51
|
Zhu Y, Liu Z, Guo Y, Li S, Qu Y, Dai L, Chen Y, Ning W, Zhang H, Ma L. Whole-genome sequencing of extrachromosomal circular DNA of cerebrospinal fluid of medulloblastoma. Front Oncol 2022; 12:934159. [PMID: 36452490 PMCID: PMC9703567 DOI: 10.3389/fonc.2022.934159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/12/2022] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Medulloblastoma (MB) is a malignant tumor associated with a poor prognosis in part due to a lack of effective detection methods. Extrachromosomal circular DNA (eccDNA) has been associated with multiple tumors. Nonetheless, little is currently known on eccDNA in MB. METHODS Genomic features of eccDNAs were identified in MB tissues and matched cerebrospinal fluid (CSF) and compared with corresponding normal samples using Circle map. The nucleotides on both sides of the eccDNAs' breakpoint were analyzed to understand the mechanisms of eccDNA formation. Bioinformatics analysis combined with the Gene Expression Omnibus (GEO) database identified features of eccDNA-related genes in MB. Lasso Cox regression model, univariate and multivariate Cox regression analysis, time-dependent ROC, and Kaplan-Meier curve were used to assess the potential diagnostic and prognostic value of the hub genes. RESULTS EccDNA was profiled in matched tumor and CSF samples from MB patients, and control, eccDNA-related genes enriched in MB were identified. The distribution of eccDNAs in the genome was closely related to gene density and the mechanism of eccDNA formation was evaluated. EccDNAs in CSF exhibited similar distribution with matched MB tissues but were differentially expressed between tumor and normal. Ten hub genes prominent in both the eccDNA dataset and the GEO database were selected to classify MB patients to either high- or low-risk groups, and a prognostic nomogram was thus established. CONCLUSIONS This study provides preliminary evidence of the characteristics and formation mechanism of eccDNAs in MB and CSF. Importantly, eccDNA-associated hub genes in CSF could be used as diagnostic and prognostic biomarkers for MB.
Collapse
Affiliation(s)
- Yi Zhu
- Department of Neurosurgery, Binzhou Medical University Hospital, Binzhou, China
| | - Zhihui Liu
- Department of Obstetrics and Gynecology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yuduo Guo
- Chinese Academy of Sciences (CAS) Key Laboratory of Infection and Immunity, Institute of biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shenglun Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yanming Qu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lin Dai
- Department of Neurosurgery, Binzhou Medical University Hospital, Binzhou, China
| | - Yujia Chen
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
52
|
Pasqualetti F, Rizzo M, Franceschi S, Lessi F, Paiar F, Buffa FM. New perspectives in liquid biopsy for glioma patients. Curr Opin Oncol 2022; 34:705-712. [PMID: 36093876 DOI: 10.1097/cco.0000000000000902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW Gliomas are the most common primary tumors of the central nervous system. They are characterized by a disappointing prognosis and ineffective therapy that has shown no substantial improvements in the past 20 years. The lack of progress in treating gliomas is linked with the inadequacy of suitable tumor samples to plan translational studies and support laboratory developments. To overcome the use of tumor tissue, this commentary review aims to highlight the potential for the clinical application of liquid biopsy (intended as the study of circulating biomarkers in the blood), focusing on circulating tumor cells, circulating DNA and circulating noncoding RNA. RECENT FINDINGS Thanks to the increasing sensitivity of sequencing techniques, it is now possible to analyze circulating nucleic acids and tumor cells (liquid biopsy). SUMMARY Although studies on the use of liquid biopsy are still at an early stage, the potential clinical applications of liquid biopsy in the study of primary brain cancer are many and have the potential to revolutionize the approach to neuro-oncology, and importantly, they offer the possibility of gathering information on the disease at any time during its history.
Collapse
Affiliation(s)
- Francesco Pasqualetti
- Department of Oncology, University of Oxford, Oxford, UK
- Radiation Oncology Unit, Pisa University Hospital
| | - Milena Rizzo
- Noncoding RNA group, Functional Genetics and Genomics Lab, Institute of Clinical Physiology (IFC), CNR, Pisa
| | | | | | | | - Francesca M Buffa
- Department of Oncology, University of Oxford, Oxford, UK
- Department of Computing Sciences, Bocconi University, Milan, Italy
| |
Collapse
|
53
|
Mellinghoff IK, Cloughesy TF. Balancing Risk and Efficiency in Drug Development for Rare and Challenging Tumors: A New Paradigm for Glioma. J Clin Oncol 2022; 40:3510-3519. [PMID: 35201903 PMCID: PMC10166355 DOI: 10.1200/jco.21.02166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/15/2021] [Accepted: 01/26/2022] [Indexed: 12/14/2022] Open
Abstract
The process of developing cancer therapies is well established and has enabled the incorporation of many new drugs and classes of agents into the standard of care for common cancers. Clinical drug development is fundamentally different for rare and difficult-to-treat solid tumors, such as glioma or pancreatic cancer. The failure to develop effective new agents for the latter diseases has discouraged the development of therapeutics for these cancers. Using glioma as an example, we describe a process toward obtaining more reliable early-stage signals of drug activity and a process toward translating those signals into clinical benefits with more efficient late-stage development. If linked together, these processes should increase the likelihood of benefit in late-stage settings at a lower cost and encourage more drug development for patients with rare and difficult-to-treat cancers.
Collapse
Affiliation(s)
- Ingo K. Mellinghoff
- Department of Neurology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Timothy F. Cloughesy
- Department of Neurology, Ronald Reagan UCLA Medical Center, University of California, Los Angeles, CA
| |
Collapse
|
54
|
Genomic Instability in Cerebrospinal Fluid Cell-Free DNA Predicts Poor Prognosis in Solid Tumor Patients with Meningeal Metastasis. Cancers (Basel) 2022; 14:cancers14205028. [PMID: 36291812 PMCID: PMC9600191 DOI: 10.3390/cancers14205028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary We established a genomic instability score using unfiltered sequencing data from meningeal metastasis (MM) cell-free circulating tumor DNA (ctDNA) samples and found that substantial genomic instability (GI) was present in cerebrospinal fluid ctDNA rather than plasma ctDNA, implying that MM lesions have a significantly increased GI status compared to primary tumors or extracranial metastatic lesions, which may suggest tumor clonal evolution. We also found that high GI status was an independent poor prognostic factor in lung adenocarcinoma MM patients, including meningeal metastasis-free survival (MFS) and overall survival (OS). Considering that genomically unstable tumors are more sensitive to PARP inhibitors, targeting GI alone or in combination with conventional therapy may be a promising treatment strategy for solid tumor patients with MM. Abstract Genomic instability (GI), which leads to the accumulation of DNA loss, gain, and rearrangement, is a hallmark of many cancers such as lung cancer, breast cancer, and colon cancer. However, the clinical significance of GI has not been systematically studied in the meningeal metastasis (MM) of solid tumors. Here, we collected both cerebrospinal fluid (CSF) and plasma samples from 56 solid tumor MM patients and isolated cell-free ctDNA to investigate the GI status using a next-generation sequencing-based comprehensive genomic profiling of 543 cancer-related genes. According to the unfiltered heterozygous mutation data-derived GI score, we found that 37 (66.1%) cases of CSF and 3 cases (6%) of plasma had a high GI status, which was further validated by low-depth whole-genome sequencing analysis. It is demonstrated that a high GI status in CSF was associated with poor prognosis, high intracranial pressure, and low Karnofsky performance status scores. More notably, a high GI status was an independent poor prognostic factor of poor MM-free survival and overall survival in lung adenocarcinoma MM patients. Furthermore, high occurrences of the co-mutation of TP53/EGFR, TP53/RB1, TP53/ERBB2, and TP53/KMT2C were found in MM patients with a high GI status. In summary, the GI status in CSF ctDNA might be a valuable prognostic indicator in solid tumor patients with MM.
Collapse
|
55
|
Umemura Y, Khan B, Weill BJ, Buthorn JJ, Skakodub A, Ridder AJ, Nevel KS, Sun Y, Boire A. Discordance Between Perceptions and Experience of Lumbar Puncture: A Prospective Study. Neurol Clin Pract 2022; 12:344-351. [PMID: 36380890 PMCID: PMC9647808 DOI: 10.1212/cpj.0000000000200061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/26/2022] [Indexed: 01/13/2023]
Abstract
Background and Objectives Novel diagnostic techniques and neurologic biomarkers have greatly expanded clinical indications for CSF studies. CSF is most commonly obtained via lumbar puncture (LP). Although it is generally believed that LPs are well tolerated, there is a lack of supportive data for this claim, and patients anticipate LP to be painful. The objective of this study was to prospectively investigate discordance between patient perception and tolerability of LP. Methods Adult patients were surveyed before and after LP regarding their perceptions and experience of LP. Physician perceptions were gathered through a web-based survey. Relative risk and Spearman correlation were used to assess the relationship between responses. Paired binomial and paired ordinal responses were compared by McNemar and paired Wilcoxon rank-sum tests. Results A total of 178 patients completed the surveys. About half of the patients (58%) reported anxiety pre-LP, at median 3.0 of 10. Physicians overpredicted patients' pre-LP anxiety (median score 5.0, p < 0.001). Experienced pain was significantly less than predicted pain (median scores 0 and 3.0, respectively, p < 0.001). Patients who predicted pain were more likely to report pain from LP (relative risk [RR] 1.3). Predicting pain was also correlated with anxiety before LP (p < 0.001). Discussion LP was generally well tolerated. The majority of patients experienced minimal pain. Anticipation of pain was correlated with both feeling anxious and experiencing pain. The results of this study can be used to reassure patients and providers that LP is indeed not as painful as imagined, which may both reduce pre-LP anxiety and improve LP tolerability.
Collapse
Affiliation(s)
- Yoshie Umemura
- Departments of Neurology (YU, BK, AJR, YS), and Radiation Oncology and Biostatistics (YS), University of Michigan, Ann Arbor; and Human Oncology and Pathogenesis Program (BJW, JJB, AS, KSN), Brain Tumor Center and Department of Neurology (AB), Memorial Sloan Kettering Cancer Center, New York
| | - Baber Khan
- Departments of Neurology (YU, BK, AJR, YS), and Radiation Oncology and Biostatistics (YS), University of Michigan, Ann Arbor; and Human Oncology and Pathogenesis Program (BJW, JJB, AS, KSN), Brain Tumor Center and Department of Neurology (AB), Memorial Sloan Kettering Cancer Center, New York
| | - Benjamin J Weill
- Departments of Neurology (YU, BK, AJR, YS), and Radiation Oncology and Biostatistics (YS), University of Michigan, Ann Arbor; and Human Oncology and Pathogenesis Program (BJW, JJB, AS, KSN), Brain Tumor Center and Department of Neurology (AB), Memorial Sloan Kettering Cancer Center, New York
| | - Justin J Buthorn
- Departments of Neurology (YU, BK, AJR, YS), and Radiation Oncology and Biostatistics (YS), University of Michigan, Ann Arbor; and Human Oncology and Pathogenesis Program (BJW, JJB, AS, KSN), Brain Tumor Center and Department of Neurology (AB), Memorial Sloan Kettering Cancer Center, New York
| | - Anna Skakodub
- Departments of Neurology (YU, BK, AJR, YS), and Radiation Oncology and Biostatistics (YS), University of Michigan, Ann Arbor; and Human Oncology and Pathogenesis Program (BJW, JJB, AS, KSN), Brain Tumor Center and Department of Neurology (AB), Memorial Sloan Kettering Cancer Center, New York
| | - Andrew J Ridder
- Departments of Neurology (YU, BK, AJR, YS), and Radiation Oncology and Biostatistics (YS), University of Michigan, Ann Arbor; and Human Oncology and Pathogenesis Program (BJW, JJB, AS, KSN), Brain Tumor Center and Department of Neurology (AB), Memorial Sloan Kettering Cancer Center, New York
| | - Kathryn S Nevel
- Departments of Neurology (YU, BK, AJR, YS), and Radiation Oncology and Biostatistics (YS), University of Michigan, Ann Arbor; and Human Oncology and Pathogenesis Program (BJW, JJB, AS, KSN), Brain Tumor Center and Department of Neurology (AB), Memorial Sloan Kettering Cancer Center, New York
| | - Yilun Sun
- Departments of Neurology (YU, BK, AJR, YS), and Radiation Oncology and Biostatistics (YS), University of Michigan, Ann Arbor; and Human Oncology and Pathogenesis Program (BJW, JJB, AS, KSN), Brain Tumor Center and Department of Neurology (AB), Memorial Sloan Kettering Cancer Center, New York
| | - Adrienne Boire
- Departments of Neurology (YU, BK, AJR, YS), and Radiation Oncology and Biostatistics (YS), University of Michigan, Ann Arbor; and Human Oncology and Pathogenesis Program (BJW, JJB, AS, KSN), Brain Tumor Center and Department of Neurology (AB), Memorial Sloan Kettering Cancer Center, New York
| |
Collapse
|
56
|
Fujita Y, Nunez-Rubiano L, Dono A, Bellman A, Shah M, Rodriguez JC, Putluri V, Kamal AHM, Putluri N, Riascos RF, Zhu JJ, Esquenazi Y, Ballester LY. IDH1 p.R132H ctDNA and D-2-hydroxyglutarate as CSF biomarkers in patients with IDH-mutant gliomas. J Neurooncol 2022; 159:261-270. [PMID: 35816267 PMCID: PMC10183250 DOI: 10.1007/s11060-022-04060-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION We aimed to evaluate IDH1 p.R132H mutation and 2-hydroxyglutarate (2HG) in cerebrospinal fluid (CSF) as biomarkers for patients with IDH-mutant gliomas. METHODS CSF was collected from patients with infiltrating glioma, and 2HG levels were measured by liquid chromatography-mass spectrometry. IDH1 p.R132H mutant allele frequency (MAF) in CSF-ctDNA was measured by digital droplet PCR (ddPCR). Tumor volume was measured from standard-of-care magnetic resonance images. RESULTS The study included 48 patients, 6 with IDH-mutant and 42 with IDH-wildtype gliomas, and 57 samples, 9 from the patients with IDH-mutant and 48 from the patients with IDH-wildtype gliomas. ctDNA was detected in 7 of the 9 samples from patients with IDH-mutant glioma, and IDH1 p.R132H mutation was detected in 5 of the 7 samples. The MAF ranged from 0.3 to 39.95%. Total 2HG level, D-2HG level, and D/L-2HG ratio in CSF were significantly higher in patients with IDH-mutant gliomas than in patients with IDH-wildtype gliomas. D-2HG level and D/L-2HG ratio correlated with total tumor volume in patients with IDH-mutant gliomas but not in patients with IDH-wildtype gliomas. CONCLUSION Our results suggest that detection of IDH1 p.R132H mutation by ddPCR and increased D-2HG level in CSF may help identify IDH-mutant gliomas. Our results also suggest that D-2HG level and D/L-2HG ratio correlate with tumor volume in patients with IDH-mutant gliomas. Further prospective studies with larger cohorts are needed to validate these findings.
Collapse
Affiliation(s)
- Yoko Fujita
- Vivian L. Smith Department of Neurosurgery McGovern Medical School, The University of Texas Health Science Center, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Luis Nunez-Rubiano
- Department of Radiology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Antonio Dono
- Vivian L. Smith Department of Neurosurgery McGovern Medical School, The University of Texas Health Science Center, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Allison Bellman
- Department of Pathology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Mauli Shah
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2130 West Holcombe Boulevard, Houston, TX, 77030, USA
| | - Juan C Rodriguez
- Vivian L. Smith Department of Neurosurgery McGovern Medical School, The University of Texas Health Science Center, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Vasanta Putluri
- Advanced Technology Core, Metabolomics Core, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Abu Hena Mostafa Kamal
- Advanced Technology Core, Metabolomics Core, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nagireddy Putluri
- Advanced Technology Core, Metabolomics Core, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Roy F Riascos
- Department of Radiology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Memorial Hermann Hospital-TMC, Houston, TX, 77030, USA
| | - Jay-Jiguang Zhu
- Vivian L. Smith Department of Neurosurgery McGovern Medical School, The University of Texas Health Science Center, 6431 Fannin Street, Houston, TX, 77030, USA
- Memorial Hermann Hospital-TMC, Houston, TX, 77030, USA
| | - Yoshua Esquenazi
- Vivian L. Smith Department of Neurosurgery McGovern Medical School, The University of Texas Health Science Center, 6431 Fannin Street, Houston, TX, 77030, USA.
- Memorial Hermann Hospital-TMC, Houston, TX, 77030, USA.
- Center for Precision Health, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Leomar Y Ballester
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, 1515 Holcombe Blvd., Unit 85, Houston, TX, 77030, USA.
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2130 West Holcombe Boulevard, Houston, TX, 77030, USA.
| |
Collapse
|
57
|
Tivey A, Church M, Rothwell D, Dive C, Cook N. Circulating tumour DNA - looking beyond the blood. Nat Rev Clin Oncol 2022; 19:600-612. [PMID: 35915225 PMCID: PMC9341152 DOI: 10.1038/s41571-022-00660-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 02/06/2023]
Abstract
Over the past decade, various liquid biopsy techniques have emerged as viable alternatives to the analysis of traditional tissue biopsy samples. Such surrogate 'biopsies' offer numerous advantages, including the relative ease of obtaining serial samples and overcoming the issues of interpreting one or more small tissue samples that might not reflect the entire tumour burden. To date, the majority of research in the area of liquid biopsies has focused on blood-based biomarkers, predominantly using plasma-derived circulating tumour DNA (ctDNA). However, ctDNA can also be obtained from various non-blood sources and these might offer unique advantages over plasma ctDNA. In this Review, we discuss advances in the analysis of ctDNA from non-blood sources, focusing on urine, cerebrospinal fluid, and pleural or peritoneal fluid, but also consider other sources of ctDNA. We discuss how these alternative sources can have a distinct yet complementary role to that of blood ctDNA analysis and consider various technical aspects of non-blood ctDNA assay development. We also reflect on the settings in which non-blood ctDNA can offer distinct advantages over plasma ctDNA and explore some of the challenges associated with translating these alternative assays from academia into clinical use.
Collapse
Affiliation(s)
- Ann Tivey
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Matt Church
- The Christie NHS Foundation Trust, Manchester, UK
| | - Dominic Rothwell
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, The University of Manchester, Manchester, UK
| | - Caroline Dive
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, The University of Manchester, Manchester, UK
| | - Natalie Cook
- Division of Cancer Sciences, The University of Manchester, Manchester, UK.
- The Christie NHS Foundation Trust, Manchester, UK.
| |
Collapse
|
58
|
Nair VS, Hui ABY, Chabon JJ, Esfahani MS, Stehr H, Nabet BY, Zhou L, Chaudhuri AA, Benson J, Ayers K, Bedi H, Ramsey M, Van Wert R, Antic S, Lui N, Backhus L, Berry M, Sung AW, Massion PP, Shrager JB, Alizadeh AA, Diehn M. Genomic Profiling of Bronchoalveolar Lavage Fluid in Lung Cancer. Cancer Res 2022; 82:2838-2847. [PMID: 35748739 PMCID: PMC9379362 DOI: 10.1158/0008-5472.can-22-0554] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
Genomic profiling of bronchoalveolar lavage (BAL) samples may be useful for tumor profiling and diagnosis in the clinic. Here, we compared tumor-derived mutations detected in BAL samples from subjects with non-small cell lung cancer (NSCLC) to those detected in matched plasma samples. Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) was used to genotype DNA purified from BAL, plasma, and tumor samples from patients with NSCLC. The characteristics of cell-free DNA (cfDNA) isolated from BAL fluid were first characterized to optimize the technical approach. Somatic mutations identified in tumor were then compared with those identified in BAL and plasma, and the potential of BAL cfDNA analysis to distinguish lung cancer patients from risk-matched controls was explored. In total, 200 biofluid and tumor samples from 38 cases and 21 controls undergoing BAL for lung cancer evaluation were profiled. More tumor variants were identified in BAL cfDNA than plasma cfDNA in all stages (P < 0.001) and in stage I to II disease only. Four of 21 controls harbored low levels of cancer-associated driver mutations in BAL cfDNA [mean variant allele frequency (VAF) = 0.5%], suggesting the presence of somatic mutations in nonmalignant airway cells. Finally, using a Random Forest model with leave-one-out cross-validation, an exploratory BAL genomic classifier identified lung cancer with 69% sensitivity and 100% specificity in this cohort and detected more cancers than BAL cytology. Detecting tumor-derived mutations by targeted sequencing of BAL cfDNA is technically feasible and appears to be more sensitive than plasma profiling. Further studies are required to define optimal diagnostic applications and clinical utility. SIGNIFICANCE Hybrid-capture, targeted deep sequencing of lung cancer mutational burden in cell-free BAL fluid identifies more tumor-derived mutations with increased allele frequencies compared with plasma cell-free DNA. See related commentary by Rolfo et al., p. 2826.
Collapse
Affiliation(s)
- Viswam S. Nair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Division of Pulmonary, Critical Care & Sleep Medicine, University of Washington School of Medicine, Seattle, Washington
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Angela Bik-Yu Hui
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Jacob J. Chabon
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Mohammad S. Esfahani
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Barzin Y. Nabet
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Li Zhou
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Aadel A. Chaudhuri
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
| | - Jalen Benson
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Kelsey Ayers
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Harmeet Bedi
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Meghan Ramsey
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Ryan Van Wert
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Sanja Antic
- Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Natalie Lui
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Leah Backhus
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Mark Berry
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Arthur W. Sung
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Pierre P. Massion
- Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Joseph B. Shrager
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Ash A. Alizadeh
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| |
Collapse
|
59
|
Improvements in Quality Control and Library Preparation for Targeted Sequencing Allowed Detection of Potentially Pathogenic Alterations in Circulating Cell-Free DNA Derived from Plasma of Brain Tumor Patients. Cancers (Basel) 2022; 14:cancers14163902. [PMID: 36010895 PMCID: PMC9405692 DOI: 10.3390/cancers14163902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Malignant gliomas are the most frequent primary brain tumors in adults. They are genetically heterogenous and invariably recur due to incomplete surgery and therapy resistance. Circulating tumor DNA (ctDNA) is a component of circulating cell-free DNA (ccfDNA) and represents genetic material that originates from the primary tumor or metastasis. Brain tumors are frequently located in the eloquent brain regions, which makes biopsy difficult or impossible due to severe postoperative complications. The analysis of ccfDNA from a patient's blood presents a plausible and noninvasive alternative. In this study, freshly frozen tumors and corresponding blood samples were collected from 84 brain tumor patients and analyzed by targeted next-generation sequencing (NGS). The cohort included 80 glioma patients, 2 metastatic cancer patients, and 2 primary CNS lymphoma (PCNSL) patients. We compared the pattern of genetic alterations in the tumor DNA (tDNA) with that of ccfDNA. The implemented technical improvements in quality control and library preparation allowed for the detection of ctDNA in 8 out of 84 patients, including 5 out of 80 glioma patients. In 32 out of 84 patients, we found potentially pathogenic genetic alterations in ccfDNA that were not detectable in tDNA. While sequencing ccfDNA from plasma has a low efficacy as a diagnostic tool for glioma patients, we concluded that further improvements in sample processing and library preparation can make liquid biopsy a valuable diagnostic tool for glioma patients.
Collapse
|
60
|
[Advances in Diagnosis and Treatment of Leptomeningeal Metastasis of Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2022; 25:517-523. [PMID: 35899451 PMCID: PMC9346159 DOI: 10.3779/j.issn.1009-3419.2022.102.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Leptomeningeal metastases (LM), a special type of metastasis in advanced lung cancer, is known for its severe clinical symptoms, rapid progression and poor prognosis. LM used to be featured with low clinical diagnosis rate, limited treatment options, poor treatment efficacy, and very short survival if treatment not given. Though cerebrospinal fluid (CSF) cytology remains to be the gold standard for the diagnosis of LM, the positive rate of the first CSF cytology even in patients with suggestive clinical symptoms and positive imaging generally does not exceed 50%, leading to a delay in the diagnosis and treatment of patients with LM. With the progress of targeted therapy for driver gene-positive lung cancer and immunotherapy for driver gene-negative lung cancer, the overall survival of patients with lung cancer has been prolonged, meanwhile incidence of LM has been increasing year by year. Current clinical research in this field center around how to improve diagnosis rate and to find effective treatment approaches. This paper reviews advances in diagnosis and treatment of LM of lung cancer..
.
Collapse
|
61
|
Zhou J, Ji N, Wang G, Zhang Y, Song H, Yuan Y, Yang C, Jin Y, Zhang Z, Zhang L, Yin Y. Metabolic detection of malignant brain gliomas through plasma lipidomic analysis and support vector machine-based machine learning. EBioMedicine 2022; 81:104097. [PMID: 35687958 PMCID: PMC9189781 DOI: 10.1016/j.ebiom.2022.104097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/01/2022] [Accepted: 05/20/2022] [Indexed: 12/25/2022] Open
Abstract
Background Most malignant brain gliomas (MBGs) are associated with dismal outcomes, mainly due to their late diagnosis. Current diagnostic methods for MBGs are based on imaging and histological examination, which limits their early detection. Here, we aimed to identify reliable plasma lipid biomarkers for non-invasive diagnosis for MBGs. Methods Untargeted lipidomic analysis was firstly performed using a discovery cohort (n=107). The data were processed by a support vector machine (SVM)-based discriminating model to retrieve a panel of candidate biomarkers. Then, a targeted quantification method was developed, and the SVM-based diagnostic model was constructed using a training cohort (n=750) and tested using a test cohort (n=225). Finally, the performance of the diagnostic model was further evaluated in an independent validation cohort (n=920) enrolled from multiple medical centers. Findings A panel of 11 plasma lipids was identified as candidate biomarkers with an accuracy of 0.999. The diagnostic model developed achieved a high performance in distinguishing MBGs patients from normal controls with an area under the receiver-operating characteristic curve (AUC) of 0.9877 and 0.9869 in the training and test cohorts, respectively. In the validation cohort, the 11 lipid panel still achieved an accuracy of 0.9641 and an AUC of 0.9866. Interpretation The present study demonstrates the applicability and robustness of utilizing a machine learning algorithm to analyze lipidomic data for efficient and reliable biomarker screening. The 11 lipid biomarkers show great potential for the non-invasive diagnosis of MBGs with high throughput. Funding A full list of funding bodies that contributed to this study can be found in the Acknowledgments section.
Collapse
Affiliation(s)
- Juntuo Zhou
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, China; Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Guangxi Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Huajie Song
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yuyao Yuan
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chunyuan Yang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yan Jin
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Zhe Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, National Clinical Research Center for Neurological Diseases, Beijing 100070, China.
| | - Yuxin Yin
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, China; Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China.
| |
Collapse
|
62
|
Shen F, Liang N, Fan Z, Zhao M, Kang J, Wang X, Hu Q, Mu Y, Wang K, Yuan M, Chen R, Guo W, Dong G, Zhao J, Bai J. Genomic Alterations Identification and Resistance Mechanisms Exploration of NSCLC With Central Nervous System Metastases Using Liquid Biopsy of Cerebrospinal Fluid: A Real-World Study. Front Oncol 2022; 12:889591. [PMID: 35814426 PMCID: PMC9259993 DOI: 10.3389/fonc.2022.889591] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/19/2022] [Indexed: 12/24/2022] Open
Abstract
Background Genomic profiling of cerebrospinal fluid (CSF) can be used to detect actionable mutations and guide clinical treatment of non-small cell lung cancer (NSCLC) patients with central nervous system (CNS) metastases. Examining the performance of CSF samples in real-world settings can confirm the potential of CSF genotyping for guiding therapy in clinical practice. Patients and Methods We included 1,396 samples from 970 NSCLC patients with CNS metastases in real-world settings. All samples underwent targeted next-generation sequencing of 1,021 cancer-relevant genes. In total, 100 CSF samples from 77 patients who had previously received targeted treatment were retrospectively analyzed to explore the mechanisms of TKI-resistance. Results For NSCLC patients with CNS metastases, CSF samples were slightly more often used for genomic sequencing in treated patients with only distant CNS metastases compared to other patients (10.96% vs. 0.81–9.61%). Alteration rates in CSF samples were significantly higher than those in plasma, especially for copy number variants (CNV). The MSAFs of CSF samples were significantly higher than those of plasma and tumor tissues (all p <0.001). Remarkably, detection rates of all actionable mutations and EGFR in CSF were higher than those in plasma samples of treated patients (all p <0.0001). For concordance between paired CSF and plasma samples that were simultaneously tested, the MSAF of the CSF was significantly higher than that of matched plasma cfDNA (p <0.001). From multiple comparisons, it can be seen that CSF better detects alterations compared to plasma, especially CNV and structural variant (SV) alterations. CSF cfDNA in identifying mutations can confer the reason for the limited efficacy of EGFR-TKIs for 56 patients (78.87%, 56/71). Conclusions This real-world large cohort study confirmed that CSF had higher sensitivity than plasma in identifying actionable mutations and showed high potential in exploring underlying resistance mechanisms. CSF can be used in genomics profiling to facilitate the broad exploration of potential resistance mechanisms for NSCLC patients with CNS metastases.
Collapse
Affiliation(s)
- Fangfang Shen
- Department of Respiratory Medicine, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zaiwen Fan
- Department of Medical Oncology, Air Force Medical Center, Chinese People's Liberation Army (PLA), Beijing, China
| | - Min Zhao
- Department of Oncology, Hebei Chest Hospital, Research Center of Hebei Lung Cancer Prevention and Treatment, Shijiazhuang, China
| | - Jing Kang
- Department of Oncology, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Xifang Wang
- Department of Medical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Qun Hu
- Department of Oncology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Yongping Mu
- Department of Clinical Laboratory Center, The Affiliated People’s Hospital of Inner Mongolia Medical University, Inner Mongolia Autonomous Region Cancer Hospital, Hohhot, China
| | - Kai Wang
- Medical Center, Geneplus-Beijing, Beijing, China
| | | | | | - Wei Guo
- Department of Respiratory Medicine, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
- *Correspondence: Jun Bai, ; Jun Zhao, ; Guilan Dong, ; Wei Guo,
| | - Guilan Dong
- Department of Medical Oncology, Tangshan People’s Hospital, Tangshan, China
- *Correspondence: Jun Bai, ; Jun Zhao, ; Guilan Dong, ; Wei Guo,
| | - Jun Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital and Institute, Beijing, China
- *Correspondence: Jun Bai, ; Jun Zhao, ; Guilan Dong, ; Wei Guo,
| | - Jun Bai
- Department of Medical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
- *Correspondence: Jun Bai, ; Jun Zhao, ; Guilan Dong, ; Wei Guo,
| |
Collapse
|
63
|
Pirosa MC, Borchmann S, Jardin F, Gaidano G, Rossi D. Controversies in the Interpretation of Liquid Biopsy Data in Lymphoma. Hemasphere 2022; 6:e727. [PMID: 35747846 PMCID: PMC9208882 DOI: 10.1097/hs9.0000000000000727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/21/2022] [Indexed: 11/25/2022] Open
Abstract
The rapid evolution of genomic technologies over the last years has led to the development of different methods for the detection, measurement and analysis of cell-free DNA fragments (cfDNA) which are shed into the bloodstream by apoptotic cells and circulate at a low concentration in plasma. In cancer patients, the proportion of tumor-derived cfDNA is defined as circulating tumor DNA. This analysis, commonly known as liquid biopsy, allows to access tumor DNA through a simple blood sampling and therefore without the need of an invasive tissue biopsy. For this reason, this tool may have several clinical applications in terms of diagnosis, prognosis, and monitoring of minimal residual disease. However, there are still several critical issues that need to be resolved. In this review, we will discuss some of the controversies around this method and its potential clinical applications.
Collapse
|
64
|
Zheng MM, Li YS, Tu HY, Sun H, Yin K, Jiang BY, Yang JJ, Zhang XC, Zhou Q, Xu CR, Wang Z, Chen HJ, Zhou DX, Wu YL. Subsequent treatments beyond progression on osimertinib in EGFR-mutated NSCLC and leptomeningeal metastases. BMC Med 2022; 20:197. [PMID: 35644609 PMCID: PMC9150343 DOI: 10.1186/s12916-022-02387-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/26/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Despite the reported efficacy of osimertinib, central nervous system (CNS) progression is still frequent in EGFR-mutated NSCLC. This study aimed to reveal site-specific resistant mechanisms to osimertinib and investigate subsequent treatments for leptomeningeal metastases (LM). METHODS EGFR-mutated NSCLC with LM who progressed on osimertinib were included. Molecular analysis of cerebrospinal fluid (CSF) at osimertinib progression was performed. Subsequent treatments of LM were collected and analyzed. RESULTS A total of 246 patients were identified. Only those with LM as a progression site on osimertinib were included (n=81). In 58 CSF-plasma pairs, more alterations were uniquely detected in CSF (77%) than in plasma (7%). These mechanisms led to 22 patients receiving matched targeted therapy. Among them, 16 (72.7%) had a clinical response. The median overall survival was 7.2 months. For non-matched therapy (n=59), the osimertinib combination had a longer median overall survival than the regimen switch in CNS-only progression (15.3 vs. 7 months, p=0.03). Finally, serial monitoring by CSF revealed the potential evolution of LM. CONCLUSIONS Private resistant mechanisms in CSF might match osimertinib-resistant LM for targeted therapy. Besides, continuing osimertinib with intensification strategy might prolong survival, especially for those with CNS-only progression. Prospective exploration is needed.
Collapse
Affiliation(s)
- Mei-Mei Zheng
- School of Medicine, South China University of Technology, Guangzhou, 510006, China.,Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Yang-Si Li
- School of Medicine, South China University of Technology, Guangzhou, 510006, China.,Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Hai-Yan Tu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Hao Sun
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Kai Yin
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Ben-Yuan Jiang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Jin-Ji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Chong-Rui Xu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Zhen Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Hua-Jun Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - De-Xiang Zhou
- Department of Neurosurgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Yi-Long Wu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China. .,Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China. .,Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
| |
Collapse
|
65
|
Balana C, Castañer S, Carrato C, Moran T, Lopez-Paradís A, Domenech M, Hernandez A, Puig J. Preoperative Diagnosis and Molecular Characterization of Gliomas With Liquid Biopsy and Radiogenomics. Front Neurol 2022; 13:865171. [PMID: 35693015 PMCID: PMC9177999 DOI: 10.3389/fneur.2022.865171] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
Gliomas are a heterogenous group of central nervous system tumors with different outcomes and different therapeutic needs. Glioblastoma, the most common subtype in adults, has a very poor prognosis and disabling consequences. The World Health Organization (WHO) classification specifies that the typing and grading of gliomas should include molecular markers. The molecular characterization of gliomas has implications for prognosis, treatment planning, and prediction of treatment response. At present, gliomas are diagnosed via tumor resection or biopsy, which are always invasive and frequently risky methods. In recent years, however, substantial advances have been made in developing different methods for the molecular characterization of tumors through the analysis of products shed in body fluids. Known as liquid biopsies, these analyses can potentially provide diagnostic and prognostic information, guidance on choice of treatment, and real-time information on tumor status. In addition, magnetic resonance imaging (MRI) is another good source of tumor data; radiomics and radiogenomics can link the imaging phenotypes to gene expression patterns and provide insights to tumor biology and underlying molecular signatures. Machine and deep learning and computational techniques can also use quantitative imaging features to non-invasively detect genetic mutations. The key molecular information obtained with liquid biopsies and radiogenomics can be useful not only in the diagnosis of gliomas but can also help predict response to specific treatments and provide guidelines for personalized medicine. In this article, we review the available data on the molecular characterization of gliomas using the non-invasive methods of liquid biopsy and MRI and suggest that these tools could be used in the future for the preoperative diagnosis of gliomas.
Collapse
Affiliation(s)
- Carmen Balana
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
- *Correspondence: Carmen Balana
| | - Sara Castañer
- Diagnostic Imaging Institute (IDI), Hospital Universitari Germans Trias I Pujol, Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Cristina Carrato
- Department of Pathology, Hospital Universitari Germans Trias I Pujol, Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Teresa Moran
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Assumpció Lopez-Paradís
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Marta Domenech
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Ainhoa Hernandez
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Josep Puig
- Department of Radiology IDI [Girona Biomedical Research Institute] IDIBGI, Hospital Universitari Dr Josep Trueta, Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Comparative Medicine and Bioimage of Catalonia, Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| |
Collapse
|
66
|
Gene alternation of cerebrospinal fluid in patients with leptomeningeal metastases of lung adenocarcinoma using next-generation sequencing. BMC Cancer 2022; 22:580. [PMID: 35614407 PMCID: PMC9131527 DOI: 10.1186/s12885-022-09597-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) provide a better prognosis in EGFR-mutant non-small cell lung cancer (NSCLC). Nevertheless, the outcome of leptomeningeal metastasis (LM) remains poor. In addition, due to limited access to intracranial tumour tissue, gene alterations associated with leptomeningeal metastasis from lung adenocarcinoma (LM-LUAD) are unclear. Methods Forty-five patients with LM-LUAD from May 2019 to June 2021 in Guangdong Sanjiu Brain Hospital were enrolled in this study. Seventy-five percent (34/45) of patients with LM harbored EGFR mutations, and patients with progressive disease (PD) of LM had 3rd-generation EGFR-TKI therapy and were defined as Cohort 1; those without 3rd-generation EGFR-TKI therapy were defined as Cohort 2. Next-generation targeted panel sequencing (NGS) was performed in each cerebrospinal fluid (CSF) sample of the two cohorts, and 9/45 LM-LUAD patients had matched plasma (PLA). Results The common gene alterations discovered in the CSF of LM-LUAD were EGFR mutation (34/45, 75%), TP53 (25/45, 56%), CDKN2A (9/45, 20%), ALK (7/45, 16%), CTNNB1 (6/45, 13%), MET (5/45, 11%), APC (4/45, 9%), FGF4 (4/45, 9%), FGF3 (4/45, 9%), ERBB2 (4/45, 9%), and PIK3CG (4/45, 9%). Cooccurring mutations of TP53 and EGFR were found in 49% (22/45) of patients and correlated with poor prognosis. CDKN2A was identified in 20% (9/45) of patients and presented slightly shorter overall survival (OS) than those without (7.1 versus 8.8 months, p = 0.2). Cohort 1 had more genes associated with poor prognosis, consisting of CDK4, CDKN2A, PIK3CG, or PIK3CA, and YES1 and MET were more likely to be detected in cohort 2. The alteration of EGFR was comparable between CSF and matched PLA. Incidences of gene alterations such as CDK4, CDKN2A, MET, SOX2, JAK2, BRAF, and PIK3CG were more likely to be identified in CSF. All mutant allele frequencies (MAF) were much higher in CSF than in matched PLA. Conclusions CSF could be a potential candidate for the genetic profiling of LM-LUAD, demonstrating the genetic characteristics of LM in EGFR-mutated lung adenocarcinoma on diverse EGFR-TKI therapies.
Collapse
|
67
|
McMahon JT, Studer M, Ulrich B, Revuelta Barbero JM, Pradilla I, Palacios-Ariza MA, Pradilla G. Circulating Tumor DNA in Adults With Glioma: A Systematic Review and Meta-Analysis of Biomarker Performance. Neurosurgery 2022; 91:231-238. [PMID: 35535984 DOI: 10.1227/neu.0000000000001982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/05/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a promising noninvasive biomarker to capture tumor genetics in patients with brain tumors. Research into its clinical utility, however, has not been standardized because the sensitivity and specificity of ctDNA remain undefined. OBJECTIVE To (1) review the primary literature about ctDNA in adults with glioma to compare the sensitivity and specificity of ctDNA in the cerebrospinal fluid vs the plasma and (2) to evaluate the effect of tumor grade on detection of ctDNA. METHODS PRISMA-guided systematic review and meta-analysis was performed using published studies that assessed ctDNA in either plasma or cerebrospinal fluid among adult patients with confirmed glioma. Summary receiver operating characteristic curves were generated using the Rücker-Schumacher method, and area under the curve (AUC) was calculated. RESULTS Meta-analysis revealed improved biomarker performance for CSF (AUC = 0.947) vs plasma (AUC = 0.741) ctDNA, although this did not reach statistical significance (P = .141). Qualitative analysis revealed greater sensitivities among single-allele PCR and small, targeted next-generation sequencing panels compared with broader panels. It additionally demonstrated higher sensitivity of ctDNA detection in high-grade vs low-grade gliomas, although these analyses were limited by a lack of specificity reporting in many studies. CONCLUSION ctDNA seems to be a highly sensitive and specific noninvasive biomarker among adults with gliomas. To maximize its performance, CSF should be studied with targeted genetic analysis platforms, particularly in high-grade gliomas. Further studies on ctDNA are needed to define its clinical utility in diagnosis, prognostication, glioblastoma pseudoprogression, and other scenarios wherein neoadjuvant therapies may be considered.
Collapse
Affiliation(s)
| | - Matthew Studer
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Bryan Ulrich
- Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Ivan Pradilla
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Gustavo Pradilla
- Department of Neurosurgery, Emory University, Atlanta, Georgia, USA
| |
Collapse
|
68
|
Alvarez-Breckenridge C, Remon J, Piña Y, Nieblas-Bedolla E, Forsyth P, Hendriks L, Brastianos PK. Emerging Systemic Treatment Perspectives on Brain Metastases: Moving Toward a Better Outlook for Patients. Am Soc Clin Oncol Educ Book 2022; 42:1-19. [PMID: 35522917 DOI: 10.1200/edbk_352320] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The diagnosis of brain metastases has historically been a dreaded, end-stage complication of systemic disease. Additionally, with the increasing effectiveness of systemic therapies that prolong life expectancy and improved imaging tools, the incidence of intracranial progression is becoming more common. Within this context, there has been increasing attention directed at understanding the molecular underpinnings of intracranial progression. Exploring the unique features of brain metastases compared with their extracranial counterparts to identify aberrant signaling pathways, which can be targeted pharmacologically, may help lead to new treatments for this patient population. Additionally, critical discoveries outside the sphere of the central nervous system are increasingly being applied to brain metastases with the emergence of immune checkpoint inhibition, becoming a prevalent treatment option for patients with brain metastases across multiple histologies. As novel treatment strategies are considered, they require thoughtful incorporation of agents that can cross the blood-brain barrier and can synergize with pre-existing agents through rational combinations. Lastly, as clinicians and scientists continue to understand key molecular features of these tumors, they will continue to influence the treatment algorithms that are developing for the management of these patients. Due to the complexity of treatment decisions for patients with brain metastases, an emerging tool is the utilization of multidisciplinary brain metastasis tumor boards to ensure optimal treatment decisions are made and that patients are provided access to applicable clinical trials. Looking to the future, the collective effort to understand the various tumor-intrinsic and tumor-extrinsic factors that promote central nervous system seeding and propagation will have the potential to change the clinical trajectory for these patients.
Collapse
Affiliation(s)
| | - Jordi Remon
- Department of Medical Oncology, HM CIOCC Barcelona (Centro Integral Oncológico Clara Campal), Hospital HM Delfos, HM Hospitales, Barcelona, Spain
| | - Yolanda Piña
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL
| | | | - Peter Forsyth
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL
| | - Lizza Hendriks
- Department of Pulmonary Diseases - GROW School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, Netherlands
| | | |
Collapse
|
69
|
Wadden J, Ravi K, John V, Babila CM, Koschmann C. Cell-Free Tumor DNA (cf-tDNA) Liquid Biopsy: Current Methods and Use in Brain Tumor Immunotherapy. Front Immunol 2022; 13:882452. [PMID: 35464472 PMCID: PMC9018987 DOI: 10.3389/fimmu.2022.882452] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022] Open
Abstract
Gliomas are tumors derived from mutations in glial brain cells. Gliomas cause significant morbidity and mortality and development of precision diagnostics and novel targeted immunotherapies are critically important. Radiographic imaging is the most common technique to diagnose and track response to treatment, but is an imperfect tool. Imaging does not provide molecular information, which is becoming critically important for identifying targeted immunotherapies and monitoring tumor evolution. Furthermore, immunotherapy induced inflammation can masquerade as tumor progression in images (pseudoprogression) and confound clinical decision making. More recently, circulating cell free tumor DNA (cf-tDNA) has been investigated as a promising biomarker for minimally invasive glioma diagnosis and disease monitoring. cf-tDNA is shed by gliomas into surrounding biofluids (e.g. cerebrospinal fluid and plasma) and, if precisely quantified, might provide a quantitative measure of tumor burden to help resolve pseudoprogression. cf-tDNA can also identify tumor genetic mutations to help guide targeted therapies. However, due to low concentrations of cf-tDNA, recovery and analysis remains challenging. Plasma cf-tDNA typically represents <1% of total cf-DNA due to the blood-brain barrier, limiting their usefulness in practice and motivating the development and use of highly sensitive and specific detection methods. This mini review summarizes the current and future trends of various approaches for cf-tDNA detection and analysis, including new methods that promise more rapid, lower-cost, and accessible diagnostics. We also review the most recent clinical case studies for longitudinal disease monitoring and highlight focus areas, such as novel accurate detection methodologies, as critical research priorities to enable translation to clinic.
Collapse
Affiliation(s)
- Jack Wadden
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
| | | | | | | | - Carl Koschmann
- Department of Pediatric Hematology and Oncology, Michigan Medicine, Ann Arbor, MI, United States
| |
Collapse
|
70
|
Ozturk EA, Caner A. Liquid Biopsy for Promising Non-invasive Diagnostic Biomarkers in Parasitic Infections. Acta Parasitol 2022; 67:1-17. [PMID: 34176040 DOI: 10.1007/s11686-021-00444-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Liquid biopsy refers to the sampling and molecular analysis of body fluids such as blood, saliva, and urine in contrast to conventional tissue biopsies. Liquid biopsy approach can offer powerful non-invasive biomarkers (circulating markers) for diagnosis and monitoring treatment response of a variety of diseases, including parasitic infections. METHODS In this review, we concentrate on cell-free DNA (cfDNA), microRNA (miRNA), and exosomes in the published literature. RESULTS Considering the high prevalence and severity of parasitic infections worldwide, circulating biomarkers can provide a new insight into the diagnosis and prognosis of parasites in the near future. Moreover, identifying and characterizing parasite- or host-derived circulating markers are important for a better understanding of the pathogenesis of parasite infection and host-parasite relationship at the molecular level. Profiling of biomarkers for parasitic diseases is a promising potential field, though further studies and optimization strategies are required, both in vitro and in vivo. CONCLUSION In this review, we discuss three approaches in the liquid biopsy including circulating cfDNA, miRNAs, and exosomes for diagnosis and evaluation of parasites and summarize circulating biomarkers in non-invasive samples during parasitic infections.
Collapse
Affiliation(s)
- Eylem Akdur Ozturk
- Department of Parasitology, Çukurova University Faculty of Medicine, Adana, Turkey
| | - Ayse Caner
- Department of Parasitology, Ege University Faculty of Medicine, 35100, Izmir, Turkey.
- Cancer Research Center, Ege University, Izmir, Turkey.
| |
Collapse
|
71
|
Diaz M, Singh P, Kotchetkov IS, Skakodub A, Meng A, Tamer C, Young RJ, Reiner AS, Panageas KS, Ramanathan LV, Pentsova E. Quantitative assessment of circulating tumor cells in cerebrospinal fluid as a clinical tool to predict survival in leptomeningeal metastases. J Neurooncol 2022; 157:81-90. [PMID: 35113288 PMCID: PMC9119011 DOI: 10.1007/s11060-022-03949-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/15/2022] [Indexed: 10/19/2022]
Abstract
PURPOSE Circulating tumor cells in cerebrospinal fluid are a quantitative diagnostic tool for leptomeningeal metastases from solid tumors, but their prognostic significance is unclear. Our objective was to evaluate CSF-CTC quantification in predicting outcomes in LM. METHODS This is a single institution retrospective study of patients with solid tumors who underwent CSF-CTC quantification using the CellSearch® platform between 04/2016 and 06/2019. Information on neuroaxis imaging, CSF results, and survival was collected. LM was diagnosed by MRI and/or CSF cytology. Survival analyses were performed using multivariable Cox proportional hazards modeling, and CSF-CTC splits associated with survival were identified through recursive partitioning analysis. RESULTS Out of 290 patients with CNS metastases, we identified a cohort of 101 patients with newly diagnosed LM. In this group, CSF-CTC count (median 200 CTCs/3 ml) predicted survival continuously (HR = 1.005, 95% CI: 1.002-1.009, p = 0.0027), and the risk of mortality doubled (HR = 2.84, 95% CI: 1.45-5.56, p = 0.0023) at the optimal cutoff of ≥ 61 CSF-CTCs/3 ml. Neuroimaging findings of LM (assessed by 3 independent neuroradiologists) were associated with a higher CSF-CTC count (median CSF-CTCs range 1.5-4 for patients without radiographic LM vs 200 for patients with radiographic LM, p < 0.001), but did not predict survival. CONCLUSION Our data shows that CSF-CTCs quantification predicts survival in newly diagnosed LM, and outperforms neuroimaging. CSF-CTC analysis can be used as a prognostic tool in patients with LM and provides quantitative assessment of disease burden in the CNS compartment.
Collapse
Affiliation(s)
- Maria Diaz
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ivan S. Kotchetkov
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Skakodub
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alicia Meng
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christel Tamer
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert J. Young
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anne S. Reiner
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Katherine S. Panageas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lakshmi V. Ramanathan
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elena Pentsova
- Department of Neurology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| |
Collapse
|
72
|
Tsui DCC, Camidge DR, Rusthoven CG. Managing Central Nervous System Spread of Lung Cancer: The State of the Art. J Clin Oncol 2022; 40:642-660. [PMID: 34985937 DOI: 10.1200/jco.21.01715] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Brain metastases (BrM) are common in both non-small-cell lung cancer and small-cell lung cancer. Substantial progress in BrM management has occurred in the past decade related to advances in both radiation and medical oncology. Recent and ongoing radiation trials have focused on increasing the candidacy for focal therapy of BrM with stereotactic radiosurgery; reducing the toxicity and improving patient selection for whole brain radiotherapy; and, in small-cell lung cancer, evaluating brain magnetic resonance imaging surveillance without prophylactic cranial irradiation, hippocampal avoidance in prophylactic cranial irradiation and whole brain radiotherapy, and the role of upfront stereotactic radiosurgery for BrM. In medical oncology, the development of multiple tyrosine kinase inhibitors with encouraging CNS activity and emerging data on the CNS activity of immune checkpoint inhibitors in some patients have opened the door to novel systemic and multidisciplinary treatment strategies for the management of BrM. Future research will focus on more robust characterizations of the CNS activity of targeted therapy and immunotherapies, as well as optimal integration and patient selection for multidisciplinary strategies involving CNS-active drugs, radiation therapy, and CNS surveillance.
Collapse
Affiliation(s)
- David Chun Cheong Tsui
- Division of Medical Oncology, University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO
| | - D Ross Camidge
- Division of Medical Oncology, University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO
| | - Chad G Rusthoven
- Department of Radiation Oncology, University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
73
|
Miller AM, Szalontay L, Bouvier N, Hill K, Ahmad H, Rafailov J, Lee AJ, Rodriguez-Sanchez MI, Yildirim O, Patel A, Bale TA, Benhamida JK, Benayed R, Arcila ME, Donzelli M, Dunkel IJ, Gilheeney SW, Khakoo Y, Kramer K, Sait SF, Greenfield JP, Souweidane MM, Haque S, Mauguen A, Berger MF, Mellinghoff IK, Karajannis MA. Next-generation sequencing of cerebrospinal fluid for clinical molecular diagnostics in pediatric, adolescent and young adult brain tumor patients. Neuro Oncol 2022; 24:1763-1772. [PMID: 35148412 PMCID: PMC9527510 DOI: 10.1093/neuonc/noac035] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Safe sampling of central nervous system tumor tissue for diagnostic purposes may be difficult if not impossible, especially in pediatric patients, and an unmet need exists to develop less invasive diagnostic tests. METHODS We report our clinical experience with minimally invasive molecular diagnostics using a clinically validated assay for sequencing of cerebrospinal fluid (CSF) cell-free DNA (cfDNA). All CSF samples were collected as part of clinical care, and results reported to both clinicians and patients/families. RESULTS We analyzed 64 CSF samples from 45 pediatric, adolescent and young adult (AYA) patients (pediatric = 25; AYA = 20) with primary and recurrent brain tumors across 12 histopathological subtypes including high-grade glioma (n = 10), medulloblastoma (n = 10), pineoblastoma (n = 5), low-grade glioma (n = 4), diffuse leptomeningeal glioneuronal tumor (DLGNT) (n = 4), retinoblastoma (n = 4), ependymoma (n = 3), and other (n = 5). Somatic alterations were detected in 30/64 samples (46.9%) and in at least one sample per unique patient in 21/45 patients (46.6%). CSF cfDNA positivity was strongly associated with the presence of disseminated disease at the time of collection (81.5% of samples from patients with disseminated disease were positive). No association was seen between CSF cfDNA positivity and the timing of CSF collection during the patient's disease course. CONCLUSIONS We identified three general categories where CSF cfDNA testing provided additional relevant diagnostic, prognostic, and/or therapeutic information, impacting clinical assessment and decision making: (1) diagnosis and/or identification of actionable alterations; (2) monitor response to therapy; and (3) tracking tumor evolution. Our findings support broader implementation of clinical CSF cfDNA testing in this population to improve care.
Collapse
Affiliation(s)
| | | | - Nancy Bouvier
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Katherine Hill
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hamza Ahmad
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Johnathan Rafailov
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alex J Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - M Irene Rodriguez-Sanchez
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Onur Yildirim
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arti Patel
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tejus A Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria Donzelli
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ira J Dunkel
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stephen W Gilheeney
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yasmin Khakoo
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kim Kramer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sameer F Sait
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jeffrey P Greenfield
- Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Neurological Surgery, Weill Cornell Medical College, New York, New York, USA,Department of Neurological Surgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Mark M Souweidane
- Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Neurological Surgery, Weill Cornell Medical College, New York, New York, USA,Department of Neurological Surgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Sofia Haque
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Berger
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ingo K Mellinghoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Pharmacology, Weill Cornell Medical College, New York, New York, USA
| | - Matthias A Karajannis
- Corresponding Author: Matthias A. Karajannis, MD, MS, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA ()
| |
Collapse
|
74
|
Treatments on the Horizon: Breast Cancer Patients with Central Nervous System Metastases. Curr Oncol Rep 2022; 24:343-350. [PMID: 35138599 DOI: 10.1007/s11912-022-01206-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW The goal of this paper is to provide a review on the current emerging management strategies as described in the literature pertaining to breast cancer and central nervous system metastases. As systemic oncology treatments evolve, so are new approaches to the management of central nervous system metastases from breast cancer. RECENT FINDINGS In this review, we describe how novel treatment strategies have evolved from standard chemotherapy to more targeted approaches, innovative drug delivery methodologies, immunotherapeutics, and radiotherapeutic approaches. We describe innovative treatment strategies on the horizon for breast cancer and central nervous metastases. Future therapeutics may be better able to penetrate through the blood-brain-barrier bypassing limitations from standard therapies. These pioneering strategies will hopefully improve patients' quality of life as well as survival.
Collapse
|
75
|
Mathis NJ, Wijetunga NA, Imber BS, Pike LRG, Yang JT. Recent Advances and Applications of Radiation Therapy for Brain Metastases. Curr Oncol Rep 2022; 24:335-342. [PMID: 35133614 DOI: 10.1007/s11912-022-01209-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW Radiation therapy (RT) is a mainstay of treatment for brain metastases from solid tumors. Treatment of these patients is complex and should focus on minimizing symptoms, preserving functional status, and prolonging survival. RECENT FINDINGS Whole-brain radiotherapy (WBRT) can lead to toxicity, and while it does reduce recurrence in the CNS, this has not been shown to provide a survival benefit. Recent advances focus on reducing the toxicity of WBRT or using more targeted radiation therapy. New paradigms including the use of proton RT for leptomeningeal metastases (LM) and stereotactic radiosurgery (SRS) before craniotomy hold promise in improving treatment efficacy and reducing toxicity. Omission or replacement of WBRT is often safe and the use of SRS is expanding to include patients with more lesions and preoperative RT. Proton RT holds promise for LM. Progress is being made in improving patient-centered outcomes and reducing toxicity for patients with brain metastases.
Collapse
Affiliation(s)
- Noah J Mathis
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - N Ari Wijetunga
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Brandon S Imber
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Luke R G Pike
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Jonathan T Yang
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
| |
Collapse
|
76
|
Kalita-de Croft P, Joshi V, Saunus JM, Lakhani SR. Emerging Biomarkers for Diagnosis, Prevention and Treatment of Brain Metastases-From Biology to Clinical Utility. Diseases 2022; 10:11. [PMID: 35225863 PMCID: PMC8884016 DOI: 10.3390/diseases10010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
Primary malignancies of the lung, skin (melanoma), and breast have higher propensity for metastatic spread to the brain. Advances in molecular tumour profiling have aided the development of targeted therapies, stereotactic radiotherapy, and immunotherapy, which have led to some improvement in patient outcomes; however, the overall prognosis remains poor. Continued research to identify new prognostic and predictive biomarkers is necessary to further impact patient outcomes, as this will enable better risk stratification at the point of primary cancer diagnosis, earlier detection of metastatic deposits (for example, through surveillance), and more effective systemic treatments. Brain metastases exhibit considerable inter- and intratumoural heterogeneity-apart from distinct histology, treatment history and other clinical factors, the metastatic brain tumour microenvironment is incredibly variable both in terms of subclonal diversity and cellular composition. This review discusses emerging biomarkers; specifically, the biological context and potential clinical utility of tumour tissue biomarkers, circulating tumour cells, extracellular vesicles, and circulating tumour DNA.
Collapse
Affiliation(s)
- Priyakshi Kalita-de Croft
- UQ Centre for Clinical Research, The University of Queensland Faculty of Medicine, Herston, QLD 4029, Australia; (V.J.); (J.M.S.)
| | - Vaibhavi Joshi
- UQ Centre for Clinical Research, The University of Queensland Faculty of Medicine, Herston, QLD 4029, Australia; (V.J.); (J.M.S.)
| | - Jodi M. Saunus
- UQ Centre for Clinical Research, The University of Queensland Faculty of Medicine, Herston, QLD 4029, Australia; (V.J.); (J.M.S.)
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, The University of Queensland Faculty of Medicine, Herston, QLD 4029, Australia; (V.J.); (J.M.S.)
- Pathology Queensland, The Royal Brisbane and Women’s Hospital Herston, Herston, QLD 4029, Australia
| |
Collapse
|
77
|
Ferguson SD, Fomchenko EI, Guerrieri RA, Glitza Oliva IC. Challenges and Advances in Diagnosis and Treatment of Leptomeningeal Disease (LMD). Front Oncol 2022; 11:800053. [PMID: 35096602 PMCID: PMC8789647 DOI: 10.3389/fonc.2021.800053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/06/2021] [Indexed: 12/11/2022] Open
Abstract
Leptomeningeal disease (LMD) is a devastating category of CNS metastasis with a very poor prognosis and limited treatment options. With maximal aggressive therapy, survival times remain short and, without treatment, prognosis is measured in weeks. Both LMD diagnosis and treatment are challenging topics within neuro-oncology. In this review, we discuss the advances in LMD diagnosis with a focus on the role of circulating tumor DNA (ctDNA) and discuss the role of targeted and immunotherapy in LMD treatment.
Collapse
Affiliation(s)
- Sherise D Ferguson
- Department of Neurosurgery, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Elena I Fomchenko
- Department of Neurosurgery, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Renato A Guerrieri
- Department of Melanoma Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| | - Isabella C Glitza Oliva
- Department of Melanoma Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, United States
| |
Collapse
|
78
|
Mair R, Mouliere F. Cell-free DNA technologies for the analysis of brain cancer. Br J Cancer 2022; 126:371-378. [PMID: 34811503 PMCID: PMC8811068 DOI: 10.1038/s41416-021-01594-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 11/08/2022] Open
Abstract
Survival for glioma patients has shown minimal improvement over the past 20 years. The ability to detect and monitor gliomas relies primarily upon imaging technologies that lack sensitivity and specificity, especially during the post-surgical treatment phase. Treatment-response monitoring with an effective liquid-biopsy paradigm may also provide the most facile clinical scenario for liquid-biopsy integration into brain-tumour care. Conceptually, liquid biopsy is advantageous when compared with both tissue sampling (less invasive) and imaging (more sensitive and specific), but is hampered by technical and biological problems. These problems predominantly relate to low concentrations of tumour-derived DNA in the bloodstream of glioma patients. In this review, we highlight methods by which the neuro-oncological scientific and clinical communities have attempted to circumvent this limitation. The use of novel biological, technological and computational approaches will be explored. The utility of alternate bio-fluids, tumour-guided sequencing, epigenomic and fragmentomic methods may eventually be leveraged to provide the biological and technological means to unlock a wide range of clinical applications for liquid biopsy in glioma.
Collapse
Affiliation(s)
- Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, Cambridge, UK.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE, Cambridge, UK.
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ, Cambridge, UK.
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, 1081 HV, Amsterdam, The Netherlands.
| |
Collapse
|
79
|
Shen E, Van Swearingen AED, Price MJ, Bulsara K, Verhaak RGW, Baëta C, Painter BD, Reitman ZJ, Salama AKS, Clarke JM, Anders CK, Fecci PE, Goodwin CR, Walsh KM. A Need for More Molecular Profiling in Brain Metastases. Front Oncol 2022; 11:785064. [PMID: 35145903 PMCID: PMC8821807 DOI: 10.3389/fonc.2021.785064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
As local disease control improves, the public health impact of brain metastases (BrM) continues to grow. Molecular features are frequently different between primary and metastatic tumors as a result of clonal evolution during neoplasm migration, selective pressures imposed by systemic treatments, and differences in the local microenvironment. However, biomarker information in BrM is not routinely obtained despite emerging evidence of its clinical value. We review evidence of discordance in clinically actionable biomarkers between primary tumors, extracranial metastases, and BrM. Although BrM biopsy/resection imposes clinical risks, these risks must be weighed against the potential benefits of assessing biomarkers in BrM. First, new treatment targets unique to a patient's BrM may be identified. Second, as BrM may occur late in a patient's disease course, resistance to initial targeted therapies and/or loss of previously identified biomarkers can occur by the time of occult BrM, rendering initial and other targeted therapies ineffective. Thus, current biomarker data can inform real-time treatment options. Third, biomarker information in BrM may provide useful prognostic information for patients. Appreciating the importance of biomarker analyses in BrM tissue, including how it may identify specific drivers of BrM, is critical for the development of more effective treatment strategies to improve outcomes for this growing patient population.
Collapse
Affiliation(s)
- Erica Shen
- Division of Neurosurgery, Department of Surgery, University of Connecticut, Farmington, CT, United States
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Amanda E. D. Van Swearingen
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC, United States
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
| | - Meghan J. Price
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
| | - Ketan Bulsara
- Division of Neurosurgery, Department of Surgery, University of Connecticut, Farmington, CT, United States
| | - Roeland G. W. Verhaak
- Division of Neurosurgery, Department of Surgery, University of Connecticut, Farmington, CT, United States
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam Universitair Medische Centra (UMC), Vrije Universiteit Amsterdam (VU) University Medical Center (VUmc), Amsterdam, Netherlands
| | - César Baëta
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
| | - Brice D. Painter
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
| | - Zachary J. Reitman
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, United States
| | - April K. S. Salama
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC, United States
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
| | - Jeffrey M. Clarke
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC, United States
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
| | - Carey K. Anders
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC, United States
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
| | - Peter E. Fecci
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
| | - C. Rory Goodwin
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
| | - Kyle M. Walsh
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
| |
Collapse
|
80
|
Santos V, Freitas C, Fernandes MGO, Sousa C, Reboredo C, Cruz-Martins N, Mosquera J, Hespanhol V, Campelo R. Liquid biopsy: the value of different bodily fluids. Biomark Med 2022; 16:127-145. [DOI: 10.2217/bmm-2021-0370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Liquid biopsies have gained an increasing interest in the last years among medical and scientific communities. Indeed, the value of liquid effusions, while less invasive and more accurate techniques, has been markedly highlighted. Peripheral blood comprises the most often analyzed sample, but recent evidences have pointed out the huge importance of other bodily fluids, including pleural and peritoneal fluids, urine, saliva and cerebrospinal fluid in the detection and monitoring of different tumor types. In face to these advances, this review aims to provide an overview of the value of tumor-associated mutations, detectable in different effusions, and how they can be used in clinical practice, namely in prognosis assessment and early disease and minimal disease recurrence detection, and in predicting the treatment response or acquired-resistance development.
Collapse
Affiliation(s)
- Vanessa Santos
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
| | - Cláudia Freitas
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
| | - Maria GO Fernandes
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Institute for Research & Innovation in Health (I3S), University of Porto, Rua Alfredo Allen, Porto, 4200135, Portugal
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, 4200135, Portugal
| | - Catarina Sousa
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
| | - Cristina Reboredo
- Department of Lung Cancer & Thoracic Tumours, Complejo Hospitalario Universitario de A Coruña, As Xubias, 84, 15006, A Coruña, La Coruña, Spain
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Institute for Research & Innovation in Health (I3S), University of Porto, Rua Alfredo Allen, Porto, 4200135, Portugal
| | - Joaquín Mosquera
- Department of Lung Cancer & Thoracic Tumours, Complejo Hospitalario Universitario de A Coruña, As Xubias, 84, 15006, A Coruña, La Coruña, Spain
| | - Venceslau Hespanhol
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Institute for Research & Innovation in Health (I3S), University of Porto, Rua Alfredo Allen, Porto, 4200135, Portugal
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, 4200135, Portugal
| | - Rosário Campelo
- Department of Lung Cancer & Thoracic Tumours, Complejo Hospitalario Universitario de A Coruña, As Xubias, 84, 15006, A Coruña, La Coruña, Spain
| |
Collapse
|
81
|
Ion Mobility Mass Spectrometry Reveals Rare Sialylated Glycosphingolipid Structures in Human Cerebrospinal Fluid. Molecules 2022; 27:molecules27030743. [PMID: 35164008 PMCID: PMC8839488 DOI: 10.3390/molecules27030743] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 01/27/2023] Open
Abstract
Gangliosides (GGs) represent an important class of biomolecules associated with the central nervous system (CNS). In view of their special role at a CNS level, GGs are valuable diagnostic markers and prospective therapeutic agents. By ion mobility separation mass spectrometry (IMS MS), recently implemented by us in the investigation of human CNS gangliosidome, we previously discovered a similarity between GG profiles in CSF and the brain. Based on these findings, we developed IMS tandem MS (MS/MS) to characterize rare human CSF glycoforms, with a potential biomarker role. To investigate the oligosaccharide and ceramide structures, the ions detected following IMS MS separation were submitted to structural analysis by collision-induced dissociation (CID) MS/MS in the transfer cell. The IMS evidence on only one mobility feature, together with the diagnostic fragment ions, allowed the unequivocal identification of isomers in the CSF. Hence, by IMS MS/MS, GalNAc-GD1c(d18:1/18:1) and GalNAc-GD1c(d18:1/18:0) having both Neu5Ac residues and GalNAc attached to the external galactose were for the first time discovered and structurally characterized. The present results demonstrate the high potential of IMS MS/MS for biomarker discovery and characterization in body fluids, and the perspectives of method implementation in clinical analyses targeting the early diagnosis of CNS diseases through molecular fingerprints.
Collapse
|
82
|
Piña Y, Yadugiri S, Yeboa DN, Ferguson SD, Forsyth PA, Oliva ICG. Advances in Diagnosis and Treatment for Leptomeningeal Disease in Melanoma. Curr Oncol Rep 2022; 24:43-54. [DOI: 10.1007/s11912-021-01162-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2021] [Indexed: 11/24/2022]
|
83
|
Deciphering Biomarkers for Leptomeningeal Metastasis in Malignant Hemopathies (Lymphoma/Leukemia) Patients by Comprehensive Multipronged Proteomics Characterization of Cerebrospinal Fluid. Cancers (Basel) 2022; 14:cancers14020449. [PMID: 35053611 PMCID: PMC8773653 DOI: 10.3390/cancers14020449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The early diagnosis of leptomeningeal disease is a challenge because it is asymptomatic in the early stages. Consequently, it is important to identify a panel of biomarkers to help in its diagnosis and/or prognosis. For this purpose, we explored a multipronged proteomics approach in cerebrospinal fluid (CSF) to determine a potential panel of biomarkers. Thus, a systematic and exhaustive characterization of more than 300 CSF samples was performed by an integrated approach by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) and functional proteomics analysis to establish protein profiles, which were useful for developing a panel of biomarkers validated by in silico approaches. Abstract In the present work, leptomeningeal disease, a very destructive form of systemic cancer, was characterized from several proteomics points of view. This pathology involves the invasion of the leptomeninges by malignant tumor cells. The tumor spreads to the central nervous system through the cerebrospinal fluid (CSF) and has a very grim prognosis; the average life expectancy of patients who suffer it does not exceed 3 months. The early diagnosis of leptomeningeal disease is a challenge because, in most of the cases, it is an asymptomatic pathology. When the symptoms are clear, the disease is already in the very advanced stages and life expectancy is low. Consequently, there is a pressing need to determine useful CSF proteins to help in the diagnosis and/or prognosis of this disease. For this purpose, a systematic and exhaustive proteomics characterization of CSF by multipronged proteomics approaches was performed to determine different protein profiles as potential biomarkers. Proteins such as PTPRC, SERPINC1, sCD44, sCD14, ANPEP, SPP1, FCGR1A, C9, sCD19, and sCD34, among others, and their functional analysis, reveals that most of them are linked to the pathology and are not detected on normal CSF. Finally, a panel of biomarkers was verified by a prediction model for leptomeningeal disease, showing new insights into the research for potential biomarkers that are easy to translate into the clinic for the diagnosis of this devastating disease.
Collapse
|
84
|
Soffietti R, Bettegowda C, Mellinghoff IK, Warren KE, Ahluwalia MS, De Groot JF, Galanis E, Gilbert MR, Jaeckle KA, Le Rhun E, Rudà R, Seoane J, Thon N, Umemura Y, Weller M, van den Bent MJ, Vogelbaum MA, Chang SM, Wen PY. Liquid biopsy in gliomas: A RANO review and proposals for clinical applications. Neuro Oncol 2022; 24:855-871. [PMID: 34999836 PMCID: PMC9159432 DOI: 10.1093/neuonc/noac004] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND There is an extensive literature highlighting the utility of blood-based liquid biopsies in several extracranial tumors for diagnosis and monitoring. METHODS The RANO (Response Assessment in Neuro-Oncology) group developed a multidisciplinary international Task Force to review the English literature on liquid biopsy in gliomas focusing on the most frequently used techniques, that is circulating tumor DNA, circulating tumor cells, and extracellular vesicles in blood and CSF. RESULTS ctDNA has a higher sensitivity and capacity to represent the spatial and temporal heterogeneity in comparison to circulating tumor cells. Exosomes have the advantages to cross an intact blood-brain barrier and carry also RNA, miRNA, and proteins. Several clinical applications of liquid biopsies are suggested: to establish a diagnosis when tissue is not available, monitor the residual disease after surgery, distinguish progression from pseudoprogression, and predict the outcome. CONCLUSIONS There is a need for standardization of biofluid collection, choice of an analyte, and detection strategies along with rigorous testing in future clinical trials to validate findings and enable entry into clinical practice.
Collapse
Affiliation(s)
- Riccardo Soffietti
- Corresponding Author: Riccardo Soffietti, MD, Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science Hospital, Via Cherasco 15, 10126 Turin, Italy ()
| | | | | | | | - Manmeet S Ahluwalia
- Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - John F De Groot
- Department of Neuro-Oncology, University of Texas, MD Anderson Cancer Center Houston, Houston, Texas, USA
| | - Evanthia Galanis
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kurt A Jaeckle
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Emilie Le Rhun
- Departments of Neurology & Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Roberta Rudà
- Department of Neurology, Castelfranco Veneto/Treviso Hospital and Division of Neuro-Oncology, Department of Neuroscience, University of Turin, Turin, Italy
| | - Joan Seoane
- Vall d’Hebron Institute of Oncology (VHIO) University Hospital, Universitat Autònoma de Barcelona, ICREA,CIBERONC, Barcelona, Spain
| | - Niklas Thon
- Division of Neuro-Oncology, Department of Neurosurgery, Ludwig Maximilians University School of Medicine, Munich, Germany
| | - Yoshie Umemura
- Division of Neuro-Oncology, Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Martin J van den Bent
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Susan M Chang
- Division of Neuro-Oncology, University of California San Francisco, San Francisco, California, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber/Brigham and Women’s Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
85
|
Pagès M, Rotem D, Gydush G, Reed S, Rhoades J, Ha G, Lo C, Fleharty M, Duran M, Jones R, Becker S, Haller M, Sinai CE, Goumnerova L, Golub TR, Love JC, Ligon KL, Wright KD, Adalsteinsson VA, Beroukhim R, Bandopadhayay P. Liquid biopsy detection of genomic alterations in pediatric brain tumors from cell-free DNA in peripheral blood, CSF, and urine. Neuro Oncol 2022; 24:1352-1363. [PMID: 34984433 PMCID: PMC9340641 DOI: 10.1093/neuonc/noab299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The ability to identify genetic alterations in cancers is essential for precision medicine; however, surgical approaches to obtain brain tumor tissue are invasive. Profiling circulating tumor DNA (ctDNA) in liquid biopsies has emerged as a promising approach to avoid invasive procedures. Here, we systematically evaluated the feasibility of profiling pediatric brain tumors using ctDNA obtained from plasma, cerebrospinal fluid (CSF), and urine. METHODS We prospectively collected 564 specimens (257 blood, 240 urine, and 67 CSF samples) from 258 patients across all histopathologies. We performed ultra-low-pass whole-genome sequencing (ULP-WGS) to assess copy number variations and estimate tumor fraction and developed a pediatric CNS tumor hybrid capture panel for deep sequencing of specific mutations and fusions. RESULTS ULP-WGS detected copy number alterations in 9/46 (20%) CSF, 3/230 (1.3%) plasma, and 0/153 urine samples. Sequencing detected alterations in 3/10 (30%) CSF, 2/74 (2.7%) plasma, and 0/2 urine samples. The only positive results were in high-grade tumors. However, most samples had insufficient somatic mutations (median 1, range 0-39) discoverable by the sequencing panel to provide sufficient power to detect tumor fractions of greater than 0.1%. CONCLUSIONS Children with brain tumors harbor very low levels of ctDNA in blood, CSF, and urine, with CSF having the most DNA detectable. Molecular profiling is feasible in a small subset of high-grade tumors. The level of clonal aberrations per genome is low in most of the tumors, posing a challenge for detection using whole-genome or even targeted sequencing methods. Substantial challenges therefore remain to genetically characterize pediatric brain tumors from liquid biopsies.
Collapse
Affiliation(s)
- Mélanie Pagès
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA,GHU-Paris—Sainte-Anne Hospital, Department of Neuropathology, Paris University, Paris, France,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Denisse Rotem
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Gregory Gydush
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Sarah Reed
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Justin Rhoades
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Gavin Ha
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Christopher Lo
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Mark Fleharty
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Madeleine Duran
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Robert Jones
- Department of Oncologic Pathology, Dana Farber/Brigham and Women’s Cancer Center, Boston, Massachusetts, USA
| | - Sarah Becker
- Department of Oncologic Pathology, Dana Farber/Brigham and Women’s Cancer Center, Boston, Massachusetts, USA
| | - Michaela Haller
- Department of Oncologic Pathology, Dana Farber/Brigham and Women’s Cancer Center, Boston, Massachusetts, USA
| | - Claire E Sinai
- Department of Oncologic Pathology, Dana Farber/Brigham and Women’s Cancer Center, Boston, Massachusetts, USA
| | - Liliana Goumnerova
- Department of Neurosurgery, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Todd R Golub
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | | | - Keith L Ligon
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Department of Neurosurgery, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Karen D Wright
- Karen Wright, MD, MS, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02115, USA ()
| | - Viktor A Adalsteinsson
- Viktor A. Adalsteinsson, PhD, Broad Institute, 450 Main Street, Cambridge, MA 02142, USA ()
| | - Rameen Beroukhim
- Corresponding Authors: Rameen Beroukhim, MD, PhD, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02115, USA ()
| | - Pratiti Bandopadhayay
- Pratiti Bandopadhayay, MBBS, PhD, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02115, USA ()
| |
Collapse
|
86
|
Fitzpatrick A, Iravani M, Mills A, Childs L, Alaguthurai T, Clifford A, Garcia-Murillas I, Van Laere S, Dirix L, Harries M, Okines A, Turner NC, Haider S, Tutt ANJ, Isacke CM. Assessing CSF ctDNA to improve diagnostic accuracy and therapeutic monitoring in breast cancer leptomeningeal metastasis. Clin Cancer Res 2021; 28:1180-1191. [PMID: 34921020 DOI: 10.1158/1078-0432.ccr-21-3017] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/23/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Cerebrospinal fluid (CSF) cytology is the gold standard diagnostic test for breast cancer leptomeningeal metastasis (BCLM), but has impaired sensitivity, often necessitating repeated lumbar puncture to confirm or refute diagnosis. Further, there is no quantitative response tool to assess response or progression during BCLM treatment. EXPERIMENTAL DESIGN Facing the challenge of working with small volume samples and the lack of common recurrent mutations in breast cancers, cell-free DNA was extracted from CSF and plasma of patients undergoing investigation for BCLM (n=30). ctDNA fraction was assessed by ultra-low pass whole genome sequencing (ulpWGS), which does not require prior tumor sequencing. RESULTS In this proof-of-concept study ctDNA was detected (fraction {greater than or equal to}0.10) in CSF of all 24 BCLM+ patients (median ctDNA fraction 0.57), regardless of negative cytology or borderline MRI imaging, whereas CSF ctDNA was not detected in the 6 BCLM- patients (median ctDNA fraction 0.03, P<0.0001). Plasma ctDNA was only detected in patients with extracranial disease progression or who had previously received whole brain radiotherapy. ctDNA fraction was highly concordant with mutant allele fraction measured by tumor mutation-specific ddPCR assays (r=0.852, P<0.0001). During intrathecal treatment, serial monitoring (n=12 patients) showed that suppression of CSF ctDNA fraction was associated with longer BCLM survival (P=0.034) and rising ctDNA fraction was detectable up to 12 weeks before clinical progression. CONCLUSION Measuring ctDNA fraction by ulpWGS is a quantitative marker demonstrating potential for timely and accurate BCLM diagnosis and therapy response monitoring, with the ultimate aim to improve management of this poor prognosis patient group.
Collapse
Affiliation(s)
- Amanda Fitzpatrick
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research
| | - Marjan Iravani
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research
| | - Adam Mills
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research
| | - Lucy Childs
- Department of Clinical Radiology, Guy's and St Thomas' NHS Foundation Trust
| | | | - Angela Clifford
- Breast Cancer Now Research Unit, Guy's Hospital, King's College London
| | - Isaac Garcia-Murillas
- Breast Cancer Now Research Centre, Institute of Cancer Research and The Royal Marsden Hospital
| | - Steven Van Laere
- Translational Cancer Research Unit, Oncology Center, General Hospital Sint-Augustinus
| | - Luc Dirix
- Translational Cancer Research Unit, Oncology Center, AZ Sint-Augustinus
| | - Mark Harries
- Clinical Oncology, Guy's and St Thomas' NHS Foundation Trust
| | | | - Nicholas C Turner
- Breast Unit, The Royal Marsden NHS Foundation Trust, and Breast Cancer Now Research Centre, The Institute of Cancer Research
| | - Syed Haider
- The Breast Cancer Now Research Centre, Institute of Cancer Research
| | - Andrew N J Tutt
- Division of Breast Cancer Research, Institute of Cancer Research London
| | - Clare M Isacke
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research
| |
Collapse
|
87
|
Li M, Hou X, Zheng L, Ma Y, Li D, Lv Y, Chen J, Zheng W, Shao Y, Mou Y, Chen L. Utilizing phenotypic characteristics of metastatic brain tumors to improve the probability of detecting circulating tumor DNA from cerebrospinal fluid in non-small-cell lung cancer patients: development and validation of a prediction model in a prospective cohort study. ESMO Open 2021; 7:100305. [PMID: 34922300 PMCID: PMC8685990 DOI: 10.1016/j.esmoop.2021.100305] [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] [Received: 07/25/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 12/18/2022] Open
Abstract
Background Circulating tumor DNA (ctDNA) in cerebrospinal fluid (CSF) has become a promising surrogate for genomic profiling of central nervous system tumors. However, suboptimal ctDNA detection rates from CSF limit its clinical utility. Thus precise screening of suitable patients is needed to maximize the clinical benefit. Patients and methods Between February 2017 and December 2020, 66 newly diagnosed non-small-cell lung cancer (NSCLC) patients with brain parenchymal metastases were prospectively enrolled as a training cohort and 30 additional patients were enrolled as an external validation cohort. CSF samples and matched primary tumor tissues were collected before treatment and subjected to next-generation sequencing (NGS). The imageological characteristics of patients’ brain tumors were evaluated by radiologists using enhanced magnetic resonance imaging images. The clinical and imageological characteristics were evaluated by complete subsets regression, Akaike information criteria, and Bayesian information criteria methods to establish the prediction model. A nomogram was then built for CSF ctDNA detection prediction. Results The somatic mutation detection rate of genes covered by our targeted NGS panel was significantly lower in CSF ctDNA (59.09%) than tumor tissue (91.84%). The Tsize (diameter of the largest intracranial lesion) and LVDmin (minimum lesion–ventricle distance for all intracranial lesions) were significantly associated with positive CSF ctDNA detection, and thus, were selected to establish the prediction model, which achieved an area under the ROC curve (AUC) of 0.819 and an accuracy of 0.800. The model’s predictive ability was further validated in the independent external cohort (AUC of 0.772, accuracy of 0.767) and by internal cross-validation. The CSF ctDNA detection rate was significantly improved from 58.18% (32/55) to 81.81% (27/33) in patients after model selection (P = 0.022). Conclusions This study developed a regression model to predict the probability of detecting CSF ctDNA using the phenotypic characteristics of metastatic brain lesions in NSCLC patients, thus, maximizing the benefits of CSF liquid biopsies. Intracranial tumor size and distance to nearest ventricle were significantly correlated with positive CSF ctDNA detection. A prediction model incorporating Tsize and LVDmin was developed and validated to evaluate the odds of CSF ctDNA positivity. The CSF ctDNA detection rate was significantly improved in patients after model selection.
Collapse
Affiliation(s)
- M Li
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P. R. China
| | - X Hou
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P. R. China
| | - L Zheng
- Department of Medical Imaging, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P. R. China
| | - Y Ma
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, P. R. China
| | - D Li
- Chemotherapy Department 2, Zhongshan City People's Hospital, Zhongshan, Guangdong, P. R. China
| | - Y Lv
- Department of Medical Imaging, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P. R. China
| | - J Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P. R. China
| | - W Zheng
- Department of Ultrasound, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P. R. China
| | - Y Shao
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, P. R. China
| | - Y Mou
- Department of Neurosurgery, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P. R. China.
| | - L Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, P. R. China.
| |
Collapse
|
88
|
Fontanilles M, Sanson M, Touat M. Liquid biopsy in neuro-oncology: are we finally there? Ann Oncol 2021; 32:1472-1474. [PMID: 34815016 DOI: 10.1016/j.annonc.2021.10.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- M Fontanilles
- Cancer Centre Henri Becquerel, Département d'oncologie médicale, Rouen, France; Normandie Université, Rouen University Hospital, UNIROUEN, IRON group, Normandy Centre for Genomic and Personalized Medicine, Inserm U1245, Rouen, France
| | - M Sanson
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - M Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France.
| |
Collapse
|
89
|
Wang M, Zhu F, Luo N, Li M, Qi Y, Wang M. Erlotinib combined with bevacizumab and chemotherapy in first line osimertinib-resistant NSCLC patient with leptomeningeal metastasis: A case report. Medicine (Baltimore) 2021; 100:e27727. [PMID: 34871271 PMCID: PMC8568434 DOI: 10.1097/md.0000000000027727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/22/2021] [Indexed: 01/05/2023] Open
Abstract
RATIONALE Leptomeningeal metastasis (LM) is a fatal complication of advanced non-small cell lung cancer (NSCLC) with a poor prognosis. Osimertinib is a promising option for NSCLC with LM harboring epidermal growth factor receptor (EGFR) mutation. However, therapeutic approaches remain a challenge for osimertinib resistant NSCLCs with LM. Although studies have reported that the first/second-generation EGFR-tyrosine kinase inhibitors were active against osimertinib-resistant NSCLC with EGFR C797S and sensitive mutation (SM), the resistance inevitably occurred due to the development of the EGFR SM/C797S/T790M triple mutations. PATIENT CONCERNS A 48-year-old woman was diagnosed with stage IV lung adenocarcinoma harboring the EGFR mutation in the combination of chest computed tomography, biopsy and amplification refractory mutation system-polymerase chain. One year and a half after oral administration of osimertinib, the patient progressed to extensive LM. DIAGNOSES Magnetic resonance images of the brain showed extensive LM. Exfoliated tumor cells from cerebrospinal fluid (CSF) were positive detected by lumbar puncture and the cytology examination. EGFR mutations (exon19 E746_T751delinsI and exon20 C797S) in CSF circulating tumor DNA were detected by next-generation sequencing (NGS). INTERVENTIONS Pemetrexed (800 mg day 1), cis-platinum (40 mg day 1-3) combined with bevacizumab (400 mg day 1) every 3 weeks were administered to the patient. After 1 cycle, due to optic nerve invasion, erlotinib was applied 150 mg/d combined with previous regimen. The patient continued erlotinib monotherapy after 6 cycles. OUTCOMES After LM, erlotinib combined with pemetrexed, cis-platinum and bevacizumab were administered to the patient for 4.25 months based on the CSF NGS. Then, the patient continued erlotinib monotherapy and appeared disease progression after 10 months. The overall survival is 35 months. LESSONS LM is a fatal complication of advanced NSCLC with a poor prognosis. NGS profiling of CSF circulating tumor DNA is important in NSCLC patients with LM and erotinib plus bevacizumab and chemotherapy is a promising option for patients with LM harboring EGFR C797S/SM.
Collapse
Affiliation(s)
- Musen Wang
- Department of Pathology, Donge People's Hospital, Donge, China
| | - Fuxin Zhu
- Department of Oncology, Donge People's Hospital, Donge, China
| | - Ningning Luo
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Mengmeng Li
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Yingxue Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Mingbo Wang
- Department of Oncology, Donge People's Hospital, Donge, China
| |
Collapse
|
90
|
Gu W, Rauschecker AM, Hsu E, Zorn KC, Sucu Y, Federman S, Gopez A, Arevalo S, Sample HA, Talevich E, Nguyen ED, Gottschall M, Nourbakhsh B, Gold CA, Cree BAC, Douglas VC, Richie MB, Shah MP, Josephson SA, Gelfand JM, Miller S, Wang L, Tihan T, DeRisi JL, Chiu CY, Wilson MR. Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid. JAMA Neurol 2021; 78:1355-1366. [PMID: 34515766 DOI: 10.1001/jamaneurol.2021.3088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Importance Cerebrospinal fluid (CSF) cytologic testing and flow cytometry are insensitive for diagnosing neoplasms of the central nervous system (CNS). Such clinical phenotypes can mimic infectious and autoimmune causes of meningoencephalitis. Objective To ascertain whether CSF metagenomic next-generation sequencing (mNGS) can identify aneuploidy, a hallmark of malignant neoplasms, in difficult-to-diagnose cases of CNS malignant neoplasm. Design, Setting, and Participants Two case-control studies were performed at the University of California, San Francisco (UCSF). The first study used CSF specimens collected at the UCSF Clinical Laboratories between July 1, 2017, and December 31, 2019, and evaluated test performance in specimens from patients with a CNS malignant neoplasm (positive controls) or without (negative controls). The results were compared with those from CSF cytologic testing and/or flow cytometry. The second study evaluated patients who were enrolled in an ongoing prospective study between April 1, 2014, and July 31, 2019, with presentations that were suggestive of neuroinflammatory disease but who were ultimately diagnosed with a CNS malignant neoplasm. Cases of individuals whose tumors could have been detected earlier without additional invasive testing are discussed. Main Outcomes and Measures The primary outcome measures were the sensitivity and specificity of aneuploidy detection by CSF mNGS. Secondary subset analyses included a comparison of CSF and tumor tissue chromosomal abnormalities and the identification of neuroimaging characteristics that were associated with test performance. Results Across both studies, 130 participants were included (median [interquartile range] age, 57.5 [43.3-68.0] years; 72 men [55.4%]). The test performance study used 125 residual laboratory CSF specimens from 47 patients with a CNS malignant neoplasm and 56 patients with other neurological diseases. The neuroinflammatory disease study enrolled 12 patients and 17 matched control participants. The sensitivity of the CSF mNGS assay was 75% (95% CI, 63%-85%), and the specificity was 100% (95% CI, 96%-100%). Aneuploidy was detected in 64% (95% CI, 41%-83%) of the patients in the test performance study with nondiagnostic cytologic testing and/or flow cytometry, and in 55% (95% CI, 23%-83%) of patients in the neuroinflammatory disease study who were ultimately diagnosed with a CNS malignant neoplasm. Of the patients in whom aneuploidy was detected, 38 (90.5%) had multiple copy number variations with tumor fractions ranging from 31% to 49%. Conclusions and Relevance This case-control study showed that CSF mNGS, which has low specimen volume requirements, does not require the preservation of cell integrity, and was orginally developed to diagnose neurologic infections, can also detect genetic evidence of a CNS malignant neoplasm in patients in whom CSF cytologic testing and/or flow cytometry yielded negative results with a low risk of false-positive results.
Collapse
Affiliation(s)
- Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco.,Department of Pathology, Stanford University, Stanford, California
| | - Andreas M Rauschecker
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco
| | - Yasemin Sucu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Hannah A Sample
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco
| | | | - Eric D Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Marc Gottschall
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Bardia Nourbakhsh
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Carl A Gold
- Department of Neurology, Stanford University, Stanford, California
| | - Bruce A C Cree
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - Vanja C Douglas
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - Megan B Richie
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - Maulik P Shah
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - S Andrew Josephson
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco.,Editor in Chief, JAMA Neurology
| | - Jeffrey M Gelfand
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Linlin Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Tarik Tihan
- Department of Pathology, University of California, San Francisco, San Francisco
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco.,Chan Zuckerberg Biohub, San Francisco, California
| | - Charles Y Chiu
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California.,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco
| | - Michael R Wilson
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco
| |
Collapse
|
91
|
Yamagishi Y, Sasaki N, Nakano Y, Matushita Y, Omura T, Shimizu S, Saito K, Kobayashi K, Narita Y, Kondo A, Shiokawa Y, Nagane M, Ichimura K. Liquid biopsy of cerebrospinal fluid for MYD88 L265P mutation is useful for diagnosis of central nervous system lymphoma. Cancer Sci 2021; 112:4702-4710. [PMID: 34523186 PMCID: PMC8586690 DOI: 10.1111/cas.15133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/30/2022] Open
Abstract
The current standard of diagnosing central nervous system (CNS) lymphoma is stereotactic biopsy, however the procedure has a risk of surgical complication. Liquid biopsy of the CSF is a less invasive, non-surgical method that can be used for diagnosing CNS lymphoma. In this study, we established a clinically applicable protocol for determining mutations in MYD88 in the CSF of patients with CNS lymphoma. CSF was collected prior to the start of chemotherapy from 42 patients with CNS lymphoma and matched tumor specimens. Mutations in MYD88 in 33 tumor samples were identified using pyrosequencing. Using 10 ng each of cellular DNA and cell-free DNA (cfDNA) extracted from the CSF, the MYD88 L265P mutation was detected using digital PCR. The conditions to judge mutation were rigorously determined. The median Target/Total value of cases with MYD88 mutations in the tumors was 5.1% in cellular DNA and 22.0% in cfDNA. The criteria to judge mutation were then determined, with a Target/Total value of 0.25% as the cutoff. When MYD88 mutations were determined based on these criteria, the sensitivity and specificity were 92.2% and 100%, respectively, with cellular DNA; and the sensitivity and specificity were 100% with cfDNA. Therefore, the DNA yield, mutated allele fraction, and accuracy were significantly higher in cfDNA compared with that in cellular DNA. Taken together, this study highlights the importance of detecting the MYD88 L265P mutation in cfDNA of the CSF for diagnosing CNS lymphoma using digital PCR, a highly accurate and clinically applicable method.
Collapse
Affiliation(s)
- Yuki Yamagishi
- Division of Brain Tumor Translational ResearchNational Cancer Center Research InstituteChuo‐kuTokyoJapan
- Department of NeurosurgeryKyorin University Facility of MedicineMitaka‐shiTokyoJapan
- Department of Brain Disease Translational ResearchJuntendo University Facility of MedicineBunkyo‐kuTokyoJapan
| | - Nobuyoshi Sasaki
- Department of NeurosurgeryKyorin University Facility of MedicineMitaka‐shiTokyoJapan
| | - Yoshiko Nakano
- Division of Brain Tumor Translational ResearchNational Cancer Center Research InstituteChuo‐kuTokyoJapan
| | - Yuko Matushita
- Division of Brain Tumor Translational ResearchNational Cancer Center Research InstituteChuo‐kuTokyoJapan
- Department of Brain Disease Translational ResearchJuntendo University Facility of MedicineBunkyo‐kuTokyoJapan
| | - Takaki Omura
- Division of Brain Tumor Translational ResearchNational Cancer Center Research InstituteChuo‐kuTokyoJapan
- Department of Neurosurgery and Neuro‐OncologyNational Cancer Center HospitalChuo‐kuTokyoJapan
| | - Saki Shimizu
- Department of NeurosurgeryKyorin University Facility of MedicineMitaka‐shiTokyoJapan
| | - Kuniaki Saito
- Department of NeurosurgeryKyorin University Facility of MedicineMitaka‐shiTokyoJapan
| | - Keiichi Kobayashi
- Department of NeurosurgeryKyorin University Facility of MedicineMitaka‐shiTokyoJapan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro‐OncologyNational Cancer Center HospitalChuo‐kuTokyoJapan
| | - Akihide Kondo
- Department of Brain Disease Translational ResearchJuntendo University Facility of MedicineBunkyo‐kuTokyoJapan
| | - Yoshiaki Shiokawa
- Department of NeurosurgeryKyorin University Facility of MedicineMitaka‐shiTokyoJapan
| | - Motoo Nagane
- Department of NeurosurgeryKyorin University Facility of MedicineMitaka‐shiTokyoJapan
| | - Koichi Ichimura
- Division of Brain Tumor Translational ResearchNational Cancer Center Research InstituteChuo‐kuTokyoJapan
- Department of Brain Disease Translational ResearchJuntendo University Facility of MedicineBunkyo‐kuTokyoJapan
| |
Collapse
|
92
|
Yu J, Sheng Z, Wu S, Gao Y, Yan Z, Bu C, Gu J, Bu Y, Deng K, Xu S, Chen Z, Zhang Q, Zemmar A, Hernesniemi J, Wang M, Liu G, Li T, Bu X. Tumor DNA From Tumor In Situ Fluid Reveals Mutation Landscape of Minimal Residual Disease After Glioma Surgery and Risk of Early Recurrence. Front Oncol 2021; 11:742037. [PMID: 34712610 PMCID: PMC8547270 DOI: 10.3389/fonc.2021.742037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/20/2021] [Indexed: 11/25/2022] Open
Abstract
The recurrence of glioma is a difficult problem in clinical treatment. The molecular markers of primary tumors after resection cannot fully represent the characteristics of recurrent tumors. Here, abundant tumor DNA was detected in tumor in situ fluid (TISF). We report that TISF-derived tumor DNA (TISF-DNA) can detect genomic changes in recurrent tumors and facilitate recurrence risk analysis, providing valuable information for diagnosis and prognosis. The tumor DNA in TISF is more representative and sensitive than that in cerebrospinal fluid. It reveals the mutational landscape of minimal residual disease after glioma surgery and the risk of early recurrence, contributing to the clinical management and clinical research of glioma patients.
Collapse
Affiliation(s)
- Jinliang Yu
- Department of Neurosurgery, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Zhiyuan Sheng
- Department of Neurosurgery, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Shuang Wu
- Department of Neurosurgery, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yushuai Gao
- Department of Neurosurgery, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Zhaoyue Yan
- Department of Neurosurgery, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Chaojie Bu
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Center for Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Jianjun Gu
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Center for Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yage Bu
- Department of Neurosurgery, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Kaiyuan Deng
- Department of Neurosurgery, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Sensen Xu
- Department of Neurosurgery, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Zhongcan Chen
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Center for Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Qianqian Zhang
- Juha International Center for Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Ajmal Zemmar
- Juha International Center for Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Juha Hernesniemi
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Center for Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Meiyun Wang
- Department of Medical Imaging, Henan Provincial People's Hospital, The People's Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Key Laboratory for Imaging Diagnosis and Research of Neurological Diseases, Henan Provincial People's Hospital, The People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Gang Liu
- Department of Center for Clinical Single Cell Biomedicine, Clinical Research Center, Department of Oncology, Henan Provincial People's Hospital, The People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Tianxiao Li
- Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Center for Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Xingyao Bu
- Department of Neurosurgery, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Juha International Central Laboratory of Neurosurgery, Henan Provincial People's Hospital, Zhengzhou, China
| |
Collapse
|
93
|
Wang Y, Jiang F, Xia R, Li M, Yao C, Li Y, Li H, Zhao Q, Shi M, Yu Y, Shao YW, Zhou G, Xia H, Miao L, Cai H. Unique Genomic Alterations of Cerebrospinal Fluid Cell-Free DNA Are Critical for Targeted Therapy of Non-Small Cell Lung Cancer With Leptomeningeal Metastasis. Front Oncol 2021; 11:701171. [PMID: 34671549 PMCID: PMC8522975 DOI: 10.3389/fonc.2021.701171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022] Open
Abstract
We reported unique molecular features of cerebrospinal fluid (CSF) of nonsmall cell lung cancer (NSCLC) patients with leptomeningeal metastasis (LM), suggesting establishing CSF as a better liquid biopsy in clinical practices. We performed next-generation panel sequencing of primary tumor tissue, plasma, and CSF from 131 NSCLC patients with LM and observed high somatic copy number variations (CNV) in CSF of NSCLC patients with LM. The status of EGFR-activating mutations was highly concordant between CSF, plasma, and primary tumors. ALK translocation was detected in 8.3% of tumor tissues but only 2.4% in CSF and 2.7% in plasma. Others such as ROS1 rearrangement, RET fusion, HER2 mutation, NTRK1 fusion, and BRAF V600E mutation were detected in 7.9% of CSF and 11.1% of tumor tissues but only 4% in plasma. Our study has shed light on the unique genomic variations of CSF and demonstrated that CSF might represent better liquid biopsy for NSCLC patients with LM.
Collapse
Affiliation(s)
- Yongsheng Wang
- Department of Respiratory Medicine & Radiology & Cardiothoracic Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Feng Jiang
- The First Affiliated Hospital/Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Ruixue Xia
- Department of Respiratory and Critical Care Medicine, Henan University Huaihe Hospital, Kaifeng, China
| | - Ming Li
- Department of Respiratory Medicine & Radiology & Cardiothoracic Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Chengyun Yao
- Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Yan Li
- Department of Respiratory Medicine & Radiology & Cardiothoracic Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Hui Li
- Department of Respiratory Medicine & Radiology & Cardiothoracic Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Qi Zhao
- Department of Respiratory Medicine & Radiology & Cardiothoracic Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Mingke Shi
- Department of Respiratory Medicine & Radiology & Cardiothoracic Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Yanzhe Yu
- Department of Respiratory Medicine & Radiology & Cardiothoracic Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Yang W Shao
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Guoren Zhou
- Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Hongping Xia
- Department of Pathology, School of Basic Medical Sciences & Sir Run Run Hospital & Key Laboratory of Antibody Technique of National Health Commission, Nanjing Medical University, Nanjing, China
| | - Liyun Miao
- Department of Respiratory Medicine & Radiology & Cardiothoracic Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| | - Hourong Cai
- Department of Respiratory Medicine & Radiology & Cardiothoracic Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing, China
| |
Collapse
|
94
|
García Molina E, Penas-Prado M. Neoplastic meningitis in solid tumours: updated review of diagnosis, prognosis, therapeutic management, and future directions. NEUROLOGÍA (ENGLISH EDITION) 2021; 37:794-805. [PMID: 34663545 DOI: 10.1016/j.nrleng.2019.10.009] [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: 07/22/2019] [Accepted: 10/14/2019] [Indexed: 10/20/2022] Open
Abstract
Neoplastic meningitis (NM) is a relatively frequent metastatic complication of cancer associated with high levels of neurological morbidity and generally poor prognosis. It appears in 5%-15% of patients with solid tumours, the most frequent being breast and lung cancer and melanoma. Symptoms are caused by involvement of the cerebral hemispheres, cranial nerves, spinal cord, and nerve roots, and are often multifocal or present with signs and symptoms of intracranial hypertension. The main diagnostic tools are the neurological examination, brain and spinal cord contrast-enhanced magnetic resonance imaging, and cerebrospinal fluid analysis including cytology, although studies have recently been conducted into the detection of tumour cells and DNA in the cerebrospinal fluid, which increases diagnostic sensitivity. With the currently available therapies, treatment aims not to cure the disease, but to delay and ameliorate the symptoms and to preserve quality of life. Treatment of NM involves a multimodal approach that may include radiotherapy, intrathecal and/or systemic chemotherapy, and surgery. Treatment should be individualised, and is based mainly on clinical practice guidelines and expert opinion. Promising clinical trials are currently being conducted to evaluate drugs with molecular and immunotherapeutic targets. This article is an updated review of NM epidemiology, clinical presentation, diagnosis, prognosis, management, and treatment; it is aimed at general neurologists and particularly at neurologists practicing in hospital settings with oncological patients.
Collapse
Affiliation(s)
- E García Molina
- Servicio de Neurología, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain.
| | - M Penas-Prado
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States
| |
Collapse
|
95
|
Rincon-Torroella J, Khela H, Bettegowda A, Bettegowda C. Biomarkers and focused ultrasound: the future of liquid biopsy for brain tumor patients. J Neurooncol 2021; 156:33-48. [PMID: 34613580 PMCID: PMC8714625 DOI: 10.1007/s11060-021-03837-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 08/28/2021] [Indexed: 01/12/2023]
Abstract
Introduction Despite advances in modern medicine, brain tumor patients are still monitored purely by clinical evaluation and imaging. Traditionally, invasive strategies such as open or stereotactic biopsies have been used to confirm the etiology of clinical and imaging changes. Liquid biopsies can enable physicians to noninvasively analyze the evolution of a tumor and a patient’s response to specific treatments. However, as a consequence of biology and the current limitations in detection methods, no blood or cerebrospinal fluid (CSF) brain tumor-derived biomarkers are used in routine clinical practice. Enhancing the presence of tumor biomarkers in blood and CSF via brain-blood barrier (BBB) disruption with MRI-guided focused ultrasound (MRgFUS) is a very compelling strategy for future management of brain tumor patients. Methods A literature review on MRgFUS-enabled brain tumor liquid biopsy was performed using Medline/Pubmed databases and clinical trial registries. Results The therapeutic applications of MRgFUS to target brain tumors have been under intense investigation. At high-intensity, MRgFUS can ablate brain tumors and target tissues, which needs to be balanced with the increased risk for damage to surrounding normal structures. At lower-intensity and pulsed-frequency, MRgFUS may be able to disrupt the BBB transiently. Thus, while facilitating intratumoral or parenchymal access to standard or novel therapeutics, BBB disruption with MRgFUS has opened the possibility of enhanced detection of brain tumor-derived biomarkers. Conclusions In this review, we describe the concept of MRgFUS-enabled brain tumor liquid biopsy and present the available preclinical evidence, ongoing clinical trials, limitations, and future directions of this application.
Collapse
Affiliation(s)
- Jordina Rincon-Torroella
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 600 N Wolfe St, Phipps 118, Baltimore, MD, 21128, USA
| | - Harmon Khela
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 600 N Wolfe St, Phipps 118, Baltimore, MD, 21128, USA
| | - Anya Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 600 N Wolfe St, Phipps 118, Baltimore, MD, 21128, USA
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 600 N Wolfe St, Phipps 118, Baltimore, MD, 21128, USA.
| |
Collapse
|
96
|
Gatto L, Franceschi E, Di Nunno V, Tosoni A, Lodi R, Brandes AA. Liquid Biopsy in Glioblastoma Management: From Current Research to Future Perspectives. Oncologist 2021; 26:865-878. [PMID: 34105205 PMCID: PMC8488799 DOI: 10.1002/onco.13858] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/02/2021] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma (GBM) is the most common primary tumor of the central nervous system. Arising from neuroepithelial glial cells, GBM is characterized by invasive behavior, extensive angiogenesis, and genetic heterogeneity that contributes to poor prognosis and treatment failure. Currently, there are several molecular biomarkers available to aid in diagnosis, prognosis, and predicting treatment outcomes; however, all require the biopsy of tumor tissue. Nevertheless, a tissue sample from a single location has its own limitations, including the risk related to the procedure and the difficulty of obtaining longitudinal samples to monitor treatment response and to fully capture the intratumoral heterogeneity of GBM. To date, there are no biomarkers in blood or cerebrospinal fluid for detection, follow-up, or prognostication of GBM. Liquid biopsy offers an attractive and minimally invasive solution to support different stages of GBM management, assess the molecular biology of the tumor, identify early recurrence and longitudinal genomic evolution, predict both prognosis and potential resistance to chemotherapy or radiotherapy, and allow patient selection for targeted therapies. The aim of this review is to describe the current knowledge regarding the application of liquid biopsy in glioblastoma, highlighting both benefits and obstacles to translation into clinical care. IMPLICATIONS FOR PRACTICE: To translate liquid biopsy into clinical practice, further prospective studies are required with larger cohorts to increase specificity and sensitivity. With the ever-growing interest in RNA nanotechnology, microRNAs may have a therapeutic role in brain tumors.
Collapse
Affiliation(s)
- Lidia Gatto
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| | - Enrico Franceschi
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| | - Vincenzo Di Nunno
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| | - Alicia Tosoni
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| | - Raffaele Lodi
- Istituto delle Scienze Neurologiche di Bologna, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)BolognaItaly
| | - Alba Ariela Brandes
- Department of Medical Oncology, Azienda Unità Sanitaria Locale (USL) of BolognaBolognaItaly
| |
Collapse
|
97
|
Detection of clonotypic DNA in the cerebrospinal fluid as a marker of central nervous system invasion in lymphoma. Blood Adv 2021; 5:5525-5535. [PMID: 34551072 PMCID: PMC8714713 DOI: 10.1182/bloodadvances.2021004512] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/16/2021] [Indexed: 11/30/2022] Open
Abstract
The NGS-MRD assay detected clonotypic DNA in 100% of CSF samples from patients who had lymphoma with parenchymal CNS involvement. Clonotypic DNA in CSF was present in 36% of newly diagnosed aggressive lymphomas and was associated with a 29% risk of CNS recurrence.
The diagnosis of parenchymal central nervous system (CNS) invasion and prediction of risk for future CNS recurrence are major challenges in the management of aggressive lymphomas, and accurate biomarkers are needed to supplement clinical risk predictors. For this purpose, we studied the results of a next-generation sequencing (NGS)–based assay that detects tumor-derived DNA for clonotypic immunoglobulin gene rearrangements in the cerebrospinal fluid (CSF) of patients with lymphomas. Used as a diagnostic tool, the NGS-minimal residual disease (NGS-MRD) assay detected clonotypic DNA in 100% of CSF samples from 13 patients with known CNS involvement. They included 7 patients with parenchymal brain disease only, whose CSF tested negative by standard cytology and flow cytometry, and 6 historical DNA aliquots collected from patients at a median of 39 months before accession, which had failed to show clonal rearrangements using standard polymerase chain reaction. For risk prognostication, we prospectively collected CSF from 22 patients with newly diagnosed B-cell lymphomas at high clinical risk of CNS recurrence, of whom 8 (36%) had detectable clonotypic DNA in the CSF. Despite intrathecal prophylaxis, a positive assay of CSF was associated with a 29% cumulative risk of CNS recurrence within 12 months of diagnosis, in contrast with a 0% risk among patients with negative CSF (P = .045). These observations suggest that detection of clonotypic DNA can aid in the diagnosis of suspected parenchymal brain recurrence in aggressive lymphoma. Furthermore, the NGS-MRD assay may enhance clinical risk assessment for CNS recurrence among patients with newly diagnosed lymphomas and help select those who may benefit most from novel approaches to CNS-directed prophylaxis.
Collapse
|
98
|
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.
Collapse
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.
| |
Collapse
|
99
|
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.
Collapse
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.
| |
Collapse
|
100
|
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: 45] [Impact Index Per Article: 15.0] [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.
Collapse
|