300 Pasteur Drive, Palo Alto, CA, 94305 USA
| | - Maxine C Umeh-Garcia
- Department of Neurosurgery, Stanford University Medical Center, 300 Pasteur Drive, Palo Alto, CA, 94305 USA
| | - Melanie Hayden Gephart
- Department of Neurosurgery, Stanford University Medical Center, 300 Pasteur Drive, Palo Alto, CA, 94305 USA; Department of Neurosurgery, Brain Tumor Center, Stanford University School of Medicine, 300 Pasteur Drive, Palo Alto, CA 94305, USA.
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24
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Natsumeda M, Kanemaru Y, Kawaguchi Y, Umezu H, Kakita A, Fujii Y. Less-invasive diagnosis of disseminated epithelioid glioblastoma harboring BRAF V600E mutation by cerebrospinal fluid analysis-A case report. Clin Case Rep 2021; 9:e04551. [PMID: 34295500 PMCID: PMC8283864 DOI: 10.1002/ccr3.4551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/31/2021] [Accepted: 06/13/2021] [Indexed: 11/11/2022] Open
Abstract
Spinal dissemination in epithelioid glioblastoma can be diagnosed by cerebrospinal fluid cytology and liquid biopsy to detect BRAF V600E mutation.
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Affiliation(s)
- Manabu Natsumeda
- Department of NeurosurgeryBrain Research InstituteNiigata UniversityNiigataJapan
| | - Yu Kanemaru
- Department of NeurosurgeryBrain Research InstituteNiigata UniversityNiigataJapan
| | - Yukie Kawaguchi
- Division of PathologyNiigata University Medical & Dental HospitalNiigataJapan
| | - Hajime Umezu
- Division of PathologyNiigata University Medical & Dental HospitalNiigataJapan
| | - Akiyoshi Kakita
- Department of PathologyBrain Research InstituteNiigata UniversityNiigataJapan
| | - Yukihiko Fujii
- Department of NeurosurgeryBrain Research InstituteNiigata UniversityNiigataJapan
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25
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Shoji Y, Furuhashi S, Kelly DF, Bilchik AJ, Hoon DSB, Bustos MA. Current status of gastrointestinal tract cancer brain metastasis and the use of blood-based cancer biomarker biopsy. Clin Exp Metastasis 2021; 39:61-69. [PMID: 33950411 DOI: 10.1007/s10585-021-10094-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/25/2021] [Indexed: 12/24/2022]
Abstract
Brain metastasis (BM) frequently occurs in patients with cutaneous melanoma, lung, and breast cancer; although, BM rarely arises from cancers of the gastrointestinal tract (GIT). The reported incidence of GIT cancer BM is less than 4%. In the last few years, effective systemic therapy has prolonged the survival of GIT patients and consequently, the incidence of developing BM is rising. Therefore, the epidemiology and biology of BM arising from GIT cancer requires a more comprehensive understanding. In spite of the development of new therapeutic agents for patients with metastatic GIT cancers, survival for patients with BM still remains poor, with a median survival after diagnosis of less than 4 months. Limited evidence suggests that early detection of isolated intra-cranial lesions will enable surgical resection plus systemic and/or radiation therapy, which may lead to an increase in overall survival. Novel diagnostic methods such as blood-based biomarker biopsies may play a crucial role in the early detection of BM. Circulating tumor cells and circulating cell-free nucleic acids are known to serve as blood biomarkers for early detection and treatment response monitoring of multiple cancers. Blood biopsy may improve early diagnosis and treatment monitoring of GIT cancers BM, thus prolonging patients' survivals.
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Affiliation(s)
- Yoshiaki Shoji
- Division of Molecular Oncology, Department of Translational Molecular Medicine, Saint John's Cancer Institute at Providence Saint John's Health Center, 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Satoru Furuhashi
- Division of Molecular Oncology, Department of Translational Molecular Medicine, Saint John's Cancer Institute at Providence Saint John's Health Center, 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Daniel F Kelly
- Pacific Neuroscience Institute, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Anton J Bilchik
- Department of Surgical Oncology, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Dave S B Hoon
- Division of Molecular Oncology, Department of Translational Molecular Medicine, Saint John's Cancer Institute at Providence Saint John's Health Center, 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Matias A Bustos
- Division of Molecular Oncology, Department of Translational Molecular Medicine, Saint John's Cancer Institute at Providence Saint John's Health Center, 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA.
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26
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Nduom EK, Gephart MH, Chheda MG, Suva ML, Amankulor N, Battiste JD, Campian JL, Dacey RG, Das S, Fecci PE, Hadjipanayis CG, Hoang KB, Jalali A, Orringer D, Patel AJ, Placantonakis D, Rodriguez A, Yang I, Yu JS, Zipfel GJ, Dunn GP, Leuthardt EC, Kim AH. Re-evaluating Biopsy for Recurrent Glioblastoma: A Position Statement by the Christopher Davidson Forum Investigators. Neurosurgery 2021; 89:129-132. [PMID: 33862619 DOI: 10.1093/neuros/nyab063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/05/2021] [Indexed: 11/15/2022] Open
Abstract
Patients with glioblastoma (GBM) need bold new approaches to their treatment, yet progress has been hindered by a relative inability to dynamically track treatment response, mechanisms of resistance, evolution of targetable mutations, and changes in mutational burden. We are writing on behalf of a multidisciplinary group of academic neuro-oncology professionals who met at the collaborative Christopher Davidson Forum at Washington University in St Louis in the fall of 2019. We propose a dramatic but necessary change to the routine management of patients with GBM to advance the field: to routinely biopsy recurrent GBM at the time of presumed recurrence. Data derived from these samples will identify true recurrence vs treatment effect, avoid treatments with little chance of success, enable clinical trial access, and aid in the scientific advancement of our understanding of GBM.
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Affiliation(s)
- Edjah K Nduom
- Department of Neurological Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Melanie Hayden Gephart
- Department of Neurological Surgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Milan G Chheda
- Departments of Medicine and Neurology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Mario L Suva
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nduka Amankulor
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - James D Battiste
- Department of Neurology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Jian L Campian
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Ralph G Dacey
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Sunit Das
- Division of Neurosurgery, University of Toronto, Toronto, Canada
| | - Peter E Fecci
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Kimberly B Hoang
- Department of Neurological Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Orringer
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, New York, USA
| | - Akash J Patel
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
| | | | - Analiz Rodriguez
- Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Isaac Yang
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jennifer S Yu
- Department of Radiation Oncology and Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Greg J Zipfel
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
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27
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Chorti E, Kebir S, Ahmed MS, Keyvani K, Umutlu L, Kanaki T, Zaremba A, Reinboldt-Jockenhoefer F, Knispel S, Gratsias E, Roesch A, Ugurel S, Scheffler B, Schadendorf D, Livingstone E, Meier F, Glas M, Zimmer L. Leptomeningeal disease from melanoma-Poor prognosis despite new therapeutic modalities. Eur J Cancer 2021; 148:395-404. [PMID: 33789203 DOI: 10.1016/j.ejca.2021.02.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE The development of leptomeningeal disease (LMD) among melanoma patients is associated with short survival. Unspecific clinical symptoms and imprecise diagnostic criteria often delay diagnosis. Because melanoma patients with LMD have been excluded from most clinical trials, the efficacy of immune checkpoint blockade (ICB) and targeted therapies (TTs) has not been adequately investigated among these patients. METHODS We performed a retrospective study in two tertiary-referral skin cancer centres to evaluate the clinical characteristics, diagnostics, treatments, and overall survival (OS) of melanoma patients with LMD between June 2011 and March 2019. RESULTS In total, 52 patients were included. The median age at LMD diagnosis was 58 years. Most patients (n = 30, 58%) were men. The median time from the first diagnosis of unresectable disease to the first diagnosis of LMD was 8.5 months (range 0-91.5 months). Most patients (65%, n = 34) were BRAF V600 mutated. Sixteen patients (31%) presented with LMD only, whereas 36 patients (69%) presented with concomitant brain metastases at LMD diagnosis. Eleven patients (21%) showed no evidence of extracranial disease. Forty-four patients (85%) had clinical symptoms at LMD diagnosis. Forty-two patients (81%) had received at least one prior therapy. Forty patients (77%) received at least one treatment after LMD diagnosis, including TT (n = 17), ICB (n = 13), bevacizumab (n = 1), radiotherapy (n = 3), and intrathecal chemotherapy (n = 1); five patients received both TT and ICB. Twelve patients (23%) received no treatment because of rapid progression of LMD. The median OS for the entire cohort was 2.9 months (95% confidence interval [CI] 1.7-4.1). Among patients receiving systemic therapy, OS was 3.7 months (95% CI 2.4-4.9). CONCLUSIONS Systemic treatment with TT or ICB seems to improve OS among patients with LMD. However, despite new therapy modalities, the prognosis of LMD remains poor.
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Affiliation(s)
- Eleftheria Chorti
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Sied Kebir
- Division of Clinical Neurooncology, Department of Neurology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Misbah S Ahmed
- Department of Dermatology, Carl Gustav Carus University Hospital, Dresden University of Technology, Dresden, Germany; Skin Cancer Centre at the University Cancer Centre, Department of Dermatology and National Centre for Tumour Diseases, Dresden, Germany
| | - Kathy Keyvani
- Institute of Neuropathology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Lale Umutlu
- Department of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Theodora Kanaki
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Anne Zaremba
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Finja Reinboldt-Jockenhoefer
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Sarah Knispel
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Emmanouil Gratsias
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Alexander Roesch
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Selma Ugurel
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Björn Scheffler
- DKFZ-Division Translational Neurooncology at the West German Cancer Centre (WTZ), University Hospital Essen, Essen, Germany; West German Cancer Center (WTZ) & German Cancer Consortium (DKTK) Partner Site, Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Dirk Schadendorf
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Elisabeth Livingstone
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany
| | - Friedegund Meier
- Department of Dermatology, Carl Gustav Carus University Hospital, Dresden University of Technology, Dresden, Germany; Skin Cancer Centre at the University Cancer Centre, Department of Dermatology and National Centre for Tumour Diseases, Dresden, Germany
| | - Martin Glas
- Division of Clinical Neurooncology, Department of Neurology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Lisa Zimmer
- Department of Dermatology, Essen University Hospital, West German Cancer Center, University of Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, Essen, Germany.
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28
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Takami H, Velásquez C, Asha MJ, Oswari S, Almeida JP, Gentili F. Creative and Innovative Methods and Techniques for the Challenges in the Management of Adult Craniopharyngioma. World Neurosurg 2021; 142:601-610. [PMID: 32987616 DOI: 10.1016/j.wneu.2020.05.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 04/05/2020] [Indexed: 10/23/2022]
Abstract
Craniopharyngioma remains a major challenge in daily clinical practice. The pathobiology of the tumor is still elusive, and there are no consensus or treatment guidelines on the optimal management strategy for this relatively rare tumor. However, recent technical and scientific advances, including genomic and radiomic profiling, innovation in surgical approaches, more precise radiotherapy protocols, targeted therapy, and restoration of lost functions all have the potential to significantly improve the outcome of patients with craniopharyngioma in the near future. Although many of these innovative tools in the new armamentarium of the clinician are still in their infancy, they could reduce craniopharyngioma-related morbidity and mortality and improve the patients' quality of life. In this article, we discuss these creative and innovative approaches that may offer solutions to the obstacles faced in treating craniopharyngioma and future possibilities in improving the care of these patients.
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Affiliation(s)
- Hirokazu Takami
- Department of Neurosurgery, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Carlos Velásquez
- Department of Neurosurgery, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Mohammed J Asha
- Department of Neurosurgery, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Selfy Oswari
- Department of Neurosurgery, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Joao Paulo Almeida
- Department of Neurosurgery, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Fred Gentili
- Department of Neurosurgery, Toronto Western Hospital, Toronto, Ontario, Canada.
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Clinical Experience of Cerebrospinal Fluid-Based Liquid Biopsy Demonstrates Superiority of Cell-Free DNA over Cell Pellet Genomic DNA for Molecular Profiling. J Mol Diagn 2021; 23:742-752. [PMID: 33781965 DOI: 10.1016/j.jmoldx.2021.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/26/2021] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) offers unique opportunities for genomic profiling of tumors involving the central nervous system but remains uncommonly used in clinical practice. We describe our clinical experience using cfDNA from CSF for routine molecular testing using Memorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer Targets (targeting 468 cancer-related genes). In all, 148 cfDNA samples were assessed, comparing results of cfDNA versus genomic DNA (gDNA; gDNA from cell pellets) derived from the same CSF sample and the primary tumor. Of these, 71.6% (106/148) were successfully sequenced. Somatic alterations (mutations and fusions) were observed in 70.8% (75/106) of the samples; 97.3% (73/75) comprised variants confirming central nervous system involvement by a previously diagnosed tumor, 14.7% (11/75) had additional variants consistent with a therapy-related resistance mechanism, and 2.7% (2/75) had variants that independently diagnosed a new primary. Among samples with paired cfDNA and gDNA sequencing results, cfDNA was more frequently positive for at least one mutation [43.6% (55/126) versus 19.8% (25/126)] and harbored 1.6× more mutations (6.94 versus 4.65; P = 0.005), with higher mean variant allele fractions (41.1% versus 13.0%; P < 0.0001). Among mutation-positive cfDNAs, the corresponding gDNA was frequently negative (44.6%; 25/55) or failed sequencing (17.8%; 9/55). Routine molecular profiling of cfDNA is superior to gDNA from CSF, facilitating the capture of mutations at high variant allele frequency, even in the context of a negative cytology.
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Tsamis KI, Sakkas H, Giannakis A, Ryu HS, Gartzonika C, Nikas IP. Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing. Mol Diagn Ther 2021; 25:207-229. [PMID: 33646562 PMCID: PMC7917176 DOI: 10.1007/s40291-021-00513-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/24/2022]
Abstract
Cerebrospinal fluid (CSF) is a clear and paucicellular fluid that circulates within the ventricular system and the subarachnoid space of the central nervous system (CNS), and diverse CNS disorders can impact its composition, volume, and flow. As conventional CSF testing suffers from suboptimal sensitivity, this review aimed to evaluate the role of next-generation sequencing (NGS) in the work-up of infectious, neoplastic, neuroimmunological, and neurodegenerative CNS diseases. Metagenomic NGS showed improved sensitivity—compared to traditional methods—to detect bacterial, viral, parasitic, and fungal infections, while the overall performance was maximized in some studies when all diagnostic modalities were used. In patients with primary CNS cancer, NGS findings in the CSF were largely concordant with the molecular signatures derived from tissue-based molecular analysis; of interest, additional mutations were identified in the CSF in some glioma studies, reflecting intratumoral heterogeneity. In patients with metastasis to the CNS, NGS facilitated diagnosis, prognosis, therapeutic management, and monitoring, exhibiting higher sensitivity than neuroimaging, cytology, and plasma-based molecular analysis. Although evidence is still rudimentary, NGS could enhance the diagnosis and pathogenetic understanding of multiple sclerosis in addition to Alzheimer and Parkinson disease. To conclude, NGS has shown potential to aid the research, facilitate the diagnostic approach, and improve the management outcomes of all the aforementioned CNS diseases. However, to establish its role in clinical practice, the clinical validity and utility of each NGS protocol should be determined. Lastly, as most evidence has been derived from small and retrospective studies, results from randomized control trials could be of significant value.
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Affiliation(s)
- Konstantinos I Tsamis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece. .,School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus.
| | - Hercules Sakkas
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Alexandros Giannakis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, 03080, Korea
| | - Constantina Gartzonika
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Ilias P Nikas
- School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus
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VanderLaan PA, Roy-Chowdhuri S. Current and future trends in non-small cell lung cancer biomarker testing: The American experience. Cancer Cytopathol 2021; 128:629-636. [PMID: 32885913 DOI: 10.1002/cncy.22313] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/04/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022]
Abstract
Biomarker testing in patients with advanced stage non-small cell lung cancer provides essential information that can be used to select the most appropriate therapy. The regular updates of guideline recommendations reflect the growing number of biomarkers that must be assessed, and as such signal the shift from single-gene assays to more comprehensive genomic profiling using next-generation sequencing modalities. Cytology and small biopsy specimens have proven to be more than adequate substrates for these types of ancillary molecular testing; however, other alternative testing substrates are beginning to emerge. These include so-called liquid biopsies as well the supernatant fluid from cytology specimens, both of which have demonstrated promise for use in the clinical realm. This review will briefly cover the current state of non-small cell lung cancer biomarker testing in the United States, with a focus on these novel nonconventional substrates that are increasingly being incorporated into testing paradigms.
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Affiliation(s)
- Paul A VanderLaan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Sinchita Roy-Chowdhuri
- Division of Pathology and Laboratory Medicine, Department of Anatomic Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Izquierdo E, Proszek P, Pericoli G, Temelso S, Clarke M, Carvalho DM, Mackay A, Marshall LV, Carceller F, Hargrave D, Lannering B, Pavelka Z, Bailey S, Entz-Werle N, Grill J, Vassal G, Rodriguez D, Morgan PS, Jaspan T, Mastronuzzi A, Vinci M, Hubank M, Jones C. Droplet digital PCR-based detection of circulating tumor DNA from pediatric high grade and diffuse midline glioma patients. Neurooncol Adv 2021; 3:vdab013. [PMID: 34169282 PMCID: PMC8218704 DOI: 10.1093/noajnl/vdab013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The use of liquid biopsy is of potential high importance for children with high grade (HGG) and diffuse midline gliomas (DMG), particularly where surgical procedures are limited, and invasive biopsy sampling not without risk. To date, however, the evidence that detection of cell-free DNA (cfDNA) or circulating tumor DNA (ctDNA) could provide useful information for these patients has been limited, or contradictory. METHODS We optimized droplet digital PCR (ddPCR) assays for the detection of common somatic mutations observed in pediatric HGG/DMG, and applied them to liquid biopsies from plasma, serum, cerebrospinal fluid (CSF), and cystic fluid collected from 32 patients. RESULTS Although detectable in all biomaterial types, ctDNA presented at significantly higher levels in CSF compared to plasma and/or serum. When applied to a cohort of 127 plasma specimens from 41 patients collected from 2011 to 2018 as part of a randomized clinical trial in pediatric non-brainstem HGG/DMG, ctDNA profiling by ddPCR was of limited use due to the small volumes (mean = 0.49 mL) available. In anecdotal cases where sufficient material was available, cfDNA concentration correlated with disease progression in two examples each of poor response in H3F3A_K27M-mutant DMG, and longer survival times in hemispheric BRAF_V600E-mutant cases. CONCLUSION Tumor-specific DNA alterations are more readily detected in CSF than plasma. Although we demonstrate the potential of the approach to assessing tumor burden, our results highlight the necessity for adequate sample collection and approach to improve detection if plasma samples are to be used.
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Affiliation(s)
- Elisa Izquierdo
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Paula Proszek
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, UK
| | - Giulia Pericoli
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | - Sara Temelso
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Matthew Clarke
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Diana M Carvalho
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Alan Mackay
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Lynley V Marshall
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
- Children & Young People’s Unit, Royal Marsden Hospital NHS Trust, Sutton, UK
| | - Fernando Carceller
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
- Children & Young People’s Unit, Royal Marsden Hospital NHS Trust, Sutton, UK
| | - Darren Hargrave
- Department of Haematology and Oncology, UCL Great Ormond Street Institute for Child Health, London, UK
| | - Birgitta Lannering
- Department of Pediatrics, Institute of Clinical Sciences, Queen Silvia Children’s Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Zdenek Pavelka
- Department of Pediatric Oncology, University Hospital Brno – Children’s Hospital, Brno, Czechia
| | - Simon Bailey
- Department of Paediatric Oncology, Great North Children’s Hospital, Newcastle University Center for Cancer, Newcastle upon Tyne, UK
| | - Natacha Entz-Werle
- Pediatric Onco-Hematology Department, University Hospital of Strasbourg, Strasbourg, France
- UMR CNRS 7021, Laboratory Bioimaging and Pathologies, Tumoral Signaling and Therapeutic Targets team, Faculty of Pharmacy, Illkirch, France
| | - Jacques Grill
- Pediatric and Adolescent Oncology and INSERM Unit U981, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy and Paris Saclay University, Villejuif, France
| | - Gilles Vassal
- Pediatric and Adolescent Oncology and INSERM Unit U981, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy and Paris Saclay University, Villejuif, France
| | - Daniel Rodriguez
- Medical Physics and Clinical Engineering, Nottingham University Hospital Trust Nottingham University Hospital Trust, Nottingham, UK
| | - Paul S Morgan
- Medical Physics and Clinical Engineering, Nottingham University Hospital Trust Nottingham University Hospital Trust, Nottingham, UK
| | - Tim Jaspan
- Department of Radiology, Nottingham University Hospital Trust, Nottingham University Hospital Trust, Nottingham, UK
| | - Angela Mastronuzzi
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | - Mara Vinci
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital-IRCCS, Rome, Italy
| | - Michael Hubank
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, UK
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
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Aili Y, Maimaitiming N, Mahemuti Y, Qin H, Wang Y, Wang Z. Liquid biopsy in central nervous system tumors: the potential roles of circulating miRNA and exosomes. Am J Cancer Res 2020; 10:4134-4150. [PMID: 33414991 PMCID: PMC7783770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023] Open
Abstract
The Central nervous system (CNS) tumor still remains the most lethal cancer, and It is hard to diagnose at an earlier stage on most occasions. It is found that recurrent disease is finally observed in patients who occurred chemo-resistance after completely primary treatment. It is a challenge that monitoring treatment efficacy and tumor recurrence of CNS tumors are full of risks and difficulties by brain biopsies. However, the brain biopsies are considered as an invasive technique with low specificity and low sensitivity. In contrast, the liquid biopsy is based on blood and cerebrospinal fluid (CSF) test, which is going to acceptable among the patients through it's minimally invasive and serial bodily fluids. The advantages of liquid biopsy are to follow the development of tumors, provide new insights in real time, and accurate medical care. The major analytical constituents of liquid biopsy contain the Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating cell-free microRNAs (cfmiRNAs), and circulating exosomes. Liquid biopsy has been widely utilized in CNS tumors in recent years, and the CTCs and ctDNA have become the hot topics for researching. In this review, we are going to explain the clinical potential of liquid biopsy biomarkers in CNS tumor by testing circulating miRNAs and exosomes to evaluate diagnose, prognosis, and response to treatment.
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Affiliation(s)
- Yirizhati Aili
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, PR China
| | - Nuersimanguli Maimaitiming
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, PR China
| | - Yusufu Mahemuti
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, PR China
| | - Hu Qin
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, PR China
| | - Yongxin Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, PR China
| | - Zengliang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical UniversityXinjiang, PR China
- Bazhou People’s HospitalXinjiang, PR China
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Abstract
PURPOSE OF REVIEW Management of metastasis to the central nervous system (CNS) has evolved, and molecular characterization of metastatic disease is now routinely done. Targeted therapies, once few in number with limited penetration into the CNS, have multiplied in number and increased in CNS coverage. This article addresses recent advances in the evaluation and clinical management of patients with CNS metastasis. RECENT FINDINGS Metastasis of cancer to the CNS can be diagnosed and characterized with novel techniques, including molecular analyses of the spinal fluid, so-called liquid biopsies. Resected parenchymal CNS metastases are now routinely subjected to genomic sequencing. For patients with CNS metastases displaying targetable mutations, a wide variety of treatment options are available, including deferral of radiation therapy in favor of a trial of an orally bioavailable targeted therapy or immunotherapy. For patients without a molecularly targetable lesion, local treatment in the form of radiation therapy, now most often stereotactic radiosurgery, is supplanting untargeted whole-brain radiation therapy. SUMMARY Technologic advances in diagnosis and management have resulted in new diagnostic and therapeutic approaches to patients with metastasis to the CNS, with resulting improvements in progression-free and overall survival.
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Pös Z, Pös O, Styk J, Mocova A, Strieskova L, Budis J, Kadasi L, Radvanszky J, Szemes T. Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes. Int J Mol Sci 2020; 21:ijms21228634. [PMID: 33207777 PMCID: PMC7697251 DOI: 10.3390/ijms21228634] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.
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Affiliation(s)
- Zuzana Pös
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jakub Styk
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Faculty of Medicine, Institute of Medical Biology, Genetics and Clinical Genetics, 811 08 Bratislava, Slovakia
| | - Angelika Mocova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | | | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Ludevit Kadasi
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jan Radvanszky
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
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Pessoa LS, Heringer M, Ferrer VP. ctDNA as a cancer biomarker: A broad overview. Crit Rev Oncol Hematol 2020; 155:103109. [PMID: 33049662 DOI: 10.1016/j.critrevonc.2020.103109] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in fluids has gained attention because ctDNA seems to identify tumor-specific abnormalities, which could be used for diagnosis, follow-up of treatment, and prognosis: the so-called liquid biopsy. Liquid biopsy is a minimally invasive approach and presents the sum of ctDNA from primary and secondary tumor sites. It has been possible not only to quantify the amount of ctDNA but also to identify (epi)genetic changes. Specific mutations in genes have been identified in the plasma of patients with several types of cancer, which highlights ctDNA as a possible cancer biomarker. However, achieving detectable concentrations of ctDNA in body fluids is not an easy task. ctDNA fragments present a short half-life, and there are no cut-off values to discriminate high and low ctDNA concentrations. Here, we discuss the use of ctDNA as a cancer biomarker, the main methodologies, the inherent difficulties, and the clinical predictive value of ctDNA.
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Affiliation(s)
- Luciana Santos Pessoa
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil; Center for Experimental Surgery, Graduate Program in Surgical Sciences, Department of Surgery, Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Manoela Heringer
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil.
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Mattox AK, Yan H, Bettegowda C. The potential of cerebrospinal fluid-based liquid biopsy approaches in CNS tumors. Neuro Oncol 2020; 21:1509-1518. [PMID: 31595305 PMCID: PMC6917400 DOI: 10.1093/neuonc/noz156] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cerebrospinal fluid (CSF) may be the best hope for minimally invasive diagnosis and treatment monitoring of central nervous system (CNS) malignancies. Discovery/validation of cell-free nucleic acid and protein biomarkers has the potential to revolutionize CNS cancer care, paving the way for presurgical evaluation, earlier detection of recurrence, and the selection of targeted therapies. While detection of mutations, changes in RNA and miRNA expression, epigenetic alterations, and elevations of protein levels have been detected in the CSF of patients with CNS tumors, most of these biomarkers remain unvalidated. In this review, we focus on the molecular changes that have been identified in a variety of CNS tumors and profile the approaches used to detect these alterations in clinical samples. We further emphasize the importance of systemic collection of CSF and the establishment of standardized collection protocols that will lead to better cross-study biomarker validation and hopefully FDA-approved clinical markers.
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Affiliation(s)
- Austin K Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hai Yan
- The Preston Robert Tisch Brain Tumor Center, Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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38
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Kang Y, Lin X, Kang D. Diagnostic value of circulating tumor DNA in molecular characterization of glioma: A meta-analysis. Medicine (Baltimore) 2020; 99:e21196. [PMID: 32871983 PMCID: PMC7437834 DOI: 10.1097/md.0000000000021196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 05/11/2020] [Accepted: 06/08/2020] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION Circulating tumor DNA (ctDNA) has provided a minimally invasive approach for the detection of genetic mutations in glioma. However, the diagnostic value of ctDNA in glioma remains unclear. This meta-analysis was designed to investigate the diagnostic value of ctDNA, compared with the current "criterion standard" tumor tissues. MATERIALS AND METHODS The included studies were collected by searching PubMed, Web of Science, Cochrane Library, and Embase databases. All statistical analyses were performed using the STATA12.0 and Meta-DiSc1.4 software. RESULT A total of 11 studies comprising 522 glioma patients met our inclusion criteria. The pooled sensitivity and specificity were 0.69 (95% confidence interval [CI] 0.66-0.73) and 0.98 (95% CI 0.96-0.99), respectively. The pooled diagnostic odds ratio was 23.27 (95% CI 13.69-39.53) and the area under the curve of the summary receiver operating characteristics curve was 0.90 (95% CI 0.89-0.92). CONCLUSIONS ctDNA analysis is an effective method to detect the genetic mutation status in glioma patients with high specificity and relatively moderate sensitivity. The application of high-throughput technologies, the detection of patients with high-grade glioma, and sampling from cerebrospinal fluid could have higher diagnostic accuracy. The improvement of detection methods and more large-sample case-control studies are required in the future.
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Affiliation(s)
| | - Xiaohua Lin
- Department of Anesthesiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
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Erker C, Tamrazi B, Poussaint TY, Mueller S, Mata-Mbemba D, Franceschi E, Brandes AA, Rao A, Haworth KB, Wen PY, Goldman S, Vezina G, MacDonald TJ, Dunkel IJ, Morgan PS, Jaspan T, Prados MD, Warren KE. Response assessment in paediatric high-grade glioma: recommendations from the Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group. Lancet Oncol 2020; 21:e317-e329. [PMID: 32502458 DOI: 10.1016/s1470-2045(20)30173-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/05/2020] [Accepted: 03/12/2020] [Indexed: 12/27/2022]
Abstract
Response criteria for paediatric high-grade glioma vary historically and across different cooperative groups. The Response Assessment in Neuro-Oncology working group developed response criteria for adult high-grade glioma, but these were not created to meet the unique challenges in children with the disease. The Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group, consisting of an international panel of paediatric and adult neuro-oncologists, clinicians, radiologists, radiation oncologists, and neurosurgeons, was established to address issues and unique challenges in assessing response in children with CNS tumours. We established a subcommittee to develop response assessment criteria for paediatric high-grade glioma. Current practice and literature were reviewed to identify major challenges in assessing the response of paediatric high-grade gliomas to various treatments. For areas in which scientific investigation was scarce, consensus was reached through an iterative process. RAPNO response assessment recommendations include the use of MRI of the brain and the spine, assessment of clinical status, and the use of corticosteroids or antiangiogenics. Imaging standards for brain and spine are defined. Compared with the recommendations for the management of adult high-grade glioma, for paediatrics there is inclusion of diffusion-weighted imaging and a higher reliance on T2-weighted fluid-attenuated inversion recovery. Consensus recommendations and response definitions have been established and, similar to other RAPNO recommendations, prospective validation in clinical trials is warranted.
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Affiliation(s)
- Craig Erker
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Dalhousie University and IWK Health Centre, Halifax, NS, Canada.
| | - Benita Tamrazi
- Department of Radiology, Keck School of Medicine, University of Southern California and Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Tina Y Poussaint
- Department of Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Sabine Mueller
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA; Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
| | - Daddy Mata-Mbemba
- Department of Diagnostic Imaging, Dalhousie University and IWK Health Centre, Halifax, NS, Canada
| | - Enrico Franceschi
- Department of Medical Oncology, Azienda USL, Bologna, Italy; IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Alba A Brandes
- Department of Medical Oncology, Azienda USL, Bologna, Italy; IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Arvind Rao
- Departments of Computational Medicine and Bioinformatics and Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Kellie B Haworth
- Division of Neuro-Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick Y Wen
- Center For Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stewart Goldman
- Department of Haematology, Oncology, Neuro-Oncology, and Stem Cell Transplantation, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Gilbert Vezina
- Department of Radiology, Children's National Medical Center, Washington, DC, USA
| | - Tobey J MacDonald
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ira J Dunkel
- Department of Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul S Morgan
- Department of Medical Physics and Clinical Engineering, Nottingham University Hospitals, Queen's Medical Centre, Nottingham, UK
| | - Tim Jaspan
- Department of Radiology, Nottingham University Hospitals, Queen's Medical Centre, Nottingham, UK
| | - Michael D Prados
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
| | - Katherine E Warren
- Department of Pediatric Oncology, Dana- Farber/Boston Children's Cancer and Blood Disorders Center, Dana-Farber Cancer Institute, Boston, MA, USA
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Glitza IC, Smalley KSM, Brastianos PK, Davies MA, McCutcheon I, Liu JKC, Ahmed KA, Arrington JA, Evernden BR, Smalley I, Eroglu Z, Khushalani N, Margolin K, Kluger H, Atkins MB, Tawbi H, Boire A, Forsyth P. Leptomeningeal disease in melanoma patients: An update to treatment, challenges, and future directions. Pigment Cell Melanoma Res 2020; 33:527-541. [PMID: 31916400 PMCID: PMC10126834 DOI: 10.1111/pcmr.12861] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/26/2019] [Accepted: 01/03/2020] [Indexed: 01/31/2023]
Abstract
In February 2018, the Melanoma Research Foundation and the Moffitt Cancer Center hosted the Second Summit on Melanoma Central Nervous System Metastases in Tampa, Florida. The meeting included investigators from multiple academic centers and disciplines. A consensus summary of the progress and challenges in melanoma parenchymal brain metastases was published (Eroglu et al., Pigment Cell & Melanoma Research, 2019, 32, 458). Here, we will describe the current state of basic, translational, clinical research, and therapeutic management, for melanoma patients with leptomeningeal disease. We also outline key challenges and barriers to be overcome to make progress in this deadly disease.
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Affiliation(s)
- Isabella C. Glitza
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Keiran S. M. Smalley
- Melanoma Research Center of Excellence, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Michael A. Davies
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ian McCutcheon
- Department of Neurosurgery, UT MD Anderson Cancer Center, Houston, TX, USA
| | - James K. C. Liu
- Department of Neuro-Oncology & Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Kamran A. Ahmed
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - John A. Arrington
- Head of Neuroradiology Section, Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Brittany R. Evernden
- Department of Neuro-Oncology & Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Inna Smalley
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Zeynep Eroglu
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Nikhil Khushalani
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Kim Margolin
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Harriet Kluger
- Department of Medical Oncology, Yale Cancer Center, New Haven, CT, USA
| | - Michael B. Atkins
- Department of Medical Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - Hussein Tawbi
- Department of Melanoma Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Adrienne Boire
- Department of Neuro-Oncology, Memorial Sloan Kettering, New York, NY, USA
| | - Peter Forsyth
- Department of Neuro-Oncology & Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Stark AC, McGrath S, Karn M, Thomson CE. Evaluation of cell-free DNA as a diagnostic marker in cerebrospinal fluid of dogs. Am J Vet Res 2020; 81:416-421. [PMID: 32343180 DOI: 10.2460/ajvr.81.5.416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether cell-free DNA (cfDNA) was detectable in CSF samples from dogs, whether CSF sample volume impacted CSF cfDNA concentration measurement, and whether CSF cfDNA concentration was associated with CNS disease category or CSF RBC count (RBCC), nucleated cell count (NCC), or protein concentration, which could aid in the diagnosis of neurologic diseases in dogs. SAMPLE 80 CSF samples collected from dogs with (n = 60) and without (20) clinical neurologic disease between February 2017 and May 2018. PROCEDURES Results for CSF RBCC, NCC, protein concentration, and cfDNA concentration were compared across CSF groups established on the basis of whether they were obtained from dogs with (case groups) or without (control group) clinical signs of neurologic disease In addition, 5 paired CSF samples representing large (3.0-mL) and small (0.5-mL) volumes, were used to evaluate whether sample volume impacted measurement of CSF cfDNA concentration. RESULTS cfDNA was detected in 76 of the 80 (95%) CSF samples used to evaluate parameters across disease categories and in all 5 of the paired samples used to evaluate whether sample volume impacted cfDNA quantification. There were no substantial differences in cfDNA concentrations identified between groups (on the basis of disease category or sample volume), and the CSF cfDNA concentration did not meaningfully correlate with CSF RBCC, NCC, or protein concentration. CONCLUSIONS AND CLINICAL RELEVANCE Although results indicated that the CSF cfDNA concentration could not be used to differentiate between categories of neurologic disease in dogs of the the present study, further investigation is warranted regarding the use of CSF analysis, including sequencing specific cfDNA mutations, for diagnosing and monitoring neurologic disease in dogs.
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Detection of Circulating Tumor DNA with a Single-Molecule Sequencing Analysis Validated for Targeted and Immunotherapy Selection. Mol Diagn Ther 2020; 23:521-535. [PMID: 31209714 PMCID: PMC6675782 DOI: 10.1007/s40291-019-00406-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Comprehensive genetic cancer profiling using circulating tumor DNA has enabled the detection of National Comprehensive Cancer Network (NCCN) guideline-recommended somatic alterations from a single, non-invasive blood draw. However, reliably detecting somatic variants at low variant allele fractions (VAFs) remains a challenge for next-generation sequencing (NGS)-based tests. We have developed the single-molecule sequencing (SMSEQ) platform to address these challenges. METHODS The OncoLBx assay utilizes the SMSEQ platform to optimize cell-free DNA extraction and library preparation with variant type-specific calling algorithms to improve sensitivity and specificity. OncoLBx is a pan-cancer panel for solid tumors targeting 75 genes and five microsatellite sites analyzing five classes of NCCN-recommended somatic variants: single-nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), fusions and microsatellite instability (MSI). Circulating DNA was extracted from plasma, followed by library preparation using SMSEQ. Analytical validation was performed according to recently published American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines and established the limit of detection (LOD), sensitivity, specificity, accuracy and reproducibility using 126 gold-standard reference samples, healthy donor samples verified by whole-exome sequencing by an external College of American Pathologists (CAP) reference lab and cell lines with known variants. Results were analyzed using a locus-specific modeling algorithm. RESULTS We have demonstrated that OncoLBx detects VAFs of ≥ 0.1% for SNVs and indels, ≥ 0.5% for fusions, ≥ 4.5 copies for CNVs and ≥ 2% for MSI, with all variant types having specificity ≥ 99.999%. Diagnostic performance of paired samples displays 80% sensitivity and > 99.999% clinical specificity. Clinical utility and performance were assessed in 416 solid tumor samples. Variants were detected in 79% of samples, for which 87.34% of positive samples had available targeted therapy.
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Yang Z, Zhao S, Zhou J, Lei S, Hu Z. Erdheim-Chester disease: a case treated with IFN-α monitored using plasma and urine cell-free DNA. Immunotherapy 2020; 12:379-387. [PMID: 32290742 DOI: 10.2217/imt-2019-0150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Erdheim-Chester disease is a rare form of non-Langerhans histiocytosis. A 40-year-old woman was diagnosed as Erdheim-Chester disease based on typical bone scintigraphy, symmetric osteosclerosis and findings of foamy, non-Langerhans histiocytes in bone marrow. BRAFV600E mutation was detected in a bone biopsy. Treatment with IFN-α showed significant improvement. The BRAFV600E mutant was detected in plasma cell-free DNA (cfDNA) by a droplet-digital PCR assay. Longitudinal analysis of BRAFV600E in plasma cfDNA showed a decreasing trend during treatment. We could not detect the mutant in urinary cfDNA. While, similar studies have detected the BRAFV600E mutant in urine, but not in plasma. A combination of allele burden assessments in plasma and urine may be helpful for detecting the residual mutant burden and monitoring therapeutic response.
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Affiliation(s)
- Zhi Yang
- Department of Nephrology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China, 610041
| | - Sha Zhao
- Department of Pathology, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China 610041
| | - Juan Zhou
- Department of Laboratory, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China, 610041
| | - Song Lei
- Department of Pathology, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China 610041
| | - Zhangxue Hu
- Department of Nephrology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu City, Sichuan Province, China, 610041
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Yan W, Xu T, Zhu H, Yu J. Clinical Applications of Cerebrospinal Fluid Circulating Tumor DNA as a Liquid Biopsy for Central Nervous System Tumors. Onco Targets Ther 2020; 13:719-731. [PMID: 32158224 PMCID: PMC6986252 DOI: 10.2147/ott.s229562] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/11/2020] [Indexed: 12/19/2022] Open
Abstract
Central nervous system (CNS) malignancies are associated with poor prognosis, as well as exceptional morbidity and mortality, likely as a result of low rates of early diagnosis and limited knowledge of the tumor growth and resistance mechanisms, dissemination, and evolution in the CNS. Monitoring patients with CNS malignancies for treatment response and tumor recurrence can be challenging because of the difficulty and risks of brain biopsies and the low specificity and sensitivity of the less invasive methodologies that are currently available. Therefore, there is an urgent need to detect and validate reliable and minimally invasive biomarkers for CNS tumors that can be used separately or in combination with current clinical practices. The circulating tumor DNA (ctDNA) of cerebrospinal fluid (CSF) samples can outline the genetic landscape of entire CNS tumors effectively and is a promising, suitable biomarker, though its role in managing CNS malignancies has not been studied extensively. This review summarizes recent studies that explore the diagnostic, prognostic, and predictive roles of CSF-ctDNA as a liquid biopsy with primary and metastatic CNS malignancies.
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Affiliation(s)
- Weiwei Yan
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China.,Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, People's Republic of China
| | - Tingting Xu
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, People's Republic of China
| | - Hui Zhu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, People's Republic of China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, People's Republic of China
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Li D, Stellpflug W, Romanski K, Kilgallon M, Speck S, Saratsis AM. Ventricular Cerebrospinal Fluid Sampling in Pediatric Diffuse Midline Glioma Patients: Institutional Experience and Review of the Literature. Front Pediatr 2020; 8:556802. [PMID: 33194892 PMCID: PMC7652764 DOI: 10.3389/fped.2020.556802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/16/2020] [Indexed: 12/03/2022] Open
Abstract
Purpose: Increasing evidence suggests that circulating biomarkers may serve diagnostic and longitudinal monitoring purposes in pediatric neuro-oncology. Mutant tumor DNA is detectable in the cerebrospinal fluid (CSF) of pediatric diffuse midline glioma (DMG) patients and quantity can reflect disease burden. CSF sampling ("liquid biopsy") via a CSF access device could therefore play a role in DMG management. Therefore, we set to evaluate the incidence of hydrocephalus (HCP) in DMG patients, and to characterize ventricular reservoir placement and access practices. Methods: A single institution retrospective review of DMG patients ≤21-years-old was performed (1984-2019). MEDLINE searches for reports of ventricular reservoir or shunt placement in DMG, and reservoir access for intraventricular chemotherapy (IVC) were performed. Results: At our institution, 62.6% of DMG patients (67/108) required intervention for HCP: 19.4% provided transient CSF access (ETV alone n = 3, EVD n = 8, unspecified n = 2), and 80.6% permanent CSF access (ETV + reservoir n = 13, shunt n = 41). Further, 22/34 patients with initially transient CSF devices required conversion to a permanent device. Five devices were revised for malfunction, one for infection. Seventeen articles cited HCP in 22 to 100% of DMG patients. IVC administration was described in 632 patients (seven articles), with 42 infectious and 63 non-infectious complications. Conclusions: Management of HCP is often necessary in children with DMG. Given the low rate of clinical risk associated with VAD placement and access, and the potential utility of longitudinal disease monitoring via CSF analysis, VAD placement could be considered in future clinical trials to guide DMG treatment.
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Affiliation(s)
- Daphne Li
- Department of Neurological Surgery, Loyola University Medical Center, Maywood, IL, United States
| | - Wendy Stellpflug
- Department of Surgery, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital, Chicago, IL, United States
| | - Kathy Romanski
- Department of Surgery, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital, Chicago, IL, United States
| | - Maureen Kilgallon
- Department of Surgery, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital, Chicago, IL, United States
| | - Stacy Speck
- Department of Surgery, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital, Chicago, IL, United States
| | - Amanda M Saratsis
- Department of Surgery, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital, Chicago, IL, United States.,Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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von Baumgarten L, Kumbrink J, Jung A, Reischer A, Flach M, Liebmann S, Metzeler KH, Holch JW, Niyazi M, Thon N, Straube A, von Bergwelt-Baildon M, Heinemann V, Kirchner T, Westphalen CB. Therapeutic management of neuro-oncologic patients - potential relevance of CSF liquid biopsy. Am J Cancer Res 2020; 10:856-866. [PMID: 31903155 PMCID: PMC6929982 DOI: 10.7150/thno.36884] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/08/2019] [Indexed: 01/09/2023] Open
Abstract
Background: In the era of precision medicine, cancer treatment is increasingly tailored according to tumor-specific genomic alterations. The analysis of tumor-derived circulating nucleic acids in cerebrospinal fluid (CSF) by next generation sequencing (NGS) may facilitate precision medicine in the field of CNS cancer. We therefore evaluated whether NGS from CSF of neuro-oncologic patients reliably detects tumor-specific genomic alterations and whether this may help to guide the management of patients with CNS cancer in clinical practice. Patient and methods: CSF samples from 27 patients with various primary and secondary CNS malignancies were collected and evaluated by NGS using a targeted, amplicon-based NGS-panel (Oncomine Focus Assay). All cases were discussed within the framework of a molecular tumor board at the Comprehensive Cancer Center Munich. Results: NGS was technically successful in 23/27 patients (85%). Genomic alterations were detectable in 20/27 patients (74%), 11/27 (40%) of which were potentially actionable. After discussion in the MTB, a change of therapeutic management was recommended in 7/27 (26%) of the cases. However, due to rapid clinical progression, only 4/27 (15%) of the patients were treated according to the recommendation. In a subset of patients (6/27, 22%), a high number of mutations of unknown significance suggestive of a high tumor mutational burden (TMB) were detected. Conclusions: NGS from cerebrospinal fluid is feasible in routine clinical practice and yields therapeutically relevant alterations in a large subset of patients. Integration of this approach into a precision cancer medicine program might help to improve therapeutic options for patients with CNS cancer.
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Mazzella A, Loi M, Mansuet-Lupo A, Bobbio A, Blons H, Damotte D, Alifano M. Clinical Characteristics, Molecular Phenotyping, and Management of Isolated Adrenal Metastases From Lung Cancer. Clin Lung Cancer 2019; 20:405-411. [DOI: 10.1016/j.cllc.2019.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/16/2019] [Accepted: 06/06/2019] [Indexed: 11/15/2022]
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Song Z, Wang W, Li M, Liu J, Zhang Y. Cytological-negative pleural effusion can be an alternative liquid biopsy media for detection of EGFR mutation in NSCLC patients. Lung Cancer 2019; 136:23-29. [PMID: 31421258 DOI: 10.1016/j.lungcan.2019.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/20/2019] [Accepted: 08/02/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Though the possibility of using malignant pleural effusions (MPEs) as alternatives for tumor tissues in epidermal growth factor receptor (EGFR) mutation test has been examined, the diagnosis of MPE is often clinically challenging, especially if the cytology is negative for malignancy. The aim of this study was to examine whether cytological-negative PE (CNPE) is useful in detecting EGFR mutation and evaluated its feasibility for predicting clinical outcomes. METHOD In this study, we performed capture-based targeted sequencing using a panel consisting of 520 lung cancer-related genes to detect EGFR mutation status in 121 MPEs and 40 CNPE samples from 161 advanced lung adenocarcinoma patients. Patients underwent TKI treatment with gefitinib, icotinib or erlotinib if EGFR sensitizing mutations were detected at their tumor biopsies or pleural effusion sediment. RESULTS We revealed a mutation detection rate of 99.2% and 100% for MPE and CNPE, respectively (p = 1). The maximum allelic fraction (maxAF) of MPE and CNPE were 57.4% and 56.8%, respectively (p = 0.77). CNPE supernatant is comparable to MPE in reflecting the mutational profile of lung adenocarcinoma. EGFR activating mutations were detected in 47.5% (19/40) of CNPE supernatant sample and 32.5% (13/40) of matched tumor biopsies. CNPE sample is superior to tumor tissues in identifying EFGR mutation. Among the 72 EGFR-TKI treated patients, 51 were cytology positive and the remaining 21 were cytology negative. Our data showed that MPE patients exhibited comparable PFS (p = 0.41) and OS (p = 0.26) with CNPE patients treated with EGFR-TKI. Among the 21 CNPE patients received TKI treatment, patients harboring either L858R or exon 19 deletion had longer PFS than patients without a detectable mutation (p = 0.036). CONCLUSION Collectively, we demonstrated that CNPE supernatant provided a comprehensive profile of NSCLC, and can serve as a reliable lipid biopsy media for EGFR mutational detection.
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Affiliation(s)
- Zhengbo Song
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Wenxian Wang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Min Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Junjun Liu
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Yiping Zhang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, 310022, China.
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Ballester LY, Glitza Oliva IC, Douse DY, Chen MM, Lan C, Haydu LE, Huse JT, Roy-Chowdhuri S, Luthra R, Wistuba II, Davies MA. Evaluating Circulating Tumor DNA From the Cerebrospinal Fluid of Patients With Melanoma and Leptomeningeal Disease. J Neuropathol Exp Neurol 2019; 77:628-635. [PMID: 29873738 DOI: 10.1093/jnen/nly046] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Circulating tumor DNA (ctDNA) refers to tumor-derived cell-free DNA that circulates in body fluids. Fluid samples are easier to collect than tumor tissue, and are amenable to serial collection at multiple time points during the course of a patient's illness. Studies have demonstrated the feasibility of performing mutation profiling from blood samples in cancer patients. However, detection of ctDNA in the blood of patients with brain tumors is suboptimal. Cerebrospinal fluid (CSF) can be obtained via lumbar puncture or intraventricular catheter, and may be a suitable fluid to assess ctDNA in patients with brain tumors. We detected melanoma-associated mutations by droplet-digital PCR (ddPCR) and next-generation sequencing in ctDNA obtained from the CSF (CSF-ctDNA) of melanoma patients with leptomeningeal disease. There is a strong correlation between mutation detection by ddPCR, the presence of circulating tumor cells in CSF and abnormalities in the MRI. However, approximately 30% of CSF samples that were negative or indeterminate for the presence of tumor cells by microscopic examination were positive for CSF-ctDNA by ddPCR. Our results demonstrate that CSF is a suitable fluid for evaluating ctDNA and ddPCR is superior to CSF-cytology for analysis of CSF in melanoma patients with leptomeningeal disease.
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Affiliation(s)
- Leomar Y Ballester
- Department of Pathology and Laboratory Medicine and Department of Neurosurgery, University of Texas Health Science Center, Houston, Texas
| | | | | | | | | | | | - Jason T Huse
- Department of Translational Molecular Pathology
- Department of Pathology
| | | | | | | | - Michael A Davies
- Department of Melanoma Medical Oncology
- Department of Translational Molecular Pathology
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Abstract
The study of cell-free DNA (cfDNA) is often challenging due to genomic DNA contamination, low concentration, and high fragmentation. Therefore, it is important to optimize pre-analytical and analytical procedures in order to maximize the performance of cfDNA-based analyses.In this chapter, we report the most common methods for the correct collection, centrifugation, storage, and DNA isolation from cell-free biological sources such as plasma, urines, cerebrospinal fluid, and pleural effusion fluid.
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Affiliation(s)
- Filippo Martignano
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
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