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Barachini S, Pardini E, Burzi IS, Sardo Infirri G, Montali M, Petrini I. Molecular and Functional Key Features and Oncogenic Drivers in Thymic Carcinomas. Cancers (Basel) 2023; 16:166. [PMID: 38201593 PMCID: PMC10778094 DOI: 10.3390/cancers16010166] [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: 11/07/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Thymic epithelial tumors, comprising thymic carcinomas and thymomas, are rare neoplasms. They differ in histology, prognosis, and association with autoimmune diseases such as myasthenia gravis. Thymomas, but not thymic carcinomas, often harbor GTF2I mutations. Mutations of CDKN2A, TP53, and CDKN2B are the most common thymic carcinomas. The acquisition of mutations in genes that control chromatin modifications and epigenetic regulation occurs in the advanced stages of thymic carcinomas. Anti-angiogenic drugs and immune checkpoint inhibitors targeting the PD-1/PD-L1 axis have shown promising results for the treatment of unresectable tumors. Since thymic carcinomas are frankly aggressive tumors, this report presents insights into their oncogenic drivers, categorized under the established hallmarks of cancer.
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Affiliation(s)
- Serena Barachini
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Eleonora Pardini
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Irene Sofia Burzi
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Gisella Sardo Infirri
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Marina Montali
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Iacopo Petrini
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
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Mo Y, Adu-Amankwaah J, Qin W, Gao T, Hou X, Fan M, Liao X, Jia L, Zhao J, Yuan J, Tan R. Unlocking the predictive potential of long non-coding RNAs: a machine learning approach for precise cancer patient prognosis. Ann Med 2023; 55:2279748. [PMID: 37983519 DOI: 10.1080/07853890.2023.2279748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
The intricate web of cancer biology is governed by the active participation of long non-coding RNAs (lncRNAs), playing crucial roles in cancer cells' proliferation, migration, and drug resistance. Pioneering research driven by machine learning algorithms has unveiled the profound ability of specific combinations of lncRNAs to predict the prognosis of cancer patients. These findings highlight the transformative potential of lncRNAs as powerful therapeutic targets and prognostic markers. In this comprehensive review, we meticulously examined the landscape of lncRNAs in predicting the prognosis of the top five cancers and other malignancies, aiming to provide a compelling reference for future research endeavours. Leveraging the power of machine learning techniques, we explored the predictive capabilities of diverse lncRNA combinations, revealing their unprecedented potential to accurately determine patient outcomes.
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Affiliation(s)
- Yixuan Mo
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
| | - Joseph Adu-Amankwaah
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
| | - Wenjie Qin
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Tan Gao
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Xiaoqing Hou
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Mengying Fan
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Xuemei Liao
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Liwei Jia
- Department of Pathology, UT Southwestern Medical Center, Dallas, UT, USA
| | - Jinming Zhao
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Pathology, The First Hospital of China Medical University, Shenyang, China
| | - Jinxiang Yuan
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Rubin Tan
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
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Zhou Z, Lu Y, Gu Z, Sun Q, Fang W, Yan W, Ku X, Liang Z, Hu G. HNRNPA2B1 as a potential therapeutic target for thymic epithelial tumor recurrence: An integrative network analysis. Comput Biol Med 2023; 155:106665. [PMID: 36791552 DOI: 10.1016/j.compbiomed.2023.106665] [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: 01/03/2023] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023]
Abstract
Thymic epithelial tumors (TETs) are rare malignant tumors, and the molecular mechanisms of both primary and recurrent TETs are poorly understood. Here we established comprehensive proteomic signatures of 15 tumors (5 recurrent and 10 non-recurrent) and 15 pair wised tumor adjacent normal tissues. We then proposed an integrative network approach for studying the proteomics data by constructing protein-protein interaction networks based on differentially expressed proteins and a machine learning-based score, followed by network modular analysis, functional enrichment annotation and shortest path inference analysis. Network modular analysis revealed that primary and recurrent TETs shared certain common molecular mechanisms, including a spliceosome module consisting of RNA splicing and RNA processing, but the recurrent TET was specifically related to the ribosome pathway. Applying the shortest path inference to the collected seed gene module identified that the ribonucleoprotein hnRNPA2B1 probably serves as a potential target for recurrent TET therapy. The drug repositioning combined molecular dynamics simulations suggested that the compound ergotamine could potentially act as a repurposing drug to treat recurrent TETs by targeting hnRNPA2B1. Our study demonstrates the value of integrative network analysis to understand proteotype robustness and its relationships with genotype, and provides hits for further research on cancer therapeutics.
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Affiliation(s)
- Ziyun Zhou
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou, 215123, China
| | - Yu Lu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Zhitao Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qiangling Sun
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China; Thoracic Cancer Institute, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wentao Fang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Ku
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou, 215123, China; Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou, 215123, China.
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