1
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Mi R, Wang Q, Liu Q, Jiang F, Ji Y. Expression and prognosis analysis of TBX2 subfamily in human lung carcinoma. Discov Oncol 2024; 15:51. [PMID: 38413457 PMCID: PMC10899548 DOI: 10.1007/s12672-024-00900-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/20/2024] [Indexed: 02/29/2024] Open
Abstract
PURPOSE Lung cancer has a high morbidity and mortality rate of all cancers worldwide. Therefore, there is an urgent need for reliable cancer markers for diagnosis and prognosis of patients with lung cancer. METHODS In this study, we used the bioinformatics database to compare the expression of the TBX2 subfamily at the transcriptional and protein levels in non-small cell lung cancer. Then, to confirm our bioinformatics analysis above, we used western bloting to determine the expression of TBX2, TBX3, TBX4 and TBX5 in human lung squamous carcinoma cell lines. Besides, low expression of TBX2 subfamily predicted a poor prognosis of patients with lung cancer. Finally, The methylation database was used to explore the relationship between the low expression of TBX2 subfamily and methylation of gene promoter region. RESULTS Our data showed a significant decrease of TBX2 subfamily expression in lung cancer tissues of several histological subtypes. Finally, the methylation of TBX2 subfamily members in the promoter region of NSCLC was significantly higher than that in normal tissues. CONCLUSION Our research provided sufficient evidence that TBX2 subfamily might play an inhibitory role in malignancy progression of lung cancer, which is promising to shed light on discovering a novel reliable cancer marker for prognosis of lung cancer patients.
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Affiliation(s)
- Rui Mi
- Department of Clinical Laboratory, Wuxi 9Th People's Hospital Affiliated to Soochow University, No.999 Liang Xi Road, Binhu District, Wuxi, 214000, Jiangsu, China
| | - Qiubo Wang
- Department of Clinical Laboratory, Wuxi 9Th People's Hospital Affiliated to Soochow University, No.999 Liang Xi Road, Binhu District, Wuxi, 214000, Jiangsu, China
| | - Qingyang Liu
- Department of Clinical Laboratory, Wuxi 9Th People's Hospital Affiliated to Soochow University, No.999 Liang Xi Road, Binhu District, Wuxi, 214000, Jiangsu, China
| | - Fengying Jiang
- Department of Clinical Laboratory, Wuxi 9Th People's Hospital Affiliated to Soochow University, No.999 Liang Xi Road, Binhu District, Wuxi, 214000, Jiangsu, China
| | - Yuan Ji
- School of Medicine, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.
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2
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Otálora-Otálora BA, López-Kleine L, Rojas A. Lung Cancer Gene Regulatory Network of Transcription Factors Related to the Hallmarks of Cancer. Curr Issues Mol Biol 2023; 45:434-464. [PMID: 36661515 PMCID: PMC9857713 DOI: 10.3390/cimb45010029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
The transcriptomic analysis of microarray and RNA-Seq datasets followed our own bioinformatic pipeline to identify a transcriptional regulatory network of lung cancer. Twenty-six transcription factors are dysregulated and co-expressed in most of the lung cancer and pulmonary arterial hypertension datasets, which makes them the most frequently dysregulated transcription factors. Co-expression, gene regulatory, coregulatory, and transcriptional regulatory networks, along with fibration symmetries, were constructed to identify common connection patterns, alignments, main regulators, and target genes in order to analyze transcription factor complex formation, as well as its synchronized co-expression patterns in every type of lung cancer. The regulatory function of the most frequently dysregulated transcription factors over lung cancer deregulated genes was validated with ChEA3 enrichment analysis. A Kaplan-Meier plotter analysis linked the dysregulation of the top transcription factors with lung cancer patients' survival. Our results indicate that lung cancer has unique and common deregulated genes and transcription factors with pulmonary arterial hypertension, co-expressed and regulated in a coordinated and cooperative manner by the transcriptional regulatory network that might be associated with critical biological processes and signaling pathways related to the acquisition of the hallmarks of cancer, making them potentially relevant tumor biomarkers for lung cancer early diagnosis and targets for the development of personalized therapies against lung cancer.
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Affiliation(s)
- Beatriz Andrea Otálora-Otálora
- Grupo de Investigación INPAC, Unidad de Investigación, Fundación Universitaria Sanitas, Bogotá 110131, Colombia
- Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 11001, Colombia
| | - Liliana López-Kleine
- Departamento de Estadística, Universidad Nacional de Colombia, Bogotá 11001, Colombia
- Correspondence: (L.L.-K.); (A.R.)
| | - Adriana Rojas
- Facultad de Medicina, Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá 110211, Colombia
- Correspondence: (L.L.-K.); (A.R.)
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3
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Yang C, Wang X, Qiu C, Zheng Z, Lin K, Tu M, Zhang K, Jiang K, Gao W. Identification of FEZ2 as a potential oncogene in pancreatic ductal adenocarcinoma. PeerJ 2022; 9:e12736. [PMID: 35036176 PMCID: PMC8742541 DOI: 10.7717/peerj.12736] [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: 07/27/2021] [Accepted: 12/12/2021] [Indexed: 12/02/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the common malignant tumors with high lethal rate and poor prognosis. Dysregulation of many genes have been reported to be involved in the occurrence and development of PDAC. However, as a highly conserved gene in eukaryotes, the role of Fasciculation and Elongation protein Zeta 2 (FEZ2) in pancreatic cancer progression is not clear. In this study, we identified the oncogenic effect of FEZ2 on PDAC. By mining of The Cancer Genome Atlas (TCGA) database, we found that FEZ2 was upregulated in PDAC tissues and FEZ2 expression was negatively regulated by its methylation. Moreover, high expression and low methylation of FEZ2 correlated with poor prognosis in PDAC patients. Besides, we found that FEZ2 could promote PDAC cells proliferation, migration and 5-FU resistance in vitro. Furthermore, Gene pathway enrichment analysis demonstrated a positive correlation between Wnt signaling activation and FEZ2 expression in PDAC patients. Western blot showed that FEZ2 knockdown significantly suppressed β-catenin expression. Collectively, our finding revealed that FEZ2 functioned as a potential oncogene on PDAC progression and migration, and the expression of FEZ2 had guidance value for the treatment and chemotherapy program of PDAC patients.
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Affiliation(s)
- Chaozhi Yang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Xuebing Wang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Chenjie Qiu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Ziruo Zheng
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Kai Lin
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Min Tu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Kai Zhang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Kuirong Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Wentao Gao
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.,Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu Province, China
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4
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Patrizi S, Pederiva F, d'Adamo AP. Whole-Genome Methylation Study of Congenital Lung Malformations in Children. Front Oncol 2021; 11:689833. [PMID: 34262872 PMCID: PMC8273538 DOI: 10.3389/fonc.2021.689833] [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: 04/01/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022] Open
Abstract
Background and Objectives The treatment of asymptomatic patients with congenital pulmonary malformations (CPMs) remains controversial, partially because the relationship between congenital lung malformations and malignancy is still undefined. Change in methylation pattern is a crucial event in human cancer, including lung cancer. We therefore studied all differentially methylated regions (DMRs) in a series of CPMs in an attempt to find methylation anomalies in genes already described in association with malignancy. Methods The DNA extracted from resected congenital lung malformations and control lung tissue was screened using Illumina MethylationEPIC arrays. Comparisons between the group of malformed samples or the malformed samples of same histology or each malformed sample and the controls and between a pleuropulmonary blastoma (PPB) and controls were performed. Moreover, each malformed sample was pairwise compared with its respective control. All differentially methylated regions (DMRs) with an adjusted p-value <0,05 were studied. Results Every comparison highlighted a number of DMRs closed to genes involved either in cell proliferation or in embryonic development or included in the Cancer Gene Census. Their abnormal methylation had been already described in lung tumors. Conclusions Methylation anomalies already described in lung tumors and also shared by the PPB were found in congenital lung malformations, regardless the histology. The presence of methylation abnormalities is suggestive of a correlation between congenital lung malformations and some step of malignant transformation.
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Affiliation(s)
- Sara Patrizi
- Medical, Surgical and Health Sciences Department, University of Trieste, Trieste, Italy
| | - Federica Pederiva
- Pediatric Surgery, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - Adamo Pio d'Adamo
- Medical, Surgical and Health Sciences Department, University of Trieste, Trieste, Italy.,Laboratory of Medical Genetics, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
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5
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Huang W, Li P, Qiu X. [A Literature Review on the Role of TBX5 in Expression and Progression of Lung Cancer: Current Perspectives]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:883-888. [PMID: 32810974 PMCID: PMC7583881 DOI: 10.3779/j.issn.1009-3419.2020.102.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
T-box转录因子(T-box transcription factor gene, TBX)基因涉及器官的发生,TBX5在人的正常心脏和肺组织中表达水平最高。TBX5的缺乏可能导致胸廓发育畸形和膈肌发育异常,其异位表达和过表达会诱导细胞凋亡和抑制细胞生长。既往研究发现了TBX5在食管腺癌、胃癌、结肠癌和乳腺癌的发生和发展中的潜在作用。我们对TBX2亚家族的基因表达和预后之间的关系进行了综述,同时探究TBX5在调控肺癌发生发展机制中的研究进展。虽然TBX5和肺癌发生之间的关系尚不明确,不过TBX5可以显著抑制人体内肿瘤生长,其表达水平和肺癌的进展呈现负相关。由此,TBX5的基因表达水平和甲基化程度是潜在的表证肺癌增殖和转移的生物标志物,具有作为肺癌治疗靶点的潜力。
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Affiliation(s)
- Weijia Huang
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Peiwei Li
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Xiaoming Qiu
- Department of Lung Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
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6
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Khalil A, Kamar A, Nemer G. Thalidomide-Revisited: Are COVID-19 Patients Going to Be the Latest Victims of Yet Another Theoretical Drug-Repurposing? Front Immunol 2020; 11:1248. [PMID: 32574274 PMCID: PMC7270289 DOI: 10.3389/fimmu.2020.01248] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/18/2020] [Indexed: 12/22/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is a worldwide threatening health issue. The progression of this viral infection occurs in the airways of the lungs with an exaggerated inflammatory response referred to as the "cytokine storm" that can lead to lethal lung injuries. In the absence of an effective anti-viral molecule and until the formulation of a successful vaccine, anti-inflammatory drugs might offer a complementary tool for controlling the associated complications of COVID-19 and thus decreasing the subsequent fatalities. Drug repurposing for several molecules has emerged as a rapid temporary solution for COVID-19. Among these drugs is Thalidomide; a historically emblematic controversial molecule that harbors an FDA approval for treating erythema nodosum leprosum (ENL) and multiple myeloma (MM). Based on just one-case report that presented positive outcomes in a patient treated amongst others with Thalidomide, two clinical trials on the efficacy and safety of Thalidomide in treating severe respiratory complications in COVID-19 patients were registered. Yet, the absence of substantial evidence on Thalidomide usage in that context along with the discontinued studies on the efficiency of this drug in similar pulmonary diseases, might cause a significant obstacle for carrying out further clinical evaluations. Herein, we will discuss the theoretical effectiveness of Thalidomide in attenuating inflammatory complications that are encountered in COVID-19 patients while pinpointing the lack of the needed evidences to move forward with this drug.
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Affiliation(s)
- Athar Khalil
- Department or Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Amina Kamar
- Vascular Medicine Program, Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
| | - Georges Nemer
- Department or Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
- Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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7
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DNA methylation landscape of triple-negative ductal carcinoma in situ (DCIS) progressing to the invasive stage in canine breast cancer. Sci Rep 2020; 10:2415. [PMID: 32051475 PMCID: PMC7015930 DOI: 10.1038/s41598-020-59260-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/16/2020] [Indexed: 11/09/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a subtype of breast cancer unresponsive to traditional receptor-targeted treatments, leading to a disproportionate number of deaths. Invasive breast cancer is believed to evolve from non-invasive ductal carcinoma in situ (DCIS). Detection of triple-negative DCIS (TN-DCIS) is challenging, therefore strategies to study molecular events governing progression of pre-invasive TN-DCIS to invasive TNBC are needed. Here, we study a canine TN-DCIS progression and investigate the DNA methylation landscape of normal breast tissue, atypical ductal hyperplasia (ADH), DCIS and invasive breast cancer. We report hypo- and hypermethylation of genes within functional categories related to cancer such as transcriptional regulation, apoptosis, signal transduction, and cell migration. DNA methylation changes associated with cancer-related genes become more pronounced at invasive breast cancer stage. Importantly, we identify invasive-only and DCIS-specific DNA methylation alterations that could potentially determine which lesions progress to invasive cancer and which could remain as pre-invasive DCIS. Changes in DNA methylation during TN-DCIS progression in this canine model correspond with gene expression patterns in human breast tissues. This study provides evidence for utilizing methylation status of gene candidates to define late-stage (DCIS and invasive), invasive stage only or DCIS stage only of TN-DCIS progression.
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8
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Khalil A, Kamar A, Nemer G. Thalidomide-Revisited: Are COVID-19 Patients Going to Be the Latest Victims of Yet Another Theoretical Drug-Repurposing? Front Immunol 2020. [PMID: 32574274 DOI: 10.3389/fimmu.2020.01248/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is a worldwide threatening health issue. The progression of this viral infection occurs in the airways of the lungs with an exaggerated inflammatory response referred to as the "cytokine storm" that can lead to lethal lung injuries. In the absence of an effective anti-viral molecule and until the formulation of a successful vaccine, anti-inflammatory drugs might offer a complementary tool for controlling the associated complications of COVID-19 and thus decreasing the subsequent fatalities. Drug repurposing for several molecules has emerged as a rapid temporary solution for COVID-19. Among these drugs is Thalidomide; a historically emblematic controversial molecule that harbors an FDA approval for treating erythema nodosum leprosum (ENL) and multiple myeloma (MM). Based on just one-case report that presented positive outcomes in a patient treated amongst others with Thalidomide, two clinical trials on the efficacy and safety of Thalidomide in treating severe respiratory complications in COVID-19 patients were registered. Yet, the absence of substantial evidence on Thalidomide usage in that context along with the discontinued studies on the efficiency of this drug in similar pulmonary diseases, might cause a significant obstacle for carrying out further clinical evaluations. Herein, we will discuss the theoretical effectiveness of Thalidomide in attenuating inflammatory complications that are encountered in COVID-19 patients while pinpointing the lack of the needed evidences to move forward with this drug.
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Affiliation(s)
- Athar Khalil
- Department or Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Amina Kamar
- Vascular Medicine Program, Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
| | - Georges Nemer
- Department or Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
- Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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Perrard J, Morel A, Meznad K, Paget-Bailly P, Dalstein V, Guenat D, Mourareau C, Clavel C, Fauconnet S, Baguet A, Mougin C, Pretet JL. DNA demethylation agent 5azadC downregulates HPV16 E6 expression in cervical cancer cell lines independently of TBX2 expression. Oncol Lett 2019; 19:1074-1081. [PMID: 31897221 DOI: 10.3892/ol.2019.11158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
HPV16 is the most carcinogenic human papillomavirus and causes >50% of cervical cancers, the majority of anal cancers and 30% of oropharyngeal squamous cell carcinomas. HPV carcinogenesis relies on the continuous expression of the two main viral oncoproteins E6 and E7 that target >150 cellular proteins. Among them, epigenetic modifiers, including DNA Methyl Transferases (DNMT), are dysregulated, promoting an aberrant methylation pattern in HPV-positive cancer cells. It has been previously reported that the treatment of HPV-positive cervical cancer cells with DNMT inhibitor 5-aza-2'-deoxycytidine (5azadC) caused the downregulation of E6 expression due to mRNA destabilization that was mediated by miR-375. Recently, the T-box transcription factor 2 (TBX2) has been demonstrated to repress HPV LCR activity. In the current study, the role of TBX2 in E6 repression was investigated in HPV16 cervical cancer cell lines following 5azadC treatment. A decrease of E6 expression was accompanied by p53 and p21 restoration. While TBX2 mRNA was upregulated in 5azadC-treated SiHa and Ca Ski cells, TBX2 protein was not detectable. Furthermore, the overexpression of TBX2 protein in cervical cancer cells did not allow the repression of E6 expression. The TBX2 transcription factor is therefore unlikely to be associated with the repression of E6 following 5azadC treatment of SiHa and Ca Ski cells.
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Affiliation(s)
- Jerome Perrard
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Adrien Morel
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 112041, Colombia
| | - Koceila Meznad
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Philippe Paget-Bailly
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Veronique Dalstein
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire, Université de Reims Champagne-Ardenne, Faculté de Médecine, 51000 Reims, France.,Centre Hospitalier Universitaire Reims, Laboratoire Biopathologie, 51000 Reims, France
| | - David Guenat
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France.,Centre National de Référence Papillomavirus, CHU Besançon, Boulevard Alexandre Fleming, 25000 Besançon, France
| | - Celine Mourareau
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire, Université de Reims Champagne-Ardenne, Faculté de Médecine, 51000 Reims, France.,Centre Hospitalier Universitaire Reims, Laboratoire Biopathologie, 51000 Reims, France
| | - Christine Clavel
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire, Université de Reims Champagne-Ardenne, Faculté de Médecine, 51000 Reims, France.,Centre Hospitalier Universitaire Reims, Laboratoire Biopathologie, 51000 Reims, France
| | - Sylvie Fauconnet
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Aurelie Baguet
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France
| | - Christiane Mougin
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France.,Centre National de Référence Papillomavirus, CHU Besançon, Boulevard Alexandre Fleming, 25000 Besançon, France
| | - Jean-Luc Pretet
- Équipe d'Accueil 3181, University of Bourgogne Franche-Comté, Laboratoire d'Excellence Lipoprotéines et Santé, Prévention et Traitement des Maladies Inflammatoires et du Cancer, 25000 Besançon, France.,Centre National de Référence Papillomavirus, CHU Besançon, Boulevard Alexandre Fleming, 25000 Besançon, France
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Chen D, Song Y, Zhang F, Wang X, Zhu E, Zhang X, Jiang G, Li S, Chen C, Chen Y. Genome-Wide Analysis of Lung Adenocarcinoma Identifies Novel Prognostic Factors and a Prognostic Score. Front Genet 2019; 10:493. [PMID: 31191611 PMCID: PMC6539224 DOI: 10.3389/fgene.2019.00493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/06/2019] [Indexed: 01/11/2023] Open
Abstract
Background and Objective Lung adenocarcinoma (LUAD) is the most common histological type of all lung cancers and is associated with genetic and epigenetic aberrations. The tumor, node, and metastasis (TNM) stage is the most authoritative indicator of the clinical outcome in LUAD patients in current clinical practice. In this study, we attempted to identify novel genetic and epigenetic modifications and integrate them as a predictor of the prognosis for LUAD, to supplement the TNM stage with additional information. Methods A dataset of 445 patients with LUAD was obtained from The Cancer Genome Atlas database. Both genetic and epigenetic aberrations were screened for their prognostic impact on overall survival (OS). A prognostic score (PS) integrating all the candidate prognostic factors was then developed and its prognostic value validated. Results A total of two micro-RNAs, two mRNAs and two DNA methylation sites were identified as prognostic factors associated with OS. The low- and high-risk patient groups, divided by their PS level, showed significantly different OS (p < 0.001) and recurrence-free survival (RFS; p = 0.005). Patients in the early stages (stages I/II) and advanced stages (stages III/IV) of LUAD could be further subdivided by PS into four subgroups. PS remained efficient in stratifying patients into different OS (p < 0.001) and RFS (p = 0.005) when the low- and high-risk subgroups were in the early stages of the disease. However, there was only a significant difference in OS (p = 0.04) but not RFS (p = 0.2), between the low-risk and high-risk subgroups when both were in advanced stages. Conclusion PS, in combination with the TNM stage, provides additional precision in stratifying patients with significantly different OS and RFS prognoses. Further studies are warranted to assess the efficiency of PS and to explain the effects of the genetic and epigenetic aberrations observed in LUAD.
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Affiliation(s)
- Donglai Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yueqiang Song
- Department of Regenerative Medicine, Stem Cell Center, Tongji University School of Medicine, Shanghai, China
| | - Fuquan Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
| | - Xiaofan Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
| | - Erjia Zhu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi Zhang
- Department of Regenerative Medicine, Stem Cell Center, Tongji University School of Medicine, Shanghai, China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Siguang Li
- Department of Regenerative Medicine, Stem Cell Center, Tongji University School of Medicine, Shanghai, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yongbing Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China
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Epigenetic Suppression of the T-box Subfamily 2 ( TBX2) in Human Non-Small Cell Lung Cancer. Int J Mol Sci 2019; 20:ijms20051159. [PMID: 30866410 PMCID: PMC6429281 DOI: 10.3390/ijms20051159] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 12/25/2022] Open
Abstract
(1) The TBX2 subfamily of transcription factors (TBXs 2, 3, 4 and 5) are markedly down-regulated in human non-small cell lung cancer (NSCLC) and exert tumor suppressor effects in lung malignancy. Yet, mechanisms underlying suppressed expression of the TBX2 subfamily in NSCLC are elusive. Here, we interrogated probable epigenetic mechanisms in suppressed expression of the TBX2 subfamily in human NSCLC. (2) TBX2 subfamily gene expression and methylation levels in NSCLC and normal lung tissues were surveyed using publicly available RNA-sequence and genome-wide methylation datasets. Methylation β-values of the four genes were statistically compared between NSCLCs and normal lung tissues, correlated with gene expression levels, and interrogated with clinicopathological variables. Expression and methylation levels of TBXs were quantified in NSCLC cells using real-time PCR and methylation-specific PCR assays, respectively. Effects of the DNA methyltransferase inhibitor 5-azacytidine (Aza) on TBX2 subfamily expression were assessed in NSCLC cells. Impact of TBX2 subfamily expression on Aza-treated cells was evaluated by RNA interference. (3) All four TBXs were significantly hypermethylated in NSCLCs relative to normal lung tissues (p < 0.05). Methylation β-values of the genes, with exception of TBX2, were significantly inversely correlated with corresponding mRNA expression levels (p < 0.05). We found no statistically significant differences in hypermethylation levels of the TBX2 subfamily by clinicopathological features including stage and tobacco history. Expression levels of the TBX genes were overall suppressed in NSCLC cells relative to normal alveolar cells. Members of the subfamily were significantly hypermethylated in all tested NSCLC cell lines relative to normal alveolar cells. Treatment with Aza induced the expression of the TBX2 subfamily concomitant with NSCLC cell growth inhibition. Further, simultaneous knockdown of the four TBX genes markedly reduced anti-growth effects of Aza in NSCLC cells. (4) Our study sheds light on new epigenetic profiles in the molecular pathogenesis of human NSCLC.
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