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Zhang R, Shi K, Hohenforst-Schmidt W, Steppert C, Sziklavari Z, Schmidkonz C, Atzinger A, Hartmann A, Vieth M, Förster S. Ability of 18F-FDG Positron Emission Tomography Radiomics and Machine Learning in Predicting KRAS Mutation Status in Therapy-Naive Lung Adenocarcinoma. Cancers (Basel) 2023; 15:3684. [PMID: 37509345 PMCID: PMC10377773 DOI: 10.3390/cancers15143684] [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: 06/18/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
OBJECTIVE Considering the essential role of KRAS mutation in NSCLC and the limited experience of PET radiomic features in KRAS mutation, a prediction model was built in our current analysis. Our model aims to evaluate the status of KRAS mutants in lung adenocarcinoma by combining PET radiomics and machine learning. METHOD Patients were retrospectively selected from our database and screened from the NSCLC radiogenomic dataset from TCIA. The dataset was randomly divided into three subgroups. Two open-source software programs, 3D Slicer and Python, were used to segment lung tumours and extract radiomic features from 18F-FDG-PET images. Feature selection was performed by the Mann-Whitney U test, Spearman's rank correlation coefficient, and RFE. Logistic regression was used to build the prediction models. AUCs from ROCs were used to compare the predictive abilities of the models. Calibration plots were obtained to examine the agreements of observed and predictive values in the validation and testing groups. DCA curves were performed to check the clinical impact of the best model. Finally, a nomogram was obtained to present the selected model. RESULTS One hundred and nineteen patients with lung adenocarcinoma were included in our study. The whole group was divided into three datasets: a training set (n = 96), a validation set (n = 11), and a testing set (n = 12). In total, 1781 radiomic features were extracted from PET images. One hundred sixty-three predictive models were established according to each original feature group and their combinations. After model comparison and selection, one model, including wHLH_fo_IR, wHLH_glrlm_SRHGLE, wHLH_glszm_SAHGLE, and smoking habits, was validated with the highest predictive value. The model obtained AUCs of 0.731 (95% CI: 0.619~0.843), 0.750 (95% CI: 0.248~1.000), and 0.750 (95% CI: 0.448~1.000) in the training set, the validation set and the testing set, respectively. Results from calibration plots in validation and testing groups indicated that there was no departure between observed and predictive values in the two datasets (p = 0.377 and 0.861, respectively). CONCLUSIONS Our model combining 18F-FDG-PET radiomics and machine learning indicated a good predictive ability of KRAS status in lung adenocarcinoma. It may be a helpful non-invasive method to screen the KRAS mutation status of heterogenous lung adenocarcinoma before selected biopsy sampling.
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Affiliation(s)
- Ruiyun Zhang
- Institute of Pathology, Medizincampus Oberfranken, Klinikum Bayreuth, Friedrich-Alexander-Universität Erlangen-Nürnberg, 95445 Bayreuth, Germany
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Kuangyu Shi
- Department of Nuclear Medicine, Inselspital Bern, 3010 Bern, Switzerland
| | | | - Claus Steppert
- Department of Pneumology, REGIOMED Klinikum Coburg, 96450 Coburg, Germany
| | - Zsolt Sziklavari
- Department of Thoracic Surgery, Klinikum Coburg, 96450 Coburg, Germany
| | - Christian Schmidkonz
- Department of Nuclear Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Armin Atzinger
- Department of Nuclear Medicine, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Michael Vieth
- Institute of Pathology, Medizincampus Oberfranken, Klinikum Bayreuth, Friedrich-Alexander-Universität Erlangen-Nürnberg, 95445 Bayreuth, Germany
| | - Stefan Förster
- Department of Nuclear Medicine, Klinikum Bayreuth, 95445 Bayreuth, Germany
- Medizincampus Oberfranken, Universitätsklinikum Erlangen, 95445 Bayreuth, Germany
- Department of Nuclear Medicine, Klinikum rechts der Isar der Technischen Universitaet Muenchen, 81675 München, Germany
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Doi Y, Tagaya H, Noge A, Semba K. Prediction of Resistance Mutations Against Upcoming Anaplastic Lymphoma Kinase Inhibitors. Target Oncol 2022; 17:695-707. [PMID: 36201110 DOI: 10.1007/s11523-022-00919-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Chromosomal aberrations involving the anaplastic lymphoma kinase (ALK) gene have been observed in approximately 4% of patients with non-small cell lung cancer (NSCLC). Although these patients clinically benefit from treatment with various ALK tyrosine kinase inhibitors (ALK-TKIs), none of these can inhibit the development of resistance mutations. Considering inevitable drug resistance and the variety of available ALK-TKIs, it is necessary to predict the pattern of drug-resistance mutations to determine the optimal treatment strategy. OBJECTIVE We aimed to establish a polymerase chain reaction (PCR)-based system to predict the development of resistance mutations against ALK-TKIs and identify therapeutic strategies using the upcoming ALK-TKIs repotrectinib (TPX-0005) and ensartinib (X-396) following recurrence on first-line alectinib treatment for ALK-positive NSCLC. METHODS An error-prone PCR-based method for predicting drug resistance mutations was established and the half-maximal inhibitory concentration (IC50) values of the predicted ALK mutations were evaluated in a Ba/F3 cell-based assay. RESULTS We predicted several resistance mutations against repotrectinib and ensartinib, and demonstrated that the next-generation ALK-TKI TPX-0131, was active against repotrectinib-resistant mutations and that the FLT3 inhibitor gilteritinib was active against ensartinib-resistant mutations. CONCLUSIONS We developed a PCR-based system for predicting drug resistance mutations. When this system was applied to repotrectinib and ensartinib, the results suggested that these drugs can be used for the second-line treatment of ALK-positive NSCLC. Predicting resistance mutations against TKIs will provide useful information to aid in the development of effective therapeutic strategies.
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Affiliation(s)
- Yuta Doi
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Hiroaki Tagaya
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Ayaka Noge
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan. .,Translational Research Center, Fukushima Medical University, Hikarigaoka, Fukushima, 960-1295, Japan.
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Vav1 accelerates Ras-driven lung cancer and modulates its tumor microenvironment. Cell Signal 2022; 97:110395. [PMID: 35752351 DOI: 10.1016/j.cellsig.2022.110395] [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] [Received: 05/13/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 11/23/2022]
Abstract
The potential impact of Vav1 on human cancer was only recently acknowledged, as it is detected as a mutant or an overexpressed gene in various cancers, including lung cancer. Vav1, which is normally and exclusively expressed in the hematopoietic system functions as a specific GDP/GTP nucleotide exchange factor (GEF), strictly regulated by tyrosine phosphorylation. To investigate whether Vav1 plays a causative or facilitating role in-vivo in lung cancer development and to examine whether it co-operates with other oncogenes, such as mutant K-Ras, we generated novel mouse strains that express: Vav1 or K-RasG12D in type II pneumocytes, as well as a transgenic mouse line that expresses both Vav1 and K-RasG12D in these cells. Coexpression of Vav1 and K-RasG12D in the lungs dramatically increased malignant lung cancer lesions, and did so significantly faster than K-RasG12D alone, strongly suggesting that these two oncogenes synergize to enhance lung tumor development. Vav1 expression alone had no apparent effects on lung tumorigenesis. The increase in lung cancer in K-RasG12D/Vav1 mice was accompanied by an increase in B-cell, T-cells, and monocyte infiltration in the tumor microenvironment. Concomitantly, ERK phosphorylation was highly elevated in the lungs of K-RasG12 D/Vav1 mice. Also, several cytokines such as IL-4 and IL-13 which play a significant role in the immune system, were elevated in lungs of Vav1 and K-RasG12 D/Vav1 mice. Our findings emphasize the contribution of Vav1 to lung tumor development through its signaling properties.
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Acker F, Stratmann J, Aspacher L, Nguyen NTT, Wagner S, Serve H, Wild PJ, Sebastian M. KRAS Mutations in Squamous Cell Carcinomas of the Lung. Front Oncol 2022; 11:788084. [PMID: 34976827 PMCID: PMC8714661 DOI: 10.3389/fonc.2021.788084] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
KRAS is one of the most commonly mutated oncogenes in cancer, enabling tumor proliferation and maintenance. After various approaches to target KRAS have failed over the past decades, the first specific inhibitor of the p.G12C mutation of KRAS was recently approved by the FDA after showing promising results in adenocarcinomas of the lung and other solid tumors. Lung cancer, the most common cancer worldwide, is a promising use case for these new therapies, as adenocarcinomas in particular frequently harbor KRAS mutations. However, in squamous cell carcinoma (SCC) of the lung, KRAS mutations are rare and their impact on clinical outcome is poorly understood. In this review, we discuss the current knowledge on the prevalence and prognostic and predictive significance of KRAS mutations in the context of SCC.
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Affiliation(s)
- Fabian Acker
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Jan Stratmann
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Lukas Aspacher
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | | | - Sebastian Wagner
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Hubert Serve
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany.,Wildlab, University Hospital MVZ GmbH, Frankfurt, Germany.,Frankfurt Institute for Advanced Studies (FIAS), Frankfurt, Germany
| | - Martin Sebastian
- Medizinische Klinik II, University Hospital Frankfurt, Frankfurt, Germany
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Chen X, Li K, Liu Z, Gai F, Zhu G, Lu S, Che N. Multigene PCR using both cfDNA and cfRNA in the supernatant of pleural effusion achieves accurate and rapid detection of mutations and fusions of driver genes in patients with advanced NSCLC. Cancer Med 2021; 10:2286-2292. [PMID: 33656807 PMCID: PMC7982639 DOI: 10.1002/cam4.3769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/16/2021] [Accepted: 01/21/2021] [Indexed: 01/29/2023] Open
Abstract
Background Pleural effusion from patients with advanced non‐small cell lung cancer (NSCLC) has been proved valuable for molecular analysis, especially when the tissue sample not available. However, simultaneous detection of multiple driver gene alterations especially the fusions is still challenging. Methods In this study, 77 patients with advanced NSCLC and pleural effusion were enrolled, 49 of whom had matched tumor tissues. Supernatants, cell sediments, and cell blocks were prepared from pleural effusion samples for detection of driver alterations by a PCR‐based 9‐gene mutation detection kit. Results Mutations in EGFR, KRAS, and HER2 were detected in DNA and cfDNA, fusions in ALK was detected in RNA and cfRNA. Compared with matched tumor tissue, the supernatant showed the highest overall sensitivity (81.3%), with 81.5% for SNV/Indels by cfDNA and 80% for fusions by cfRNA, followed by cell blocks (71.0%) and the cell sediments (66.7%). Within the group of treatment‐naïve patients or malignant cells observed in the cell sediments, supernatant showed higher overall sensitivity (89.5% and 92.3%) with both 100% for fusions. Conclusions CfDNA and cfRNA derived from pleural effusion supernatant have been successfully tested with a PCR‐based multigene detection kit. Pleural effusion supernatant seems a preferred material for detection of multigene alterations to guide treatment decision of advanced NSCLC.
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Affiliation(s)
- Xuejing Chen
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis And Thoracic Tumor Research Institute, Beijing, China
| | - Kun Li
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis And Thoracic Tumor Research Institute, Beijing, China
| | - Zichen Liu
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis And Thoracic Tumor Research Institute, Beijing, China
| | - Fei Gai
- Medical Department, Amoy Diagnostics Co., Ltd., Xiamen, China
| | - Guanshan Zhu
- Medical Department, Amoy Diagnostics Co., Ltd., Xiamen, China
| | - Shun Lu
- Department of Oncology, Shanghai Chest Hospital Shanghai Jiaotong University, Shanghai, China
| | - Nanying Che
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis And Thoracic Tumor Research Institute, Beijing, China
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