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Udomruk S, Orrapin S, Pruksakorn D, Chaiyawat P. Size distribution of cell-free DNA in oncology. Crit Rev Oncol Hematol 2021; 166:103455. [PMID: 34464717 DOI: 10.1016/j.critrevonc.2021.103455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA (cfDNA) in liquid biopsy test is a novel promising biomarker in the advancement of cancer management, including early diagnosis, screening, prognosis, identification of actionable targets, and serial tumor monitoring. The specific size pattern of DNA fragments derived from cancer cells is observed to differ from that of cfDNA fragments shed by non-cancer cells. Research into the physiological and biological properties of cfDNA reveals the molecular signature carried by each cfDNA fragments, which can reflect their tissue origins, as well as the mutational profiles with significant genetic alterations. Understanding the fragmentation and size distribution of cfDNA might be a valuable hotspot in liquid biopsy research, with the potential to drive innovation in oncology.
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Affiliation(s)
- Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Santhasiri Orrapin
- Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Department of Orthopedics, Faculty of Medicine, Chiang Mai University, 110 Intawaroros, Sriphoom, Muang, Chiang Mai 50200, Thailand.
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand.
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Karschnia P, Le Rhun E, Vogelbaum MA, van den Bent M, Grau SJ, Preusser M, Soffietti R, von Baumgarten L, Westphal M, Weller M, Tonn JC. The evolving role of neurosurgery for central nervous system metastases in the era of personalized cancer therapy. Eur J Cancer 2021; 156:93-108. [PMID: 34425408 DOI: 10.1016/j.ejca.2021.07.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022]
Abstract
Recent therapeutic advances involving the use of systemic targeted treatments and immunotherapeutic agents in patients with advanced cancers have translated into improved survival rates. Despite the emergence of such promising pharmacological therapies and extended survival, the frequency of metastases in the central nervous system has steadily increased. Effective medical and surgical therapies are available for many patients with brain metastases and need to be incorporated into multi-disciplinary care protocols. The role of neurosurgeons is evolving within these multi-disciplinary care teams. Surgical resection of brain metastases can provide immediate relief from neurological symptoms due to large lesions and provides the histopathological diagnosis in cases of no known primary malignancy. In situations where immunotherapy is part of the oncological treatment plan, surgery may be proposed for expeditious relief of edema to remove the need for steroids. In patients with multiple brain metastases and mixed response to therapeutics or radiosurgery, tumour resampling allows tissue analysis for druggable targets or to distinguish radiation effects from progression. Ventriculo-peritoneal shunting may improve quality of life in patients with hydrocephalus associated with leptomeningeal tumour dissemination and may allow for time to administer more therapy thus prolonging overall survival. Addressing the limited efficacy of many oncological drugs for brain metastases due to insufficient blood-brain barrier penetrance, clinical trial protocols in which surgical specimens are analysed after pre-surgical administration of therapeutics offer pharmacodynamic insights. Comprehensive neurosurgical assessment remains an integral element of multi-disciplinary oncological care of patients with brain metastases and is integral to tumour biology research and therapeutic advancement.
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Affiliation(s)
- Philipp Karschnia
- Department of Neurosurgery, Ludwig-Maximilians-University School of Medicine, Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Germany
| | - Emilie Le Rhun
- Department of Neurosurgery & Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | | | - Martin van den Bent
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Stefan J Grau
- Department of Neurosurgery, University Hospital of Cologne, Cologne, Germany
| | - Matthias Preusser
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Riccardo Soffietti
- Department of Neuro-Oncology, University and City of Health and Science Hospital, Turin, Italy
| | - Louisa von Baumgarten
- Department of Neurosurgery, Ludwig-Maximilians-University School of Medicine, Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Hospital Hamburg, Hamburg, Germany
| | - Michael Weller
- Department of Neurology & Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Joerg-Christian Tonn
- Department of Neurosurgery, Ludwig-Maximilians-University School of Medicine, Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, Germany.
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Mouliere F, Smith CG, Heider K, Su J, van der Pol Y, Thompson M, Morris J, Wan JCM, Chandrananda D, Hadfield J, Grzelak M, Hudecova I, Couturier D, Cooper W, Zhao H, Gale D, Eldridge M, Watts C, Brindle K, Rosenfeld N, Mair R. Fragmentation patterns and personalized sequencing of cell-free DNA in urine and plasma of glioma patients. EMBO Mol Med 2021; 13:e12881. [PMID: 34291583 PMCID: PMC8350897 DOI: 10.15252/emmm.202012881] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
Glioma-derived cell-free DNA (cfDNA) is challenging to detect using liquid biopsy because quantities in body fluids are low. We determined the glioma-derived DNA fraction in cerebrospinal fluid (CSF), plasma, and urine samples from patients using sequencing of personalized capture panels guided by analysis of matched tumor biopsies. By sequencing cfDNA across thousands of mutations, identified individually in each patient's tumor, we detected tumor-derived DNA in the majority of CSF (7/8), plasma (10/12), and urine samples (10/16), with a median tumor fraction of 6.4 × 10-3 , 3.1 × 10-5 , and 4.7 × 10-5 , respectively. We identified a shift in the size distribution of tumor-derived cfDNA fragments in these body fluids. We further analyzed cfDNA fragment sizes using whole-genome sequencing, in urine samples from 35 glioma patients, 27 individuals with non-malignant brain disorders, and 26 healthy individuals. cfDNA in urine of glioma patients was significantly more fragmented compared to urine from patients with non-malignant brain disorders (P = 1.7 × 10-2 ) and healthy individuals (P = 5.2 × 10-9 ). Machine learning models integrating fragment length could differentiate urine samples from glioma patients (AUC = 0.80-0.91) suggesting possibilities for truly non-invasive cancer detection.
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104
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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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105
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Poynton E, Okosun J. Liquid biopsy in lymphoma: Is it primed for clinical translation? EJHAEM 2021; 2:616-627. [PMID: 35844685 PMCID: PMC9175672 DOI: 10.1002/jha2.212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022]
Abstract
The simultaneous growth in our understanding of lymphoma biology and the burgeoning therapeutic options has come with a renewed drive for precision‐based approaches and how best to incorporate them into contemporary and future patient care. In the hunt for accurate and sensitive biomarkers, liquid biopsies, particularly circulating tumour DNA, have come to the forefront as a promising tool in multiple cancer types including lymphomas, with considerable implications for clinical practice. Liquid biopsy analyses could supplement existing tissue biopsies with distinct advantages including the minimally invasive nature and the ease with which it can be repeated during a patient's clinical journey. Circulating tumour DNA (ctDNA) analyses has been and continues to be evaluated across lymphoma subtypes with potential applications as a diagnostic, disease monitoring and treatment selection tool. To make the leap into the clinic, these assays must demonstrate accuracy, reliability and a quick turnaround to be employed in the real‐time clinical management of lymphoma patients. Here, we review the available ctDNA assays and discuss key practical and technical issues around improving sensitivity. We then focus on their potential roles in several lymphoma subtypes exemplified by recent studies and provide a glimpse of different features that can be analysed beyond ctDNA.
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Affiliation(s)
- Edward Poynton
- Centre for Haemato‐Oncology Barts Cancer Institute, Queen Mary University of London London UK
| | - Jessica Okosun
- Centre for Haemato‐Oncology Barts Cancer Institute, Queen Mary University of London London UK
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106
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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: 6] [Impact Index Per Article: 2.0] [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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107
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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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108
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Park JH, de Lomana ALG, Marzese DM, Juarez T, Feroze A, Hothi P, Cobbs C, Patel AP, Kesari S, Huang S, Baliga NS. A Systems Approach to Brain Tumor Treatment. Cancers (Basel) 2021; 13:3152. [PMID: 34202449 PMCID: PMC8269017 DOI: 10.3390/cancers13133152] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022] Open
Abstract
Brain tumors are among the most lethal tumors. Glioblastoma, the most frequent primary brain tumor in adults, has a median survival time of approximately 15 months after diagnosis or a five-year survival rate of 10%; the recurrence rate is nearly 90%. Unfortunately, this prognosis has not improved for several decades. The lack of progress in the treatment of brain tumors has been attributed to their high rate of primary therapy resistance. Challenges such as pronounced inter-patient variability, intratumoral heterogeneity, and drug delivery across the blood-brain barrier hinder progress. A comprehensive, multiscale understanding of the disease, from the molecular to the whole tumor level, is needed to address the intratumor heterogeneity resulting from the coexistence of a diversity of neoplastic and non-neoplastic cell types in the tumor tissue. By contrast, inter-patient variability must be addressed by subtyping brain tumors to stratify patients and identify the best-matched drug(s) and therapies for a particular patient or cohort of patients. Accomplishing these diverse tasks will require a new framework, one involving a systems perspective in assessing the immense complexity of brain tumors. This would in turn entail a shift in how clinical medicine interfaces with the rapidly advancing high-throughput (HTP) technologies that have enabled the omics-scale profiling of molecular features of brain tumors from the single-cell to the tissue level. However, several gaps must be closed before such a framework can fulfill the promise of precision and personalized medicine for brain tumors. Ultimately, the goal is to integrate seamlessly multiscale systems analyses of patient tumors and clinical medicine. Accomplishing this goal would facilitate the rational design of therapeutic strategies matched to the characteristics of patients and their tumors. Here, we discuss some of the technologies, methodologies, and computational tools that will facilitate the realization of this vision to practice.
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Affiliation(s)
- James H. Park
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
| | | | - Diego M. Marzese
- Balearic Islands Health Research Institute (IdISBa), 07010 Palma, Spain;
| | - Tiffany Juarez
- St. John’s Cancer Institute, Santa Monica, CA 90401, USA; (T.J.); (S.K.)
| | - Abdullah Feroze
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA; (A.F.); (A.P.P.)
| | - Parvinder Hothi
- Swedish Neuroscience Institute, Seattle, WA 98122, USA; (P.H.); (C.C.)
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Seattle, WA 98122, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Seattle, WA 98122, USA; (P.H.); (C.C.)
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Seattle, WA 98122, USA
| | - Anoop P. Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA; (A.F.); (A.P.P.)
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Santosh Kesari
- St. John’s Cancer Institute, Santa Monica, CA 90401, USA; (T.J.); (S.K.)
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
- Departments of Microbiology, Biology, and Molecular Engineering Sciences, University of Washington, Seattle, WA 98105, USA
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Marei HE, Althani A, Afifi N, Hasan A, Caceci T, Pozzoli G, Cenciarelli C. Current progress in chimeric antigen receptor T cell therapy for glioblastoma multiforme. Cancer Med 2021; 10:5019-5030. [PMID: 34145792 PMCID: PMC8335808 DOI: 10.1002/cam4.4064] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
Glioblastoma multiforme (GBM) is one of the deadliest brain tumors with an unfavorable prognosis and overall survival of approximately 20 months following diagnosis. The current treatment for GBM includes surgical resections and chemo‐ and radiotherapeutic modalities, which are not effective. CAR‐T immunotherapy has been proven effective for CD19‐positive blood malignancies, and the application of CAR‐T cell therapy for solid tumors including GBM offers great hope for this aggressive tumor which has a limited response to current treatments. CAR‐T technology depends on the use of patient‐specific T cells genetically engineered to express specific tumor‐associated antigens (TAAs). Interaction of CAR‐T cells with tumor cells triggers the destruction/elimination of these cells by the induction of cytotoxicity and the release of different cytokines. Despite the great promise of CAR‐T cell‐based therapy several challenges exist. These include the heterogeneity of GBM cancer cells, aberrant various signaling pathways involved in tumor progression, antigen escape, the hostile inhibitory GBM microenvironment, T cell dysfunction, blood‐brain barrier, and defective antigen presentation. All need to be addressed before full application at the clinical level can begin. Herein we provide a focused review of the rationale for the use of different types of CAR‐T cells (including FcγRs), the different GBM‐associated antigens, the challenges still facing CAR‐T‐based therapy, and means to overcome such challenges. Finally, we enumerate currently completed and ongoing clinical trials, highlighting the different ways such trials are designed to overcome specific problems. Exploitation of the full potential of CAR‐T cell therapy for GBM depends on their solution.
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Affiliation(s)
- Hany E Marei
- Department of Cytology and Histology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Asmaa Althani
- Biomedical Research Center, Qatar University, Doha, Qatar
| | | | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha, Qatar
| | - Thomas Caceci
- Biomedical Sciences, Virginia Maryland College of Veterinary Medicine, Blacksburg, Virginia, USA
| | - Giacomo Pozzoli
- Pharmacology Unit, Fondazione Policlinico A. Gemelli, IRCCS, Rome, Italy
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Pellerino A, Brastianos PK, Rudà R, Soffietti R. Leptomeningeal Metastases from Solid Tumors: Recent Advances in Diagnosis and Molecular Approaches. Cancers (Basel) 2021; 13:2888. [PMID: 34207653 PMCID: PMC8227730 DOI: 10.3390/cancers13122888] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 06/05/2021] [Indexed: 12/13/2022] Open
Abstract
Leptomeningeal metastases (LM) from solid tumors represent an unmet need of increasing importance due to an early use of MRI for diagnosis and improvement of outcome of some molecular subgroups following targeted agents and immunotherapy. In this review, we first discussed factors limiting the efficacy of targeted agents in LM, such as the molecular divergence between primary tumors and CNS lesions and CNS barriers at the level of the normal brain, brain tumors and CSF. Further, we reviewed pathogenesis and experimental models and modalities, such as MRI (with RANO and ESO/ESMO criteria), CSF cytology and liquid biopsy, to improve diagnosis and monitoring following therapy. Efficacy and limitations of targeted therapies for LM from EGFR-mutant and ALK-rearranged NSCLC, HER2-positive breast cancer and BRAF-mutated melanomas are reported, including the use of intrathecal administration or modification of traditional cytotoxic compounds. The efficacy of checkpoint inhibitors in LM from non-druggable tumors, in particular triple-negative breast cancer, is discussed. Last, we focused on some recent techniques to improve drug delivery.
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Affiliation(s)
- Alessia Pellerino
- Department of Neuro-Oncology, University and City of Health and Science Hospital, 10126 Turin, Italy; (R.R.); (R.S.)
| | - Priscilla K. Brastianos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02115, USA;
| | - Roberta Rudà
- Department of Neuro-Oncology, University and City of Health and Science Hospital, 10126 Turin, Italy; (R.R.); (R.S.)
- Department of Neurology, Castelfranco Veneto and Brain Tumor Board Treviso Hospital, 31100 Treviso, Italy
| | - Riccardo Soffietti
- Department of Neuro-Oncology, University and City of Health and Science Hospital, 10126 Turin, Italy; (R.R.); (R.S.)
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Watanabe K, Nakamura Y, Low SK. Clinical implementation and current advancement of blood liquid biopsy in cancer. J Hum Genet 2021; 66:909-926. [PMID: 34088974 DOI: 10.1038/s10038-021-00939-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/23/2021] [Indexed: 12/14/2022]
Abstract
Liquid biopsies have been receiving tremendous attentions as easy, rapid, and non-invasive tools for cancer diagnosis. Liquid biopsy can be performed repeatedly for disease monitoring and is expected to overcome the limitations of tissue biopsies. With the advancement of next generation sequencing technologies, it is now possible to detect minute amount of tumor-derived circulation tumor DNA (ctDNA) from blood samples. Importantly, ctDNA detection could be complementary to tissue biopsies or tumor biomarkers particularly in cases of which tumor biopsy is clinically difficult to obtain. Here, we introduce the up-to-date technologies used in cfDNA-based liquid biopsy and review the clinical utilities of ctDNA in cancer screening, detection of minimal residual diseases, selection of molecular-targeted drugs, as well as monitoring of treatment responsiveness. We also discuss the challenges and future perspectives of liquid biopsy implementation in clinical setting.
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Affiliation(s)
- Kazunori Watanabe
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Gastroenterological Surgery II, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yusuke Nakamura
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Siew-Kee Low
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
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Huang S, Jin L, Yang J, Duan Y, Zhang M, Zhou C, Zhang YH. Characteristics of Central Nervous System (CNS) Involvement in Children With Non-Hodgkin's Lymphoma (NHL) and the Diagnostic Value of CSF Flow Cytometry in CNS Positive Disease. Technol Cancer Res Treat 2021; 20:15330338211016372. [PMID: 34060372 PMCID: PMC8173989 DOI: 10.1177/15330338211016372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE To investigate the characteristics of central nervous system (CNS) involvement in children with non-Hodgkin's lymphoma (NHL) and the value of flow cytometry (FC) in the diagnosis of CNS disease in pediatric NHL. METHODS The data of 56 newly diagnosed pediatric NHL patients with CNS involvement (CNS+/mass, CNS+/palsy, CNS+/CSF) were analyzed. The proportions and formats of CNS disease in different pathological types were compared. In addition, FC and conventional cytology (CC) of cerebrospinal fluid (CSF) were carried out in 383 newly diagnosed NHL cases. RESULTS A total of 383 children with NHL were enrolled. Among these patients, 56 (14.6%) were diagnosed with positive CNS involvement (CNS+), 33 had bulky disease (tumor diameter >10 cm), 32 had bone marrow invasion, 32 had lactate dehydrogenase levels >1000 U/L, and 25 had invasion of more than 4 organs at the time of diagnosis. There were 14 patients with T lymphoblastic lymphoma (T-LBL), 9 with B lymphoblastic lymphoma (B-LBL), 26 with Burkitt's lymphoma (BL), and 2 with Epstein-Barr virus-positive diffuse large B cell lymphoma (EBV + DLBCL). Among the 56 CNS+ patients, 35 were CSF-positive (CSF+); there were 2 patients who were CSF+ via CC detection and 35 who were CSF+ via FC detection. The difference between CC and FC was statistically significant (P < 0.01). In the T-LBL group, 14 patients were CNS+/CSF, and in the B-LBL group, 8 were CNS+/mass. In the BL group, 22 patients were CNS+/mass and 15 were CNS+/CSF. In the anaplastic large-cell lymphoma group, 5 patients were CNS+/mass. Nine of the 56 CNS+ patients had events. The 2-year overall survival rate was 87% ± 0.046%, and the 2-year event-free survival rate was 76.2% ± 0.07%. CONCLUSION CNS+ diagnoses were more common in pediatric NHL patients with bulky disease and/or bone marrow involvement and/or involvement of more than 4 organs at the time of diagnosis, and they were also common in the EBV + DLBCL and BL groups. FC of CSF showed important clinical significance in the diagnosis of CNS disease in pediatric NHL patients, and it can be used to significantly improve the CNS+ detection rate.
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Affiliation(s)
- Shuang Huang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Ling Jin
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Jing Yang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yanlong Duan
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Meng Zhang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chunju Zhou
- Pathology Department, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yong-Hong Zhang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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Urine as a Source of Liquid Biopsy for Cancer. Cancers (Basel) 2021; 13:cancers13112652. [PMID: 34071230 PMCID: PMC8199052 DOI: 10.3390/cancers13112652] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Tissue biopsy is essential for diagnosis and characterization of a tumor. Recently circulating tumor cells and other tumor-derived nucleic acid can be detected from blood, which is called liquid biopsy. Now this concept has been expanded to many other body fluids including urine. Urine is the least invasive method to obtain a liquid biopsy and can be done anywhere, which allows longitudinal repeated sampling. Here, we review the latest update on urine liquid biopsy in urological and non-urological cancers. Abstract Tissue biopsy is the gold standard for diagnosis and morphological and immunohistochemical analyses to characterize cancer. However, tissue biopsy usually requires an invasive procedure, and it can be challenging depending on the condition of the patient and the location of the tumor. Even liquid biopsy analysis of body fluids such as blood, saliva, gastric juice, sweat, tears and cerebrospinal fluid may require invasive procedures to obtain samples. Liquid biopsy can be applied to circulating tumor cells (CTCs) or nucleic acids (NAs) in blood. Recently, urine has gained popularity due to its less invasive sampling, ability to easily repeat samples, and ability to follow tumor evolution in real-time, making it a powerful tool for diagnosis and treatment monitoring in cancer patients. With the development and advancements in extraction methods of urinary substances, urinary NAs have been found to be closely related to carcinogenesis, metastasis, and therapeutic response, not only in urological cancers but also in non-urological cancers. This review mainly highlights the components of urine liquid biopsy and their utility and limitations in oncology, especially in non-urological cancers.
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Molecular Profiles of Brain Metastases: A Focus on Heterogeneity. Cancers (Basel) 2021; 13:cancers13112645. [PMID: 34071176 PMCID: PMC8198739 DOI: 10.3390/cancers13112645] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Precision cancer medicine depends on the characterization of tumor samples, usually by a single-tumor biopsy, to administer an optimal therapeutic. However, primary tumors and their metastases are often heterogeneous. A metastatic lesion may harbor a completely different genetic makeup to that of its parent tumor, and a single tumor sampling may be ineffective in selecting the most efficient therapy. Brain metastases, due to their low availability and specific microenvironment, pose a particular challenge for precision medicine. In this review, we highlight the genetic landscape of brain metastases, with a particular focus on their heterogeneity. To illustrate this problem, we present phenotypic alterations in brain metastases originating from lung cancer, breast cancer, and melanoma. This article may help clinicians better understand alterations in brain metastases and the relevance of their heterogeneity. Abstract Brain metastasis is a common and devastating clinical entity. Intratumor heterogeneity in brain metastases poses a crucial challenge to precision medicine. However, advances in next-generation sequencing, new insight into the pathophysiology of driver mutations, and the creation of novel tumor models have allowed us to gain better insight into the genetic landscapes of brain metastases, their temporal evolution, and their response to various treatments. A plethora of genomic studies have identified the heterogeneous clonal landscape of tumors and, at the same time, introduced potential targets for precision medicine. As an example, we present phenotypic alterations in brain metastases originating from three malignancies with the highest brain metastasis frequency: lung cancer, breast cancer, and melanoma. We discuss the barriers to precision medicine, tumor heterogeneity, the significance of blood-based biomarkers in tracking clonal evolution, the phylogenetic relationship between primary and metastatic tumors, blood–brain barrier heterogeneity, and limitations to ongoing research.
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Li S, Ke L, Meng X, Zhou H, Zhang X, Wu H, Yu J, Zhang H. Next Generation Sequencing in the Management of Leptomeningeal Metastases of Non-Small Cell Lung Cancer: A Case Report and Literature Review. Recent Pat Anticancer Drug Discov 2021; 16:108-116. [PMID: 33245275 DOI: 10.2174/1574892815666201127114224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/15/2020] [Accepted: 11/10/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Diagnosis of Leptomeningeal Metastases (LM) from Non-Small Cell Lung Cancer (NSCLC) is usually based on clinical symptoms, Cerebral-Spinal Fluid (CSF) cytology, and neuro-imaging. However, early diagnosis of LM in NSCLC is challenging due to the low sensitivity of these approaches. The Next-Generation Sequencing (NGS) using CSF could help improve the diagnosis of LM and guide its treatment options. CASE PRESENTATION We report a 39-year-old male NSCLC patient with negative molecular testing results in the lung cancer tissue sample. The patient developed symptoms of LM with the negative CSF cytology and MRI; however, the NGS analysis of CSF revealed an EGFR exon 19 del mutation. The patient attained 6 months of Progression-Free Survival (PFS) by treating with erlotinib and anlotinib before the neurological symptoms appeared again. EGFR Thr790Met was positive in the CSF but negative in his plasma. The patient was then treated with osimertinib therapy and the response was maintained for more than 1 year. RESULTS & DISCUSSION This case is the first study reporting the clinical benefit of using the combination of erlotinib and anlotinib for the treatment of LM with the EGFR 19 del, osimertinib with EGFR T790M mutation in CSF, but negative gene mutation in the blood or lung tumor biopsy specimens. Our results support that genetic analysis should be performed with CSF samples in all cases of suspected LM when the results of testing for EGFR/ALK/ROS1 mutation in blood samples or tumor biopsy specimens are negative, as these patients could benefit from treatment of TKIs in a poor prognostic setting. CONCLUSION In parallel to current patents, NGS could be applied as a novel strategy in the managing of NSCLC patients with LM.
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Affiliation(s)
- Shuo Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Linping Ke
- Department of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
| | - Xue Meng
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Haiyan Zhou
- Department of Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Xiqin Zhang
- Department of Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Huaguo Wu
- Department of Head and Neck Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Hui Zhang
- Department of Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, China
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Primary central nervous system lymphoma: status and advances in diagnosis, molecular pathogenesis, and treatment. Chin Med J (Engl) 2021; 133:1462-1469. [PMID: 32452898 PMCID: PMC7339152 DOI: 10.1097/cm9.0000000000000844] [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] [Indexed: 12/16/2022] Open
Abstract
Primary central nervous system lymphoma (PCNSL) is a rare group of extra-nodal non-Hodgkin lymphoma which is confined to the central nervous system or eyes. This article aims to present a brief profile of PCNSL diagnosis and treatment in immunocompetent patients. The authors retrieved information from the PubMed database up to September 2019. The annual incidence of PCNSL increased over the last four decades. The prognosis of PCNSL has improved mainly due to the introduction and wide-spread use of high-dose methotrexate, which is now the backbone of all first-line treatment polychemotherapy regimens. Gene expression profiling and next-generation sequencing analyses have revealed mutations that induce activation of nuclear factor-κB, B cell antigen receptor, and Janus kinases/signal transducer and activator of transcription proteins signal pathways. Some novel agents are investigated in the treatment of relapsed PCNSL including immunotherapy and targeted therapy. In particular, lenalidomide and ibrutinib have demonstrated durable efficiency. Treatment of PCNSL has evolved in the last 40 years and survival outcomes have improved in most patient groups, but there is still room to improve outcome by optimizing current chemotherapy and novel agents.
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Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE. Nat Commun 2021; 12:2717. [PMID: 33976150 PMCID: PMC8113516 DOI: 10.1038/s41467-021-22901-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a promising noninvasive biomarker for cell death. Here, we propose an algorithm, CelFiE, to accurately estimate the relative abundances of cell types and tissues contributing to cfDNA from epigenetic cfDNA sequencing. In contrast to previous work, CelFiE accommodates low coverage data, does not require CpG site curation, and estimates contributions from multiple unknown cell types that are not available in external reference data. In simulations, CelFiE accurately estimates known and unknown cell type proportions from low coverage and noisy cfDNA mixtures, including from cell types composing less than 1% of the total mixture. When used in two clinically-relevant situations, CelFiE correctly estimates a large placenta component in pregnant women, and an elevated skeletal muscle component in amyotrophic lateral sclerosis (ALS) patients, consistent with the occurrence of muscle wasting typical in these patients. Together, these results show how CelFiE could be a useful tool for biomarker discovery and monitoring the progression of degenerative disease. Tissue damage and turnover lead to the release of DNA in the blood and can be used to monitor changes in tissue state. Here, the authors developed a tool to accurately estimate the proportion of cell types contributing to cell-free DNA in the blood, with an application to pregnant women and ALS patients.
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118
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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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ctDNA-Based Liquid Biopsy of Cerebrospinal Fluid in Brain Cancer. Cancers (Basel) 2021; 13:cancers13091989. [PMID: 33919036 PMCID: PMC8122255 DOI: 10.3390/cancers13091989] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/18/2022] Open
Abstract
The correct characterisation of central nervous system (CNS) malignancies is crucial for accurate diagnosis and prognosis and also the identification of actionable genomic alterations that can guide the therapeutic strategy. Surgical biopsies are performed to characterise the tumour; however, these procedures are invasive and are not always feasible for all patients. Moreover, they only provide a static snapshot and can miss tumour heterogeneity. Currently, monitoring of CNS cancer is performed by conventional imaging techniques and, in some cases, cytology analysis of the cerebrospinal fluid (CSF); however, these techniques have limited sensitivity. To overcome these limitations, a liquid biopsy of the CSF can be used to obtain information about the tumour in a less invasive manner. The CSF is a source of cell-free circulating tumour DNA (ctDNA), and the analysis of this biomarker can characterise and monitor brain cancer. Recent studies have shown that ctDNA is more abundant in the CSF than plasma for CNS malignancies and that it can be sequenced to reveal tumour heterogeneity and provide diagnostic and prognostic information. Furthermore, analysis of longitudinal samples can aid patient monitoring by detecting residual disease or even tracking tumour evolution at relapse and, therefore, tailoring the therapeutic strategy. In this review, we provide an overview of the potential clinical applications of the analysis of CSF ctDNA and the challenges that need to be overcome in order to translate research findings into a tool for clinical practice.
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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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121
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Shi L, Tang J, Tao H, Guo L, Wu W, Wu H, Liu Z, Tong L, Wu W, Li H, Meng Q, Xu L, Che N, Liu Z. Detection of EGFR Mutations in Cerebrospinal Fluid of EGFR-Mutant Lung Adenocarcinoma With Brain Metastases. Front Oncol 2021; 11:622142. [PMID: 33828979 PMCID: PMC8019917 DOI: 10.3389/fonc.2021.622142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/04/2021] [Indexed: 12/14/2022] Open
Abstract
Background We aimed to investigate the feasibility of detecting epidermal growth factor receptor (EGFR) mutations in cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) and plasma of advanced lung adenocarcinoma (LADC) with brain metastases (BMs) by droplet digital polymerase chain reaction (ddPCR). Methods Thirty advanced LADC patients with BMs were enrolled, and their matched CSF and plasma samples were collected. Droplet digital PCR was used to test cfDNA in CSF and plasma for EGFR mutation status. The clinical response and prognosis were evaluated. Results Out of 30 patients, there were 21 females and 9 males, aged 34-75 years. In all of the cases, CSF cytology were negative. In ddPCR assays, 10 patients (33.3%) had EGFR mutation in CSF, including 3 cases of EGFR T790M mutation, and 16 patients (53.3%) had EGFR mutation in plasma, including 6 cases of EGFR T790M mutation. Five patients with activating EGFR mutations in CSF achieved an intracranial partial response (iPR) after combination treatment with the first-generation EGFR-tyrosine kinase inhibitors. Three patients with EGFR T790M mutations in CSF achieved iPR after second-line osimertinib treatment. The median overall survival and intracranial progression-free survival were 17.0 months and 11.0 months, respectively. Conclusion It was feasible to test EGFR mutation in cerebrospinal fluid and plasma. In LADC patients with brain metastasis, cerebrospinal fluid can be used as a liquid biopsy specimen to guide treatment strategy by monitoring EGFR mutation status.
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Affiliation(s)
- Liang Shi
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Junfang Tang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hong Tao
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Lili Guo
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Weihua Wu
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hongbo Wu
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zichen Liu
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Li Tong
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Wei Wu
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hongxia Li
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qiyi Meng
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Liyan Xu
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Nanying Che
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zhe Liu
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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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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Utility of Cerebrospinal Fluid Cell-Free DNA in Patients with EGFR-Mutant Non-Small-Cell Lung Cancer with Leptomeningeal Metastasis. Target Oncol 2021; 16:207-214. [PMID: 33566300 DOI: 10.1007/s11523-021-00791-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Leptomeningeal metastasis (LM) is a fatal complication of advanced non-small-cell lung cancer (NSCLC). OBJECTIVE The aim of this study was to evaluate the utility of cerebrospinal fluid (CSF) as a medium for epidermal growth factor receptor (EGFR) mutation testing in clinical practice. PATIENTS AND METHODS We prospectively enrolled patients with EGFR-mutant NSCLC who underwent CSF sampling for suspected LM. The supernatant of CSF after routine cytology examination was collected. The diagnosis of LM was established according to EANO-ESMO criteria. CSF and plasma cell-free DNA (cfDNA) were retrieved for EGFR mutation testing. RESULTS Fifty-one patients with a median age of 62.7 years were enrolled. The median duration from initial diagnosis to CSF sampling was 23.0 months and most patients (94.1%) had received at least one EGFR-tyrosine kinase inhibitor. Adenocarcinoma cells were found in 37 CSF samples (72.5%), and 48 (94.1%) patients had confirmed or probable LM. Thirty-five of these 48 patients (72.9%) had valid EGFR mutation-testing results using CSF cfDNA and tended to have higher white blood cell counts and positive cytology in their CSF compared to those with invalid mutation testing results. The overall detection rate of EGFR mutation in CSF cfDNA was 68.8%, and the T790M detection rate was 14.6%. In 37 patients with paired CSF and plasma samples, the concordance rate of the EGFR mutation results was 29.7%. CONCLUSIONS For patients with EGFR-mutant NSCLC with LM, CSF supernatant is a valuable source for EGFR mutation testing and may provide important information.
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Bobillo S, Crespo M, Escudero L, Mayor R, Raheja P, Carpio C, Rubio-Perez C, Tazón-Vega B, Palacio C, Carabia J, Jiménez I, Nieto JC, Montoro J, Martínez-Ricarte F, Castellvi J, Simó M, Puigdefàbregas L, Abrisqueta P, Bosch F, Seoane J. Cell free circulating tumor DNA in cerebrospinal fluid detects and monitors central nervous system involvement of B-cell lymphomas. Haematologica 2021; 106:513-521. [PMID: 32079701 PMCID: PMC7849551 DOI: 10.3324/haematol.2019.241208] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/18/2020] [Indexed: 11/10/2022] Open
Abstract
The levels of cell free circulating tumor DNA (ctDNA) in plasma correlate with treatment response and outcome in systemic lymphomas. Notably, in brain tumors, the levels of ctDNA in the cerebrospinal fluid (CSF) are higher than in plasma. Nevertheless, their role in central nervous system (CNS) lymphomas remains elusive. We evaluated the CSF and plasma from 19 patients: 6 restricted CNS lymphomas, 1 systemic and CNS lymphoma, and 12 systemic lymphomas. We performed whole exome sequencing or targeted sequencing to identify somatic mutations of the primary tumor, then variant-specific droplet digital polymerase chain reaction was designed for each mutation. At time of enrollment, we found ctDNA in the CSF of all patients with restricted CNS lymphoma but not in patients with systemic lymphoma without CNS involvement. Conversely, plasma ctDNA was detected in only 2 out of 6 patients with restricted CNS lymphoma with lower variant allele frequencies than CSF ctDNA. Moreover, we detected CSF ctDNA in one patient with CNS lymphoma in complete remission and in one patient with systemic lymphoma, 3 and 8 months before CNS relapse was confirmed, indicating that CSF ctDNA might detect CNS relapse earlier than conventional methods. Finally, in two cases with CNS lymphoma, CSF ctDNA was still detected after treatment even though no tumoral cells were observed by flow cytometry (FC), indicating that CSF ctDNA detected residual disease better than FC. In conclusion, CSF ctDNA can detect CNS lesions better than plasma ctDNA and FC. In addition, CSF ctDNA predicted CNS relapse in CNS and systemic lymphomas.
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Affiliation(s)
- Sabela Bobillo
- Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Marta Crespo
- Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Laura Escudero
- Translational Research Program, Vall Hebron Institute of Oncology (VHIO)
| | - Regina Mayor
- Translational Research Program, Vall Hebron Institute of Oncology (VHIO)
| | - Priyanka Raheja
- Vall Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Cecilia Carpio
- Vall Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | | | - Bárbara Tazón-Vega
- Vall Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Carlos Palacio
- Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Júlia Carabia
- Vall Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Isabel Jiménez
- Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Juan C Nieto
- Vall Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Julia Montoro
- Vall Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | | | | | - Marc Simó
- Department of Nuclear Medicine, Vall Hebron University Hospital
| | - Lluis Puigdefàbregas
- Vall Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Pau Abrisqueta
- Vall Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Francesc Bosch
- Vall Hebron University Hospital, Universitat Autònoma de Barcelona, Department of Medicine
| | - Joan Seoane
- Translational Research Program, Vall Hebron Institute of Oncology (VHIO)
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Masmudi-Martín M, Zhu L, Sanchez-Navarro M, Priego N, Casanova-Acebes M, Ruiz-Rodado V, Giralt E, Valiente M. Brain metastasis models: What should we aim to achieve better treatments? Adv Drug Deliv Rev 2021; 169:79-99. [PMID: 33321154 DOI: 10.1016/j.addr.2020.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/16/2020] [Accepted: 12/04/2020] [Indexed: 02/07/2023]
Abstract
Brain metastasis is emerging as a unique entity in oncology based on its particular biology and, consequently, the pharmacological approaches that should be considered. We discuss the current state of modelling this specific progression of cancer and how these experimental models have been used to test multiple pharmacologic strategies over the years. In spite of pre-clinical evidences demonstrating brain metastasis vulnerabilities, many clinical trials have excluded patients with brain metastasis. Fortunately, this trend is getting to an end given the increasing importance of secondary brain tumors in the clinic and a better knowledge of the underlying biology. We discuss emerging trends and unsolved issues that will shape how we will study experimental brain metastasis in the years to come.
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126
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Liu Y, Yang S, Zhao J, He Z, Ma J, Guo Y, Wang W, Yoshizawa A, Prelaj A, Tiseo M, Normanno N, Van Schil PE, Wang Q, Yang X. Cell-free DNA from cerebrospinal fluid can be used to detect the EGFR mutation status of lung adenocarcinoma patients with central nervous system metastasis. Transl Lung Cancer Res 2021; 10:914-925. [PMID: 33718032 PMCID: PMC7947414 DOI: 10.21037/tlcr-21-62] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background EGFR tyrosine kinase inhibitors (TKIs) have revolutionized the therapeutic approach for EGFR mutated patients. However, acquired resistance to EGFR-TKI therapy is unavoidable. Repeat biopsy cannot be used, and peripheral blood detection shows a low positive rate in cases of brain-only disease progression. Methods Droplet digital polymerase chain reaction (PCR) (ddPCR) was performed on the plasma and cerebrospinal fluid (CSF) samples of 79 lung adenocarcinoma (LUAD) patients with EGFR mutations and central nervous system (CNS) metastasis. The differences in the EGFR mutation status between the paired plasma and CSF samples were assessed, and the role of CSF testing as a predictor of overall survival was evaluated. Results The CSF of patients with neurological symptoms, EGFR-TKI treatment, or leptomeningeal metastasis (LM) had a significantly higher positive rate of EGFR mutation compared to the plasma samples (P=0.001, P=0.035, P=0.019, respectively). Moreover, EGFR mutation status in CSF was consistent with neurological symptoms and LM (kappa =0.455, P<0.001; kappa =0.508, P<0.001; respectively). For the patients with brain metastasis, EGFR mutation-positive rate in CSF samples was lower than that in plasma samples (28.3% vs. 64.2%, P<0.001), while the patients with LM had the opposite result (84.6% vs. 38.5%, P=0.004). Moreover, patients with EGFR mutation in their CSF experienced worse survival [hazard ratio (HR) =2.93, 95% confidence interval (CI): 1.45–5.92; P=0.003, P adjust <0.0001]. Conclusions The EGFR mutation status of CSF was different from that of plasma and is correlated with patient prognosis. CSF could be helpful in detecting the EGFR mutation status of patients, particularly in cases of LM.
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Affiliation(s)
- Yang Liu
- Department of Radiotherapy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Sen Yang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,Department of Neurology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiuzhou Zhao
- Department of Molecular Pathology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Zhen He
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jie Ma
- Department of Molecular Pathology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Yongjun Guo
- Department of Molecular Pathology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Henan Key Laboratory of Molecular Pathology, Zhengzhou, China
| | - Wei Wang
- Henan Medical Association, Zhengzhou, China
| | - Akihiko Yoshizawa
- Department of Diagnostic Pathology, Kyoto University Hospital, Sakyo-ku, Kyoto, Japan
| | - Arsela Prelaj
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy.,Department of Electronics, Information, and Bioengineering, Polytechnic University of Milan, Milan, Italy
| | - Marcello Tiseo
- Department of Medicine and Surgery, University of Parma and Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-"Fondazione G. Pascale", Naples, Italy
| | - Paul E Van Schil
- Department of Thoracic and Vascular Surgery, University Hospital of Antwerp, Edegem, Belgiu
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Xiaopeng Yang
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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127
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Shah M, Takayasu T, Zorofchian Moghadamtousi S, Arevalo O, Chen M, Lan C, Duose D, Hu P, Zhu JJ, Roy-Chowdhuri S, Riascos RF, Chen H, Luthra R, Esquenazi Y, Ballester LY. Evaluation of the Oncomine Pan-Cancer Cell-Free Assay for Analyzing Circulating Tumor DNA in the Cerebrospinal Fluid in Patients with Central Nervous System Malignancies. J Mol Diagn 2021; 23:171-180. [PMID: 33531134 DOI: 10.1016/j.jmoldx.2020.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 10/09/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Available tools to evaluate patients with central nervous system (CNS) tumors such as magnetic resonance imaging (MRI), cerebrospinal fluid (CSF) cytology, and brain biopsies, have significant limitations. MRI and CSF cytology have poor specificity and sensitivity, respectively, and brain biopsies are invasive. Circulating tumor DNA in CSF (CSF-ctDNA) could be used as a biomarker in patients with CNS tumors, but studies in this area are limited. We evaluated four CSF-ctDNA extraction methods and analyzed mutations in CSF-ctDNA with the Oncomine Pan-Cancer cell-free assay. CSF-ctDNA was extracted from 38 patients with primary or metastatic CNS tumors and 10 patients without CNS malignancy. Commercial ctDNA controls were used for assay evaluation. CSF-ctDNA yields ranged from 3.65 to 3120 ng. Mutations were detected in 39.5% of samples. TP53 was the most commonly mutated gene and copy number alterations were detected in CCND1, MYC, and ERBB2/HER2. Twenty-five percent of CSF-cytology-negative samples showed mutations in CSF-ctDNA. There was good concordance between mutations in CSF-ctDNA and matching tumors. The QIAamp Circulating Nucleic Acid Kit was the optimal method for extraction of CSF-ctDNA and the Oncomine cell-free DNA assay is suitable for detection of mutations in CSF-ctDNA. Analysis of CSF-ctDNA is more sensitive than CSF-cytology and has the potential to improve the diagnosis and monitoring of patients with CNS tumors.
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Affiliation(s)
- Mauli Shah
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Takeshi Takayasu
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Soheil Zorofchian Moghadamtousi
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Octavio Arevalo
- Department of Radiology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Melissa Chen
- Department of Radiology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chieh Lan
- Division of Pathology and Laboratory Medicine, Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Duose
- Division of Pathology and Laboratory Medicine, Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter Hu
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jay-Jiguang Zhu
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center, Houston, Texas; Memorial Hermann Hospital, Texas Medical Center, Houston, Texas
| | - Sinchita Roy-Chowdhuri
- Division of Pathology and Laboratory Medicine, Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roy F Riascos
- Department of Radiology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Hui Chen
- Division of Pathology and Laboratory Medicine, Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Division of Pathology and Laboratory Medicine, Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas; Division of Pathology and Laboratory Medicine, Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yoshua Esquenazi
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center, Houston, Texas; Memorial Hermann Hospital, Texas Medical Center, Houston, Texas.
| | - Leomar Y Ballester
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas; Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center, Houston, Texas; Memorial Hermann Hospital, Texas Medical Center, Houston, Texas.
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128
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Angus L, Deger T, Jager A, Martens JWM, de Weerd V, van Heuvel I, van den Bent MJ, Sillevis Smitt PAE, Kros JM, Bindels EMJ, Heitzer E, Sleijfer S, Jongen JLM, Wilting SM. Detection of Aneuploidy in Cerebrospinal Fluid from Patients with Breast Cancer Can Improve Diagnosis of Leptomeningeal Metastases. Clin Cancer Res 2021; 27:2798-2806. [PMID: 33514525 DOI: 10.1158/1078-0432.ccr-20-3954] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/04/2020] [Accepted: 01/25/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Detection of leptomeningeal metastasis is hampered by limited sensitivities of currently used techniques: MRI and cytology of cerebrospinal fluid (CSF). Detection of cell-free tumor DNA in CSF has been proposed as a tumor-specific candidate to detect leptomeningeal metastasis at an earlier stage. The aim of this study was to investigate mutation and aneuploidy status in CSF-derived cell-free DNA (cfDNA) of patients with breast cancer with a clinical suspicion of leptomeningeal metastasis. EXPERIMENTAL DESIGN cfDNA was isolated from stored remnant CSF and analyzed by targeted next-generation sequencing (NGS; n = 30) and the modified fast aneuploidy screening test-sequencing system (mFAST-SeqS; n = 121). The latter method employs selective amplification of long interspaced nuclear elements sequences that are present throughout the genome and allow for fast and cheap detection of aneuploidy. We compared these results with the gold standard to diagnose leptomeningeal metastasis: cytology. RESULTS Leptomeningeal metastasis was cytology proven in 13 of 121 patients. Low DNA yields resulted in insufficient molecular coverage of NGS for the majority of samples (success rate, 8/30). The mFAST-SeqS method, successful in 112 of 121 (93%) samples, detected genome-wide aneuploidy in 24 patients. Ten of these patients had cytology-proven leptomeningeal metastasis; 8 additional patients were either concurrently diagnosed with central nervous system metastases by radiological means or developed these soon after the lumbar puncture. The remaining six cases were suspected of leptomeningeal metastasis, but could not be confirmed by cytology or imaging. Aneuploidy was associated with development of leptomeningeal metastasis and significantly worse overall survival. CONCLUSIONS Aneuploidy in CSF-derived cfDNA may provide a promising biomarker to improve timely detection of leptomeningeal metastasis.
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Affiliation(s)
- Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Teoman Deger
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Irene van Heuvel
- Department of Neurology, The Brain Tumor Center at Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Martin J van den Bent
- Department of Neurology, The Brain Tumor Center at Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Peter A E Sillevis Smitt
- Department of Neurology, The Brain Tumor Center at Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Eric M J Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ellen Heitzer
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Joost L M Jongen
- Department of Neurology, The Brain Tumor Center at Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
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Díaz Méndez AB, Tremante E, Regazzo G, Brandner S, Rizzo MG. Time to focus on circulating nucleic acids for diagnosis and monitoring of gliomas: A systematic review of their role as biomarkers. Neuropathol Appl Neurobiol 2021; 47:471-487. [PMID: 33403678 DOI: 10.1111/nan.12691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 11/30/2022]
Abstract
Gliomas are diffusely growing tumours arising from progenitors within the central nervous system. They encompass a range of different molecular types and subtypes, many of which have a well-defined profile of driver mutations, copy number changes and DNA methylation patterns. A majority of gliomas will require surgical intervention to relieve raised intracranial pressure and reduce tumour burden. A proportion of tumours, however, are located in neurologically sensitive areas and a biopsy poses a significant risk of a deficit. A majority of gliomas recur after surgery, and monitoring tumour burden of the recurrence is currently achieved by imaging. However, most imaging modalities have limitations in assessing tumour burden and infiltration into adjacent brain, and sometimes imaging is unable to discriminate between tumour recurrence and pseudo-progression. Liquid biopsies, obtained from body fluids such as cerebrospinal fluid or blood, contain circulating nucleic acids or extracellular vesicles containing tumour-derived components. The studies for this systematic review were selected according to PRISMA criteria, and suggest that the detection of circulating tumour-derived nucleic acids holds great promises as biomarker to aid diagnosis and prognostication by monitoring tumour progression, and thus can be considered a pathway towards personalized medicine.
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Affiliation(s)
- Ana Belén Díaz Méndez
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Elisa Tremante
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Regazzo
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK.,Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Maria G Rizzo
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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130
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Fujioka Y, Hata N, Akagi Y, Kuga D, Hatae R, Sangatsuda Y, Michiwaki Y, Amemiya T, Takigawa K, Funakoshi Y, Sako A, Iwaki T, Iihara K, Mizoguchi M. Molecular diagnosis of diffuse glioma using a chip-based digital PCR system to analyze IDH, TERT, and H3 mutations in the cerebrospinal fluid. J Neurooncol 2021; 152:47-54. [PMID: 33417137 PMCID: PMC7910241 DOI: 10.1007/s11060-020-03682-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE Conventional genetic analyzers require surgically obtained tumor tissues to confirm the molecular diagnosis of diffuse glioma. Recent technical breakthroughs have enabled increased utilization of cell-free tumor DNA (ctDNA) in body fluids as a reliable resource for molecular diagnosis in various cancers. Here, we tested the application of a chip-based digital PCR system for the less invasive diagnosis (i.e., liquid biopsy) of diffuse glioma using the cerebrospinal fluid (CSF). METHODS CSF samples from 34 patients with diffuse glioma were collected from the surgical field during craniotomy. Preoperative lumbar CSF collection was also performed in 11 patients. Extracted ctDNA was used to analyze diagnostic point mutations in IDH1 R132H, TERT promoter (C228T and C250T), and H3F3A (K27M) on the QuantStudio® 3D Digital PCR System. These results were compared with their corresponding tumor DNA samples. RESULTS We detected either of the diagnostic mutations in tumor DNA samples from 28 of 34 patients. Among them, we achieved precise molecular diagnoses using intracranial CSF in 20 (71%). Univariate analyses revealed that the World Health Organization (WHO) grade (p = 0.0034), radiographic enhancement (p = 0.0006), and Mib1 index (p = 0.01) were significant predictors of precise CSF-based molecular diagnosis. We precisely diagnosed WHO grade III or IV diffuse gliomas using lumbar CSF obtained from 6 (87%) of 7 patients with tumors harboring any mutation. CONCLUSION We established a novel, non-invasive molecular diagnostic method using a chip-based digital PCR system targeting ctDNA derived from CSF with high sensitivity and specificity, especially for high-grade gliomas.
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Affiliation(s)
- Yutaka Fujioka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Yojiro Akagi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yuhei Michiwaki
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Takeo Amemiya
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kosuke Takigawa
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yusuke Funakoshi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Aki Sako
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Toru Iwaki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Iihara
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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131
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Smyth LM, Reichel JB, Tang J, Patel JAA, Meng F, Selcuklu DS, Houck-Loomis B, You D, Samoila A, Schiavon G, Li BT, Razavi P, Piscuoglio S, Reis-Filho JS, Taylor BS, Baselga J, Solit DB, Hyman DM, Berger MF, Chandarlapaty S. Utility of Serial cfDNA NGS for Prospective Genomic Analysis of Patients on a Phase I Basket Study. JCO Precis Oncol 2021; 5:PO.20.00184. [PMID: 34250397 DOI: 10.1200/po.20.00184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/18/2020] [Accepted: 10/28/2020] [Indexed: 01/06/2023] Open
Abstract
PURPOSE Cell-free DNA (cfDNA) analysis offers a noninvasive means to access the tumor genome. Despite limited sensitivity of broad-panel sequencing for detecting low-frequency mutations in cfDNA, it may enable more comprehensive genomic characterization in patients with sufficiently high disease burden. We investigated the utility of large-panel cfDNA sequencing in patients enrolled to a Phase I AKT1-mutant solid tumor basket study. METHODS Patients had AKT1 E17K-mutant solid tumors and were treated on the multicenter basket study (ClinicalTrials.gov identifier: NCT01226316) of capivasertib, an AKT inhibitor. Serial plasma samples were prospectively collected and sequenced using exon-capture next-generation sequencing (NGS) analysis of 410 genes (Memorial Sloan Kettering [MSK]-Integrated Molecular Profiling of Actionable Cancer Target [IMPACT]) and allele-specific droplet digital polymerase chain reaction (ddPCR) for AKT1 E17K. Tumor DNA (tDNA) NGS (MSK-IMPACT) was also performed on available pretreatment tissue biopsy specimens. RESULTS Among 25 patients, pretreatment plasma samples were sequenced to an average coverage of 504×. Somatic mutations were called in 20/25 (80%), with mutant allele fractions highly concordant with ddPCR of AKT1 E17K (r 2 = 0.976). Among 17 of 20 cfDNA-positive patients with available tDNA for comparison, mutational concordance was acceptable, with 82% of recurrent mutations shared between tissue and plasma. cfDNA NGS captured additional tumor heterogeneity, identifying mutations not observed in tDNA in 38% of patients, and revealed oncogenic mutations in patients without available baseline tDNA. Longitudinal cfDNA NGS (n = 98 samples) revealed distinct patterns of clonal dynamics in response to therapy. CONCLUSION Large gene panel cfDNA NGS is feasible for patients with high disease burden and is concordant with single-analyte approaches, providing a robust alternative to ddPCR with greater breadth. cfDNA NGS can identify heterogeneity and potentially biologically informative and clinically relevant alterations.
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Affiliation(s)
| | | | - Jiabin Tang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Fanli Meng
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Daoqi You
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Gaia Schiavon
- R&D Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - José Baselga
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - David M Hyman
- Memorial Sloan Kettering Cancer Center, New York, NY
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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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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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Dudley JC, Diehn M. Detection and Diagnostic Utilization of Cellular and Cell-Free Tumor DNA. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 16:199-222. [PMID: 33228464 DOI: 10.1146/annurev-pathmechdis-012419-032604] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Because cancer is caused by an accumulation of genetic mutations, mutant DNA released by tumors can be used as a highly specific biomarker for cancer. Although this principle was described decades ago, the advent and falling costs of next-generation sequencing have made the use of tumor DNA as a biomarker increasingly practical. This review surveys the use of cellular and cell-free DNA for the detection of cancer, with a focus on recent technological developments and applications to solid tumors. It covers (a) key principles and technology enabling the highly sensitive detection of tumor DNA; (b) assessment of tumor DNA in plasma, including for genotyping, minimal residual disease detection, and early detection of localized cancer; (c) detection of tumor DNA in body cavity fluids, such as urine or cerebrospinal fluid; and (d) challenges posed to the use of tumor DNA as a biomarker by the phenomenon of benign clonal expansions.
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Affiliation(s)
- Jonathan C Dudley
- Ludwig Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA;
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Durin L, Pradines A, Basset C, Ulrich B, Keller L, Dongay V, Favre G, Mazieres J, Guibert N. Liquid Biopsy of Non-Plasma Body Fluids in Non-Small Cell Lung Cancer: Look Closer to the Tumor! Cells 2020; 9:cells9112486. [PMID: 33207539 PMCID: PMC7698102 DOI: 10.3390/cells9112486] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/19/2022] Open
Abstract
Liquid biopsy is a rapidly emerging field due to an increasing number of oncogenic drivers and a better understanding of resistance mechanisms to targeted therapies in non-small cell lung cancer (NSCLC). The sensitivity of the most widely used blood-based assays is, however, limited in particular in cases of low tumor volume where shed of tumor-derived material can be limited. A negative result thus requires biopsy confirmation using minimally invasive sampling procedures that can result in small specimens, which are often not suitable for genotyping. Liquid biopsy is not limited to plasma, and tumor DNA circulating in other body fluids such as urine, pleural fluid, cerebrospinal fluid, or cytology specimen-derived supernatant can be exploited. In comparison to cell blocks, these fluids in close contact to the tumor may contain a more abundant and less analytically demanding tumor DNA. In this review, we discuss the potential applications of circulating tumor DNA derived from cytology samples in NSCLC, from early stage (screening, nodule characterization) to metastatic disease.
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Affiliation(s)
- Lucile Durin
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
| | - Anne Pradines
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
| | - Céline Basset
- Cytology Department, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France;
| | - Bryan Ulrich
- Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Laura Keller
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
| | - Vincent Dongay
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
| | - Gilles Favre
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
- University of Toulouse III—Paul Sabatier, 31062 Toulouse, France
| | - Julien Mazieres
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- University of Toulouse III—Paul Sabatier, 31062 Toulouse, France
| | - Nicolas Guibert
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- University of Toulouse III—Paul Sabatier, 31062 Toulouse, France
- Correspondence: ; Tel.: +33-567771836
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Choudhury NJ, Yang SR, Arcila M, Mohanty AS, Boire A, Drilon A. Genomic Characterization of a RET Inhibitor-Resistant RET Fusion-Positive Lung Cancer by CSF Cell-Free DNA Hybrid Capture-Based Sequencing. JCO Precis Oncol 2020; 4:2000188. [PMID: 33381675 DOI: 10.1200/po.20.00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
- Noura J Choudhury
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Soo-Ryum Yang
- Department of Pathology, Diagnostic Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcila
- Department of Pathology, Diagnostic Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abhinita S Mohanty
- Department of Pathology, Diagnostic Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Adrienne Boire
- Department of Neurology, Human Oncology and Pathogenesis Program, Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
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Dhanyamraju PK, Patel TN, Dovat S. Medulloblastoma: "Onset of the molecular era". Mol Biol Rep 2020; 47:9931-9937. [PMID: 33159234 DOI: 10.1007/s11033-020-05971-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
Among brain tumors, Medulloblastoma (MB) is one of the most common, malignant, pediatric tumors of the cerebellum. It accounts for ~20% of all childhood central nervous system (CNS) tumors. Despite, tremendous advances in drug development processes, as well as novel drugs for MB the morbidity and mortality rates, remain high. Craniospinal radiation, high-dose chemotherapy, and surgical resection are the primary therapeutic strategies. Tremendous progress in the field of "genomics" with vast amounts of data has led to the identification of four distinct molecular subgroups in medulloblastoma: WNT group, SHH group, group-III, and group-IV. The identification of these subgroups has led to individualized treatment strategies for each subgroup. Here, we discuss the various molecular subgroups of medulloblastoma as well as the differences between them. We also highlight the latest treatment strategies available for medulloblastoma.
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Affiliation(s)
- Pavan Kumar Dhanyamraju
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
| | - Trupti N Patel
- Department of Integrative Biology, Vellore Institute of Technology, Vellore, India
| | - Sinisa Dovat
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
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Cecchini MJ, Yi ES. Liquid biopsy is a valuable tool in the diagnosis and management of lung cancer. J Thorac Dis 2020; 12:7048-7056. [PMID: 33282410 PMCID: PMC7711358 DOI: 10.21037/jtd.2020.04.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsy refers to the use of various body fluids to test for circulating biological elements derived from the tumor. Liquid biopsy has taken on an increasingly important role in lung cancer diagnosis, molecular characterization, surveillance, monitoring, and determining mechanisms of resistance. These assays can utilize various sources of cell-free DNA (cfDNA) including blood, pleural fluid, urine, and others to detect tumor associated alterations. With the increasing power of next-generation sequencing technologies and the development of assays such as digital droplet PCR, rare tumor alleles can be detected in cfDNA to determine key characteristics of the tumor. Current assays, while effective, are still challenged by limited sensitivity and capacity to single genes or small panels of genes, though this is rapidly expanding. Nevertheless, testing of cfDNA has been shown to be valuable in detecting resistance to targeted inhibitors, particularly for detection of T790M in EGFR and monitoring response to therapy. With the continued development of more powerful and sensitive assays, these techniques will empower clinicians to better characterize early stage disease and can be used in the screening of high-risk patients, which may eliminate the requirement for tissue diagnosis in some settings. That said, since the majority of these alterations are not specific to lung cancer, there will continue to be a need for tissue in at least the initial diagnosis. Used in conjugation with tissue sampling, these assays will assist the treating clinician and the pathologist to better characterize individual tumors, even in the setting of limited tissue.
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Affiliation(s)
- Matthew J Cecchini
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Eunhee S Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
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139
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Escudero L, Llort A, Arias A, Diaz-Navarro A, Martínez-Ricarte F, Rubio-Perez C, Mayor R, Caratù G, Martínez-Sáez E, Vázquez-Méndez É, Lesende-Rodríguez I, Hladun R, Gros L, Ramón Y Cajal S, Poca MA, Puente XS, Sahuquillo J, Gallego S, Seoane J. Circulating tumour DNA from the cerebrospinal fluid allows the characterisation and monitoring of medulloblastoma. Nat Commun 2020; 11:5376. [PMID: 33110059 PMCID: PMC7591522 DOI: 10.1038/s41467-020-19175-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/30/2020] [Indexed: 02/08/2023] Open
Abstract
The molecular characterisation of medulloblastoma, the most common paediatric brain tumour, is crucial for the correct management and treatment of this heterogenous disease. However, insufficient tissue sample, the presence of tumour heterogeneity, or disseminated disease can challenge its diagnosis and monitoring. Here, we report that the cerebrospinal fluid (CSF) circulating tumour DNA (ctDNA) recapitulates the genomic alterations of the tumour and facilitates subgrouping and risk stratification, providing valuable information about diagnosis and prognosis. CSF ctDNA also characterises the intra-tumour genomic heterogeneity identifying small subclones. ctDNA is abundant in the CSF but barely present in plasma and longitudinal analysis of CSF ctDNA allows the study of minimal residual disease, genomic evolution and the characterisation of tumours at recurrence. Ultimately, CSF ctDNA analysis could facilitate the clinical management of medulloblastoma patients and help the design of tailored therapeutic strategies, increasing treatment efficacy while reducing excessive treatment to prevent long-term secondary effects.
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Affiliation(s)
- Laura Escudero
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Anna Llort
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Alexandra Arias
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Ander Diaz-Navarro
- Dpto. de Bioquímica y Biología Molecular, IUOPA-Universidad de Oviedo, 33006, Oviedo, Spain.,CIBERONC, Barcelona, Spain
| | - Francisco Martínez-Ricarte
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain.,Universitat Autònoma de Barcelona (UAB), 08193, Cerdanyola del Vallès, Spain
| | - Carlota Rubio-Perez
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Regina Mayor
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Ginevra Caratù
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Elena Martínez-Sáez
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Élida Vázquez-Méndez
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | | | - Raquel Hladun
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Luis Gros
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Santiago Ramón Y Cajal
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Maria A Poca
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain.,Universitat Autònoma de Barcelona (UAB), 08193, Cerdanyola del Vallès, Spain
| | - Xose S Puente
- Dpto. de Bioquímica y Biología Molecular, IUOPA-Universidad de Oviedo, 33006, Oviedo, Spain.,CIBERONC, Barcelona, Spain
| | - Juan Sahuquillo
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain.,Universitat Autònoma de Barcelona (UAB), 08193, Cerdanyola del Vallès, Spain
| | - Soledad Gallego
- Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron University Hospital, 08035, Barcelona, Spain.,Universitat Autònoma de Barcelona (UAB), 08193, Cerdanyola del Vallès, Spain
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, 08035, Barcelona, Spain. .,CIBERONC, Barcelona, Spain. .,Universitat Autònoma de Barcelona (UAB), 08193, Cerdanyola del Vallès, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
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140
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Zheng MM, Li YS, Tu HY, Jiang BY, Yang JJ, Zhou Q, Xu CR, Yang XR, Wu YL. Genotyping of Cerebrospinal Fluid Associated With Osimertinib Response and Resistance for Leptomeningeal Metastases in EGFR-Mutated NSCLC. J Thorac Oncol 2020; 16:250-258. [PMID: 33122107 DOI: 10.1016/j.jtho.2020.10.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/16/2020] [Accepted: 10/02/2020] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Patients with NSCLC with leptomeningeal metastases (LM) presented dismal prognosis. Cerebrospinal fluid (CSF) is suggested as a medium of liquid biopsy of LM. However, the clinical implications of CSF genotyping on treatment outcomes remained elusive. METHODS Patients with EGFR-mutated advanced NSCLC with LM were included: cohort 1, patients with LM who were treated with osimertinib with CSF and plasma genotyping performed before the first dosing of osimertinib (baseline, n = 45); cohort 2, CSF genotyping on progression on osimertinib and development of LM (the progression event on osimertinib is the diagnosis of LM, n = 35). Circulating tumor DNA in CSF underwent next-generation sequencing. RESULTS Sensitivity of CSF genotyping for EGFR-sensitizing mutations was 93.3% (42 of 45) and 97.1% (34 of 35) in cohorts 1 and 2, respectively. In cohort 1, patients with EGFR exon 19 deletion had higher median intracranial progression free survival (iPFS) than those with EGFR exon 21 L858R mutation (11.9 versus 2.8 mo; p = 0.02). Median iPFS was significantly longer in patients with T790M-positive CSF genotyping (15.6 mo) than T790M-negative CSF (7.0 mo, p = 0.04). Concurrent CDK4 (2.8 versus 11.6 mo, p = 0.002) and CDKN2A (2.5 versus 9.6 mo, p = 0.04) mutation with EGFR-sensitizing mutations indicated lower median iPFS. Patients with T790M-negative CSF, EGFR exon 21 L858R mutation, concurrent FGF3 alteration, and over first-line osimertinib had shortened iPFS. In cohort 2, possible EGFR-related and EGFR-independent resistance mechanisms were found including C797S mutation, MET dysregulation, and TP53 plus RB1 co-occurrence. Patients with loss of T790M in CSF had a shorter median iPFS (7.4 mo) compared with those with reserved T790M (13.6 mo, p = 0.01). CONCLUSIONS Genotyping of CSF indicated heterogeneous response to osimertinib and revealed the genetic characteristic of LM on osimertinib failure in patients with EGFR-mutated NSCLC diagnosed with LM.
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Affiliation(s)
- Mei-Mei Zheng
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Yang-Si Li
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Hai-Yan Tu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Ben-Yuan Jiang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Jin-Ji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Chong-Rui Xu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Xiao-Rong Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China.
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141
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Bruzek AK, Ravi K, Muruganand A, Wadden J, Babila CM, Cantor E, Tunkle L, Wierzbicki K, Stallard S, Dickson RP, Wolfe I, Mody R, Schwartz J, Franson A, Robertson PL, Muraszko KM, Maher CO, Garton HJL, Qin T, Koschmann C. Electronic DNA Analysis of CSF Cell-free Tumor DNA to Quantify Multi-gene Molecular Response in Pediatric High-grade Glioma. Clin Cancer Res 2020; 26:6266-6276. [PMID: 33087334 DOI: 10.1158/1078-0432.ccr-20-2066] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/07/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Pediatric high-grade glioma (pHGG) diagnosis portends poor prognosis and therapeutic monitoring remains difficult. Tumors release cell-free tumor DNA (cf-tDNA) into cerebrospinal fluid (CSF), allowing for potential detection of tumor-associated mutations by CSF sampling. We hypothesized that direct, electronic analysis of cf-tDNA with a handheld platform (Oxford Nanopore MinION) could quantify patient-specific CSF cf-tDNA variant allele fraction (VAF) with improved speed and limit of detection compared with established methods. EXPERIMENTAL DESIGN We performed ultra-short fragment (100-200 bp) PCR amplification of cf-tDNA for clinically actionable alterations in CSF and tumor samples from patients with pHGG (n = 12) alongside nontumor CSF (n = 6). PCR products underwent rapid amplicon-based sequencing by Oxford Nanopore Technology (Nanopore) with quantification of VAF. Additional comparison to next-generation sequencing (NGS) and droplet digital PCR (ddPCR) was performed. RESULTS Nanopore demonstrated 85% sensitivity and 100% specificity in CSF samples (n = 127 replicates) with 0.1 femtomole DNA limit of detection and 12-hour results, all of which compared favorably with NGS. Multiplexed analysis provided concurrent analysis of H3.3A (H3F3A) and H3C2 (HIST1H3B) mutations in a nonbiopsied patient and results were confirmed by ddPCR. Serial CSF cf-tDNA sequencing by Nanopore demonstrated correlation of radiological response on a clinical trial, with one patient showing dramatic multi-gene molecular response that predicted long-term clinical response. CONCLUSIONS Nanopore sequencing of ultra-short pHGG CSF cf-tDNA fragments is feasible, efficient, and sensitive with low-input samples thus overcoming many of the barriers restricting wider use of CSF cf-tDNA diagnosis and monitoring in this patient population.
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Affiliation(s)
- Amy K Bruzek
- Department of Neurosurgery, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Karthik Ravi
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Ashwath Muruganand
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jack Wadden
- Department of Computer Engineering, University of Michigan, Ann Arbor, Michigan
| | - Clarissa May Babila
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Evan Cantor
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Leo Tunkle
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kyle Wierzbicki
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Stefanie Stallard
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Robert P Dickson
- Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Ian Wolfe
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Rajen Mody
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | | | - Andrea Franson
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Patricia L Robertson
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Karin M Muraszko
- Department of Neurosurgery, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Cormac O Maher
- Department of Neurosurgery, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Hugh J L Garton
- Department of Neurosurgery, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Tingtin Qin
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Carl Koschmann
- Department of Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan.
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142
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Ramkissoon LA, Pegram W, Haberberger J, Danziger N, Lesser G, Strowd R, Dahiya S, Cummings TJ, Bi WL, Abedalthagafi M, Sathyan P, McGregor K, Reddy P, Severson E, Williams E, Lin D, Edgerly C, Huang RSP, Hemmerich A, Creeden J, Brown C, Venstrom J, Hegde P, Ross JS, Alexander BM, Elvin J, Ramkissoon SH. Genomic Profiling of Circulating Tumor DNA From Cerebrospinal Fluid to Guide Clinical Decision Making for Patients With Primary and Metastatic Brain Tumors. Front Neurol 2020; 11:544680. [PMID: 33192972 PMCID: PMC7604477 DOI: 10.3389/fneur.2020.544680] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 09/09/2020] [Indexed: 12/04/2022] Open
Abstract
Despite advances in systemic therapies for solid tumors, the development of brain metastases remains a significant contributor to overall cancer mortality and requires improved methods for diagnosing and treating these lesions. Similarly, the prognosis for malignant primary brain tumors remains poor with little improvement in overall survival over the last several decades. In both primary and metastatic central nervous system (CNS) tumors, the challenge from a clinical perspective centers on detecting CNS dissemination early and understanding how CNS lesions differ from the primary tumor, in order to determine potential treatment strategies. Acquiring tissue from CNS tumors has historically been accomplished through invasive neurosurgical procedures, which restricts the number of patients to those who can safely undergo a surgical procedure, and for which such interventions will add meaningful value to the care of the patient. In this review we discuss the potential of analyzing cell free DNA shed from tumor cells that is contained within the cerebrospinal fluid (CSF) as a sensitive and minimally invasive method to detect and characterize primary and metastatic tumors in the CNS.
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Affiliation(s)
- Lori A Ramkissoon
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Worthy Pegram
- Foundation Medicine, Inc., Morrisville, NC, United States
| | | | | | - Glenn Lesser
- Section of Medical Oncology and Hematology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States
| | - Roy Strowd
- Section of Medical Oncology and Hematology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States
| | - Sonika Dahiya
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MI, United States
| | - Thomas J Cummings
- Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, United States
| | - Malak Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | | | | | | | - Eric Severson
- Foundation Medicine, Inc., Morrisville, NC, United States
| | - Erik Williams
- Foundation Medicine, Inc., Morrisville, NC, United States
| | - Douglas Lin
- Foundation Medicine, Inc., Cambridge, MA, United States
| | - Claire Edgerly
- Foundation Medicine, Inc., Morrisville, NC, United States
| | | | | | - James Creeden
- Foundation Medicine, Inc., Cambridge, MA, United States
| | | | | | - Priti Hegde
- Foundation Medicine, Inc., Cambridge, MA, United States
| | | | | | - Julia Elvin
- Foundation Medicine, Inc., Cambridge, MA, United States
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., Morrisville, NC, United States.,Department of Pathology and Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, United States
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143
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Nakano Y, Watanabe Y, Honda-Kitahara M, Yamagishi Y, Niizuma H, Niihori T, Sasahara Y, Sonoda Y, Narita Y, Nagane M, Kure S, Ichimura K. Utility of a bridged nucleic acid clamp for liquid biopsy: Detecting BRAF V600E in the cerebrospinal fluid of a patient with brain tumor. Pediatr Blood Cancer 2020; 67:e28651. [PMID: 32776443 DOI: 10.1002/pbc.28651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Yoshiko Nakano
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Pediatric Oncology/Hematology, Osaka City General Hospital, Osaka, Japan
| | - Yuko Watanabe
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan.,Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Mai Honda-Kitahara
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuki Yamagishi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan.,Department of Neurosurgery, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Hidetaka Niizuma
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Yoji Sasahara
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Yukihiko Sonoda
- Department of Neurosurgery, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Motoo Nagane
- Department of Neurosurgery, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
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144
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Li J, Zhao S, Lee M, Yin Y, Li J, Zhou Y, Ballester LY, Esquenazi Y, Dashwood RH, Davies PJA, Parsons DW, Li XN, Huang Y, Sun D. Reliable tumor detection by whole-genome methylation sequencing of cell-free DNA in cerebrospinal fluid of pediatric medulloblastoma. SCIENCE ADVANCES 2020; 6:6/42/eabb5427. [PMID: 33067228 PMCID: PMC7567591 DOI: 10.1126/sciadv.abb5427] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/01/2020] [Indexed: 05/11/2023]
Abstract
Medulloblastoma (MB), the most common form of pediatric brain malignancy, has a low frequency of oncogenic mutations but pronouncedly abnormal DNA methylation changes. Epigenetic analysis of circulating cell-free tumor DNA (ctDNA) by liquid biopsy offers an approach for real-time monitoring of tumor status without tumor dissection. In this study, we identified 6598 differentially methylated CpGs in both MB tumors and the ctDNA isolated from matched cerebrospinal fluid (CSF) compared with normal cerebellum, which could be used to detect MB tumor occurrence and determine its subtype. Furthermore, DNA methylation changes in serial CSF samples could be used to monitor the treatment response and tumor recurrence. Integrating our data with large public datasets, we identified reliable MB DNA methylation signatures in ctDNA that have potential diagnostic and prognostic values. Our study sets the stage for exploiting epigenetic markers in CSF to improve the clinical management of patients with MB.
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Affiliation(s)
- Jia Li
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Sibo Zhao
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Hematology and Oncology, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Minjung Lee
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yue Yin
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Jin Li
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Leomar Y Ballester
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yoshua Esquenazi
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Roderick H Dashwood
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Peter J A Davies
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - D Williams Parsons
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiao-Nan Li
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA.
- Program of Precision Medicine PDOX Modeling of Pediatric Cancers, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA.
| | - Deqiang Sun
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA.
- Gomics Technology Corporation, 7707 Fannin Street, Suite 200, Houston, TX 77054, USA
- Department of Cardiology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
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145
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Cerebrospinal fluid circulating tumour DNA as a liquid biopsy for central nervous system malignancies. Curr Opin Neurol 2020; 33:736-741. [DOI: 10.1097/wco.0000000000000869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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146
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Cheng P, Feng F, Yang H, Jin S, Lai C, Wang Y, Bi J. Detection and significance of exosomal mRNA expression profiles in the cerebrospinal fluid of patients with meningeal carcinomatosis. J Mol Neurosci 2020; 71:790-803. [PMID: 32959225 DOI: 10.1007/s12031-020-01701-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/07/2020] [Indexed: 01/05/2023]
Abstract
Exosomes are cell-derived membrane vesicles with cargo that can be transported into receiver cells to exert their biological roles. Exosomal RNA signature profiles and exosome-derived proteomics are often used to explore the molecular regulation of diseases, and can mirror the conditional state of their tissue of origin, thus serving as biomarkers. The onset of meningeal carcinomatosis (MC) is concealed, and early diagnosis is difficult. To enable early diagnosis of MC, it is essential to identify new biomarkers. Few studies have investigated the function of exosomes in MC. In this study, high-throughput sequencing was used to examine the mRNA profiles of exosomes in the cerebrospinal fluid (CSF) of patients with MC. We further analyzed the functions and signaling pathways associated with the differentially expressed genes in exosomes to reveal the putative mechanisms by which the exosomal mRNAs function in MC. In summary, this study identified biomarker candidates for MC, and provided new insights into the significant role of exosomal mRNA regulation in MC.
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Affiliation(s)
- Peng Cheng
- Department of Neural Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, People's Republic of China
| | - Feifei Feng
- Department of Respiratory Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, People's Republic of China
| | - Hui Yang
- Department of Neural Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, People's Republic of China
| | - Suqin Jin
- Department of Neural Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, People's Republic of China
| | - Chao Lai
- Department of Neural Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, People's Republic of China.
| | - Yun Wang
- Department of Neural Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, People's Republic of China.
| | - Jianzhong Bi
- Department of Neural Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, People's Republic of China
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147
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Song Y, Liu P, Huang Y, Guan Y, Han X, Shi Y. Osimertinib Quantitative and Gene Variation Analyses in Cerebrospinal Fluid and Plasma of a Non-small Cell Lung Cancer Patient with Leptomeningeal Metastases. Curr Cancer Drug Targets 2020; 19:666-673. [PMID: 30332963 DOI: 10.2174/1568009618666181017114111] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Leptomeningeal metastases (LM) are much more frequent in patients of non-small lung cancer (NSCLC) harboring epidermal growth factor receptor (EGFR) mutations. Osimertinib, a third-generation epidermal growth factor receptor-tyrosine kinase inhibitor (EGFRTKI) shows promising efficacy for LM. OBJECTIVE The aim of this study was to analyze the concentration of osimertinib and gene variation of circulating tumor DNA (ctDNA) in human plasma and cerebrospinal fluid (CSF). Furthermore, we explored whether ctDNA in CSF might be used as a biomarker to predict and monitor therapeutic responses. METHODS The dynamic paired CSF and blood samples were collected from the NSCLC patient with LM acquired EGFR-TKI resistance. A method based on ultra-high performance liquid chromatography- tandem mass spectrometry (UPLC-MS/MS) was developed and validated for detecting osimertinib in CSF and plasma samples. Gene variations of ctDNA were tested by next-generation sequencing with a panel of 1021 genes. RESULTS The concentrations of osimertinib in CSF were significantly lower than that in plasma (penetration rate was 1.47%). Mutations included mTOR, EGFR, CHECK1, ABCC11, and TP53 were explored in ctDNA from plasma and CSF samples. The detected mutation rate of CSF samples was higher than that of plasma samples (50% vs. 25%). Our data further revealed that the variations allele frequency (VAF) and molecular tumor burden index (mTBI) of ctDNA derived from CSF exhibited the negative correlation with efficacy of treatment. CONCLUSION ctDNA from CSF might be a useful biomarker for monitoring the efficacy of treatment and an effective complement to nuclear magnetic resonance imaging (MRI) for LM.
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Affiliation(s)
- Yuanyuan Song
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Peng Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Yu Huang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Xiaohong Han
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China.,Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing 100021, China
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148
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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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149
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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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150
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Zhao Y, He JY, Cui JZ, Meng ZQ, Zou YL, Guo XS, Chen X, Wang X, Yan LT, Han WX, Li C, Guo L, Bu H. Detection of genes mutations in cerebrospinal fluid circulating tumor DNA from neoplastic meningitis patients using next generation sequencing. BMC Cancer 2020; 20:690. [PMID: 32711494 PMCID: PMC7382072 DOI: 10.1186/s12885-020-07172-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 07/13/2020] [Indexed: 02/08/2023] Open
Abstract
Background This study profiled the somatic genes mutations and the copy number variations (CNVs) in cerebrospinal fluid (CSF)-circulating tumor DNA (ctDNA) from patients with neoplastic meningitis (NM). Methods A total of 62 CSF ctDNA samples were collected from 58 NM patients for the next generation sequencing. The data were bioinformatically analyzed by (Database for Annotation, Visualization and Integrated Discovery) DAVID software. Results The most common mutated gene was TP53 (54/62; 87.10%), followed by EGFR (44/62; 70.97%), PTEN (39/62; 62.90%), CDKN2A (32/62; 51.61%), APC (27/62: 43.55%), TET2 (27/62; 43.55%), GNAQ (18/62; 29.03%), NOTCH1 (17/62; 27.42%), VHL (17/62; 27.42%), FLT3 (16/62; 25.81%), PTCH1 (15/62; 24.19%), BRCA2 (13/62; 20.97%), KDR (10/62; 16.13%), KIT (9/62; 14.52%), MLH1 (9/62; 14.52%), ATM (8/62; 12.90%), CBL (8/62; 12.90%), and DNMT3A (7/62; 11.29%). The mutated genes were enriched in the PI3K-Akt signaling pathway by the KEGG pathway analysis. Furthermore, the CNVs of these genes were also identified in these 62 samples. The mutated genes in CSF samples receiving intrathecal chemotherapy and systemic therapy were enriched in the ERK1/2 signaling pathway. Conclusions This study identified genes mutations in all CSF ctDNA samples, indicating that these mutated genes may be acted as a kind of biomarker for diagnosis of NM, and these mutated genes may affect meningeal metastasis through PI3K-Akt signaling pathway.
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Affiliation(s)
- Yue Zhao
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Jun Ying He
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Jun Zhao Cui
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Zi-Qi Meng
- Wenzhou Medical University, Wenzhou, China
| | - Yue Li Zou
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Xiao Su Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Xin Chen
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Xueliang Wang
- San Valley Biotechnology Incorporated, Beijing, China
| | - Li-Tian Yan
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Wei Xin Han
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Chunyan Li
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Li Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China
| | - Hui Bu
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Shijiazhuang, Hebei, China.
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