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Huang H, Kai Z, Wang Y, Zhang X, Wang J, Zhang W, Xue Q, Zhang H, Jin H, Meng P, Zhang S, Yang Y, Yang H, Liang W, Zha G, Luo P, Xu Y, Shi W, Ruan Z. Evaluating personalized circulating tumor DNA detection for early-stage lung cancer. Cancer Med 2024; 13:e6817. [PMID: 38112031 PMCID: PMC11112296 DOI: 10.1002/cam4.6817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/20/2023] [Accepted: 12/03/2023] [Indexed: 12/20/2023] Open
Abstract
Circulating tumor DNA (ctDNA) has been widely used as a minimally invasive biomarker in clinical routine. However, a number of factors such as panel design, sample quality, patients' disease stages are known to influence ctDNA detection sensitivity. In this study, we systematically evaluated common factors associated with the variability of ctDNA detection in plasma and investigated ctDNA abundance in bronchoalveolar lavage (BAL). Whole exome profiling was conducted on 61 tumor tissue samples to identify tumor-specific variants, which were then used to design personalized assay MarRyDa® for ctDNA detection. DNA extracted from BAL fluid and plasma were genotyped using MarRyDa® platform. Our analysis showed that histological subtypes and disease stages had significant differences in ctDNA detection rate. Furthermore, we found that DNA purified from BAL supernatants contains the highest levels of ctDNA compared with BAL precipitates and plasma; therefore, utilizing BAL supernatants for tumor detection might provide additional benefits. Finally, we demonstrated that tumor cellularity played significant roles in the design of personalized ctDNA panel which eventually impacts ctDNA detection sensitivity. We suggest setting a flexible criteria for sample quality control and utilization of BAL might benefit more patients in clinics.
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Affiliation(s)
- Haihua Huang
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
| | - Zhentian Kai
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd.ShanghaiChina
| | - Yuchen Wang
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
| | - Xiaomiao Zhang
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
| | - Jin Wang
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
| | - Wei Zhang
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
| | - Qian Xue
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
| | - Hang Zhang
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
| | - Hansong Jin
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
| | - Peize Meng
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
| | - Shuilong Zhang
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd.ShanghaiChina
| | - Yueyue Yang
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd.ShanghaiChina
| | - Honghua Yang
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd.ShanghaiChina
| | - Wanning Liang
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd.ShanghaiChina
| | - Guangbing Zha
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd.ShanghaiChina
| | - Peng Luo
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd.ShanghaiChina
| | - Yan Xu
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd.ShanghaiChina
| | - Weiwei Shi
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd.ShanghaiChina
| | - Zheng Ruan
- Department of Thoracic SurgeryShanghai First People's HospitalShanghaiChina
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Dlugolecka M, Szymanski J, Zareba L, Homoncik Z, Domagala-Kulawik J, Polubiec-Kownacka M, Czystowska-Kuzmicz M. Characterization of Extracellular Vesicles from Bronchoalveolar Lavage Fluid and Plasma of Patients with Lung Lesions Using Fluorescence Nanoparticle Tracking Analysis. Cells 2021; 10:3473. [PMID: 34943982 PMCID: PMC8699990 DOI: 10.3390/cells10123473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
The current lack of reliable methods for quantifying extracellular vesicles (EVs) isolated from complex biofluids significantly hinders translational applications in EV research. The recently developed fluorescence nanoparticle tracking analysis (FL-NTA) allows for the detection of EV-associated proteins, enabling EV content determination. In this study, we present the first comprehensive phenotyping of bronchopulmonary lavage fluid (BALF)-derived EVs from non-small cell lung cancer (NSCLC) patients using classical EV-characterization methods as well as the FL-NTA method. We found that EV immunolabeling for the specific EV marker combined with the use of the fluorescent mode NTA analysis can provide the concentration, size, distribution, and surface phenotype of EVs in a heterogeneous solution. However, by performing FL-NTA analysis of BALF-derived EVs in comparison to plasma-derived EVs, we reveal the limitations of this method, which is suitable only for relatively pure EV isolates. For more complex fluids such as plasma, this method appears to not be sensitive enough and the measurements can be compromised. Our parallel presentation of NTA-based phenotyping of plasma and BALF EVs emphasizes the great impact of sample composition and purity on FL-NTA analysis that has to be taken into account in the further development of FL-NTA toward the detection of EV-associated cancer biomarkers.
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Affiliation(s)
- Magdalena Dlugolecka
- Chair and Department of Biochemistry, Doctoral School, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland;
| | - Jacek Szymanski
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
- Chair and Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (L.Z.); (Z.H.)
| | - Lukasz Zareba
- Chair and Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (L.Z.); (Z.H.)
| | - Zuzanna Homoncik
- Chair and Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (L.Z.); (Z.H.)
| | - Joanna Domagala-Kulawik
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, Banacha 1a, 02-097 Warsaw, Poland;
| | | | - Malgorzata Czystowska-Kuzmicz
- Chair and Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (L.Z.); (Z.H.)
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Roncarati R, Lupini L, Miotto E, Saccenti E, Mascetti S, Morandi L, Bassi C, Rasio D, Callegari E, Conti V, Rinaldi R, Lanza G, Gafà R, Papi A, Frassoldati A, Sabbioni S, Ravenna F, Casoni GL, Negrini M. Molecular testing on bronchial washings for the diagnosis and predictive assessment of lung cancer. Mol Oncol 2020; 14:2163-2175. [PMID: 32441866 PMCID: PMC7463327 DOI: 10.1002/1878-0261.12713] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/04/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Cytopathological analyses of bronchial washings (BWs) collected during fibre‐optic bronchoscopy are often inconclusive for lung cancer diagnosis. To address this issue, we assessed the suitability of conducting molecular analyses on BWs, with the aim to improve the diagnosis and outcome prediction of lung cancer. The methylation status of RASSF1A, CDH1, DLC1 and PRPH was analysed in BW samples from 91 lung cancer patients and 31 controls, using a novel two‐colour droplet digital methylation‐specific PCR (ddMSP) technique. Mutations in ALK, BRAF, EGFR, ERBB2, KRAS, MAP2K1, MET, NRAS, PIK3CA, ROS1 and TP53 and gene fusions of ALK, RET and ROS1 were also investigated, using next‐generation sequencing on 73 lung cancer patients and 14 tumour‐free individuals. Our four‐gene methylation panel had significant diagnostic power, with 97% sensitivity and 74% specificity (relative risk, 7.3; odds ratio, 6.1; 95% confidence interval, 12.7–127). In contrast, gene mutation analysis had a remarkable value for predictive, but not for diagnostic, purposes. Actionable mutations in EGFR, HER2 and ROS1 as well as in other cancer genes (KRAS, PIK3CA and TP53) were detected. Concordance with gene mutations uncovered in tumour biopsies was higher than 90%. In addition, bronchial‐washing analyses permitted complete patient coverage and the detection of additional actionable mutations. In conclusion, BWs are a useful material on which to perform molecular tests based on gene panels: aberrant gene methylation and mutation analyses could be performed as approaches accompanying current diagnostic and predictive assays during the initial workup phase. This study establishes the grounds for further prospective investigation.
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Affiliation(s)
- Roberta Roncarati
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy.,CNR, Institute of Genetics and Biomedical Research, National Research Council of Italy, Milano, Italy
| | - Laura Lupini
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy
| | - Elena Miotto
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy
| | - Elena Saccenti
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy
| | - Susanna Mascetti
- Azienda Ospedaliero-Universitaria di Ferrara, Division of Respiratory Endoscopy, S. Anna Hospital, Cona, Italy
| | - Luca Morandi
- Azienda Ospedaliero-Universitaria di Ferrara, Division of Respiratory Endoscopy, S. Anna Hospital, Cona, Italy
| | - Cristian Bassi
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy.,Laboratorio per le Tecnologie delle Terapie Avanzate, Tecnopolo, University of Ferrara, Italy
| | - Debora Rasio
- Department of Clinical and Molecular Medicine, Sant' Andrea Hospital, University "La Sapienza", Rome, Italy
| | - Elisa Callegari
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy
| | - Valentina Conti
- Pneumology Division, State Hospital, San Marino, Republic of San Marino
| | - Rosa Rinaldi
- Division of Anatomic Pathology, Carlo Poma Hospital, Mantova, Italy
| | - Giovanni Lanza
- Azienda Ospedaliero-Universitaria di Ferrara, Division of Anatomic Pathology, S. Anna Hospital, Cona, Italy.,Department of Medical Sciences, University of Ferrara, Italy
| | - Roberta Gafà
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy.,Azienda Ospedaliero-Universitaria di Ferrara, Division of Anatomic Pathology, S. Anna Hospital, Cona, Italy
| | - Alberto Papi
- Azienda Ospedaliero-Universitaria di Ferrara, Division of Respiratory Endoscopy, S. Anna Hospital, Cona, Italy.,Department of Medical Sciences, University of Ferrara, Italy
| | - Antonio Frassoldati
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy.,Azienda Ospedaliero-Universitaria di Ferrara, Medical Oncology Unit, S. Anna Hospital, Cona, Italy
| | - Silvia Sabbioni
- Laboratorio per le Tecnologie delle Terapie Avanzate, Tecnopolo, University of Ferrara, Italy.,Department of Life Sciences and Biotechnology, University of Ferrara, Italy
| | - Franco Ravenna
- Division of Pneumology and Intensive Respiratory Unit, Carlo Poma Hospital, Mantova, Italy
| | - Gian L Casoni
- Azienda Ospedaliero-Universitaria di Ferrara, Division of Respiratory Endoscopy, S. Anna Hospital, Cona, Italy
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Italy.,Laboratorio per le Tecnologie delle Terapie Avanzate, Tecnopolo, University of Ferrara, Italy
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