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Zhao Y, Zhang Z, Qiu JH, Li RY, Sun ZG. Catching cancer signals in the blood: Innovative pathways for early esophageal cancer diagnosis. World J Gastroenterol 2025; 31:101838. [PMID: 40093671 PMCID: PMC11886526 DOI: 10.3748/wjg.v31.i10.101838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Revised: 01/23/2025] [Accepted: 02/05/2025] [Indexed: 02/26/2025] Open
Abstract
In recent years, significant progress has been made in the application of DNA methylation for the early detection of esophageal cancer (EC). As an epigenetic modification, DNA methylation allows for noninvasive screening by detecting the methylation status of circulating tumor DNA. Studies have shown that the methylation of genes such as SHOX2, SEPTIN9, EPO, and RNF180 significantly improves diagnostic sensitivity and specificity. Currently, SEPTIN9 has been approved by the Food and Drug Administration for colorectal cancer screening, while SHOX2 and EPO show promising results in EC, and RNF180 has potential in gastrointestinal tumors. This editorial reviews the study by Liu et al, which demonstrated the potential of combining the methylation of these four genes for early EC screening. In addition to their roles in early diagnosis, DNA methylation markers are gaining attention because of their roles in predicting recurrence and in postoperative follow-up. By monitoring changes in methylation levels, these markers can provide valuable insights into treatment efficacy and long-term management. As research progresses, liquid biopsy technology is expected to become an essential tool in the precision diagnosis and treatment of EC, benefiting patients significantly.
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Affiliation(s)
- Yue Zhao
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan 250063, Shandong Province, China
| | - Zhan Zhang
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan 250063, Shandong Province, China
| | - Jian-Hao Qiu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan 250063, Shandong Province, China
| | - Rong-Yang Li
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan 250063, Shandong Province, China
| | - Zhen-Guo Sun
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan 250063, Shandong Province, China
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Kong Z, Zhou P, Xu J, Zhang Y, Wang Y. RFX2 downregulates RASSF1 expression and YAP phosphorylation through Hippo signaling to promote immune escape in lung adenocarcinoma. Cell Div 2025; 20:7. [PMID: 40069841 PMCID: PMC11895337 DOI: 10.1186/s13008-025-00147-z] [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: 10/16/2024] [Accepted: 02/27/2025] [Indexed: 03/15/2025] Open
Abstract
OBJECTIVE Regulatory Factor X (RFX) transcription factors have been implicated in different cancers. Ras association domain family (RASSF) has been shown clinical significance in lung cancer. This paper was to investigate the interaction of RFX2 and RASSF1 in lung adenocarcinoma (LUAD). METHODS The transcriptome differences of LUAD patients in GSE32863, GSE43458, and GSE21933 datasets were analyzed. A-549 and NCI-H358 cell lines after overexpression of RFX2 were co-cultured with activated CD8+ T cells, and the release of IFN-γ, GZMB, PRF1 by CD8+ T cells, and PD-L1 in the LUAD cells were detected. Cell viability, invasion, and apoptosis were analyzed by CCK-8, Transwell, and TUNEL assays. Dual-luciferase assay and ChIP were conducted to detect the interaction between RFX2 and RASSF1 promoter. An in vivo tumor model was constructed to monitor tumor growth. YAP protein levels and phosphorylation were measured. A-549 and NCI-H358 cells treated with DMSO or PY-60 after RFX2 overexpression were co-cultured with activated CD8+ T cells. RESULTS RFX2 was notably downregulated in LUAD. RFX2 overexpression increased infiltrating CD8+ T cells within transplanted tumors and inhibited immune escape, proliferation, and invasion of LUAD cells. RFX2 was enriched in the RASSF1 promoter, and RFX2 activated RASSF1 transcription by binding to the RASSF1 promoter. RASSF1 knockdown reversed the ability of RFX2 overexpression to inhibit immune escape. RFX2 depletion downregulated RASSF1, which reduced YAP phosphorylation, thus affecting the Hippo pathway to promote the immune escape. CONCLUSION RFX2 Loss in LUAD downregulates RASSF1 expression and YAP phosphorylation, thereby promoting immune escape through Hippo signaling.
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Affiliation(s)
- Zhenzhen Kong
- Department of Laboratory, Wujin Hospital Affiliated With Jiangsu University, No. 2 of Yongning North Road, Changzhou, 213002, Jiangsu, People's Republic of China
- The Wujin Clinical College of Xuzhou Medical University, Xuzhou, 221006, Jiangsu, People's Republic of China
| | - Ping Zhou
- Department of Medical Laboratory, Xuzhou Mining Group General Hospital, Xuzhou, 221011, Jiangsu, People's Republic of China
| | - Jiahao Xu
- Department of Laboratory, Wujin Hospital Affiliated With Jiangsu University, No. 2 of Yongning North Road, Changzhou, 213002, Jiangsu, People's Republic of China
- The Wujin Clinical College of Xuzhou Medical University, Xuzhou, 221006, Jiangsu, People's Republic of China
| | - Ying Zhang
- Department of Laboratory, Wujin Hospital Affiliated With Jiangsu University, No. 2 of Yongning North Road, Changzhou, 213002, Jiangsu, People's Republic of China
- The Wujin Clinical College of Xuzhou Medical University, Xuzhou, 221006, Jiangsu, People's Republic of China
| | - Yong Wang
- Department of Laboratory, Wujin Hospital Affiliated With Jiangsu University, No. 2 of Yongning North Road, Changzhou, 213002, Jiangsu, People's Republic of China.
- The Wujin Clinical College of Xuzhou Medical University, Xuzhou, 221006, Jiangsu, People's Republic of China.
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Bi L, Wang X, Li J, Li W, Wang Z. Epigenetic modifications in early stage lung cancer: pathogenesis, biomarkers, and early diagnosis. MedComm (Beijing) 2025; 6:e70080. [PMID: 39991629 PMCID: PMC11843169 DOI: 10.1002/mco2.70080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 01/03/2025] [Accepted: 01/09/2025] [Indexed: 02/25/2025] Open
Abstract
The integration of liquid biopsy with epigenetic markers offers significant potential for early lung cancer detection and personalized treatment. Epigenetic alterations, including DNA methylation, histone modifications, and noncoding RNA changes, often precede genetic mutations and are critical in cancer progression. In this study, we explore how liquid biopsy, combined with epigenetic markers, can provide early detection of lung cancer, potentially predicting onset up to 4 years before clinical diagnosis. We discuss the challenges of targeting epigenetic regulators, which could disrupt cellular balance if overexploited, and the need for maintaining key gene expressions in therapeutic applications. This review highlights the promise and challenges of using liquid biopsy and epigenetic markers for early-stage lung cancer diagnosis, with a focus on optimizing treatment strategies for personalized and precision medicine.
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Affiliation(s)
- Lingfeng Bi
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease‐related Molecular Network, State Key Laboratory of Respiratory Health and MultimorbidityWest China Hospital, Sichuan UniversityChengduSichuanChina
- Institute of Respiratory Health, Frontiers Science Center for Disease‐Related Molecular NetworkWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Xin Wang
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease‐related Molecular Network, State Key Laboratory of Respiratory Health and MultimorbidityWest China Hospital, Sichuan UniversityChengduSichuanChina
- Institute of Respiratory Health, Frontiers Science Center for Disease‐Related Molecular NetworkWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Jiayi Li
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease‐related Molecular Network, State Key Laboratory of Respiratory Health and MultimorbidityWest China Hospital, Sichuan UniversityChengduSichuanChina
- Institute of Respiratory Health, Frontiers Science Center for Disease‐Related Molecular NetworkWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease‐related Molecular Network, State Key Laboratory of Respiratory Health and MultimorbidityWest China Hospital, Sichuan UniversityChengduSichuanChina
- Institute of Respiratory Health, Frontiers Science Center for Disease‐Related Molecular NetworkWest China Hospital, Sichuan UniversityChengduSichuanChina
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan UniversityChengduSichuanChina
- The Research Units of West China, Chinese Academy of Medical SciencesWest China HospitalChengduSichuanChina
| | - Zhoufeng Wang
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease‐related Molecular Network, State Key Laboratory of Respiratory Health and MultimorbidityWest China Hospital, Sichuan UniversityChengduSichuanChina
- Institute of Respiratory Health, Frontiers Science Center for Disease‐Related Molecular NetworkWest China Hospital, Sichuan UniversityChengduSichuanChina
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan UniversityChengduSichuanChina
- The Research Units of West China, Chinese Academy of Medical SciencesWest China HospitalChengduSichuanChina
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Yu Y, Lu XH, Mu JS, Meng JY, Sun JS, Chen HX, Yan Y, Meng K. N6-methyladenosine-modified long non-coding RNA KIF9-AS1 promotes stemness and sorafenib resistance in hepatocellular carcinoma by upregulating SHOX2 expression. World J Gastroenterol 2024; 30:5174-5190. [PMID: 39735272 PMCID: PMC11612700 DOI: 10.3748/wjg.v30.i48.5174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 09/26/2024] [Accepted: 11/08/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a prevalent and aggressive tumor. Sorafenib is the first-line treatment for patients with advanced HCC, but resistance to sorafenib has become a significant challenge in this therapy. Cancer stem cells play a crucial role in sorafenib resistance in HCC. Our previous study revealed that the long non-coding RNA (lncRNA) KIF9-AS1 is an oncogenic gene in HCC. However, the role of KIF9-AS1 in drug resistance and cancer stemness in HCC remains unclear. Herein, we aimed to investigate the function and mechanism of the lncRNA KIF9-AS1 in cancer stemness and drug resistance in HCC. AIM To describe the role of the lncRNA KIF9-AS1 in cancer stemness and drug resistance in HCC and elucidate the underlying mechanism. METHODS Tumor tissue and adjacent non-cancerous tissue samples were collected from HCC patients. Sphere formation was quantified via a tumor sphere assay. Cell viability, proliferation, and apoptosis were evaluated via Cell Counting Kit-8, flow cytometry, and colony formation assays, respectively. The interactions between the lncRNA KIF9-AS1 and its downstream targets were confirmed via RNA immunoprecipitation and coimmunoprecipitation. The tumorigenic role of KIF9-AS1 was validated in a mouse model. RESULTS Compared with that in normal controls, the expression of the lncRNA KIF9-AS1 was upregulated in HCC tissues. Knockdown of KIF9-AS1 inhibited stemness and attenuated sorafenib resistance in HCC cells. Mechanistically, N6-methyladenosine modification mediated by methyltransferase-like 3/insulin-like growth factor 2 mRNA-binding protein 1 stabilized and increased the expression of KIF9-AS1. Additionally, KIF9-AS1 increased the stability and expression of short stature homeobox 2 by promoting ubiquitin-specific peptidase 1-induced deubiquitination. Furthermore, depletion of KIF9-AS1 alleviated sorafenib resistance in a xenograft mouse model of HCC. CONCLUSION The N6-methyladenosine-modified lncRNA KIF9-AS1 promoted stemness and sorafenib resistance in HCC by upregulating short stature homeobox 2 expression.
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MESH Headings
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/metabolism
- Sorafenib/pharmacology
- Sorafenib/therapeutic use
- Humans
- Liver Neoplasms/genetics
- Liver Neoplasms/drug therapy
- Liver Neoplasms/pathology
- Liver Neoplasms/metabolism
- Drug Resistance, Neoplasm/genetics
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Animals
- Neoplastic Stem Cells/drug effects
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Mice
- Gene Expression Regulation, Neoplastic
- Up-Regulation
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Adenosine/pharmacology
- Cell Line, Tumor
- Male
- Cell Proliferation/drug effects
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Xenograft Model Antitumor Assays
- Apoptosis/drug effects
- Mice, Nude
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Methyltransferases/metabolism
- Methyltransferases/genetics
- Female
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Affiliation(s)
- Yong Yu
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Xiang-Hong Lu
- Department of Intensive Care Medicine, The First Medical Center, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Jin-Song Mu
- Department of Intensive Care Medicine, The Fifth Medical Center, Chinese People’s Liberation Army General Hospital, Beijing 100039, China
| | - Jiang-Yun Meng
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Jiang-Shan Sun
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Hai-Xu Chen
- Institute of Geriatrics and National Clinical Research Center of Geriatrics Disease, The Second Medical Center, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Yang Yan
- Department of General Surgery, The First Medical Center, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Ke Meng
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
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Shan Y, Teng Y, Guan C, Mao Z, Lu C, Ding W, Zhang J. Combined ultrasound endoscopy-guided fine-needle aspiration with DNA methylation of SHOX2 and RASSF1A genes to enhance the auxiliary diagnostic precision of pancreatic cancer. Heliyon 2024; 10:e34028. [PMID: 39071574 PMCID: PMC11282983 DOI: 10.1016/j.heliyon.2024.e34028] [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: 01/18/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
The purpose of this study was to assess the influence and the clinical effectiveness of the short stature homeobox 2 (SHOX2) and ras association domain family 1A (RASSF1A) genes by tissue sampling through ultrasound endoscopy-guided fine-needle aspiration (EUS-FNA) as auxiliary diagnostic tools for pancreatic cancer (PC). Methylation markers were detected in 96 patients using real-time fluorescence quantitative PCR (qPCR), and the performance of this diagnostic assay was compared with CA19-9, CEA, and puncture fluid-based exfoliative cytology using receiver operating characteristic curve (ROC) analysis. The PC group exhibited higher methylation rates for SHOX2, RASSF1A, and the combined assay of both genes compared to the control group (95.7 % vs. 54.0 %, 78.3 % vs. 36.0 %, and 73.9 % vs. 16.0 %, P < 0.05). The areas under the ROC curve (AUC) for CA19-9, CEA, liquid-based exfoliative cytology, SHOX2, RASSF1A, the combination of SHOX2 and RASSF1A, the combination assay with CEA, CA19-9, and liquid-based exfoliative cytology were 0.827, 0.692, 0.767, 0.770, 0.732, 0.870, 0.870, 0.933, and 0.900, respectively. Therefore, the methylation assay based on the combined SHOX2 and RASSF1A genes in EUS-FNA puncture fluid is more effective than using a single gene, liquid-based exfoliative cytology, or intravenous tumor markers for diagnosing PC. Combining the conventional marker CA19-9 enhances the diagnostic value, making it a promising approach to complement histology and cytology.
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Affiliation(s)
- Yangyang Shan
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
- Department of General Practice, Affiliated Hospital 2 of Nantong University, Nantong, Jiangsu, 226006, PR China
| | - Ying Teng
- Department of General Practice Medicine, and Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Chengqi Guan
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Zhenbiao Mao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Cuihua Lu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Weifeng Ding
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Jianfeng Zhang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, PR China
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Zhao J, Lu Y, Ren X, Bian T, Feng J, Sun H, Liu L, She B, Liu Y, Ke H. Association of the SHOX2 and RASSF1A methylation levels with the pathological evolution of early-stage lung adenocarcinoma. BMC Cancer 2024; 24:687. [PMID: 38840077 PMCID: PMC11154976 DOI: 10.1186/s12885-024-12452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
Background The methylation of SHOX2 and RASSF1A shows promise as a potential biomarker for the early screening of lung cancer, offering a solution to remedy the limitations of morphological diagnosis. The aim of this study is to diagnose lung adenocarcinoma by measuring the methylation levels of SHOX2 and RASSF1A, and provide an accurate pathological diagnosis to predict the invasiveness of lung cancer prior to surgery.Material and methods The methylation levels of SHOX2 and RASSF1A were quantified using a LungMe® test kit through methylation-specific PCR (MS-PCR). The diagnostic efficacy of SHOX2 and RASSF1A and the cutoff values were validated using ROC curve analysis. The hazardous factors influencing the invasiveness of lung adenocarcinoma were calculated using multiple regression.Results: The cutoff values of SHOX2 and RASSF1A were 8.3 and 12.0, respectively. The sensitivities of LungMe® in IA, MIA and AIS patients were 71.3% (122/171), 41.7% (15/36), and 16.1% (5/31) under the specificity of 94.1% (32/34) for benign lesions. Additionally, the methylation level of SHOX2, RASSF1A and LungMe® correlated with the high invasiveness of clinicopathological features, such as age, gender, tumor size, TNM stage, pathological type, pleural invasion and STAS. The tumor size, age, CTR values and LungMe® methylation levels were identified as independent hazardous factors influencing the invasiveness of lung adenocarcinoma.Conclusion: SHOX2 and RASSF1A combined methylation can be used as an early detection indicator of lung adenocarcinoma. SHOX2 and RASSF1A combined (LungMe®) methylation is significantly correlated to age, gender, tumor size, TNM stage, pathological type, pleural invasion and STAS. The SHOX2 and RASSF1A methylation levels, tumor size and CTR values could predict the invasiveness of the tumor prior to surgery, thereby providing guidance for the surgical procedure.
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Affiliation(s)
- Jiaping Zhao
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Yu Lu
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Xiaosha Ren
- Department of Academic Development, Shanghai methyldia technology Co. Ltd, No. 412 Huiqing Road , Shanghai, 201203, China
| | - Tingting Bian
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Jia Feng
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Hui Sun
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Lei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Bin She
- Department of Academic Development, Shanghai methyldia technology Co. Ltd, No. 412 Huiqing Road , Shanghai, 201203, China
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Tellgen Corporation Co. Ltd, No. 115, Lane 572, Bibo Road, Pilot Free Trade Zone, Shanghai, 201203, China
| | - Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China.
| | - Honggang Ke
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China.
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Lan Z, Zhang J, Yang F, Ma X, He R. Utility of SHOX2 and RASSF1A gene methylation detection on the residual cytology material from endobronchial ultrasound-guided transbronchial needle aspiration. Cytojournal 2024; 21:19. [PMID: 38887695 PMCID: PMC11181472 DOI: 10.25259/cytojournal_114_2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/29/2024] [Indexed: 06/20/2024] Open
Abstract
Objective This study aims to assess the effectiveness of Short Stature Homeobox 2 (SHOX2) and RAS Association Domain Family 1 Isoform A (RASSF1A) gene methylation detection in residual liquid-based cytology (LBC) materials from Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) and investigate the diagnostic accuracy of a comprehensive diagnostic approach. Material and Methods Between June 2022 and May 2023, a total of 110 cases that underwent EBUS-TBNA were enrolled in the study. SHOX2 and RASSF1A genes methylation detection using the residual cytological material, LBC, and cell block (CB) were conducted for each EBUS-TBNA case. The sensitivity and specificity of cytology, CB histopathology, SHOX2, and RASSF1A methylation in diagnosing EBUS-TBNA samples were determined based on follow-up data. Results Among the 72 cases confirmed as pulmonary carcinomas, the methylation test yielded positive results in 24 adenocarcinoma cases, 10 squamous cell carcinoma cases, and 14 small cell carcinoma cases. The sensitivity of the comprehensive diagnosis (combining LBC, CB, and methylation detection) in distinguishing metastatic pulmonary epithelial malignancies in mediastinal and hilar lymph nodes or masses from benign lesions was higher (97.22%, 70/72) than that of morphological diagnosis alone (LBC and CB) (88.89%, 64/72; P < 0.05). Conclusion SHOX2 and RASSF1A methylation detection demonstrates a high sensitivity and negative predictive value in the identification of pulmonary epithelial malignancies and holds promise as a valuable ancillary approach to enhance morphological diagnosis of EBUS-TBNA.
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Affiliation(s)
- Zhihua Lan
- Department of Pathology, the First Affiliated Hospital of Hengyang Medical School, Hengyang, Hunan, China
| | - Jing Zhang
- Department of Pathology, the First Affiliated Hospital of Hengyang Medical School, Hengyang, Hunan, China
| | - Fang Yang
- Department of Anorectal Surgery in Traditional Chinese Medicine, the First Affiliated Hospital of Hengyang Medical School, Hengyang, Hunan, China
| | - Xin Ma
- Department of Pathology, the First Affiliated Hospital of Hengyang Medical School, Hengyang, Hunan, China
| | - Rongfang He
- Department of Pathology, the First Affiliated Hospital of Hengyang Medical School, Hengyang, Hunan, China
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Cui X, Lin Q, Chen M, Wang Y, Wang Y, Wang Y, Tao J, Yin H, Zhao T. Long-read sequencing unveils novel somatic variants and methylation patterns in the genetic information system of early lung cancer. Comput Biol Med 2024; 171:108174. [PMID: 38442557 DOI: 10.1016/j.compbiomed.2024.108174] [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: 01/07/2024] [Revised: 01/25/2024] [Accepted: 02/18/2024] [Indexed: 03/07/2024]
Abstract
Lung cancer poses a global health challenge, necessitating advanced diagnostics for improved outcomes. Intensive efforts are ongoing to pinpoint early detection biomarkers, such as genomic variations and DNA methylation, to elevate diagnostic precision. We conducted long-read sequencing on cancerous and adjacent non-cancerous tissues from a patient with lung adenocarcinoma. We identified somatic structural variations (SVs) specific to lung cancer by integrating data from various SV calling methods and differentially methylated regions (DMRs) that were distinct between these two tissue samples, revealing a unique methylation pattern associated with lung cancer. This study discovered over 40,000 somatic SVs and over 180,000 DMRs linked to lung cancer. We identified approximately 700 genes of significant relevance through comprehensive analysis, including genes intricately associated with many lung cancers, such as NOTCH1, SMOC2, CSMD2, and others. Furthermore, we observed that somatic SVs and DMRs were substantially enriched in several pathways, such as axon guidance signaling pathways, which suggests a comprehensive multi-omics impact on lung cancer progression across various biological investigation levels. These datasets can potentially serve as biomarkers for early lung cancer detection and may hold significant value in clinical diagnosis and treatment applications.
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Affiliation(s)
- Xinran Cui
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China
| | - Qingyan Lin
- Department of Respiratory and Critical Care, Heilongjiang Provincial Hospital, 405 Gorokhovaya Street, Harbin, Heilongjiang, 150000, China
| | - Ming Chen
- Institute of Bioinformatics, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China
| | - Yidan Wang
- Department of Respiratory and Critical Care, Heilongjiang Provincial Hospital, 405 Gorokhovaya Street, Harbin, Heilongjiang, 150000, China
| | - Yiwen Wang
- Tanwei College, Tsinghua University, Shuangqing Road, Beijing, 100084, China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China.
| | - Jiang Tao
- School of Computer Science and Technology, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China.
| | - Honglei Yin
- Department of Respiratory and Critical Care, Heilongjiang Provincial Hospital, 405 Gorokhovaya Street, Harbin, Heilongjiang, 150000, China.
| | - Tianyi Zhao
- School of Medicine, Harbin Institute of Technology, 92 West Da Zhi St, Harbin, Heilongjiang, 150000, China.
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Du C, Tan L, Xiao X, Xin B, Xiong H, Zhang Y, Ke Z, Yin J. Detection of the DNA methylation of seven genes contribute to the early diagnosis of lung cancer. J Cancer Res Clin Oncol 2024; 150:77. [PMID: 38315228 PMCID: PMC10844440 DOI: 10.1007/s00432-023-05588-z] [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: 09/22/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Low-dose Computed Tomography (CT) is used for the detection of pulmonary nodules, but the ambiguous risk evaluation causes overdiagnosis. Here, we explored the significance of the DNA methylation of 7 genes including TAC1, CDO1, HOXA9, ZFP42, SOX17, RASSF1A and SHOX2 in the blood cfDNA samples in distinguishing lung cancer from benign nodules and healthy individuals. METHOD A total of 149 lung cancer patients [72 mass and 77 ground-glass nodules (GGNs)], 5 benign and 48 healthy individuals were tested and analyzed in this study. The lasso-logistic regression model was built for distinguishing cancer and control/healthy individuals or IA lung cancer and non-IA lung cancer cases. RESULTS The positive rates of methylation of 7 genes were higher in the cancer group as compared with the healthy group. We constructed a model using age, sex and the ΔCt value of 7 gene methylation to distinguish lung cancer from benign and healthy individuals. The sensitivity, specificity and AUC (area under the curve) were 86.7%, 81.4% and 0.891, respectively. Also, we assessed the significance of 7 gene methylation together with patients' age and sex in distinguishing of GGNs type from the mass type. The sensitivity, specificity and AUC were 77.1%, 65.8% and 0.753, respectively. Furthermore, the methylation positive rates of CDO1 and SHOX2 were different between I-IV stages of lung cancer. Specifically, the positive rate of CDO1 methylation was higher in the non-IA group as compared with the IA group. CONCLUSION Collectively, this study reveals that the methylation of 7 genes has a big significance in the diagnosis of lung cancer with high sensitivity and specificity. Also, the 7 genes present with certain significance in distinguishing the GGN type lung cancer, as well as different stages.
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Affiliation(s)
- Chaoxiang Du
- Department of Thoracic Surgery, Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, China
- Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Lijie Tan
- Department of Thoracic Surgery, Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, China
- Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Xiao Xiao
- School of Physics, Changchun University of Science and Technology, Changchun, 130022, China
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Beibei Xin
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Hui Xiong
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Yuying Zhang
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China
| | - Zhonghe Ke
- Shanghai Rightongene Biotechnology Co. Ltd., Shanghai, 201403, China.
| | - Jun Yin
- Department of Thoracic Surgery, Cancer Center, Zhongshan Hospital of Fudan University, Shanghai, China.
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Xie B, Dong W, He F, Peng F, Zhang H, Wang W. The Combination of SHOX2 and RASSF1A DNA Methylation Had a Diagnostic Value in Pulmonary Nodules and Early Lung Cancer. Oncology 2024; 102:759-774. [PMID: 38262380 DOI: 10.1159/000534275] [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: 02/06/2023] [Accepted: 09/19/2023] [Indexed: 01/25/2024]
Abstract
INTRODUCTION The study explored the effects of SHOX2 and RASSF1A DNA methylation in lung cancer (LC). METHOD Bronchoalveolar lavage fluid (BALF) samples as well as LC and normal adjacent tissues were collected from 72 LC patients and 35 patients with benign pulmonary nodules. Quantitative analysis of SHOX2 and RASSF1A DNA methylation was performed in benign pulmonary nodules and different stages of LC. The diagnostic value of SHOX2 and RASSF1A DNA methylation in LC and benign pulmonary nodules was determined by receiver operating characteristics analysis. Gain/loss-of-function experiments were constructed in LC cells and mouse models of xenograft and pulmonary nodule metastasis. The levels of SHOX2 and transfer-associated genes were tested through quantitative reverse transcription polymerase chain reaction and Western blot. Malignant phenotype of LC cells was assessed by functional experiment. The tumor volume and weight of mice in xenograft models were measured. Pulmonary nodule metastasis was determined through HE staining assay. 5-azacytidine appeared as a positive control drug. RESULT SHOX2 DNA methylation or RASSF1A DNA methylation had diagnostic efficiency in pulmonary nodules and early LC, with the two combined having better diagnostic value. SHOX2 expression was upregulated in LC. Similar to 5-azacytidine, SHOX2 knockdown inhibited LC cell viability, migration, and invasion in vitro as well as restrained LC tumorigenesis and pulmonary nodule metastasis in vivo, whereas overexpressed SHOX2 had the opposite effects. CONCLUSION The combination of SHOX2 and RASSF1A DNA methylation had a diagnostic value in pulmonary nodules and early LC. SHOX2 positively modulated the tumorigenesis and metastasis of LC by regulating DNA methylation processes.
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Affiliation(s)
- Bin Xie
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Wenyan Dong
- Department of Geriatric Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fengping He
- Central Laboratory, Yue Bei People's Hospital, Shaoguan, China
| | - Feng Peng
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Honghua Zhang
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Wei Wang
- Medical Integration and Practice Center of Shandong University, Jinan, China
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Ramazi S, Dadzadi M, Sahafnejad Z, Allahverdi A. Epigenetic regulation in lung cancer. MedComm (Beijing) 2023; 4:e401. [PMID: 37901797 PMCID: PMC10600507 DOI: 10.1002/mco2.401] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 10/31/2023] Open
Abstract
Lung cancer is indeed a major cause of cancer-related deaths worldwide. The development of tumors involves a complex interplay of genetic, epigenetic, and environmental factors. Epigenetic mechanisms, including DNA methylation (DNAm), histone modifications, and microRNA expression, play a crucial role in this process. Changes in DNAm patterns can lead to the silencing of important genes involved in cellular functions, contributing to the development and progression of lung cancer. MicroRNAs and exosomes have also emerged as reliable biomarkers for lung cancer. They can provide valuable information about early diagnosis and treatment assessment. In particular, abnormal hypermethylation of gene promoters and its effects on tumorigenesis, as well as its roles in the Wnt signaling pathway, have been extensively studied. Epigenetic drugs have shown promise in the treatment of lung cancer. These drugs target the aberrant epigenetic modifications that are involved in the development and progression of the disease. Several factors have been identified as drug targets in non-small cell lung cancer. Recently, combination therapy has been discussed as a successful strategy for overcoming drug resistance. Overall, understanding the role of epigenetic mechanisms and their targeting through drugs is an important area of research in lung cancer treatment.
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Affiliation(s)
- Shahin Ramazi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Maedeh Dadzadi
- Department of BiotechnologyFaculty of Advanced Science and TechnologyTehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Zahra Sahafnejad
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Abdollah Allahverdi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
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Lin LP, Tan MTT. Biosensors for the detection of lung cancer biomarkers: A review on biomarkers, transducing techniques and recent graphene-based implementations. Biosens Bioelectron 2023; 237:115492. [PMID: 37421797 DOI: 10.1016/j.bios.2023.115492] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 07/10/2023]
Abstract
Lung cancer remains the leading cause of cancer-related death. In addition to chest X-rays and computerised tomography, the detection of cancer biomarkers serves as an emerging diagnostic tool for lung cancer. This review explores biomarkers including the rat sarcoma gene, the tumour protein 53 gene, the epidermal growth factor receptor, the neuron-specific enolase, the cytokeratin-19 fragment 21-1 and carcinoembryonic antigen as potential indicators of lung cancer. Biosensors, which utilise various transduction techniques, present a promising solution for the detection of lung cancer biomarkers. Therefore, this review also explores the working principles and recent implementations of transducers in the detection of lung cancer biomarkers. The transducing techniques explored include optical techniques, electrochemical techniques and mass-based techniques for detecting biomarkers and cancer-related volatile organic compounds. Graphene has outstanding properties in terms of charge transfer, surface area, thermal conductivity and optical characteristics, on top of allowing easy incorporation of other nanomaterials. Exploiting the collective merits of both graphene and biosensor is an emerging trend, as evidenced by the growing number of studies on graphene-based biosensors for the detection of lung cancer biomarkers. This work provides a comprehensive review of these studies, including information on modification schemes, nanomaterials, amplification strategies, real sample applications, and sensor performance. The paper concludes with a discussion of the challenges and future outlook of lung cancer biosensors, including scalable graphene synthesis, multi-biomarker detection, portability, miniaturisation, financial support, and commercialisation.
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Affiliation(s)
- Lih Poh Lin
- Faculty of Engineering and Technology, Tunku Abdul Rahman University of Management and Technology, 53300, Kuala Lumpur, Malaysia; Centre for Multimodal Signal Processing, Tunku Abdul Rahman University of Management and Technology, 53300, Kuala Lumpur, Malaysia
| | - Michelle Tien Tien Tan
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500, Semenyih, Malaysia.
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Ji XY, Li H, Chen HH, Lin J. Diagnostic performance of RASSF1A and SHOX2 methylation combined with EGFR mutations for differentiation between small pulmonary nodules. J Cancer Res Clin Oncol 2023; 149:8557-8571. [PMID: 37097393 DOI: 10.1007/s00432-023-04745-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND AND AIM Aberrant methylation of Ras association domain family 1, isoform A (RASSF1A), and short-stature homeobox gene 2 (SHOX2) promoters has been validated as a pair of valuable biomarkers for diagnosing early lung adenocarcinomas (LUADs). Epidermal growth factor receptor (EGFR) is the key driver mutation in lung carcinogenesis. This study aimed to investigate the aberrant promoter methylation of RASSF1A and SHOX2, and the genetic mutation of EGFR in 258 specimens of early LUADs. METHODS We retrospectively selected 258 paraffin-embedded samples of pulmonary nodules measuring 2 cm or less in diameter and evaluated the diagnostic performance of individual biomarker assays and multiple panels between noninvasive (group 1) and invasive lesions (groups 2A and 2B). Then, we investigated the interaction between genetic and epigenetic alterations. RESULTS The degree of RASSF1A and SHOX2 promoter methylation and EGFR mutation was significantly higher in invasive lesions than in noninvasive lesions. The three biomarkers distinguished between noninvasive and invasive lesions with reliable sensitivity and specificity: 60.9% sensitivity [95% confidence interval (CI) 52.41-68.78] and 80.0% specificity (95% CI 72.14-86.07). The novel panel biomarkers could further discriminate among three invasive pathological subtypes (area under the curve value > 0.6). The distribution of RASSF1A methylation and EGFR mutation was considerably exclusive in early LUAD (P = 0.002). CONCLUSION DNA methylation of RASSF1A and SHOX2 is a pair of promising biomarkers, which may be used in combination with other driver alterations, such as EGFR mutation, to support the differential diagnosis of LUADs, especially for stage I.
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Affiliation(s)
- Xiang-Yu Ji
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Hong Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Hui-Hui Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jie Lin
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China.
- National Virtual and Reality Experimental Education Center for Medical Morphology, Southern Medical University, Guangzhou, People's Republic of China.
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Carbajo-García MC, Juarez-Barber E, Segura-Benítez M, Faus A, Trelis A, Monleón J, Carmona-Antoñanzas G, Pellicer A, Flanagan JM, Ferrero H. H3K4me3 mediates uterine leiomyoma pathogenesis via neuronal processes, synapsis components, proliferation, and Wnt/β-catenin and TGF-β pathways. Reprod Biol Endocrinol 2023; 21:9. [PMID: 36703136 PMCID: PMC9878797 DOI: 10.1186/s12958-023-01060-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Uterine leiomyomas (UL) are the most common benign tumor in women of reproductive age. Their pathology remains unclear, which hampers the development of safe and effective treatments. Raising evidence suggests epigenetics as a main mechanism involved in tumor development. Histone modification is a key component in the epigenetic regulation of gene expression. Specifically, the histone mark H3K4me3, which promotes gene expression, is altered in many tumors. In this study, we aimed to identify if the histone modification H3K4me3 regulates the expression of genes involved in uterine leiomyoma pathogenesis. METHODS Prospective study integrating RNA-seq (n = 48) and H3K4me3 CHIP-seq (n = 19) data of uterine leiomyomas versus their adjacent myometrium. Differentially expressed genes (FDR < 0.01, log2FC > 1 or < - 1) were selected following DESeq2, edgeR, and limma analysis. Their differential methylation and functional enrichment (FDR < 0.05) were respectively analyzed with limma and ShinyGO. RESULTS CHIP-seq data showed a global suppression of H3K4me3 in uterine leiomyomas versus their adjacent myometrial tissue (p-value< 2.2e-16). Integrating CHIP-seq and RNA-seq data highlighted that transcription of 696/922 uterine leiomyoma-related differentially expressed genes (DEG) (FDR < 0.01, log2FC > 1 or < - 1) was epigenetically mediated by H3K4me3. Further, 50 genes were differentially trimethylated (FDR < 0.05), including 33 hypertrimethylated/upregulated, and 17 hypotrimethylated/downregulated genes. Functional enrichment analysis of the latter showed dysregulation of neuron-related processes and synapsis-related cellular components in uterine leiomyomas, and a literature review study of these DEG found additional implications with tumorigenesis (i.e. aberrant proliferation, invasion, and dysregulation of Wnt/β-catenin, and TGF-β pathways). Finally, SATB2, DCX, SHOX2, ST8SIA2, CAPN6, and NPTX2 proto-oncogenes were identified among the hypertrimethylated/upregulated DEG, while KRT19, ABCA8, and HOXB4 tumor suppressor genes were identified among hypotrimethylated/downregulated DEG. CONCLUSIONS H3K4me3 instabilities alter the expression of oncogenes and tumor suppressor genes, inducing aberrant proliferation, and dysregulated Wnt/β-catenin, and TGF-β pathways, that ultimately promote uterine leiomyoma progression. The reversal of these histone modifications may be a promising new therapeutic alternative for uterine leiomyoma patients.
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Affiliation(s)
- María Cristina Carbajo-García
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain
- Departamento de Pediatría, Obstetricia y Ginecología, Universidad de Valencia, Valencia, Spain
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Elena Juarez-Barber
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain
| | - Marina Segura-Benítez
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain
- Departamento de Pediatría, Obstetricia y Ginecología, Universidad de Valencia, Valencia, Spain
| | - Amparo Faus
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain
| | | | - Javier Monleón
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | | | - Antonio Pellicer
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain
- IVIRMA Rome, Rome, Italy
| | - James M Flanagan
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Hortensia Ferrero
- Fundación IVI, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain.
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Ding P, Peng B, Li G, Sun X, Wang G. Glucosamine-phosphate N-acetyltransferase 1 and its DNA methylation can be biomarkers for the diagnosis and prognosis of lung cancer. J Clin Lab Anal 2022; 36:e24628. [PMID: 35929347 PMCID: PMC9459321 DOI: 10.1002/jcla.24628] [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: 04/14/2022] [Revised: 07/04/2022] [Accepted: 07/16/2022] [Indexed: 12/05/2022] Open
Abstract
Objective Lung cancer ranking high in the cancer‐related list has long perplexed patients, in which glucosamine‐phosphate N‐acetyltransferase 1 (GNPNAT1) is found to be highly expressed. Besides, DNA methylation is perceived as a biomarker to assess the prognosis of patients with various cancers. However, the correlation between GNPNAT1 and DNA methylation and the role of GNPNAT1 in lung cancer remain vague. Methods Principal component analysis (PCA), heatmap, volcano map, Venn diagram, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to screen out the candidate genes. The viability, migration, and invasion of lung cancer cells were detected by CCK‐8 and Transwell assays. An xenograft tumor mouse model was established. The relative expressions of GNPNAT1, E‐cadherin, vimentin, Matrix metalloproteinase‐2 (MMP‐2), tissue inhibitor of metalloproteinase‐2 (TIMP‐2), E2F1, and cyclin D1 in cells or xenograft tumor tissues were quantified by Western blot, RT‐qPCR, or immunohistochemistry assay. Results GNPNAT1 was screened as the research object. GNPNAT1 methylation was downregulated, while GNPNAT1 expression was upregulated in lung cancer tissues. The methylation and mRNA levels of GNPNAT1 were correlated with the patient prognosis. GNPNAT1 increased cell viability, migration and invasion, and promoted the xenograft tumor volume and weight, whereas shGNPNAT1 acted oppositely. Moreover, expressions of Vimentin, MMP‐2, E2F1, and cyclin D1 were increased, but E‐cadherin and TIMP‐2 expressions were decreased by overexpressed GNPNAT1, whilst GNPNAT1 knockdown ran conversely. Conclusion GNPNAT1 and methylated GNPNAT1 coverage are biomarkers for the diagnosis and prognosis of lung cancer.
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Affiliation(s)
- Peikun Ding
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
| | - Bin Peng
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
| | - Guofeng Li
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
| | - Xuefeng Sun
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
| | - Guangsuo Wang
- Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University
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Nayak C, Singh SK. Integrated Transcriptome Profiling Identifies Prognostic Hub Genes as Therapeutic Targets of Glioblastoma: Evidenced by Bioinformatics Analysis. ACS OMEGA 2022; 7:22531-22550. [PMID: 35811900 PMCID: PMC9260928 DOI: 10.1021/acsomega.2c01820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Glioblastoma (GBM) is the most devastating and frequent type of primary brain tumor with high morbidity and mortality. Despite the use of surgical resection followed by radio- and chemotherapy as standard therapy, the progression of GBM remains dismal with a median overall survival of <15 months. GBM embodies a populace of cancer stem cells (GSCs) that is associated with tumor initiation, invasion, therapeutic resistance, and post-treatment reoccurrence. However, understanding the potential mechanisms of stemness and their candidate biomarkers remains limited. Hence in this investigation, we aimed to illuminate potential candidate hub genes and key pathways associated with the pathogenesis of GSC in the development of GBM. The integrated analysis discovered differentially expressed genes (DEGs) between the brain cancer tissues (GBM and GSC) and normal brain tissues. Multiple approaches, including gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were employed to functionally annotate the DEGs and visualize them through the R program. The significant hub genes were identified through the protein-protein interaction network, Venn diagram analysis, and survival analysis. We observed that the upregulated DEGs were prominently involved in the ECM-receptor interaction pathway. The downregulated genes were mainly associated with the axon guidance pathway. Five significant hub genes (CTNNB1, ITGB1, TNC, EGFR, and SHOX2) were screened out through multiple analyses. GO and KEGG analyses of hub genes uncovered that these genes were primarily enriched in disease-associated pathways such as the inhibition of apoptosis and the DNA damage repair mechanism, activation of the cell cycle, EMT (epithelial-mesenchymal transition), hormone AR (androgen receptor), hormone ER (estrogen receptor), PI3K/AKT (phosphatidylinositol 3-kinase and AKT), RTK (receptor tyrosine kinase), and TSC/mTOR (tuberous sclerosis complex and mammalian target of rapamycin). Consequently, the epigenetic regulatory network disclosed that hub genes played a vital role in the progression of GBM. Finally, candidate drugs were predicted that can be used as possible drugs to treat GBM patients. Overall, our investigation offered five hub genes (CTNNB1, ITGB1, TNC, EGFR, and SHOX2) that could be used as precise diagnostic and prognostic candidate biomarkers of GBM and might be used as personalized therapeutic targets to obstruct gliomagenesis.
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Gao H, Yang J, He L, Wang W, Liu Y, Hu Y, Ge M, Ding J, Ye Q. The Diagnostic Potential of SHOX2 and RASSF1A DNA Methylation in Early Lung Adenocarcinoma. Front Oncol 2022; 12:849024. [PMID: 35837113 PMCID: PMC9273978 DOI: 10.3389/fonc.2022.849024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveMethylation of the promoters of SHOX2 and RASSF1A are potentially informative biomarkers for the diagnosis of early lung adenocarcinoma (LUAD). Abnormal methylation of SHOX2 and RASSF1A promoters may promote the occurrence and facilitate the progression of LUAD.Materials and MethodsWe selected 54 patients with early LUAD and 31 patients with benign lung nodules as a NJDT cohort and evaluated their DNA methylation and mRNA sequencing levels. The DNA methylation sequencing, mRNA sequencing, and clinical data for patients with LUAD were obtained from The Cancer Genome Atlas, and served as a TCGA cohort. We evaluated the diagnostic potential of a SHOX2 and RASSF1A combined promoter methylation assay for detection of early LUAD in the NJDT cohort. Then we explored the promoter methylation levels of SHOX2 and RASSF1A and their gene expression between normal and tumor samples at different stages in both cohorts. Pathways enriched between tumor and normal samples of methylation-positive patients in the NJDT cohort were analyzed.ResultsIn the NJDT cohort, the sensitivity of the combined promoter methylation assay on tumor samples was 74.07%, the sensitivity on paired tumor and paracancerous samples was 77.78%, and the specificities in both contexts were 100%. The combined promoter methylation-positive patients had clinicopathologic features including older age, larger tumors, deeper invasion, and higher Ki-67 expression. In both cohorts, SHOX2 expression increased and RASSF1A expression decreased in tumor samples. The promoter methylation level of SHOX2 and RASSF1A was significantly higher in tumor samples at stage I-II than that in normal samples. The promoter methylation levels of these two genes were both negative associated with their expression in early tumor samples. In the NJDT cohort, methylation-positive patients of both individual SHOX2 and RASSF1A assays exhibited upregulation of folate acid metabolism and nucleotide metabolism in tumor samples. The SHOX2 methylation-positive and RASSF1A methylation-positive patients showed the downregulation of pathways related to cell proliferation and apoptosis and pathways involved in DNA repair, cell growth and cell adhesion, respectively.ConclusionThe combined promoter methylation assay for SHOX2 and RASSF1A can be used for screening and diagnosis of early LUAD, with good sensitivity and specificity. The promoter methylation levels of SHOX2 and RASSF1A were associated with their abnormal mRNA expression, and affected DNA instability, cell proliferation, apoptosis and tumor microenvironment in patients with LUAD.
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Affiliation(s)
- Hong Gao
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jun Yang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Lu He
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Wei Wang
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yanhong Liu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yue Hu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Meiling Ge
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jie Ding
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Qing Ye
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- *Correspondence: Qing Ye,
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Wu J, Li P. Detection of short stature homeobox 2 and RAS-associated domain family 1 subtype A DNA methylation in interventional pulmonology. World J Clin Cases 2021; 9:5391-5397. [PMID: 34307592 PMCID: PMC8281403 DOI: 10.12998/wjcc.v9.i20.5391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/07/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
One of the most important aspects of interventional pulmonology is to obtain tissue or liquid samples of the chest to diagnose a respiratory disease; however, it is still possible to obtain insufficient tissue or cytologic specimens. Indeed, methylation detection is an effective method by which to establish a diagnosis. This review focuses on the clinical application of short stature homeobox 2 and RAS-associated domain family 1 subtype A DNA methylation detection in interventional pulmonology, including bronchoscopic fluid biopsy, transbronchial needle aspiration, and pleural effusion.
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Affiliation(s)
- Jian Wu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Peng Li
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
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Li N, Zeng Y, Tai M, Lin B, Zhu D, Luo Y, Ren X, Zhu X, Li L, Wu H, Huang J. Analysis of the Prognostic Value and Gene Expression Mechanism of SHOX2 in Lung Adenocarcinoma. Front Mol Biosci 2021; 8:688274. [PMID: 34262939 PMCID: PMC8273341 DOI: 10.3389/fmolb.2021.688274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/26/2021] [Indexed: 01/15/2023] Open
Abstract
Background: Detection of SHOX2 methylation has been used to assist in the early diagnosis of lung cancer in many hospitals as SHOX2 may be important in the tumorigenesis of lung cancer. However, there are few studies on the mRNA expression, methylation, and molecular mechanism of SHOX2 in lung cancer. We aimed to explore the role of SHOX2 in lung adenocarcinoma (LUAD). Methods: First, we examined the differential expression of SHOX2 mRNA and methylation in cancerous and normal tissues using databases. Second, we analyzed the relationship between SHOX2 expression and common clinical parameters in LUAD patients. Third, we further explored the methylated level and its specific location of SHOX2 and the mainly factors of SHOX2 gene expression. Finally, we screened the correlatively expressed genes to analyze the pathways from the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes using DAVID. Results: We found that the mRNA expression of SHOX2 was higher in multiple cancers, including LUAD and lung squamous cell carcinoma (LUSC), than in normal tissues. Among LUAD patients, SHOX2 expression was higher in patients of middle–young age, with smoking history, in advanced stages, and with nodal distant metastasis. In addition, our results showed that patients with high expression of SHOX2 are prone to recurrence, poor differentiation, and poor prognosis. Thus, we identified that SHOX2 might be an oncogene for LUAD progression. The main factor influencing the high expression of SHOX2 mRNA may be DNA methylation, followed by copy number variation (CNV), but not by gene mutations in LUAD. Unexpectedly, we found that SHOX2 undergoes hypomethylation in the gene body instead of hypermethylation in the promoter. Additionally, SHOX2 has cross talk in the PI3K–Akt signaling pathway and ECM–receptor interaction. Conclusion:SHOX2 is highly expressed in most cancers. SHOX2 gene expression might be mainly regulated by methylation of its gene body in LUAD, and its high expression or hypomethylation indicates poor differentiation and poor prognosis. SHOX2 could be involved in PI3K–Akt and other important cancer-related signaling pathways to promote tumorigenesis.
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Affiliation(s)
- Nanhong Li
- Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yu Zeng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Min Tai
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Biyun Lin
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Di Zhu
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Yi Luo
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Xinle Ren
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Xiaoying Zhu
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Lanlan Li
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Hongrong Wu
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jian Huang
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Department of Pathology, Guangdong Medical University, Zhanjiang, China
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Yang J, Jia Y, Wang B, Yang S, Du K, Luo Y, Li Y, Zhu B. Circular RNA CHST15 Sponges miR-155-5p and miR-194-5p to Promote the Immune Escape of Lung Cancer Cells Mediated by PD-L1. Front Oncol 2021; 11:595609. [PMID: 33777742 PMCID: PMC7991744 DOI: 10.3389/fonc.2021.595609] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/27/2021] [Indexed: 12/19/2022] Open
Abstract
Background The effects of up-regulated CircCHST15 on lung cancer remained unclear. In this study, the role of CircCHST15 in lung cancer was investigated. Methods Dual-luciferase reporter verified the bioinformatics prediction that CircCHST15 targeted miR-155-5p and miR-194-5p. The correlation between CircCHST15 and PD-L1 was analyzed by Pearson analysis. CCK-8 and colony formation was performed to determine the viability and proliferation of lung cancer cells. After the lung cancer (subcutaneous-xenotransplant) model was established in mice, the T cell subtype and related cytokines in mouse tumor tissues were detected by flow cytometry and ELISA. Moreover, the expressions of CircCHST15, miR-155-5p, miR-194-5p, immune-related, and proliferation-related factors of the lung cancer cells or mice tumor tissues were detected by immunohistochemistry, RT-qPCR, or Western blot. Results CircCHST15 and PD-L1 were high-expressed in lung cancer, and the two was positively correlated. CircCHST15 targeted miR-155-5p and miR-194-5p, the later further targeted PD-L1. Lung cancer cell viability and proliferation were increased by miR-155-5p and inhibited by miR-194-5p. CircCHST15 located in the cytoplasm promoted tumor growth, down-regulated the expressions of miR-155-5p and miR-194-5p, and up-regulated the expressions of PD-L1, Ki-67, PCNA, CCL17, CCL22, IFN-γ, TNF-β, and IL-10. Also, CircCHST15 decreased the CD8+ cells in mouse blood and tumor, but increased the Tregs in mouse tumor. PD-L1 inhibitor showed an opposite effect to CircCHST15 on mouse tumors. Conclusion CircCHST15 sponged miR-155-5p and miR-194-5p to promote the PD-L1-mediated immune escape of lung cancer cells.
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Affiliation(s)
- Jianru Yang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yang Jia
- Department of Plastic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Bing Wang
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shengrong Yang
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Kun Du
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yujie Luo
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yunhe Li
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bing Zhu
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Zeng Y, Li N, Chen R, Liu W, Chen T, Zhu J, Zeng M, Cheng J, Huang J. Screening of hub genes associated with prognosis in non-small cell lung cancer by integrated bioinformatics analysis. Transl Cancer Res 2020; 9:7149-7164. [PMID: 35117319 PMCID: PMC8798611 DOI: 10.21037/tcr-20-1073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/12/2020] [Indexed: 12/18/2022]
Abstract
Background Lung cancer is an intractable disease and the second leading cause of cancer-related deaths and morbidity in the world. This study conducted a bioinformatics analysis to identify critical genes associated with poor prognosis in non-small cell lung cancer (NSCLC). Methods We downloaded three datasets (GSE33532, GSE27262, and GSE18842) from the gene expression omnibus (GEO), and used the GEO2R online tools to identify the differentially expressed genes (DEGs). We then used the Search Tool for Retrieval of Interacting Genes (STRING) database to establish a protein-protein interaction (PPI) network and used the Cytoscape software to perform a module analysis of the PPI network. A Kaplan-Meier plotter was used to perform the overall survival (OS) analysis, and the Gene Expression Profiling Interactive Analysis (GEPIA) database was used for expression level analysis of hub genes. Further, the UALCAN database was used to validate the relationship between the gene expression level of each hub gene and clinical characteristics. Results We identified 254 DEGs, which were composed of 66 up-regulated genes and 188 down-regulated genes. Out of these, five DEGs were identified as hub genes (CDC20, BUB1, CCNB2, CCNB1, UBE2C) by constructing a PPI network. The use of a Kaplan-Meier plotter to generate patient survival curves suggested a strong relationship between the five hub genes with worse OS. Validation of the above results using the GEPIA database showed that all the hub genes were highly expressed in NSCLC tissues. Using the UALACN data mining platform, we found that the five hub genes are correlated with tumor stage and the status of node metastasis in NSCLC patients. Conclusions We identified five hub DEGs that might provide perspectives in the explorations of pathogenesis and treatments for NSCLC.
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Affiliation(s)
- Yu Zeng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Graduate School, Guangdong Medical University, Zhanjiang, China
| | - Nanhong Li
- Graduate School, Guangdong Medical University, Zhanjiang, China.,Pathological Diagnosis and Research Center, Affiliated Hospital, Guangdong Medical University, Zhanjiang, China
| | - Riken Chen
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Wang Liu
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Tao Chen
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Graduate School, Guangdong Medical University, Zhanjiang, China
| | - Jinru Zhu
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Graduate School, Guangdong Medical University, Zhanjiang, China
| | - Mingqing Zeng
- First Clinical School of Medicine, Guangdong Medical University, Zhanjiang, China
| | - Junfen Cheng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jian Huang
- Pathological Diagnosis and Research Center, Affiliated Hospital, Guangdong Medical University, Zhanjiang, China
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Sarne V, Huter S, Braunmueller S, Rakob L, Jacobi N, Kitzwögerer M, Wiesner C, Obrist P, Seeboeck R. Promoter Methylation of Selected Genes in Non-Small-Cell Lung Cancer Patients and Cell Lines. Int J Mol Sci 2020; 21:E4595. [PMID: 32605217 PMCID: PMC7369760 DOI: 10.3390/ijms21134595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 01/03/2023] Open
Abstract
Specific gene promoter DNA methylation is becoming a powerful epigenetic biomarker in cancer diagnostics. Five genes (CDH1, CDKN2Ap16, RASSF1A, TERT, and WT1) were selected based on their frequently published potential as epigenetic markers. Diagnostic promoter methylation assays were generated based on bisulfite-converted DNA pyrosequencing. The methylation patterns of 144 non-small-cell lung cancer (NSCLC) and 7 healthy control formalin-fixed paraffin-embedded (FFPE) samples were analyzed to evaluate the applicability of the putative diagnostic markers. Statistically significant changes in methylation levels are shown for TERT and WT1. Furthermore, 12 NSCLC and two benign lung cell lines were characterized for promoter methylation. The in vitro tests involved a comparison of promoter methylation in 2D and 3D cultures, as well as therapeutic tests investigating the impact of CDH1/CDKN2Ap16/RASSF1A/TERT/WT1 promoter methylation on sensitivity to tyrosine kinase inhibitor (TKI) and DNA methyl-transferase inhibitor (DNMTI) treatments. We conclude that the selected markers have potential and putative impacts as diagnostic or even predictive marker genes, although a closer examination of the resulting protein expression and pathway regulation is needed.
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MESH Headings
- Aged
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cadherins/genetics
- Cadherins/metabolism
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- DNA Methylation
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Male
- Middle Aged
- Prognosis
- Promoter Regions, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- Victoria Sarne
- Department Life Sciences, IMC University of Applied Sciences Krems, 3500 Krems, Austria; (V.S.); (S.B.); (L.R.); (N.J.); (C.W.)
| | - Samuel Huter
- Pathologylab Dr. Obrist & Dr. Brunhuber OG, 6511 Zams, Austria; (S.H.); (P.O.)
| | - Sandrina Braunmueller
- Department Life Sciences, IMC University of Applied Sciences Krems, 3500 Krems, Austria; (V.S.); (S.B.); (L.R.); (N.J.); (C.W.)
| | - Lisa Rakob
- Department Life Sciences, IMC University of Applied Sciences Krems, 3500 Krems, Austria; (V.S.); (S.B.); (L.R.); (N.J.); (C.W.)
| | - Nico Jacobi
- Department Life Sciences, IMC University of Applied Sciences Krems, 3500 Krems, Austria; (V.S.); (S.B.); (L.R.); (N.J.); (C.W.)
| | - Melitta Kitzwögerer
- Clinical Institute of Pathology, University Hospital St. Poelten, Karl Landsteiner University of Health Sciences, 3100 St. Pölten, Austria;
| | - Christoph Wiesner
- Department Life Sciences, IMC University of Applied Sciences Krems, 3500 Krems, Austria; (V.S.); (S.B.); (L.R.); (N.J.); (C.W.)
| | - Peter Obrist
- Pathologylab Dr. Obrist & Dr. Brunhuber OG, 6511 Zams, Austria; (S.H.); (P.O.)
| | - Rita Seeboeck
- Department Life Sciences, IMC University of Applied Sciences Krems, 3500 Krems, Austria; (V.S.); (S.B.); (L.R.); (N.J.); (C.W.)
- Clinical Institute of Pathology, University Hospital St. Poelten, Karl Landsteiner University of Health Sciences, 3100 St. Pölten, Austria;
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