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Azad TD, Nanjo S, Jin MC, Chabon JJ, Kurtz DM, Chaudhuri AA, Connolly ID, Hui ABY, Liu CL, Merriott D, Ko R, Yoo C, Carter J, Chen E, Bonilla R, Hata A, Katakami N, Irie K, Yano S, Okimoto R, Bivona TG, Newman AM, Iv M, Nagpal S, Gephart MH, Alizadeh AA, Diehn M. Quantification of cerebrospinal fluid tumor DNA in lung cancer patients with suspected leptomeningeal carcinomatosis. NPJ Precis Oncol 2024; 8:121. [PMID: 38806586 PMCID: PMC11133465 DOI: 10.1038/s41698-024-00582-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
Cerebrospinal fluid tumor-derived DNA (CSF-tDNA) analysis is a promising approach for monitoring the neoplastic processes of the central nervous system. We applied a lung cancer-specific sequencing panel (CAPP-Seq) to 81 CSF, blood, and tissue samples from 24 lung cancer patients who underwent lumbar puncture (LP) for suspected leptomeningeal disease (LMD). A subset of the cohort (N = 12) participated in a prospective trial of osimertinib for refractory LMD in which serial LPs were performed before and during treatment. CSF-tDNA variant allele fractions (VAFs) were significantly higher than plasma circulating tumor DNA (ctDNA) VAFs (median CSF-tDNA, 32.7%; median plasma ctDNA, 1.8%; P < 0.0001). Concentrations of tumor DNA in CSF and plasma were positively correlated (Spearman's ρ, 0.45; P = 0.03). For LMD diagnosis, cytology was 81.8% sensitive and CSF-tDNA was 91.7% sensitive. CSF-tDNA was also strongly prognostic for overall survival (HR = 7.1; P = 0.02). Among patients with progression on targeted therapy, resistance mutations, such as EGFR T790M and MET amplification, were common in peripheral blood but were rare in time-matched CSF, indicating differences in resistance mechanisms based on the anatomic compartment. In the osimertinib cohort, patients with CNS progression had increased CSF-tDNA VAFs at follow-up LP. Post-osimertinib CSF-tDNA VAF was strongly prognostic for CNS progression (HR = 6.2, P = 0.009). Detection of CSF-tDNA in lung cancer patients with suspected LMD is feasible and may have clinical utility. CSF-tDNA improves the sensitivity of LMD diagnosis, enables improved prognostication, and drives therapeutic strategies that account for spatial heterogeneity in resistance mechanisms.
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Affiliation(s)
- Tej D Azad
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Shigeki Nanjo
- Department of Medicine, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Respiratory Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | - Michael C Jin
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - David M Kurtz
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Comprehensive Cancer Center, Rochester, MN, USA
| | - Ian D Connolly
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Angela Bik-Yu Hui
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David Merriott
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Ryan Ko
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Christopher Yoo
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Justin Carter
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Emily Chen
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Rene Bonilla
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Akito Hata
- Department of Medical Oncology, Kobe Minimally Invasive Cancer Center, Kobe, Japan
| | - Nobuyuki Katakami
- Department of Medical Oncology, Takarazuka City Hospital, Hyogo, Japan
| | - Kei Irie
- Department of Pharmaceutics, Faculty of Pharmaceutical Science, Kobe Gakuin University, Kobe, Japan
| | - Seiji Yano
- Department of Respiratory Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | - Ross Okimoto
- Department of Medicine, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Aaron M Newman
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Michael Iv
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Seema Nagpal
- Department of Neurology, Stanford University, Stanford, CA, USA
| | | | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
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Goldberg M, Mondragon-Soto MG, Altawalbeh G, Meyer B, Aftahy AK. New Breakthroughs in the Diagnosis of Leptomeningeal Carcinomatosis: A Review of Liquid Biopsies of Cerebrospinal Fluid. Cureus 2024; 16:e55187. [PMID: 38558729 PMCID: PMC10980855 DOI: 10.7759/cureus.55187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Leptomeningeal carcinomatosis represents a terminal stage and is a devastating complication of cancer. Despite its high incidence, current diagnostic methods fail to accurately detect this condition in a timely manner. This failure to diagnose leads to the refusal of treatment and the absence of clinical trials, hampering the development of new therapy strategies. The use of liquid biopsy is revolutionizing the field of diagnostic oncology. The dynamic and non-invasive detection of tumor markers has enormous potential in cancer diagnostics and treatment. Leptomeningeal carcinomatosis is a condition where invasive tissue biopsy is not part of the routine diagnostic analysis, making liquid biopsy an essential diagnostic tool. Several elements in cerebrospinal fluid (CSF) have been investigated as potential targets of liquid biopsy, including free circulating tumor cells, free circulating nucleic acids, proteins, exosomes, and even non-tumor cells as part of the dynamic tumor microenvironment. This review aims to summarize current breakthroughs in the research on liquid biopsy, including the latest breakthroughs in the identification of tumor cells and nucleic acids, and give an overview of future directions in the diagnosis of leptomeningeal carcinomatosis.
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Affiliation(s)
- Maria Goldberg
- Department of Neurosurgery, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, DEU
| | | | - Ghaith Altawalbeh
- Department of Neurosurgery, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, DEU
| | - Bernhard Meyer
- Department of Neurosurgery, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, DEU
| | - Amir Kaywan Aftahy
- Department of Neurosurgery, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, DEU
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Tsakonas G, Tadigotla V, Chakrabortty SK, Stragliotto G, Chan D, Lewensohn R, Yu W, Skog JK, Hydbring P, Ekman S. Cerebrospinal fluid as a liquid biopsy for molecular characterization of brain metastasis in patients with non-small cell lung cancer. Lung Cancer 2023; 182:107292. [PMID: 37423059 DOI: 10.1016/j.lungcan.2023.107292] [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: 02/28/2023] [Revised: 05/11/2023] [Accepted: 07/02/2023] [Indexed: 07/11/2023]
Abstract
OBJECTIVES Non-small cell lung cancer (NSCLC) with brain metastases (BM) is a challenging clinical issue with poor prognosis. No data exist regarding extensive genetic analysis of cerebrospinal fluid (CSF) and its correlation to associated tumor compartments. MATERIALS AND METHODS We designed a study across multiple NSCLC patients with matched material from four compartments; primary tumor, BM, plasma and CSF. We performed enrichment-based targeted next-generation sequencing analysis of ctDNA and exosomal RNA in CSF and plasma and compared the outcome with the solid tumor compartments. RESULTS An average of 105 million reads per sample was generated with fractions of mapped reads exceeding 99% in all samples and with a mean coverage above 10,000x. We observed a high degree of overlap in variants between primary lung tumor and BM. Variants specific for the BM/CSF compartment included in-frame deletions in AR, FGF10 and TSC1 and missense mutations in HNF1a, CD79B, BCL2, MYC, TSC2, TET2, NRG1, MSH3, NOTCH3, VHL and EGFR. CONCLUSION Our approach of combining ctDNA and exosomal RNA analyses in CSF presents a potential surrogate for BM biopsy. The specific variants that were only observed in the CNS compartments could serve as targets for individually tailored therapies in NSCLC patients with BM.
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Affiliation(s)
- Georgios Tsakonas
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | - Dalin Chan
- Exosome Diagnostics, Inc., a Bio-Techne Brand, Waltham, MA, USA
| | - Rolf Lewensohn
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden
| | - Wei Yu
- Exosome Diagnostics, Inc., a Bio-Techne Brand, Waltham, MA, USA
| | - Johan K Skog
- Exosome Diagnostics, Inc., a Bio-Techne Brand, Waltham, MA, USA
| | - Per Hydbring
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Simon Ekman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden
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Chiang CL, Ho HL, Yeh YC, Lee CC, Huang HC, Shen CI, Luo YH, Chen YM, Chiu CH, Chou TY. Efficacy of different platforms in detecting EGFR mutations using cerebrospinal fluid cell-free DNA from non-small-cell lung cancer patients with leptomeningeal metastases. Thorac Cancer 2023; 14:1251-1259. [PMID: 36977550 PMCID: PMC10175033 DOI: 10.1111/1759-7714.14866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Cell-free tumor DNA (ctDNA) obtained through liquid biopsy is useful for the molecular analysis of advanced non-small-cell lung cancer (NSCLC). Few studies have directly compared analysis platforms in terms of their diagnostic performance in analyzing ctDNA obtained from the cerebrospinal fluid (CSF) of patients with leptomeningeal metastasis (LM). METHODS We prospectively analyzed patients with epidermal growth factor receptor (EGFR)-mutant NSCLC who were subjected to CSF analysis for suspected LM. To detect EGFR mutations, CSF ctDNA was analyzed using the cobas EGFR Mutation Test and droplet digital polymerase chain reaction (ddPCR). CSF samples from osimertinib-refractory patients with LM were also subjected to next-generation sequencing (NGS). RESULTS Significantly higher rates of valid results (95.1% vs. 78%, respectively, p = 0.04) and EGFR common mutation detection (94.3% vs. 77.1%, respectively, p = 0.047) were obtained through ddPCR than through the cobas EGFR Mutation Test. The sensitivities of ddPCR and cobas were 94.3% and 75.6%, respectively. The concordance rate for EGFR mutation detection through ddPCR and the cobas EGFR Mutation Test was 75.6% and that for EGFR mutation detection in CSF and plasma ctDNA was 28.1%. In osimertinib-resistant CSF samples, all original EGFR mutations were detected through NGS. MET amplification and CCDC6-RET fusion were demonstrated in one patient each (9.1%). CONCLUSIONS The cobas EGFR Mutation Test, ddPCR, and NGS appear to be feasible methods for analyzing CSF ctDNA in patients with NSCLC and LM. In addition, NGS may provide comprehensive information regarding the mechanisms underlying osimertinib resistance.
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Affiliation(s)
- Chi-Lu Chiang
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hsiang-Ling Ho
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Chen Yeh
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Cheng-Chia Lee
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hsu-Ching Huang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chia-I Shen
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yung-Hung Luo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yuh-Min Chen
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chao-Hua Chiu
- Taipei Cancer Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Teh-Ying Chou
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Pathology, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
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Prognosticators of osimertinib treatment outcomes in patients with EGFR-mutant non-small cell lung cancer and leptomeningeal metastasis. J Cancer Res Clin Oncol 2023; 149:5-14. [PMID: 36318332 DOI: 10.1007/s00432-022-04396-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/05/2022] [Indexed: 02/01/2023]
Abstract
PURPOSE Leptomeningeal metastasis (LM) is a serious complication of non-small cell lung cancer (NSCLC), particularly in patients with EGFR mutations. In this study, we investigated the survival outcomes of patients with EGFR-mutant NSCLC who have developed LM and explored the factors associated with their survival. METHODS From April 2018 to November 2021, patients with EGFR-mutant NSCLC who underwent cerebrospinal fluid (CSF) sampling under the clinical suspicion of LM were enrolled. The patients' clinicodemographic characteristics, treatment history including whole-brain radiation therapy (WBRT), overall survival (OS), and intracranial progression-free survival (icPFS) were measured. EGFR mutations in cell-free tumor DNA (ctDNA) of CSF, including T790M mutation, were analyzed. RESULTS We enrolled 62 patients with NSCLC. The median time form diagnosis to LM was 23.1 months and 16 (25.8%) patients had history of prior third-generation EGFR-TKI use. EGFR mutation in CSF ctDNA was detected in 53 patients (85.5%); of them, 10 (16.1%) had T790M mutation. The patients' icPFS and OS after osimertinib were 6.43 and 9.37 months, respectively, and were comparable among patients with different sensitive EGFR mutations, indicating that EGFR mutation status did not affect osimertinib efficacy. Patients who received WBRT after LM had numerically higher icPFS and OS compared to those without. Multivariate analysis revealed that lack of prior exposure to third-generation EGFR-TKI was associated with better OS. CONCLUSIONS Osimertinib is effective in patients with EGFR-mutant NSCLC who developed LM and prior third-generation EGFR-TKI use was associated with poor survival in these patients. The role of WBRT warrants further investigation.
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Gao T, Chen F, Li M. Sequencing of cerebrospinal fluid in non-small-cell lung cancer patients with leptomeningeal metastasis: A systematic review. Cancer Med 2022; 12:2248-2261. [PMID: 36000927 PMCID: PMC9939157 DOI: 10.1002/cam4.5163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 07/14/2022] [Accepted: 08/12/2022] [Indexed: 11/07/2022] Open
Abstract
Leptomeningeal metastasis (LM) refers to the dissemination of malignant cells in the subarachnoid space, pia, and arachnoid mater and is a severe condition associated with metastatic solid tumors. The most common solid tumor that develops into LM is lung cancer and the incidence increased in patients with advanced non-small-cell lung cancer (NSCLC) with targetable mutations. However, tissue biopsy of LM is inaccessible, leading to the paucity of genomic profiles of LM to guide targeted treatments and explore biological mechanisms. In recent years, liquid biopsy is considered a minimally invasive and dynamic method to trace the genomic alterations of cancer cells and some studies started to perform sequencing of cerebrospinal fluid (CSF) in patients with LM to reveal the targeted mutations and genomic profiles. In this review, we focused on studies performed sequencing of CSF in NSCLC patients with LM and summarized the sequencing results and their commonality. As the only way to reveal the genomic landscapes of LM, our review provided evidence that sequencing of CSF is a promising management method in LM patients to dynamically guide target therapy and monitor intracranial tumor response. Furthermore, it reveals a unique genomic profile of LM including driver genes, drug-resistant mutations, and a number of copy number variations. Sequencing of CSF in LM patients seems to provide more comprehensive genomic information than we expected and the biological significance behind the genomic alternations needs further study.
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Affiliation(s)
- Tianqi Gao
- Department of OncologyThe Second Hospital of Dalian Medical UniversityDalianChina
| | - Fengxi Chen
- Department of OncologyThe Second Hospital of Dalian Medical UniversityDalianChina
| | - Man Li
- Department of OncologyThe Second Hospital of Dalian Medical UniversityDalianChina
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Luo YH, Liang KH, Huang HC, Shen CI, Chiang CL, Wang ML, Chiou SH, Chen YM. State-of-the-Art Molecular Oncology of Lung Cancer in Taiwan. Int J Mol Sci 2022; 23:ijms23137037. [PMID: 35806042 PMCID: PMC9266727 DOI: 10.3390/ijms23137037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/14/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Lung cancers are life-threatening malignancies that cause great healthcare burdens in Taiwan and worldwide. The 5-year survival rate for Taiwanese patients with lung cancer is approximately 29%, an unsatisfactorily low number that remains to be improved. We first reviewed the molecular epidemiology derived from a deep proteogenomic resource in Taiwan. The nuclear factor erythroid 2-related factor 2 (NRF2)antioxidant mechanism was discovered to mediate the oncogenesis and tumor progression of lung adenocarcinoma. Additionally, DNA replication, glycolysis and stress response are positively associated with tumor stages, while cell-to-cell communication, signaling, integrin, G protein coupled receptors, ion channels and adaptive immunity are negatively associated with tumor stages. Three patient subgroups were discovered based on the clustering analysis of protein abundance in tumors. The first subgroup is associated with more advanced cancer stages and visceral pleural invasion, as well as higher mutation burdens. The second subgroup is associated with EGFR L858R mutations. The third subgroup is associated with PI3K/AKT pathways and cell cycles. Both EGFR and PI3K/AKT signaling pathways have been shown to induce NRF2 activation and tumor cell proliferation. We also reviewed the clinical evidence of patient outcomes in Taiwan given various approved targeted therapies, such as EGFR-tyrosine kinase inhibitors and anaplastic lymphoma kinase (ALK)inhibitors, in accordance with the patients’ characteristics. Somatic mutations occurred in EGFR, KRAS, HER2 and BRAF genes, and these mutations have been detected in 55.7%, 5.2%, 2.0% and 0.7% patients, respectively. The EGFR mutation is the most prevalent targetable mutation in Taiwan. EML4-ALK translocations have been found in 9.8% of patients with wild-type EGFR. The molecular profiling of advanced NSCLC is critical to optimal therapeutic decision-making. The patient characteristics, such as mutation profiles, protein expression profiles, drug-resistance profiles, molecular oncogenic mechanisms and patient subgroup systems together offer new strategies for personalized treatments and patient care.
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Affiliation(s)
- Yung-Hung Luo
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.-H.L.); (H.-C.H.); (C.-I.S.); (C.-L.C.)
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Kung-Hao Liang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Hsu-Ching Huang
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.-H.L.); (H.-C.H.); (C.-I.S.); (C.-L.C.)
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Chia-I Shen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.-H.L.); (H.-C.H.); (C.-I.S.); (C.-L.C.)
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Chi-Lu Chiang
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.-H.L.); (H.-C.H.); (C.-I.S.); (C.-L.C.)
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Mong-Lien Wang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Correspondence: (S.-H.C.); (Y.-M.C.); Tel.: +886-2-28757865 (Y.-M.C.)
| | - Yuh-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.-H.L.); (H.-C.H.); (C.-I.S.); (C.-L.C.)
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Correspondence: (S.-H.C.); (Y.-M.C.); Tel.: +886-2-28757865 (Y.-M.C.)
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Chiang CL, Shen CI, Huang HC, Chang HJ, Huang YT, Chiu CH. Cytology–Based Specimen Triage for Epidermal Growth Factor Receptor Mutation Testing of Malignant Pleural Effusions in Non–Small Cell Lung Cancer. Front Oncol 2022; 12:810124. [PMID: 35141163 PMCID: PMC8819005 DOI: 10.3389/fonc.2022.810124] [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: 11/06/2021] [Accepted: 01/04/2022] [Indexed: 11/15/2022] Open
Abstract
Introduction Malignant pleural effusions are common in non–small cell lung cancer (NSCLC). Molecular testing is among the most critical steps in the management of patients with advanced NSCLC. However, the optimal approach for epidermal growth factor receptor (EGFR) mutation testing in such effusion samples remains unclear. Methods We prospectively collected effusion samples from patients with EGFR–mutant NSCLC. Following sample centrifugation, genomic DNA and cell–free DNA were respectively extracted from the sediment and supernatants. EGFR mutation was detected through a real–time PCR assay. Results A total of 108 effusions from 78 patients were examined, with 12 and 96 obtained before and after EGFR tyrosine kinase inhibitor treatment, respectively. Carcinoma cells or atypical cells were identified in 73 effusions (67.6%). EGFR mutations were detected in 86 (79.6%) sediment and 84 (77.8%) supernatant samples. Among the effusions with positive cytological findings, the EGFR mutation detection rates were 95.9% (70/73) and 86.3% (63/73) in the sediment and supernatants, respectively. Among the effusions with negative cytological findings, the corresponding detection rates were 45.7% (16/35) and 60% (21/35), respectively. Current clinical practice is to arrange EGFR mutation testing only for sediment from cytologically positive effusions. Through the proposed cytology–based specimen triage, wherein sediment and supernatants with positive and negative cytological findings, respectively, are tested, the detection rate was increased from 64.8% (70/108) to 84.3% (91/108). At half of the cost, this strategy provided a detection rate only slightly lower than the rate in a combined test of all the sediment and supernatants (87.0%, 94/108). Conclusions The separate extraction of DNA from sediment and supernatants obtained from centrifuged effusion samples can improve the overall EGFR mutation detection rate. The present cytology–based specimen triage is an efficient strategy for EGFR mutation testing in patients with EGFR–mutant NSCLC.
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Affiliation(s)
- Chi-Lu Chiang
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chia-I Shen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsu-Ching Huang
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Han-Jhih Chang
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Ting Huang
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chao-Hua Chiu
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- *Correspondence: Chao-Hua Chiu,
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Wang P, Zhang H, Chen P, Sun Z, Zhang Z, Yin Q, Sun H, Yu J. The Presence of Genomic Instability in Cerebrospinal Fluid in Patients with Meningeal Metastasis. Cancer Manag Res 2021; 13:4853-4863. [PMID: 34188538 PMCID: PMC8232886 DOI: 10.2147/cmar.s295368] [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: 12/04/2020] [Accepted: 05/17/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose This study aimed to explore the genomic instability in cerebrospinal fluid (CSF) in patients with meningeal metastasis (MM). Material and Methods We collected the blood and CSF samples of 15 MM patients and one brain parenchymal metastasis (BPM) patient. A panel of 543 cancer-related genes was conducted to analyze the status of genomic instability in CSF and plasma cell-free DNA (cfDNA) of all patients. Subsequently, nine patients underwent low-depth whole-genome sequencing (WGS) analysis to verify the existence of genomic instability, followed by genomic scoring by the application of aneuploidy scores. Diagnosis-specific graded prognostic assessment (DS-GPA) score was utilized to assess the clinical status of MM patients. Results There was significant difference in gene mutation between CSF cfDNA and plasma cfDNA in MM patients. Among them, 12 MM patients developed genomic instability in their CSF cfDNA, while the remaining 3 had stable genetic profile. Besides, BPM patients showed genomic stability in his CSF and paraffin-embedded tissue sections. No genomic instability was noticed in plasma cfDNA of all patients. Sensitive mutations on EGFR, ERBB2, ALK and KRAS genes and increased gene copy numbers of MET and ERBB2 were detected in 10 MM patients with genomic instability, as well as the EGFR gene mutation in one MM case with genomic stability. Additionally, MM patients with genomic instability had lower overall survival and higher aneuploidy scores and tumor mutation burden compared with those with genomic stability. Moreover, MM patients with higher DS-GPA scores benefited from better survival. Conclusion Genomic instability existed in the CSF cfDNA rather than plasma cfDNA of MM patients, which might be the underlying cause of the differences in MM.
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Affiliation(s)
- Peng Wang
- Department of Neuro-Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China.,Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, People's Republic of China
| | - Henghui Zhang
- Genecast Biotechnology Co., Ltd, Wuxi, 214000, People's Republic of China
| | - Peng Chen
- Genecast Biotechnology Co., Ltd, Wuxi, 214000, People's Republic of China
| | - Zengfeng Sun
- Department of Neuro-Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China.,Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, People's Republic of China
| | - Zhen Zhang
- Department of Neuro-Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China.,Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, People's Republic of China
| | - Qiang Yin
- Department of Neuro-Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China.,Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, People's Republic of China
| | - Huaibo Sun
- Genecast Biotechnology Co., Ltd, Wuxi, 214000, People's Republic of China
| | - Jinpu Yu
- Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, People's Republic of China.,Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
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