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Yu Z, Li J, Deng Y, Li C, Ye M, Zhang Y, Huang Y, Wang X, Zhao X, Liu J, Liu Z, Yin X, Mei L, Hou Y, Hu Q, Huang Y, Wang R, Fu H, Qiu R, Xu J, Gong Z, Zhang D, Zhang X. Lung tumor discrimination by deep neural network model CanDo via DNA methylation in bronchial lavage. iScience 2024; 27:110079. [PMID: 38883836 PMCID: PMC11176796 DOI: 10.1016/j.isci.2024.110079] [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: 01/08/2024] [Revised: 05/02/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
Bronchoscopic-assisted discrimination of lung tumors presents challenges, especially in cases with contraindications or inaccessible lesions. Through meta-analysis and validation using the HumanMethylation450 database, this study identified methylation markers for molecular discrimination in lung tumors and designed a sequencing panel. DNA samples from 118 bronchial washing fluid (BWF) specimens underwent enrichment via multiplex PCR before targeted methylation sequencing. The Recursive Feature Elimination Cross-Validation and deep neural network algorithm established the CanDo classification model, which incorporated 11 methylation features (including 8 specific to the TBR1 gene), demonstrating a sensitivity of 98.6% and specificity of 97.8%. In contrast, bronchoscopic rapid on-site evaluation (bronchoscopic-ROSE) had lower sensitivity (87.7%) and specificity (80%). Further validation in 33 individuals confirmed CanDo's discriminatory potential, particularly in challenging cases for bronchoscopic-ROSE due to pathological complexity. CanDo serves as a valuable complement to bronchoscopy for the discriminatory diagnosis and stratified management of lung tumors utilizing BWF specimens.
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Affiliation(s)
- Zezhong Yu
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jieyi Li
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing 314033, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing 314006, China
| | - Yi Deng
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chun Li
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Maosong Ye
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yong Zhang
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yuqing Huang
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing 314006, China
| | - Xintao Wang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing 314033, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing 314006, China
| | - Xiaokai Zhao
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing 314033, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing 314006, China
| | - Jie Liu
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zilong Liu
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xia Yin
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lijiang Mei
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yingyong Hou
- Department of Pathology Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qin Hu
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yao Huang
- Department of Pulmonary, Taikang Xianlin Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210046, China
| | - Rongping Wang
- Department of Pulmonary, Taikang Xianlin Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210046, China
| | - Huiyu Fu
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing 314006, China
| | - Rumeng Qiu
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing 314006, China
| | - Jiahuan Xu
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing 314006, China
| | - Ziying Gong
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing 314033, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing 314006, China
- Department of R&D, Shanghai Yunying Biopharmaceutical Technology Co., Ltd., Shanghai 201612, China
| | - Daoyun Zhang
- Jiaxing Key Laboratory of Precision Medicine and Companion Diagnostics, Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing 314033, China
- Department of R&D, Zhejiang Yunying Medical Technology Co., Ltd., Jiaxing 314006, China
- Department of R&D, Shanghai Yunying Biopharmaceutical Technology Co., Ltd., Shanghai 201612, China
| | - Xin Zhang
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Department of Pulmonary, Taikang Xianlin Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210046, China
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Zhang X, Yu Z, Xu Y, Chao Y, Hu Q, Li C, Ye M, Zhu X, Cui L, Bai J, Gong Y, Guan Y, Zhou M, Huang J, Zhang H, Ren T, Shen Q, Wang K, Hou Y, Xia X, Pu X, Carbone DP, Zhang X. Utility of cell-free DNA from bronchial washing fluid in diagnosis and genomic determination for radiology-suspected pulmonary nodules. Br J Cancer 2022; 127:2154-2165. [PMID: 36253524 PMCID: PMC9727069 DOI: 10.1038/s41416-022-01969-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/05/2022] [Accepted: 08/23/2022] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Bronchial washing fluid (BWF) is a less-invasive specimen. Due to the limited sensitivity of BWF cellular component diagnosis, the aim of this study was to explore the potential role of BWF supernatant as a source of liquid biopsy of lung cancer. METHODS This prospective study enrolled 76 suspected and 5 progressed lung cancer patients. Transbronchial biopsy tissues, BWF supernatant (BWF_Sup) and BWF precipitant (BWF_Pre) were tested by a targeted panel of 1021 genes. RESULTS BWF_Sup cell-free DNA (cfDNA) was superior to tissue biopsy and BWF_Pre in determining mutational allele frequency, tumour mutational burden, and chromosomal instability. Moreover, BWF_Sup and BWF_Pre achieved comparable efficacy to tissue samples in differentiating malignant and benign patients, but only BWF_Sup persisted differentiated performance after excluding 55 malignancies pathologically diagnosed by bronchoscopic biopsy. Among 67 malignant patients, 82.1% and 71.6% of tumour-derived mutations (TDMs) were detected in BWF_Sup and BWF_Pre, respectively, and the detectability of TDMs in BWF_Sup was independent of the cytological examination of BWF. BWF_Sup outperformed BWF_Pre in providing more subclonal information and thus might yield advantage in tracking drug-resistant markers. CONCLUSIONS BWF_Sup cfDNA is a reliable medium for lung cancer diagnosis and genomic profiles and may provide important information for subsequent therapeutic regimens.
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Affiliation(s)
- Xinyu Zhang
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Zhuo Yu
- Beijing Tsinghua Changgung Hospital, 168 Litang Road, Changping District, 102218, Beijing, China
| | - Yaping Xu
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Yencheng Chao
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Qin Hu
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Chun Li
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Maosong Ye
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Xiuli Zhu
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Liang Cui
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Jing Bai
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Yuhua Gong
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Yanfang Guan
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Min Zhou
- Ruijin Hospital, Shanghai Jiao Tong University, No. 197 Ruijin Second Road, Huangpu District, 200025, Shanghai, China
| | - Jian'an Huang
- First People's Hospital, Suzhou University, No. 899 Pinghai Road, Gusu District, 215008, Suzhou, China
| | - Hua Zhang
- Zhengzhou Central Hospital, Zhengzhou University, No. 195 Tongbai Road, Zhongyuan District, 450000, Zhengzhou, China
| | - Tao Ren
- Shanghai Sixth People's Hospital, No 600 Yishan Road, Xuhui District, 200233, Shanghai, China
| | - Qian Shen
- First Affiliated Hospital of Zhejiang University, No. 79 Qingchun Road, Shangcheng District, 310002, Hangzhou, China
| | - Kai Wang
- Fourth Affiliated Hospital of Zhejiang University, No 88 Jiefang Road, Shangcheng District, 310002, Hangzhou, China
| | - Yingyong Hou
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Xingxiang Pu
- Department of Thoracic Medical Oncology, Hunan Cancer Hospital/the affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Yuelu District, 410013, Changsha, Hunan, China.
| | - David P Carbone
- Comprehensive Cancer Center, The Ohio State University, 460W 12th Ave., Columbus, OH, 43210, USA.
| | - Xin Zhang
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China.
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Sato Y. Clinical utility of liquid biopsy-based companion diagnostics in the non-small-cell lung cancer treatment. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:630-642. [PMID: 36338524 PMCID: PMC9630093 DOI: 10.37349/etat.2022.00104] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
Recently, technological advances in the detection and biological characterization of circulating tumor DNA (ctDNA) have enabled the implementation of liquid biopsy testing into clinical practice. Methods for analysis of liquid biopsies have rapidly evolved over the past few years and have continued to advance, thus providing details about tumor biological characteristics such as tumor progression, metastasis, tumor heterogeneity, genomic mutation profile, clonal evolution, etc. In tandem with technological advances, the implementation of liquid biopsy in routine clinical settings has proceeded. In 2016, the Food and Drug Administration (FDA) approved the first ctDNA liquid biopsy test to detect epidermal growth factor receptor (EGFR) gene mutations in patients with non-small-cell lung cancer (NSCLC) as a companion diagnostic for molecular targeted drug of EGFR-tyrosine kinase inhibitor (TKI, EGFR-TKI). More recently, multigene panel assays of liquid biopsy have been approved as companion diagnostics and have been used in routine clinical settings. The estimation of blood tumor mutation burden (bTMB) to predict the efficacy of immune checkpoint inhibitor (ICI) treatment can be one of the promising approaches to liquid biopsy. The next stage of implementation of liquid biopsy for routine clinical settings is for monitoring of ctDNA after surgical treatment to predict prognosis and to detect disease relapse earlier than conventional imaging diagnosis. Its clinical utility is under assessment in several clinical trials. This review introduces recent advances in liquid biopsy methodology, the development of biomarkers, and its clinical utility in the treatment of NSCLC patients.
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Affiliation(s)
- Yoshiharu Sato
- DNA Chip Research Inc., Tokyo 105-0022, Japan,Correspondence: Yoshiharu Sato, DNA Chip Research Inc., 1-15-1 Kaigan, Minato-ku, Tokyo 105-0022, Japan.
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