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Wang X, Shi J, Liu Z. Advancements in the diagnosis and treatment of sub‑centimeter lung cancer in the era of precision medicine (Review). Mol Clin Oncol 2024; 20:28. [PMID: 38414512 PMCID: PMC10895471 DOI: 10.3892/mco.2024.2726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024] Open
Abstract
Lung cancer is the malignancy with the highest global mortality rate and imposes a substantial burden on society. The increasing popularity of lung cancer screening has led to increasing number of patients being diagnosed with pulmonary nodules due to their potential for malignancy, causing considerable distress in the affected population. However, the diagnosis and treatment of sub-centimeter grade pulmonary nodules remain controversial. The evolution of genetic detection technology and the development of targeted drugs have positioned the diagnosis and treatment of lung cancer in the precision medicine era, leading to a marked improvement in the survival rate of patients with lung cancer. It has been established that lung cancer driver genes serve a key role in the development and progression of sub-centimeter lung cancer. The present review aimed to consolidate the findings on genes associated with sub-centimeter lung cancer, with the intent of serving as a reference for future studies and the personalized management of sub-centimeter lung cancer through genetic testing.
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Affiliation(s)
- Xiao Wang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Jingwei Shi
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, P.R. China
| | - Zhengcheng Liu
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
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2
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Xu D, Li C, Zhang Y, Zhang J. DNA methylation molecular subtypes for prognosis prediction in lung adenocarcinoma. BMC Pulm Med 2022; 22:133. [PMID: 35392867 PMCID: PMC8991665 DOI: 10.1186/s12890-022-01924-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/30/2022] [Indexed: 02/06/2023] Open
Abstract
Aims Lung cancer is one of the main results in tumor-related mortality. Methylation differences reflect critical biological features of the etiology of LUAD and affect prognosis. Methods In the present study, we constructed a prediction prognostic model integrating various DNA methylation used high-throughput omics data for improved prognostic evaluation. Results Overall 21,120 methylation sites were identified in the training dataset. Overall, 237 promoter genes were identified by genomic annotation of 205 CpG loci. We used Akakike Information Criteria (AIC) to obtain the validity of data fitting, but to prevent overfitting. After AIC clustering, specific methylation sites of cg19224164 and cg22085335 were left. Prognostic analysis showed a significant difference among the two groups (P = 0.017). In particular, the hypermethylated group had a poor prognosis, suggesting that these methylation sites may be a marker of prognosis. Conclusion The model might help in the identification of unknown biomarkers in predicting patient prognosis in LUAD. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-022-01924-0.
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Affiliation(s)
- Duoduo Xu
- Wenzhou Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, No. 9 Jiaowei Road, Lucheng District, Wenzhou City, Zhejiang Province, China
| | - Cheng Li
- Department of Otolaryngology Head and Neck Surgery, The Central Hospital of Wuhan, Tongji Medical College Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Youjing Zhang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizhou Zhang
- Wenzhou Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, No. 9 Jiaowei Road, Lucheng District, Wenzhou City, Zhejiang Province, China.
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Testa U, Pelosi E, Castelli G. Molecular charcterization of lung adenocarcinoma combining whole exome sequencing, copy number analysis and gene expression profiling. Expert Rev Mol Diagn 2021; 22:77-100. [PMID: 34894979 DOI: 10.1080/14737159.2022.2017774] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Lung cancer is the leading cause of cancer mortality worldwide; lung adenocarcinoma (LUAD) corresponds to about 40% of lung cancers. LUAD is a genetically heterogeneous disease and the definition of this heterogeneity is of fundamental importance for prognosis and treatment. AREAS COVERED Based on primary literature, this review provides an updated analysis of multiomics studies based on the study of mutation profiling, copy number alterations and gene expression allowing for definition of molecular subgroups, prognostic factors based on molecular biomarkers, and identification of therapeutic targets. The authors sum up by providing the reader with their expert opinion on the potentialities of multiomics analysis of LUADs. EXPERT OPINION A detailed and comprehensive study of the co-occurring genetic abnormalities characterizing different LUAD subsets represents a fundamental tool for a better understanding of the disease heterogeneity and for the identification of subgroups of patients responding or resistant to targeted treatments and for the discovery of new therapeutic targets. It is expected that a comprehensive characterization of LUADs may provide a fundamental contribution to improve the survival of LUAD patients.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
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Zhou C, Wang Y, Lei L, Ji MH, Yang JJ, Xia H. Identifying Common Genes Related to Platelet and Immunity for Lung Adenocarcinoma Prognosis Prediction. Front Mol Biosci 2020; 7:563142. [PMID: 33195410 PMCID: PMC7658298 DOI: 10.3389/fmolb.2020.563142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022] Open
Abstract
Background Although 1000s of immune-related and platelet receptor-related genes have been identified in lung adenocarcinoma, their role in prognosis prediction remains unclear. Methods We downloaded mRNA data from the Cancer Genome Atlas Dataset (TCGA), and GSE68465 or GSE14814 data sets from the Gene Expression Omnibus (GEO) database. Results The high-risk group’s overall survival (OS) time was lower than that of the low-risk group’s in TCGA (p = 1.15e-03). Additionally, the risk score was an independent prognostic survival factor for lung adenocarcinoma patients in TCGA (HR = 2.136, 95%CI = 1.553–2.937, p < 0.001). The model’s prognostic performance was verified with two independent GEO cohorts (GSE68465 and GSE14814). We also developed a nomogram and provided free webpage prediction tools.1 The mechanism of the high-risk group in this risk score may be have been related to somatic mutations and copy number changes. In addition, this risk score can distinguish the prognosis of the other two cancers (ACC, p < 0.001 and KIRP, p < 0.001). Also, among the other seven cancers, the OS prognosis for high and low risk groups show wide variation (p < 0.05). Conclusion Our research demonstrates that CCNA2 and TGFB2 are potential diagnostic and prognostic biomarkers, as well as therapeutic targets in lung adenocarcinoma (LUAD). We also determined a novel and reliable prognostic score for lung adenocarcinoma prognosis. The online nomogram prediction tool that contains this risk score may also help clinical medical staff.
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Affiliation(s)
- Chengmao Zhou
- School of Medicine, Southeast University, Nanjing, China
| | - Ying Wang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Lei
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mu-Huo Ji
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jian-Jun Yang
- School of Medicine, Southeast University, Nanjing, China.,Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongping Xia
- School of Medicine, Southeast University, Nanjing, China.,Department of Pathology, School of Basic Medical Sciences & Sir Run Run Hospital & State Key Laboratory of Reproductive Medicine & Key Laboratory of Antibody Technique of National Health Commission, Nanjing Medical University, Nanjing, China
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Yu X, Zhang Y. Identification of a long non-coding RNA signature for predicting prognosis and biomarkers in lung adenocarcinoma. Oncol Lett 2020; 19:2793-2800. [PMID: 32218832 PMCID: PMC7068299 DOI: 10.3892/ol.2020.11400] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have a number of functions in various cellular processes and are potential prognostic factors for lung adenocarcinoma (LUAD). A gene risk model could provide novel evidence to improve the prediction of overall outcomes and provide more potential biomarkers. The present study aimed improve a previously published method of gene signature construction to make it more robust and accurate. The lncRNA expression profiles from 594 patients with LUAD were obtained from The Cancer Genome Atlas (TCGA) database and samples were divided into high- and low-risk groups based on median risk scores calculated using a prognosis-related risk score formula. Univariate Cox regression, least absolute shrinkage and selection operator algorithm and multivariate Cox regression were performed to construct a gene signature based on the differentially expressed lncRNAs in patients with LUAD. The robustness and accuracy of the present model was assessed using area under the calculated curves (AUC) and Kaplan-Meier (K-M) survival analysis of the high- and low-risk cohorts. Potential biomarkers associated with survival status were then identified using K-M survival analysis and potential biomarker functions were predicted using enrichment analysis of co-expressed mRNAs. The gene signature constructed contained 44 lncRNAs. The AUCs for 3- and 5-year survival with the model were 0.836 and 0.818, respectively, of a time-dependent receiver operator characteristic curve. Moreover, lncRNAs AC124804.1 and MIR34AHG were identified using K-M survival analysis and the potential function of these two lncRNAs was predicted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment. The present lncRNA model provides novel insight which may improve prediction of prognosis for patients with LUAD and identify potentially novel biomarkers for the diagnosis.
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Affiliation(s)
- Xiaolin Yu
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100078, P.R. China
| | - Yanxia Zhang
- Department of Respiratory, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing 100078, P.R. China
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Saab S, Zalzale H, Rahal Z, Khalifeh Y, Sinjab A, Kadara H. Insights Into Lung Cancer Immune-Based Biology, Prevention, and Treatment. Front Immunol 2020; 11:159. [PMID: 32117295 PMCID: PMC7026250 DOI: 10.3389/fimmu.2020.00159] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is the number one cause of cancer-related deaths. The malignancy is characterized by dismal prognosis and poor clinical outcome mostly due to advanced-stage at diagnosis, thereby inflicting a heavy burden on public health worldwide. Recent breakthroughs in immunotherapy have greatly benefited a subset of lung cancer patients, and more importantly, they are undauntedly bringing forth a paradigm shift in the drugs approved for cancer treatment, by introducing "tumor-type agnostic therapies". Yet, and to fulfill immunotherapy's potential of personalized cancer treatment, demarcating the immune and genomic landscape of cancers at their earliest possible stages will be crucial to identify ideal targets for early treatment and to predict how a particular patient will fare with immunotherapy. Recent genomic surveys of premalignant lung cancer have shed light on early alterations in the evolution of lung cancer. More recently, the advent of immunogenomic technologies has provided prodigious opportunities to study the multidimensional landscape of lung tumors as well as their microenvironment at the molecular, genomic, and cellular resolution. In this review, we will summarize the current state of immune-based therapies for cancer, with a focus on lung malignancy, and highlight learning outcomes from clinical and preclinical studies investigating the naïve immune biology of lung cancer. The review also collates immunogenomic-based evidence from seminal reports which collectively warrant future investigations of premalignancy, the tumor-adjacent normal-appearing lung tissue, pulmonary inflammatory conditions such as chronic obstructive pulmonary disease, as well as systemic microbiome imbalance. Such future directions enable novel insights into the evolution of lung cancers and, thus, can provide a low-hanging fruit of targets for early immune-based treatment of this fatal malignancy.
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Affiliation(s)
- Sara Saab
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hussein Zalzale
- School of Medicine, American University of Beirut, Beirut, Lebanon
| | - Zahraa Rahal
- School of Medicine, American University of Beirut, Beirut, Lebanon
| | - Yara Khalifeh
- School of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Humam Kadara
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Jakubek YA, Chang K, Sivakumar S, Yu Y, Giordano MR, Fowler J, Huff CD, Kadara H, Vilar E, Scheet P. Large-scale analysis of acquired chromosomal alterations in non-tumor samples from patients with cancer. Nat Biotechnol 2020; 38:90-96. [PMID: 31685958 PMCID: PMC8082517 DOI: 10.1038/s41587-019-0297-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 09/25/2019] [Indexed: 01/21/2023]
Abstract
Mosaicism, the presence of subpopulations of cells bearing somatic mutations, is associated with disease and aging and has been detected in diverse tissues, including apparently normal cells adjacent to tumors. To analyze mosaicism on a large scale, we surveyed haplotype-specific somatic copy number alterations (sCNAs) in 1,708 normal-appearing adjacent-to-tumor (NAT) tissue samples from 27 cancer sites and in 7,149 blood samples from The Cancer Genome Atlas. We find substantial variation across tissues in the rate, burden and types of sCNAs, including those spanning entire chromosome arms. We document matching sCNAs in the NAT tissue and the adjacent tumor, suggesting a shared clonal origin, as well as instances in which both NAT tissue and tumor tissue harbor a gain of the same oncogene arising in parallel from distinct parental haplotypes. These results shed light on pan-tissue mutations characteristic of field cancerization, the presence of oncogenic processes adjacent to cancer cells.
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Affiliation(s)
- Y A Jakubek
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - K Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - S Sivakumar
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y Yu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M R Giordano
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - E Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Wang C, Shen H. Commentary: Premalignant genomic data tracing the evolution of lung adenocarcinoma. EBioMedicine 2019; 42:16-17. [PMID: 30956168 PMCID: PMC6491914 DOI: 10.1016/j.ebiom.2019.03.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 11/19/2022] Open
Affiliation(s)
- Cheng Wang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
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