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Zhao Z, Yin W, Peng X, Cai Q, He B, Shi S, Peng W, Tu G, Li Y, Li D, Tao Y, Peng M, Wang X, Yu F. A Machine-Learning Approach to Developing a Predictive Signature Based on Transcriptome Profiling of Ground-Glass Opacities for Accurate Classification and Exploring the Immune Microenvironment of Early-Stage LUAD. Front Immunol 2022; 13:872387. [PMID: 35693786 PMCID: PMC9178173 DOI: 10.3389/fimmu.2022.872387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Screening for early-stage lung cancer with low-dose computed tomography is recommended for high-risk populations; consequently, the incidence of pure ground-glass opacity (pGGO) is increasing. Ground-glass opacity (GGO) is considered the appearance of early lung cancer, and there remains an unmet clinical need to understand the pathology of small GGO (<1 cm in diameter). The objective of this study was to use the transcriptome profiling of pGGO specimens <1 cm in diameter to construct a pGGO-related gene risk signature to predict the prognosis of early-stage lung adenocarcinoma (LUAD) and explore the immune microenvironment of GGO. pGGO-related differentially expressed genes (DEGs) were screened to identify prognostic marker genes with two machine learning algorithms. A 15-gene risk signature was constructed from the DEGs that were shared between the algorithms. Risk scores were calculated using the regression coefficients for the pGGO-related DEGs. Patients with Stage I/II LUAD or Stage IA LUAD and high-risk scores had a worse prognosis than patients with low-risk scores. The prognosis of high-risk patients with Stage IA LUAD was almost identical to that of patients with Stage II LUAD, suggesting that treatment strategies for patients with Stage II LUAD may be beneficial in high-risk patients with Stage IA LUAD. pGGO-related DEGs were mainly enriched in immune-related pathways. Patients with high-risk scores and high tumor mutation burden had a worse prognosis and may benefit from immunotherapy. A nomogram was constructed to facilitate the clinical application of the 15-gene risk signature. Receiver operating characteristic curves and decision curve analysis validated the predictive ability of the nomogram in patients with Stage I LUAD in the TCGA-LUAD cohort and GEO datasets.
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Affiliation(s)
- Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wei Yin
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Shuai Shi
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Weilin Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Guangxu Tu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yunping Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
| | | | - Yongguang Tao
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- National Health Council (NHC) Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, China
| | - Muyun Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Xiang Wang, ; Muyun Peng, ; Fenglei Yu,
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Xiang Wang, ; Muyun Peng, ; Fenglei Yu,
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Xiang Wang, ; Muyun Peng, ; Fenglei Yu,
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Mehrabiani KM, Cheng RR, Onuchic JN. Expanding Direct Coupling Analysis to Identify Heterodimeric Interfaces from Limited Protein Sequence Data. J Phys Chem B 2021; 125:11408-11417. [PMID: 34618469 DOI: 10.1021/acs.jpcb.1c07145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Direct coupling analysis (DCA) is a global statistical approach that uses information encoded in protein sequence data to predict spatial contacts in a three-dimensional structure of a folded protein. DCA has been widely used to predict the monomeric fold at amino acid resolution and to identify biologically relevant interaction sites within a folded protein. Going beyond single proteins, DCA has also been used to identify spatial contacts that stabilize the interaction in protein complex formation. However, extracting this higher order information necessary to predict dimer contacts presents a significant challenge. A DCA evolutionary signal is much stronger at the single protein level (intraprotein contacts) than at the protein-protein interface (interprotein contacts). Therefore, if DCA-derived information is to be used to predict the structure of these complexes, there is a need to identify statistically significant DCA predictions. We propose a simple Z-score measure that can filter good predictions despite noisy, limited data. This new methodology not only improves our prediction ability but also provides a quantitative measure for the validity of the prediction.
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Affiliation(s)
- Kareem M Mehrabiani
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States.,Department of Physics & Astronomy, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States.,Department of Biosciences, Rice University, Houston, Texas 77005, United States
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PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids. J Mol Model 2020; 26:290. [PMID: 32986131 DOI: 10.1007/s00894-020-04508-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/04/2020] [Indexed: 02/05/2023]
Abstract
Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q-Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.
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Chen MC, Li Y, Zhu YH, Ge F, Yu DJ. SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network. J Chem Inf Model 2020; 60:3295-3303. [DOI: 10.1021/acs.jcim.9b01207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ming-Cai Chen
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei 200, Nanjing 210094, P. R. China
| | - Yang Li
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei 200, Nanjing 210094, P. R. China
- Department of Computational Medicine and Bioinformatics, University of Michigan, Washtenaw 100, Ann Arbor, Michigan 48109-2218, United States
| | - Yi-Heng Zhu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei 200, Nanjing 210094, P. R. China
| | - Fang Ge
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei 200, Nanjing 210094, P. R. China
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei 200, Nanjing 210094, P. R. China
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