1
|
Ramazi S, Daddzadi 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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Shahin Ramazi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Meadeh Daddzadi
- 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
| |
Collapse
|
2
|
Celik B, Pasin O, Sen S, Tuncer SB, Kayım ZY, Erciyas SK, Erdogan OS, Gultaslar BK, Ghafour AA, Yazıcı H, Olgac NV. DNA methylation of KIFC1 gene in determination of histological diagnosis, prognosis and metastasis of lung cancer. Pathol Res Pract 2023; 249:154742. [PMID: 37666088 DOI: 10.1016/j.prp.2023.154742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/29/2023] [Accepted: 08/03/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND One of the main features of cancer, especially lung cancer (LC), is abnormal cell division. Abnormal expression of kinesin family member C1 (KIFC1/HSET), which is involved in mitotic cell division and ensures equatorial alignment of chromosomes during division, is observed in both premalignant and malignant lesions. There are no studies in the literature addressing the role of KIFC1 in the diagnosis and follow-up of LC. In this study, we investigated the epigenetic role of KIFC1 in the diagnosis, stage, and prognosis of various histological subtypes diagnosed with LC. MATERIAL AND METHODS The expression and methylation status of the KIFC1 gene were examined after DNA/RNA isolation in tumor, conjugate normal tissue, and blood samples from 39 patients diagnosed with LC and in blood samples from 39 healthy controls. Changes in KIFC1 gene expression were examined by the Quantitative Real Time-PCR (qRT-PCR) method after cDNA synthesis following RNA isolation. The Methylation-Specific PCR (MSP) method was used to determine the methylation status of the KIFC1 gene. In this study, the expression/methylation profiles of the KIFC1 gene and the clinical and pathological characteristics of the patients were analyzed by statistical methods. RESULT Hypomethylation was detected in 95.8% of the 62.1% of patients' tissues with increased KIFC1 gene expression. The expression level of the KIFC1 gene was found to be increased 3.2-fold in the tumor tissues of the patients compared with the conjugated normal tissues and 2.4-fold in the serum of the patients compared with the healthy serum. Statistical comparison of patients' clinical parameters and methylation and expression results revealed statistical significance between KIFC1 expression and metastasis, tumor stage and tumor grade. CONCLUSION In conclusion, the increase in the expression level of the KIFC1 gene is higher in patients diagnosed with LC than in the healthy population, and therefore, the increase in the expression level of the KIFC1 gene due to hypomethylation can be used as a screening biomarker in LC. It can also be considered that the methylation profile of the KIFC1 gene may be a potential biomarker for determining the subtype of squamous cell carcinoma in LC. The results of the study need to be analyzed and continued with a larger number of patients.
Collapse
Affiliation(s)
- Betul Celik
- Istanbul University, Institute of Graduate Studies in Health Sciences, Department of Cancer Genetics, Istanbul, Türkiye; Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye; Molecular Biology Department, Erzincan Binali Yıldırım University, Erzincan, Türkiye.
| | - Ozge Pasin
- Department of Biostatistics, Bezmialem University, Istanbul, Türkiye.
| | - Sena Sen
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Seref Bugra Tuncer
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Zubeyde Yalnız Kayım
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Seda Kılıc Erciyas
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Ozge Sukruoglu Erdogan
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Busra Kurt Gultaslar
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Arash Adamnejad Ghafour
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Hulya Yazıcı
- Istanbul Arel University, Arel Medical Faculty, Department of Medical Biology and Genetics, Istanbul, Türkiye.
| | - Necat Vakur Olgac
- Istanbul University, Institute of Graduate Studies in Health Sciences, Department of Cancer Genetics, Istanbul, Türkiye; Tumor Pathology Department, Department of Clinical Oncology, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| |
Collapse
|
3
|
Liu D, Yao L, Ding X, Zhou H. Multi-omics immune regulatory mechanisms in lung adenocarcinoma metastasis and survival time. Comput Biol Med 2023; 164:107333. [PMID: 37586202 DOI: 10.1016/j.compbiomed.2023.107333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/23/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023]
Abstract
Lung adenocarcinoma (LUAD) is the most common type of lung cancer. Despite previous research on immune mechanisms and related molecules in LUAD, the specific regulatory mechanisms of these molecules in the immune microenvironment remain unclear. Furthermore, the impact of regulatory genes or RNA on LUAD metastasis and survival time is yet to be understood. To address these gaps, we collected a substantial amount of data, including 17,226 gene expression profiles from 1,018 samples, 370,640 methylation sites from 461 samples, and 248 miRNAs from 513 samples. Our aim was to explore the genes, miRNAs, and methylation sites associated with LUAD progression. Leveraging the regulatory functions of miRNAs and methylation sites, we identified target and regulated genes. Through the utilization of LASSO and survival analysis, we pinpointed 22 key genes that play pivotal roles in the immune regulatory mechanism of LUAD. Notably, the expression levels of these 22 genes demonstrated significant discriminatory power in predicting LUAD patient survival time. Additionally, our deep learning model accurately predicted distant metastasis in LUAD patients using the expression levels of these genes. Further pathway enrichment analysis revealed that these 22 genes are significantly enriched in pathways closely linked to LUAD progression. Through Immune Infiltration Assay, we observed that T cell CD4 memory resting, monocytes, and macrophages.M2 were the three most abundant cell types in the immune microenvironment of LUAD. These cells are known to play crucial roles in tumor growth, invasion, and metastasis. Single-cell data analysis further validated the functional significance of these genes, indicating their involvement not only in immune cells but also in epithelial cells, showcasing significant differential expression. Overall, this study sheds light on the regulatory mechanisms underlying the immune microenvironment of LUAD by identifying key genes associated with LUAD progression. The findings provide insights into potential prognostic markers and therapeutic targets.
Collapse
Affiliation(s)
- Dan Liu
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Lulu Yao
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China
| | - Xiaolei Ding
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China.
| | - Huan Zhou
- Department of Medical Oncology, The Second Hospital of Dalian Medical University, Dalian, China.
| |
Collapse
|
4
|
Mogoantă CA, Ciolofan MS, Istrate-Ofițeru AM, Mogoantă SȘ, Roșu GC, Anghelina F, Căpitanescu AN, Opriscan IC, Ionovici N, Mitroi MR, Badea O, Iovănescu G. HPV and Other Risk Factors Involved in Pharyngeal Neoplasm-Clinical and Morphopathological Correlations in the Southwestern Region of Romania. Pathogens 2023; 12:984. [PMID: 37623944 PMCID: PMC10458356 DOI: 10.3390/pathogens12080984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Oropharyngeal squamous cell carcinoma (OPSCC) development is strongly associated with risk factors like smoking, chronic alcohol consumption, and the living environment, but also chronic human papilloma virus (HPV) infection, which can trigger cascade cellular changes leading to a neoplastic transformation. The prevalence of these factors differs among different world regions, and the prevention, diagnosis, and prognosis of OPSCC are highly dependent on them. We performed a retrospective study on 406 patients diagnosed with OPSCC in our region that were classified according to the tumor type, localization and diagnosis stage, demographic characteristics, risk factors, and histological and immunohistochemical features. We found that most of the patients were men from urban areas with a smoking habit, while most of the women in our study were diagnosed with tonsillar OPSCC and had a history of chronic alcoholism. During the immunohistochemical study, we analyzed the tumor immunoreactivity against anti-p16 and anti-HPV antibodies as markers of HPV involvement in tumor progression, as well as the correlation with the percentage of intratumoral nuclei immunomarked with the anti-Ki 67 antibody in serial samples. We observed that the percentage of Ki67-positive nuclei increased proportionally with the presence of intratumoral HPV; thus, active HPV infection leads to an increase in the rate of tumor progression. Our results support the implementation of strategies for OPSCC prevention and early diagnosis and can be a starting point for future studies aiming at adapting surgical and oncological treatment according to the HPV stage for better therapeutic results.
Collapse
Affiliation(s)
- Carmen Aurelia Mogoantă
- ENT Department, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (C.A.M.); (M.S.C.); (F.A.); (A.-N.C.); (M.R.M.)
| | - Mircea Sorin Ciolofan
- ENT Department, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (C.A.M.); (M.S.C.); (F.A.); (A.-N.C.); (M.R.M.)
| | | | | | - Gabriela-Camelia Roșu
- Histology Department, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Florin Anghelina
- ENT Department, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (C.A.M.); (M.S.C.); (F.A.); (A.-N.C.); (M.R.M.)
| | - Alina-Nicoleta Căpitanescu
- ENT Department, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (C.A.M.); (M.S.C.); (F.A.); (A.-N.C.); (M.R.M.)
| | | | - Nina Ionovici
- Department of Occupational Medicine, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Mihaela Roxana Mitroi
- ENT Department, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (C.A.M.); (M.S.C.); (F.A.); (A.-N.C.); (M.R.M.)
| | - Oana Badea
- Department of Modern Languages, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Gheorghe Iovănescu
- ENT Department, Faculty of Medicine, University of Medicine and Pharmacy Victor Babes, 300041 Timisoara, Romania;
| |
Collapse
|
5
|
Xu Y, Xu J, Qiao R, Zhong H, Xia J, Zhong R. Loss of BLK expression as a potential predictor of poor prognosis and immune checkpoint blockade response in NSCLC and contribute to tumor progression. Transl Oncol 2023; 33:101671. [PMID: 37068401 PMCID: PMC10127141 DOI: 10.1016/j.tranon.2023.101671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/16/2023] [Accepted: 04/08/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Immune checkpoint blockade (ICB) has been proved to have significant anti-tumor effect in the clinical treatment of non-small cell lung cancer (NSCLC). Therefore, biomarkers predicting ICB response can provide better treatment for patients with NSCLC. METHODS Differential expression genes (DEGs) were identified by ImmuCellAI database. Copy number alteration (CNA) was analyzed by cBioPortal. The predicted efficiency of 4 genes on cancer immunotherapy was assessed by ROC analysis. The survival value of BLK was analyzed by Kaplan-Meier plotter and Prognoscan analysis. Clinical significance of BLK IHC-TMA score in NSCLC was also explored. The CCK-8 assay, wound healing assay, western blot assay in vitro and subcutaneous xenograft experiments in vivo were used for investigating the functions of BLK. The RNA-sequencing were performed to screen BLK regulated genes and conducted for GO/KEGG enrichment analysis. The transcriptional regulatory factor of BLK promoter region was predicted by ChIP-seq analysis. RESULTS 39 common DEGs between ICB Response (R) group and No Response (NR) group with NSCLC were identified, in which the CNA frequency of BLK deletion (> 6%) was found. The predicted efficiency of BLK on immunotherapy was performed best in NSCLC (AUC>0.7). Low expression of BLK was related to NSCLC with significantly poor prognosis. BLK overexpression can inhibit growth of NSCLC via activating apoptosis pathway, inhibiting the G2M checkpoint and Glycolysis pathway. The enrichment analysis indicated that BLK regulated genes related to oncogenic potential in NSCLC. Besides, BLK expression was inhibited via H3K27me3 modification in A549 and H1299 cells. BLK mRNA level was negatively correlated with methylation and positively correlated with the tumor purity in NSCLC. CONCLUSION Our study provides strong evidence that low expression of BLK may serve as a biomarker for poor prognosis in NSCLC, while response to ICB therapy and contributes to NSCLC tumor progression.
Collapse
Affiliation(s)
- Yingqi Xu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No.241 Huaihai West Road, Shanghai 200030, China.
| | - Jianlin Xu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No.241 Huaihai West Road, Shanghai 200030, China.
| | - Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No.241 Huaihai West Road, Shanghai 200030, China.
| | - Hua Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No.241 Huaihai West Road, Shanghai 200030, China.
| | - Jinjing Xia
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No.241 Huaihai West Road, Shanghai 200030, China.
| | - Runbo Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No.241 Huaihai West Road, Shanghai 200030, China.
| |
Collapse
|
6
|
Sulewska A, Pilz L, Manegold C, Ramlau R, Charkiewicz R, Niklinski J. A Systematic Review of Progress toward Unlocking the Power of Epigenetics in NSCLC: Latest Updates and Perspectives. Cells 2023; 12:cells12060905. [PMID: 36980246 PMCID: PMC10047383 DOI: 10.3390/cells12060905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Epigenetic research has the potential to improve our understanding of the pathogenesis of cancer, specifically non-small-cell lung cancer, and support our efforts to personalize the management of the disease. Epigenetic alterations are expected to have relevance for early detection, diagnosis, outcome prediction, and tumor response to therapy. Additionally, epi-drugs as therapeutic modalities may lead to the recovery of genes delaying tumor growth, thus increasing survival rates, and may be effective against tumors without druggable mutations. Epigenetic changes involve DNA methylation, histone modifications, and the activity of non-coding RNAs, causing gene expression changes and their mutual interactions. This systematic review, based on 110 studies, gives a comprehensive overview of new perspectives on diagnostic (28 studies) and prognostic (25 studies) epigenetic biomarkers, as well as epigenetic treatment options (57 studies) for non-small-cell lung cancer. This paper outlines the crosstalk between epigenetic and genetic factors as well as elucidates clinical contexts including epigenetic treatments, such as dietary supplements and food additives, which serve as anti-carcinogenic compounds and regulators of cellular epigenetics and which are used to reduce toxicity. Furthermore, a future-oriented exploration of epigenetic studies in NSCLC is presented. The findings suggest that additional studies are necessary to comprehend the mechanisms of epigenetic changes and investigate biomarkers, response rates, and tailored combinations of treatments. In the future, epigenetics could have the potential to become an integral part of diagnostics, prognostics, and personalized treatment in NSCLC.
Collapse
Affiliation(s)
- Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Correspondence: (A.S.); (J.N.)
| | - Lothar Pilz
- Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Christian Manegold
- Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Correspondence: (A.S.); (J.N.)
| |
Collapse
|
7
|
Czarnecka-Chrebelska KH, Mukherjee D, Maryanchik SV, Rudzinska-Radecka M. Biological and Genetic Mechanisms of COPD, Its Diagnosis, Treatment, and Relationship with Lung Cancer. Biomedicines 2023; 11. [PMID: 36830984 DOI: 10.3390/biomedicines11020448] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the most prevalent chronic adult diseases, with significant worldwide morbidity and mortality. Although long-term tobacco smoking is a critical risk factor for this global health problem, its molecular mechanisms remain unclear. Several phenomena are thought to be involved in the evolution of emphysema, including airway inflammation, proteinase/anti-proteinase imbalance, oxidative stress, and genetic/epigenetic modifications. Furthermore, COPD is one main risk for lung cancer (LC), the deadliest form of human tumor; formation and chronic inflammation accompanying COPD can be a potential driver of malignancy maturation (0.8-1.7% of COPD cases develop cancer/per year). Recently, the development of more research based on COPD and lung cancer molecular analysis has provided new light for understanding their pathogenesis, improving the diagnosis and treatments, and elucidating many connections between these diseases. Our review emphasizes the biological factors involved in COPD and lung cancer, the advances in their molecular mechanisms' research, and the state of the art of diagnosis and treatments. This work combines many biological and genetic elements into a single whole and strongly links COPD with lung tumor features.
Collapse
|
8
|
Li B, Jiang C, Xu Y, Fan X, Yang L, Zou B, Fan B, Wang L. Genome-wide DNA methylation signature predict clinical benefit of bevacizumab in non-small cell lung cancer. BMC Cancer 2022; 22:828. [PMID: 35906610 PMCID: PMC9338664 DOI: 10.1186/s12885-022-09918-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Background The efficacy of bevacizumab in non-small cell lung cancer (NSCLC) patients is unsatisfactory, and the selection of suitable patients is still challenging. Given the epigenetic modifications can contribute to an aberrant regulation of angiogenesis and microenvironment, we investigated DNA methylation profiles to determine clinical benefit of bevacizumab in NSCLC patients. Methods Genome-wide DNA methylation profiling was performed in NSCLC patients treated with chemotherapy in combination with bevacizumab. Patients were divided into better prognosis group (A group) and inferior prognosis group (B group) based on their survival. The difference of methylation patterns and respective functional enrichment analysis were performed between two groups. Prognostic DNA methylation signature for bevacizumab was established with the least absolute shrinkage and selection operator regression analyses. TISIDB database was further used to infer immunological relationship for prognostic related DNA methylation. Results Twenty patients were included in this study, and significantly distinct methylation patterns were observed between patients with different prognosis. Related genes of different methylation regions were significantly enriched in the biological process of cell projection assembly, neutrophil mediated immunity, and pathway of VEGFA-VEGFR2 signaling pathway, neutrophil degranulation. A 10-gene DNA methylation signature for prognosis prediction was established with the C-index of 0.76. And host genes of signature were found to be related to the abundance of ActCD4, Th1, ActCD8, NKT and neutrophil cells. Conclusion The 10-gene DNA methylation signature could serve as a novel biomarker to predict the clinical benefit of bevacizumab therapy and improve this anti-tumor approach for NSCLC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09918-1.
Collapse
Affiliation(s)
- Butuo Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Chao Jiang
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yiyue Xu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Xinyu Fan
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Linlin Yang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Bing Zou
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Bingjie Fan
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Linlin Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China.
| |
Collapse
|
9
|
Petrovic D, Bodinier B, Dagnino S, Whitaker M, Karimi M, Campanella G, Haugdahl Nøst T, Polidoro S, Palli D, Krogh V, Tumino R, Sacerdote C, Panico S, Lund E, Dugué PA, Giles GG, Severi G, Southey M, Vineis P, Stringhini S, Bochud M, Sandanger TM, Vermeulen RCH, Guida F, Chadeau-Hyam M. Epigenetic mechanisms of lung carcinogenesis involve differentially methylated CpG sites beyond those associated with smoking. Eur J Epidemiol 2022; 37:629-640. [PMID: 35595947 PMCID: PMC9288379 DOI: 10.1007/s10654-022-00877-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/25/2022] [Indexed: 12/24/2022]
Abstract
Smoking-related epigenetic changes have been linked to lung cancer, but the contribution of epigenetic alterations unrelated to smoking remains unclear. We sought for a sparse set of CpG sites predicting lung cancer and explored the role of smoking in these associations. We analysed CpGs in relation to lung cancer in participants from two nested case-control studies, using (LASSO)-penalised regression. We accounted for the effects of smoking using known smoking-related CpGs, and through conditional-independence network. We identified 29 CpGs (8 smoking-related, 21 smoking-unrelated) associated with lung cancer. Models additionally adjusted for Comprehensive Smoking Index-(CSI) selected 1 smoking-related and 49 smoking-unrelated CpGs. Selected CpGs yielded excellent discriminatory performances, outperforming information provided by CSI only. Of the 8 selected smoking-related CpGs, two captured lung cancer-relevant effects of smoking that were missed by CSI. Further, the 50 CpGs identified in the CSI-adjusted model complementarily explained lung cancer risk. These markers may provide further insight into lung cancer carcinogenesis and help improving early identification of high-risk patients.
Collapse
Affiliation(s)
- Dusan Petrovic
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
- Department and Division of Primary Care Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Barbara Bodinier
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Sonia Dagnino
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Matthew Whitaker
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Maryam Karimi
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Bureau de Biostatistique et d'Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Oncostat U1018, Inserm, Équipe Labellisée Ligue Contre Le Cancer, Université Paris-Saclay, Villejuif, France
| | - Gianluca Campanella
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Therese Haugdahl Nøst
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute-ISPO, Florence, Italy
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rosario Tumino
- Hyblean Association for Epidemiological Research, AIRE- ONLUS, Ragusa, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology Città Della Salute e della Scienza University-Hospital, Via Santena 7, 10126, Turin, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Eiliv Lund
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- The Norwegian Cancer Registry, Oslo, Norway
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Gianluca Severi
- Centre for Research in Epidemiology and Population Health, Inserm (Institut National de La Sante Et de a Recherche Medicale), Villejuif, France
| | - Melissa Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Australia
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Silvia Stringhini
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
- Department and Division of Primary Care Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Murielle Bochud
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
| | - Torkjel M Sandanger
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Roel C H Vermeulen
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
- Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht, Utrecht, The Netherlands
| | - Florence Guida
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Group of Genetic Epidemiology, International Agency for Research on Cancer (IARC) - World Health Organization (WHO), Lyon, France
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK.
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
10
|
Liu C, Xiang X, Han S, Lim HY, Li L, Zhang X, Ma Z, Yang L, Guo S, Soo R, Ren B, Wang L, Goh BC. Blood-based liquid biopsy: Insights into early detection and clinical management of lung cancer. Cancer Lett 2022; 524:91-102. [PMID: 34656690 DOI: 10.1016/j.canlet.2021.10.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/22/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022]
Abstract
Currently, early detection of lung cancer relies on the characterisation of images generated from computed tomography (CT). However, lung tissue biopsy, a highly invasive surgical procedure, is required to confirm CT-derived diagnostic results with very high false-positive rates. Hence, a non-invasive or minimally invasive biomarkers is essential to complement the existing low-dose CT (LDCT) for early detection, improve responses to a certain treatment, predict cancer recurrence, and to evaluate prognosis. In the past decade, liquid biopsies (e.g., blood) have been demonstrated to be highly effective for lung cancer biomarker discovery. In this review, the roles of emerging liquid biopsy-derived biomarkers such as circulating nucleic acids, circulating tumour cells (CTCs), long non-coding RNA (lncRNA), and microRNA (miRNA), as well as exosomes, have been highlighted. The advantages and limitations of these blood-based minimally invasive biomarkers have been discussed. Furthermore, the current progress of the identified biomarkers for clinical management of lung cancer has been summarised. Finally, a potential strategy for the early detection of lung cancer, using a combination of LDCT scans and well-validated biomarkers, has been discussed.
Collapse
Affiliation(s)
- Cuiliu Liu
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Xiaoqiang Xiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Shuangqing Han
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Hannah Ying Lim
- Department of Pharmacy, Faculty of Science, National University of Singapore, 117543, Singapore
| | - Lingrui Li
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Xing Zhang
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Zhaowu Ma
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Li Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuliang Guo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ross Soo
- Department of Haematology-Oncology, National University Cancer Institute, 119228, Singapore
| | - Boxu Ren
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China.
| | - Lingzhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore.
| | - Boon Cher Goh
- Department of Haematology-Oncology, National University Cancer Institute, 119228, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
| |
Collapse
|
11
|
Ntzifa A, Londra D, Rampias T, Kotsakis A, Georgoulias V, Lianidou E. DNA Methylation Analysis in Plasma Cell-Free DNA and Paired CTCs of NSCLC Patients before and after Osimertinib Treatment. Cancers (Basel) 2021; 13:cancers13235974. [PMID: 34885084 PMCID: PMC8656722 DOI: 10.3390/cancers13235974] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Osimertinib has been an effective second-line treatment in EGFR mutant NSCLC patients; however, resistance inevitably occurs. DNA methylation has been previously implicated in NSCLC progression and often in therapy resistance, however its distinct role in osimertinib resistance is not elucidated as yet. In the present study, we directly compared DNA methylation of nine selected genes (RASSF1A, RASSF10, APC, WIF-1, BRMS1, SLFN11, RARβ, SHISA3, and FOXA1) in plasma-cfDNA and paired CTCs of NSCLC patients who were longitudinally monitored during osimertinib treatment. Peripheral blood (PB) from 42 NSCLC patients was obtained at two time points: (a) baseline: before treatment with osimertinib and (b) at progression of disease (PD). DNA methylation of the selected genes was detected in plasma-cfDNA (n = 80) and in paired CTCs (n = 74). Direct comparison of DNA methylation of six genes between plasma-cfDNA and paired CTC samples (n = 70) revealed a low concordance, indicating that CTCs and cfDNA give complementary information. DNA methylation analysis of plasma-cfDNA and CTCs indicated that when at least one of these genes was methylated there was a statistically significant increase at PD compared to baseline (p = 0.031). For the first time, DNA methylation analysis in plasma-cfDNA and paired CTCs of NSCLC patients during osimertinib therapy indicated that DNA methylation of these genes could be a possible resistance mechanism.
Collapse
Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.N.); (D.L.)
| | - Dora Londra
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.N.); (D.L.)
| | - Theodoros Rampias
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | - Athanasios Kotsakis
- Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece;
| | - Vassilis Georgoulias
- Department of Medical Oncology, Hellenic Oncology Research Group (HORG), 11471 Athens, Greece;
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece; (A.N.); (D.L.)
- Correspondence: ; Tel.: +30-210-727-4311
| |
Collapse
|
12
|
Ao C, Gao L, Yu L. Research progress in predicting DNA methylation modifications and the relation with human diseases. Curr Med Chem 2021; 29:822-836. [PMID: 34533438 DOI: 10.2174/0929867328666210917115733] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/05/2021] [Accepted: 07/11/2021] [Indexed: 11/22/2022]
Abstract
DNA methylation is an important mode of regulation in epigenetic mechanisms, and it is one of the research foci in the field of epigenetics. DNA methylation modification affects a series of biological processes, such as eukaryotic cell growth, differentiation and transformation mechanisms, by regulating gene expression. In this review, we systematically summarized the DNA methylation databases, prediction tools for DNA methylation modification, machine learning algorithms for predicting DNA methylation modification, and the relationship between DNA methylation modification and diseases such as hypertension, Alzheimer's disease, diabetic nephropathy, and cancer. An in-depth understanding of DNA methylation mechanisms can promote accurate prediction of DNA methylation modifications and the treatment and diagnosis of related diseases.
Collapse
Affiliation(s)
- Chunyan Ao
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xi'an, China
| |
Collapse
|
13
|
Kang C, Wang D, Zhang X, Wang L, Wang F, Chen J. Construction and Validation of a Lung Cancer Diagnostic Model Based on 6-Gene Methylation Frequency in Blood, Clinical Features, and Serum Tumor Markers. Comput Math Methods Med 2021; 2021:9987067. [PMID: 34257703 DOI: 10.1155/2021/9987067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/02/2021] [Indexed: 12/25/2022]
Abstract
Lung cancer has a high mortality rate. Promoting early diagnosis and screening of lung cancer is the most effective way to enhance the survival rate of lung cancer patients. Through computer technology, a comprehensive evaluation of genetic testing results and basic clinical information of lung cancer patients could effectively diagnose early lung cancer and indicate cancer risks. This study retrospectively collected 70 pairs of lung cancer tissue samples and normal human tissue samples. The methylation frequencies of 6 genes (FHIT, p16, MGMT, RASSF1A, APC, DAPK) in lung cancer patients, the basic clinical information, and tumor marker levels of these patients were analyzed. Then, the python package "sklearn" was employed to build a support vector machine (SVM) classifier which performed 10-fold cross-validation to construct diagnostic models that could identify lung cancer risk of suspected cases. Receiver operation characteristic (ROC) curves were drawn, and the performance of the combined diagnostic model based on several factors (clinical information, tumor marker level, and methylation frequency of 6 genes in blood) was shown to be better than that of models with only one pathological feature. The AUC value of the combined model was 0.963, and the sensitivity, specificity, and accuracy were 0.900, 0.971, and 0.936, respectively. The above results revealed that the diagnostic model based on these features was highly reliable, which could screen and diagnose suspected early lung cancer patients, contributing to increasing diagnosis rate and survival rate of lung cancer patients.
Collapse
|
14
|
Lianidou E. Detection and relevance of epigenetic markers on ctDNA: recent advances and future outlook. Mol Oncol 2021; 15:1683-1700. [PMID: 33942482 PMCID: PMC8169441 DOI: 10.1002/1878-0261.12978] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy, a minimally invasive approach, is a highly powerful clinical tool for the real-time follow-up of cancer and overcomes many limitations of tissue biopsies. Epigenetic alterations have a high potential to provide a valuable source of innovative biomarkers for cancer, owing to their stability, frequency, and noninvasive accessibility in bodily fluids. Numerous DNA methylation markers are now tested in circulating tumor DNA (ctDNA) as potential biomarkers, in various types of cancer. DNA methylation in combination with liquid biopsy is very powerful in identifying circulating epigenetic biomarkers of clinical importance. Blood-based epigenetic biomarkers have a high potential for early detection of cancer since DNA methylation in plasma can be detected early during cancer pathogenesis. In this review, we summarize the latest findings on DNA methylation markers in ctDNA for early detection, prognosis, minimal residual disease, risk of relapse, treatment selection, and resistance, for breast, prostate, lung, and colorectal cancer.
Collapse
Affiliation(s)
- Evi Lianidou
- Analysis of Circulating Tumor CellsLaboratory of Analytical ChemistryDepartment of ChemistryUniversity of AthensGreece
| |
Collapse
|
15
|
Abstract
The epigenetic landscape, which in part includes DNA methylation, chromatin organization, histone modifications, and noncoding RNA regulation, greatly contributes to the heterogeneity that makes developing effective therapies for lung cancer challenging. This review will provide an overview of the epigenetic alterations that have been implicated in all aspects of cancer pathogenesis and progression as well as summarize clinical applications for targeting epigenetics in the treatment of lung cancer.
Collapse
Affiliation(s)
- Yvonne L Chao
- Department of Medicine, Division of Hematology and Oncology, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| | - Chad V Pecot
- Department of Medicine, Division of Hematology and Oncology, University of North Carolina, Chapel Hill, North Carolina 27514, USA
| |
Collapse
|
16
|
Freitas C, Sousa C, Machado F, Serino M, Santos V, Cruz-Martins N, Teixeira A, Cunha A, Pereira T, Oliveira HP, Costa JL, Hespanhol V. The Role of Liquid Biopsy in Early Diagnosis of Lung Cancer. Front Oncol 2021; 11:634316. [PMID: 33937034 PMCID: PMC8085425 DOI: 10.3389/fonc.2021.634316] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsy is an emerging technology with a potential role in the screening and early detection of lung cancer. Several liquid biopsy-derived biomarkers have been identified and are currently under ongoing investigation. In this article, we review the available data on the use of circulating biomarkers for the early detection of lung cancer, focusing on the circulating tumor cells, circulating cell-free DNA, circulating micro-RNAs, tumor-derived exosomes, and tumor-educated platelets, providing an overview of future potential applicability in the clinical practice. While several biomarkers have shown exciting results, diagnostic performance and clinical applicability is still limited. The combination of different biomarkers, as well as their combination with other diagnostic tools show great promise, although further research is still required to define and validate the role of liquid biopsies in clinical practice.
Collapse
Affiliation(s)
- Cláudia Freitas
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Catarina Sousa
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Francisco Machado
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Mariana Serino
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Vanessa Santos
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal
- Laboratory of Neuropsychophysiology, Faculty of Psychology and Education Sciences, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - Armando Teixeira
- Institute for Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- Faculty of Engineering, University of Porto, Porto, Portugal
| | - António Cunha
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
- Department of Engineering, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Tania Pereira
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
| | - Hélder P. Oliveira
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - José Luís Costa
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Venceslau Hespanhol
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| |
Collapse
|
17
|
Fu Y, Zhuang X, Xia X, Li X, Xiao K, Liu X. Correlation Between Promoter Hypomethylation and Increased Expression of Syncytin-1 in Non-Small Cell Lung Cancer. Int J Gen Med 2021; 14:957-965. [PMID: 33776474 PMCID: PMC7989540 DOI: 10.2147/ijgm.s294392] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/19/2021] [Indexed: 12/15/2022] Open
Abstract
Introduction Syncytin-1 is a human endogenous retroviral (HERVW) envelope protein, which has been implicated in trophoblast and cancer cell fusions as well as in immunomodulatory functions. We investigated syncytin-1 expression and promoter methylation in non-small cell lung cancer (NSCLC) and the adjacent, para-carcinoma tissues. In addition, the correlation to patient survival differentiation of between 5-year survival and death group was analyzed. Methods Survival ratio was calculated by Kaplan-Meier survival curve. Death risk assessment was executed by Cox risk regression model. The 5ʹ-LTR methylation level of HERVW promoter was detected by EpiTYPER method. Results Syncytin-1 expression in NSCLC tissue was found to be significantly higher than in para-carcinoma tissues. Moreover, the 5-year survival group has a lower syncytin-1 expression than the death group. Clinical stage and the percentage of syncytin-1 positive cells were top risk factors according to Cox ratio risk regression model analysis. While the methylation level of the 5ʹ-LTR in HERVW gene promoter was relatively lower in NSCLC than para-carcinoma tissues, the methylation status of a CpG-2 site overlapping the Oct-1 binding site was found to be an important element potentially involved in the epigenetic regulation of HERVW gene expression. Conclusion These findings suggest that syncytin-1 could be a biomarker for the diagnosis/prognosis of NSCLC, and further studies are required to elucidate the exact role of syncytin-1 in the development of NSCLC as well as the underlying molecular mechanism for syncytin-1 function and regulation.
Collapse
Affiliation(s)
- Yang Fu
- Department of Reproductive Medicine Center, Jinan Maternity and Child Care Hospital, Jinan, 250001, People's Republic of China
| | - Xuewei Zhuang
- Department of Clinical Laboratory Medicine, Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250031, People's Republic of China.,Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, People's Republic of China
| | - Xiyan Xia
- Department of Microbial Immune, Jinan Vocational College of Nursing, Jinan, 250012, People's Republic of China
| | - Xiaohui Li
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, People's Republic of China
| | - Ke Xiao
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, People's Republic of China
| | - Xiaojing Liu
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, People's Republic of China
| |
Collapse
|
18
|
Su SF, Liu CH, Cheng CL, Ho CC, Yang TY, Chen KC, Hsu KH, Tseng JS, Chen HW, Chang GC, Yu SL, Li KC. Genome-Wide Epigenetic Landscape of Lung Adenocarcinoma Links HOXB9 DNA Methylation to Intrinsic EGFR-TKI Resistance and Heterogeneous Responses. JCO Precis Oncol 2021; 5:PO.20.00151. [PMID: 34036228 PMCID: PMC8140798 DOI: 10.1200/po.20.00151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/15/2020] [Accepted: 01/08/2021] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) show efficacy in treating patients with lung adenocarcinoma with EGFR-activating mutations. However, a significant subset of targeted patients fail to respond. Unlike acquired resistance (AR), intrinsic resistance (IR) remains poorly understood. We investigated whether epigenomic factors contribute to patient-to-patient heterogeneity in the EGFR-TKI response and aimed to characterize the IR subpopulation that obtains no benefit from EGFR-TKIs. PATIENTS AND METHODS We conducted genome-wide DNA methylation profiling of 79 tumors sampled from patients with advanced lung adenocarcinoma before they received EGFR-TKI treatment and analyzed the patient responses. Pyrosequencing was performed in a validation cohort of 163 patients with EGFR-activating mutations. RESULTS A DNA methylation landscape of 216 CpG sites with differential methylation was established to elucidate the association of DNA methylation with the characteristics and EGFR-TKI response status of the patients. Functional analysis of 37 transcription-repressive sites identified the enrichment of transcription factors, notably homeobox (HOX) genes. DNA methylation of HOXB9 (cg13643585) in the enhancer region yielded 88% sensitivity for predicting drug response (odds ratio [OR], 6.64; 95% CI, 1.98 to 25.23; P = .0009). Pyrosequencing validated that HOXB9 gained methylation in patients with a poor EGFR-TKI response (OR, 3.06; 95% CI, 1.13 to 8.19; P = .019). CONCLUSION Our data suggest that homeobox DNA methylation could be a novel tumor cellular state that can aid the precise categorization of tumor heterogeneity in the study of IR to EGFR-TKIs. We identified, for the first time, an epigenomic factor that can potentially complement DNA mutation status in discriminating patients with lung adenocarcinoma who are less likely to benefit from EGFR-TKI treatment, thereby leading to improved patient management in precision medicine.
Collapse
Affiliation(s)
- Sheng-Fang Su
- Institute of Statistical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Oncology, National Taiwan University, College of Medicine, Taipei, Taiwan.,YongLin Institute of Health, YongLin Scholar, National Taiwan University, Taipei, Taiwan
| | - Chia-Hsin Liu
- Institute of Statistical Sciences, Academia Sinica, Taipei, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Chiou-Ling Cheng
- NTU Centers for Genomic and Precision Medicine, National Taiwan University, College of Medicine, Taipei, Taiwan
| | - Chao-Chi Ho
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University, College of Medicine, Taipei, Taiwan
| | - Tsung-Ying Yang
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Kun-Chieh Chen
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Applied Chemistry, National Chi Nan University, Nantou, Taiwan
| | - Kuo-Hsuan Hsu
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.,Internal Medicine, Division of Critical Care and Respiratory Therapy, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jeng-Sen Tseng
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Huei-Wen Chen
- Graduate Institute of Toxicology, National Taiwan University, College of Medicine, Taipei, Taiwan
| | - Gee-Chen Chang
- Department of Internal Medicine, Division of Chest Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan.,Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Sung-Liang Yu
- NTU Centers for Genomic and Precision Medicine, National Taiwan University, College of Medicine, Taipei, Taiwan.,Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, College of Medicine, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pathology and Graduate Institute of Pathology, National Taiwan University, College of Medicine, Taipei, Taiwan.,Institute of Medical Device and Imaging, National Taiwan University, College of Medicine, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University, College of Medicine, Taipei, Taiwan
| | - Ker-Chau Li
- Institute of Statistical Sciences, Academia Sinica, Taipei, Taiwan.,Department of Statistics, University of California, Los Angeles, Los Angeles, CA
| |
Collapse
|
19
|
Mastoraki S, Balgkouranidou I, Tsaroucha E, Klinakis A, Georgoulias V, Lianidou E. KMT2C promoter methylation in plasma-circulating tumor DNA is a prognostic biomarker in non-small cell lung cancer. Mol Oncol 2020; 15:2412-2422. [PMID: 33159839 PMCID: PMC8410531 DOI: 10.1002/1878-0261.12848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/26/2020] [Accepted: 11/06/2020] [Indexed: 01/08/2023] Open
Abstract
MLL3 histone methyltransferase, encoded by the KMT2C gene, is a tumor suppressor that has an essential role in cell‐type‐specific gene expression. We evaluated the prognostic significance of KMT2C promoter methylation as a circulating epigenetic biomarker in plasma cell‐free DNA (cfDNA) in non‐small cell lung cancer (NSCLC). We examined the methylation status of KMT2C promoter using a novel highly specific and sensitive real‐time methylation‐specific PCR (MSP) assay in (a) operable NSCLC: 48 fresh‐frozen NSCLC tissues, their corresponding adjacent non‐neoplastic tissues, and 48 matched plasma samples; (b) metastatic NSCLC: 91 plasma samples; and (c) 60 plasma samples from healthy donors (HD). KMT2C promoter methylation in plasma cfDNA was detected in 7/48 (14.6%) patients with operable and in 18/91 (19.8%) patients with advanced NSCLC but in none (0/60, 0%) of the plasma samples from HD. In operable NSCLC, in corresponding adjacent non‐neoplastic tissue samples, KMT2C promoter methylation was detected in 3/48 (6.3%) cases. Moreover, in operable NSCLC, KMT2C promoter methylation in plasma cfDNA was related to reduced disease‐free survival (ΗR = 0.239; P = 0.001) and worse overall survival (OS; HR = 0.342, P = 0.023). In metastatic NSCLC, KMT2C promoter methylation in plasma cfDNA was related to worse progression‐free survival (PFS; HR = 0.431; P = 0.005) and worse OS (HR = 0.306; P < 0.001). Our data strongly suggest that the detection of KMT2C promoter methylation in plasma cfDNA predicts poor prognosis in patients with both operable and metastatic NSCLCs. KMT2C promoter methylation in plasma cfDNA therefore merits further evaluation and validation as a noninvasive circulating epigenetic biomarker.
Collapse
Affiliation(s)
- Sofia Mastoraki
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Greece
| | - Ioanna Balgkouranidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Greece
| | - Emily Tsaroucha
- 8th Department of Pulmonary Diseases, 'Sotiria' General Hospital for Chest Diseases, Athens, Greece
| | | | | | - Evi Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Greece
| |
Collapse
|
20
|
Abstract
Lung cancer is the most common cancer and the leading cause of cancer-related morbidity and mortality worldwide. As early symptoms of lung cancer are minimal and non-specific, many patients are diagnosed at an advanced stage. Despite a concerted effort to diagnose lung cancer early, no biomarkers that can be used for lung cancer screening and prognosis prediction have been established so far. As global DNA demethylation and gene-specific promoter DNA methylation are present in lung cancer, DNA methylation biomarkers have become a major area of research as potential alternative diagnostic methods to detect lung cancer at an early stage. This review summarizes the emerging DNA methylation changes in lung cancer tumorigenesis, focusing on biomarkers for early detection and their potential clinical applications in lung cancer.
Collapse
Affiliation(s)
- Yoonki Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, South Korea
| |
Collapse
|
21
|
Abstract
Lung carcinoma is one of the most common human cancers and is estimated to have an incidence of approximately 2 million new cases per year worldwide with a 20% mortality rate. Lung cancer represents one of the leading causes of cancer related death in the world. Of all cancer types to affect the pulmonary system, non-small cell lung carcinoma comprises approximately 80-85% of all tumors. In the past few decades cytogenetic and advanced molecular techniques have helped define the genomic landscape of lung cancer, and in the process, revolutionized the clinical management and treatment of patients with advanced non-small cell lung cancer. The discovery of specific, recurrent genetic abnormalities has led to the development of targeted therapies that have extended the life expectancy of patients who develop carcinoma of the lungs. Patients are now routinely treated with targeted therapies based on identifiable molecular alterations or other predictive biomarkers which has led to a revolution in the field of pulmonary pathology and oncology. Numerous different testing modalities, with various strengths and limitations now exist which complicate diagnostic algorithms, however recently emerging consensus guidelines and recommendations have begun to standardize the way to approach diagnostic testing of lung carcinoma. Herein we provide an overview of the molecular genetic landscape of non-small cell lung carcinoma, with attention to those clinically relevant alterations which drive management, as well as review current recommendations for molecular testing.
Collapse
Affiliation(s)
- David Ilan Suster
- Department of Pathology, Rutgers University, New Jersey Medical School, Newark, NJ, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
22
|
Kim JY, Choi JK, Jung H. Genome-wide methylation patterns predict clinical benefit of immunotherapy in lung cancer. Clin Epigenetics 2020; 12:119. [PMID: 32762727 PMCID: PMC7410160 DOI: 10.1186/s13148-020-00907-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023] Open
Abstract
Background It is crucial to unravel molecular determinants of responses to immune checkpoint blockade (ICB) therapy because only a small subset of advanced non-small cell lung cancer (NSCLC) patients responds to ICB therapy. Previous studies were concentrated on genomic and transcriptomic markers (e.g., mutation burden and immune gene expression). However, these markers are not sufficient to accurately predict a response to ICB therapy. Results Here, we analyzed DNA methylomes of 141 advanced NSCLC samples subjected to ICB therapy (i.e., anti-programmed death-1) from two independent cohorts (60 and 81 patients from our and IDIBELL cohorts). Integrative analysis of patients with matched transcriptome data in our cohort (n = 28) at pathway level revealed significant overlaps between promoter hypermethylation and transcriptional repression in nonresponders relative to responders. Fifteen immune-related pathways, including interferon signaling, were identified to be enriched for both hypermethylation and repression. We built a reliable prognostic risk model based on eight genes using LASSO model and successfully validated the model in independent cohorts. Furthermore, we found 30 survival-associated molecular interaction networks, in which two or three hypermethylated genes showed significant mutual exclusion across nonresponders. Conclusions Our study demonstrates that methylation patterns can provide insight into molecular determinants underlying the clinical benefit of ICB therapy.
Collapse
Affiliation(s)
- Jeong Yeon Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea. .,Penta Medix Co., Ltd., Seongnam-si, Gyeongi-do, 13449, Republic of Korea.
| | - Hyunchul Jung
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea. .,Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK.
| |
Collapse
|
23
|
Noguera-Uclés JF, Boyero L, Salinas A, Cordero Varela JA, Benedetti JC, Bernabé-Caro R, Sánchez-Gastaldo A, Alonso M, Paz-Ares L, Molina-Pinelo S. The Roles of Imprinted SLC22A18 and SLC22A18AS Gene Overexpression Caused by Promoter CpG Island Hypomethylation as Diagnostic and Prognostic Biomarkers for Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2020; 12:cancers12082075. [PMID: 32726996 PMCID: PMC7466018 DOI: 10.3390/cancers12082075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
Genomic imprinting is a process that involves one gene copy turned-off in a parent-of-origin-dependent manner. The regulation of imprinted genes is broadly dependent on promoter methylation marks, which are frequently associated with both oncogenes and tumor suppressors. The purpose of this study was to assess the DNA methylation patterns of the imprinted solute-carrier family 22 member 18 (SLC22A18) and SLC22A18 antisense (SLC22A18AS) genes in non-small cell lung cancer (NSCLC) patients to study their relevance to the disease. We found that both genes were hypomethylated in adenocarcinoma and squamous cell carcinoma patients. Due to this imprinting loss, SLC22A18 and SLC22A18AS were found to be overexpressed in NSCLC tissues, which is significantly more evident in lung adenocarcinoma patients. These results were validated through analyses of public databases of NSCLC patients. The reversed gene profile of both genes was achieved in vitro by treatment with ademetionine. We then showed that high SLC22A18 and SLC22A18AS expression levels were significantly associated with worsening disease progression. In addition, low levels of SLC22A18AS were also correlated with better overall survival for lung adenocarcinoma patients. We found that SLC22A18 and SLC22A18AS knockdown inhibits cell proliferation in vitro. All these results suggest that both genes may be useful as diagnostic and prognostic biomarkers in NSCLC, revealing novel therapeutic opportunities.
Collapse
Affiliation(s)
- José Francisco Noguera-Uclés
- Institute of Biomedicine of Seville (IBiS) (HUVR, CSIC, Universidad de Sevilla), 41013 Seville, Spain; (J.F.N.-U.); (L.B.); (A.S.); (J.A.C.V.); (J.C.B.); (R.B.-C.); (A.S.-G.); (M.A.)
| | - Laura Boyero
- Institute of Biomedicine of Seville (IBiS) (HUVR, CSIC, Universidad de Sevilla), 41013 Seville, Spain; (J.F.N.-U.); (L.B.); (A.S.); (J.A.C.V.); (J.C.B.); (R.B.-C.); (A.S.-G.); (M.A.)
| | - Ana Salinas
- Institute of Biomedicine of Seville (IBiS) (HUVR, CSIC, Universidad de Sevilla), 41013 Seville, Spain; (J.F.N.-U.); (L.B.); (A.S.); (J.A.C.V.); (J.C.B.); (R.B.-C.); (A.S.-G.); (M.A.)
| | - Juan Antonio Cordero Varela
- Institute of Biomedicine of Seville (IBiS) (HUVR, CSIC, Universidad de Sevilla), 41013 Seville, Spain; (J.F.N.-U.); (L.B.); (A.S.); (J.A.C.V.); (J.C.B.); (R.B.-C.); (A.S.-G.); (M.A.)
| | - Johana Cristina Benedetti
- Institute of Biomedicine of Seville (IBiS) (HUVR, CSIC, Universidad de Sevilla), 41013 Seville, Spain; (J.F.N.-U.); (L.B.); (A.S.); (J.A.C.V.); (J.C.B.); (R.B.-C.); (A.S.-G.); (M.A.)
- Medical Oncology Department, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain
| | - Reyes Bernabé-Caro
- Institute of Biomedicine of Seville (IBiS) (HUVR, CSIC, Universidad de Sevilla), 41013 Seville, Spain; (J.F.N.-U.); (L.B.); (A.S.); (J.A.C.V.); (J.C.B.); (R.B.-C.); (A.S.-G.); (M.A.)
- Medical Oncology Department, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain
| | - Amparo Sánchez-Gastaldo
- Institute of Biomedicine of Seville (IBiS) (HUVR, CSIC, Universidad de Sevilla), 41013 Seville, Spain; (J.F.N.-U.); (L.B.); (A.S.); (J.A.C.V.); (J.C.B.); (R.B.-C.); (A.S.-G.); (M.A.)
- Medical Oncology Department, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain
| | - Miriam Alonso
- Institute of Biomedicine of Seville (IBiS) (HUVR, CSIC, Universidad de Sevilla), 41013 Seville, Spain; (J.F.N.-U.); (L.B.); (A.S.); (J.A.C.V.); (J.C.B.); (R.B.-C.); (A.S.-G.); (M.A.)
- Medical Oncology Department, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain
| | - Luis Paz-Ares
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
- H12O-CNIO Lung Cancer Clinical Research Unit, Instituto de Investigación Hospital 12 de Octubre & Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
- Medical Oncology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Sonia Molina-Pinelo
- Institute of Biomedicine of Seville (IBiS) (HUVR, CSIC, Universidad de Sevilla), 41013 Seville, Spain; (J.F.N.-U.); (L.B.); (A.S.); (J.A.C.V.); (J.C.B.); (R.B.-C.); (A.S.-G.); (M.A.)
- Medical Oncology Department, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
- Correspondence:
| |
Collapse
|
24
|
Liu Y, Mao C, Wang M, Liu N, Ouyang L, Liu S, Tang H, Cao Y, Liu S, Wang X, Xiao D, Chen C, Shi Y, Yan Q, Tao Y. Cancer progression is mediated by proline catabolism in non-small cell lung cancer. Oncogene 2020; 39:2358-76. [PMID: 31911619 DOI: 10.1038/s41388-019-1151-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 12/05/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022]
Abstract
Dysregulated metabolism contributes to cancer initiation and progression, but the key drivers of these pathways are just being discovered. Here, we report a critical role for proline catabolism in non-small cell lung cancer (NSCLC). Proline dehydrogenase (PRODH) is activated to reduce proline levels by the chromatin remodeling factor lymphoid-specific helicase (LSH), an epigenetic driver of NSCLC. PRODH promotes NSCLC tumorigenesis by inducing epithelial to mesenchymal transition (EMT) and IKKα-dependent inflammatory genes, including CXCL1, LCN2, and IL17C. Consistently, proline addition promotes the expression of these inflammatory genes, as well as EMT, tumor cell proliferation, and migration in vitro and tumor growth in vivo, while the depletion or inhibition of PRODH blocks these phenotypes. In summary, we reveal an essential metabolic pathway amenable to targeting in NSCLC.
Collapse
|
25
|
Advani S, Braithwaite D. Optimizing selection of candidates for lung cancer screening: role of comorbidity, frailty and life expectancy. Transl Lung Cancer Res 2019; 8:S454-S459. [PMID: 32038937 PMCID: PMC6987350 DOI: 10.21037/tlcr.2019.10.03] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/23/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Shailesh Advani
- Cancer Prevention and Control Program, Department of Oncology, Georgetown University School of Medicine, Washington, DC, USA
- Social Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dejana Braithwaite
- Cancer Prevention and Control Program, Department of Oncology, Georgetown University School of Medicine, Washington, DC, USA
| |
Collapse
|
26
|
Xiao Z, Chen X, Lu X, Zhong X, Ling Y. Accuracy Evaluation of Circular RNA in Diagnosing Lung Cancer in a Chinese Population. Dis Markers 2019; 2019:7485389. [PMID: 31781305 PMCID: PMC6855014 DOI: 10.1155/2019/7485389] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/17/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022]
Abstract
Circular RNA (circRNA) is a class of recently discovered noncoding RNA. circRNAs can be used as a potent noninvasive biological marker of cancer owing to their varying expression levels among different cancers. This meta-analysis was performed to assess the accuracy of circRNAs in diagnosing lung cancer. A total of eight studies identified through searching the PubMed, Web of Science, Cochrane Library, and Embase from inception to March 20, 2019 were eligible for this meta-analysis. The pooled sensitivity, specificity, positive likelihood ratios, negative likelihood ratios, and diagnostic odds ratio were 0.77 (95% confidence interval (CI): 0.73-0.80; I 2 = 8.98%), 0.76 (95% CI: 0.69-0.82; I 2 = 63.12%), 3.17 (95% CI: 2.43-4.14; I 2 = 33.18%), 0.31 (95% CI: 0.26-0.37; I 2 = 20.36%), and 10.26 (95% CI: 6.87-15.31; I 2 = 97.18%), respectively. The area under the receiver operating characteristic curve was 0.78 (95% CI: 0.74-0.81). The study confirmed the use of circRNAs in diagnosing lung cancer in a Chinese population.
Collapse
Affiliation(s)
- Zhihao Xiao
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Xinglei Chen
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Xiaodan Lu
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Xuexin Zhong
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Yihui Ling
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
27
|
Leiro-Fernandez V, De Chiara L, Rodríguez-Girondo M, Botana-Rial M, Valverde D, Núñez-Delgado M, Fernández-Villar A. Methylation Assessment for the Prediction of Malignancy in Mediastinal Adenopathies Obtained by Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration in Patients with Lung Cancer. Cancers (Basel) 2019; 11:cancers11101408. [PMID: 31547177 PMCID: PMC6826358 DOI: 10.3390/cancers11101408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022] Open
Abstract
The evaluation of mediastinal lymph nodes is critical for the correct staging of patients with lung cancer (LC). Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive technique for mediastinal staging, though unfortunately lymph node micrometastasis is often missed by cytological analysis. The aim of this study was to evaluate the predictive capacity of methylation biomarkers and provide a classification rule for predicting malignancy in false negative EBUS-TBNA samples. The study included 112 patients with a new or suspected diagnosis of LC that were referred to EBUS-TBNA. Methylation of p16/INK4a, MGMT, SHOX2, E-cadherin, DLEC1, and RASSF1A was quantified by nested methylation-specific qPCR in 218 EBUS-TBNA lymph node samples. Cross-validated linear regression models were evaluated to predict malignancy. According to EBUS-TBNA and final diagnosis, 90 samples were true positives for malignancy, 110 were true negatives, and 18 were false negatives. MGMT, SHOX2, and E-cadherin were the methylation markers that better predicted malignancy. The model including sex, age, short axis diameter and standard uptake value of adenopathy, and SHOX2 showed 82.7% cross-validated sensitivity and 82.4% specificity for the detection of malignant lymphadenopathies among negative cytology samples. Our results suggest that the predictive model approach proposed can complement EBUS-TBNA for mediastinal staging.
Collapse
Affiliation(s)
- Virginia Leiro-Fernandez
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
- Correspondence: (L.D.C.); (V.L.-F.)
| | - Loretta De Chiara
- Department of Biochemistry, Genetics and Immunology, Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain;
- Correspondence: (L.D.C.); (V.L.-F.)
| | - Mar Rodríguez-Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
- SiDOR Research Group, Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
| | - Maribel Botana-Rial
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
| | - Diana Valverde
- Department of Biochemistry, Genetics and Immunology, Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain;
| | - Manuel Núñez-Delgado
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
| | - Alberto Fernández-Villar
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
| |
Collapse
|
28
|
Yang G, Xiao Z, Tang C, Deng Y, Huang H, He Z. Recent advances in biosensor for detection of lung cancer biomarkers. Biosens Bioelectron 2019; 141:111416. [DOI: 10.1016/j.bios.2019.111416] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/28/2019] [Accepted: 06/04/2019] [Indexed: 12/20/2022]
|
29
|
Hong Y, Choi HM, Cheong HS, Shin HD, Choi CM, Kim WJ. Epigenome-Wide Association Analysis of Differentially Methylated Signals in Blood Samples of Patients with Non-Small-Cell Lung Cancer. J Clin Med 2019; 8:jcm8091307. [PMID: 31450665 PMCID: PMC6780065 DOI: 10.3390/jcm8091307] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is a common form of cancer and the leading cause of cancer-related deaths worldwide. Early diagnosis using noninvasive biomarkers may play an important role in increasing the survival rate of patients with lung cancer. Biomarkers of DNA methylation in blood samples may improve the early diagnosis of lung cancer. Here, we used peripheral blood samples obtained from 150 patients diagnosed with non-small-cell lung cancer (NSCLC) and 150 healthy controls. The latter were selected by frequency matching with the 150 patients with NSCLC, based on age, sex, and smoking status. Genome-wide methylation profiles were obtained using a MethylationEPIC BeadChip Kit, which covers the 850k bp cytosine–phosphate–guanine site. This analysis showed two significant differentially methylated changes (cg12169243 [DPH6] and cg25429010 [IMP3]) associated with NSCLC in current smokers, six changes (cg09245319, cg17183999 [USP7], cg06366994 [CPE], cg24992236 [MEG9], cg22144719, and cg22448179 [epidermal growth factor receptor]) associated with epidermal growth factor receptor mutation in patients with adenocarcinoma, and four changes (cg25021476 [RSL24D1], cg04989085 [FAM113B], cg20905681 [CKAP4], and cg26379694) associated with advanced-stage NSCLC compared with stage I NSCLC. The validation of these DNA methylation changes and further research on the related genes may help develop easily accessible biomarkers for the early diagnosis or prognosis of NSCLC.
Collapse
Affiliation(s)
- Yoonki Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea
| | - Hye-Mi Choi
- Division of Biomedical Convergence, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, 04107, Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, 04107, Korea
- Department of Life Science, Sogang University, Seoul 121-742, Korea
| | - Chang Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea.
| | - Woo Jin Kim
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 200-701, Korea.
| |
Collapse
|
30
|
Yeh SJ, Chang CA, Li CW, Wang LHC, Chen BS. Comparing progression molecular mechanisms between lung adenocarcinoma and lung squamous cell carcinoma based on genetic and epigenetic networks: big data mining and genome-wide systems identification. Oncotarget 2019; 10:3760-3806. [PMID: 31217907 PMCID: PMC6557199 DOI: 10.18632/oncotarget.26940] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) is the predominant type of lung cancer in the world. Lung adenocarcinoma (LADC) and lung squamous cell carcinoma (LSCC) are subtypes of NSCLC. We usually regard them as different disease due to their unique molecular characteristics, distinct cells of origin and dissimilar clinical response. However, the differences of genetic and epigenetic progression mechanism between LADC and LSCC are complicated to analyze. Therefore, we applied systems biology approaches and big databases mining to construct genetic and epigenetic networks (GENs) with next-generation sequencing data of LADC and LSCC. In order to obtain the real GENs, system identification and system order detection are conducted on gene regulatory networks (GRNs) and protein-protein interaction networks (PPINs) for each stage of LADC and LSCC. The core GENs were extracted via principal network projection (PNP). Based on the ranking of projection values, we got the core pathways in respect of KEGG pathway. Compared with the core pathways, we found significant differences between microenvironments, dysregulations of miRNAs, epigenetic modifications on certain signaling transduction proteins and target genes in each stage of LADC and LSCC. Finally, we proposed six genetic and epigenetic multiple-molecule drugs to target essential biomarkers in each progression stage of LADC and LSCC, respectively.
Collapse
Affiliation(s)
- Shan-Ju Yeh
- Laboratory of Automatic Control, Signaling Processing, and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chien-An Chang
- Laboratory of Automatic Control, Signaling Processing, and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Cheng-Wei Li
- Laboratory of Automatic Control, Signaling Processing, and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Lily Hui-Ching Wang
- Department of Medical Science, Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Bor-Sen Chen
- Laboratory of Automatic Control, Signaling Processing, and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.,Department of Electrical Engineering, Yuan Ze University, Chungli 32003, Taiwan
| |
Collapse
|
31
|
Calabrese F, Lunardi F, Pezzuto F, Fortarezza F, Vuljan SE, Marquette C, Hofman P. Are There New Biomarkers in Tissue and Liquid Biopsies for the Early Detection of Non-Small Cell Lung Cancer? J Clin Med 2019; 8:jcm8030414. [PMID: 30917582 PMCID: PMC6463117 DOI: 10.3390/jcm8030414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/11/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is one of the most lethal malignancies worldwide, mainly due to its late diagnoses. The detection of molecular markers on samples provided from routine bronchoscopy including several liquid-based cytology tests (e.g., bronchoaspirate, bronchoalveolar lavage) and/or on easily obtained specimens such as sputum could represent a new approach to improve the sensitivity in lung cancer diagnoses. Recently growing interest has been reported for "noninvasive" liquid biopsy as a valuable source for molecular profiling. Unfortunately, a biomarker and/or composition of biomarkers capable of detecting early-stage lung cancer has yet to be discovered even if in the last few years there has been, through the use of revolutionary new technologies, an explosion of lung cancer biomarkers. Assay sensitivity and specificity need to be improved particularly when new approaches and/or tools are used. We have focused on the most important markers detected in tissue, and on several cytological specimens and liquid biopsies overall.
Collapse
Affiliation(s)
- Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Francesca Lunardi
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Federica Pezzuto
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Francesco Fortarezza
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Stefania Edith Vuljan
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Charles Marquette
- University Côte d'Azur, University Nice Hospital, FHU OncoAge, Department of Pneumology, Pasteur Hospital, 06001 Nice, France.
- University Côte d'Azur, CNRS, INSERM, IRCAN, Team 4, FHU OncoAge, 06001 Nice, France.
| | - Paul Hofman
- University Côte d'Azur, CNRS, INSERM, IRCAN, Team 4, FHU OncoAge, 06001 Nice, France.
- University Côte d'Azur, University Nice Hospital, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, 06001 Nice, France.
- University Côte d'Azur, Biobank (BB-0033-00025), FHU OncoAge, Pasteur Hospital, 06001 Nice, France.
| |
Collapse
|
32
|
Wu S, Wu D, Pan Y, Liu H, Shao Z, Wang M. Correlation between EZH2 and CEP55 and lung adenocarcinoma prognosis. Pathol Res Pract 2019; 215:292-301. [PMID: 30527357 DOI: 10.1016/j.prp.2018.11.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/08/2018] [Accepted: 11/23/2018] [Indexed: 01/24/2023]
Abstract
OBJECTIVE Recently, accumulated evidence indicates that the enhancer of zeste homologue 2 (EZH2) is highly expressed in a wide range of cancer types, including NSCLC. The downstream genes regulated by EZH2 were screened using bioinformatics analysis. This study aimed to analyse the correlation between the downstream genes of EZH2 and the prognosis of lung adenocarcinoma. METHODS Expression and methylation data of lung adenocarcinoma were downloaded from The Cancer Genome Atlas (TCGA) (https://cancergenome.nih.gov/) database, and data were categorized into EZH2 overexpression and EZH2 downregulation groups according to EZH2 expression. The genes that showed opposite trends of methylation and expression changes were screened, and the association of gene expression was calculated. Based on the String database, a protein association analysis was conducted to identify genes related to EZH2, which are referred to as EZH2 regulation candidate genes. According to gene expression (GSE27262) and methylation (GSE66836) chip data in the Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/) database, the genes with differential expression and methylation in lung adenocarcinoma tissues were analysed, and the trends of EZH2 regulation candidate gene expression and methylation were verified to identify the EZH2 regulation candidate genes. Subsequently, MethHC (http://methhc.mbc.nctu.edu.tw/php/index.php) and UALCAN (http://ualcan.path.uab.edu/index.html) were employed to verify changes in the expression and methylation of EZH2 downstream regulation candidate genes and to analyse the correlation between these genes and the prognosis of lung adenocarcinoma. RESULTS Expression and methylation data of lung adenocarcinoma were downloaded from TCGA database and categorized into EZH2 overexpression and EZH2 downregulation groups according to EZH2 expression. A total of 337 genes that showed opposite trends of methylation and expression changes were obtained. The protein association analysis using the String (https://string-db.org/) database showed that 61 genes interact with EZH2 and 61 genes represent EZH2 downstream regulation candidate genes. Moreover, 222 genes obtained from GSE27262 and GSE66836 chip data were negatively correlated with methylation and expression changes, and centrosomal protein 55 (CEP55) was identified as the EZH2 downstream regulation candidate gene. CEP55 was upregulated in lung adenocarcinoma tissues and showed low methylation. According to gene expression data from TCGA database, CEP55 and EZH2 exhibit higher levels in lung adenocarcinoma tissue than in adjacent normal tissue. Finally, the survival analysis revealed that EZH2 is not associated with the prognosis of lung adenocarcinoma, while CEP55 is related to lung adenocarcinoma prognosis. CONCLUSION Taken together, these results indicate that changes in EZH2 expression lead to changes in CEP55 expression in lung adenocarcinoma, and these changes are associated with its prognosis.
Collapse
|
33
|
Moon DH, Kwon SO, Kim WJ, Hong Y. Identification of Serial DNA Methylation Changes in the Blood Samples of Patients with Lung Cancer. Tuberc Respir Dis (Seoul) 2018; 82:126-132. [PMID: 30302959 PMCID: PMC6435926 DOI: 10.4046/trd.2018.0042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/21/2018] [Accepted: 07/31/2018] [Indexed: 12/21/2022] Open
Abstract
Background The development of lung cancer results from the interaction between genetic mutations and dynamic epigenetic alterations, although the exact mechanisms are not completely understood. Changes in DNA methylation may be a promising biomarker for early detection and prognosis of lung cancer. We evaluated the serial changes in genome-wide DNA methylation patterns in blood samples of lung cancer patients. Methods Blood samples were obtained for three consecutive years from three patients (2 years before, 1 year before, and after lung cancer detection) and from three control subjects (without lung cancer). We used the MethylationEPIC BeadChip method, which covers the 850,000 bp cytosine-phosphate-guanine (CpG) site, to conduct an epigenome-wide analysis. Significant differentially methylated regions (DMRs) were identified using p-values <0.05 in a correlation test identifying serial methylation changes and serial increase or decrease in β value above 0.1 for three consecutive years. Results We found three significant CpG sites with differentially methylated β values and 7,105 CpG sites with significant correlation from control patients without lung cancer. However, there were no significant DMRs. In contrast, we found 11 significant CpG sites with differentially methylated β values and 10,562 CpG sites with significant correlation from patients with lung cancer. There were two significant DMRs: cg21126229 (RNF212) and cg27098574 (BCAR1). Conclusion This study revealed DNA methylation changes that might be implicated in lung cancer development. The DNA methylation changes may be the possible candidate target regions for the early detection and prevention of lung cancer.
Collapse
Affiliation(s)
- Da Hye Moon
- Department of Internal Medicine, Kangwon National University Hospital, Chuncheon, Korea
| | - Sung Ok Kwon
- Biomedical Research Institute, Kangwon National University Hospital, Chuncheon, Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University Hospital, Chuncheon, Korea.,Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Yoonki Hong
- Department of Internal Medicine, Kangwon National University Hospital, Chuncheon, Korea.,Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea.
| |
Collapse
|
34
|
Hong Y, Hong SH, Oh YM, Shin SH, Choi SS, Kim WJ. Identification of lung cancer specific differentially methylated regions using genome-wide DNA methylation study. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-018-0034-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
35
|
Catacchio I, Scattone A, Silvestris N, Mangia A. Immune Prophets of Lung Cancer: The Prognostic and Predictive Landscape of Cellular and Molecular Immune Markers. Transl Oncol 2018; 11:825-835. [PMID: 29729581 PMCID: PMC6050352 DOI: 10.1016/j.tranon.2018.04.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths throughout the world. The majority of patients are diagnosed with locally advanced or metastatic disease when surgery, the best curative option, is no longer feasible. Thus, the prognosis of lung cancer remains poor and heterogeneous and new biomarkers are needed. As the immune system plays a pivotal role in cancer, the study of tumor microenvironment, with regard to the immune component, may provide valuable information for a better comprehension of the pathogenesis and progression of the disease. Through a detailed and critical evaluation of the most recent publications on this topic, we provide evidences of the prognostic and predictive significance of immune markers in tumor and in peripheral blood of lung cancer patients: from the landscape of immune cells (macrophages, neutrophils, lymphocytes and natural killer) and their cytokines, to the analysis of immune-checkpoints (PD-L1 and CTLA4), up to the genetic and epigenetic regulation of the immune response (immune gene signatures and miRNA). We also argue about the lights and shadows related to immune marker use in clinical practice, emphasizing on one hand the importance of their assessment in the choice of therapeutic treatment, on the other, the difficulty in their determination and reproducibility of literature data. The following review gives a foundation and a suggestion for future studies investigating tumor immunology in lung cancer.
Collapse
Affiliation(s)
- Ivana Catacchio
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori, Bari 70124, Italy
| | - Anna Scattone
- Pathology Department, IRCCS-Istituto Tumori, Bari 70124, Italy
| | | | - Anita Mangia
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori, Bari 70124, Italy.
| |
Collapse
|
36
|
Abstract
Background Lung cancer is the second most common cancer and the leading cause of cancer death for both men and women. Although low-dose CT (LDCT) is recommended for lung cancer screening in high-risk populations and may decrease lung cancer mortality, there is a need to improve the accuracy of lung cancer screening to decrease over-diagnosis and morbidity. Blood and serum-based biomarkers, including EarlyCDT-lung and microRNA based biomarkers, are promising adjuncts to LDCT in lung cancer screening. We evaluated the diagnostic performance of EarlyCDT-lung, micro-RNA signature classifier (MSC), and miR-test, and their impact on lung cancer-related mortality and all-cause mortality. Methods References were identified using searches of PubMed, EMBASE, and Ovid Medline® from January 2000 to November 2015. Phase three or greater studies in the English language evaluating the diagnostic performance of EarlyCDT-lung, MSC, and miR-test were selected for inclusion. Results Three phase 3 studies were identified, one evaluating EarlyCDT-lung, one evaluating miR-Test, and one evaluating MSC respectively. No phase 4 or 5 studies were identified. All three biomarker assays show promise for the detection of lung cancer. MSC shows promise when used in conjunction with LDCT for lung cancer detection, achieving a positive likelihood ratio of 18.6 if both LDCT and MSC are positive, and a negative likelihood ratio of 0.03 if both LDCT and MSC are negative. However, there is a paucity of high-quality studies that can guide clinical implementation. Conclusions There is currently no high quality evidence to support or guide the implementation of these biomarkers in clinical practice. Reports of further research at stages four and five for these, and other promising methods, is required. Electronic supplementary material The online version of this article (10.1186/s12885-018-4024-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gavin C W Chu
- Toronto Western Hospital Family Health Team, Department of Family and Community Medicine, University of Toronto, 2W428, 399 Bathurst Street, Toronto, ON, M5T 2S8, Canada.,Department of Family and Community Medicine, University of Toronto, 500 University Avenue, 5th Floor, Room 348, Toronto, ON, M5G 1V7, Canada
| | - Kim Lazare
- North York General Hospital Family Medicine Teaching Unit, Department of Family and Community Medicine, University of Toronto, 4 South, 4001 Leslie Street, Toronto, ON, M6H 2Z7, Canada
| | - Frank Sullivan
- Department of Family and Community Medicine, University of Toronto, 500 University Avenue, 5th Floor, Room 348, Toronto, ON, M5G 1V7, Canada. .,Division of Population & Behavioural Sciences, Medical School, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK.
| |
Collapse
|
37
|
Han L, Xu G, Xu C, Liu B, Liu D. Potential prognostic biomarkers identified by DNA methylation profiling analysis for patients with lung adenocarcinoma. Oncol Lett 2018; 15:3552-3557. [PMID: 29467875 PMCID: PMC5796271 DOI: 10.3892/ol.2018.7790] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/23/2017] [Indexed: 12/15/2022] Open
Abstract
Lung adenocarcinoma is frequently occurring type of lung cancer with high metastatic risk. We performed a DNA methylation profiling analysis to identify possible prognostic markers involved in lung adenocarcinoma. DNA methylation profiling data (GSE66386) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially methylated genes were identified using a limma package. GO enrichment analysis was performed to identify vital functions related to differential gene methylation, and pathway analysis was performed to assess the associations between different proteins with regard to regulation of cell function and metabolism. The screening results showed a total of 112,662 differentially methylated genes in lung adenocarcinoma patients compared with those of the normal controls. These CpGs were involved in 16,705 genes. The skeletal system development (P=9.46E-27) and embryonic organ morphogenesis (P=8.67E-24) were found to be involved in lung adenocarcinoma. The cancer (P=3.64E-07), Rap1 signaling (P=9.21E-05) and calcium signaling (P=9.21E-05) pathways constituted the important pathways associated with lung adenocarcinoma. In conclusion, methylated PTPRF, HOXD3, HOXD13 and CACNA1A are potential markers and may be utilized for the diagnosis and therapy of lung adenocarcinoma.
Collapse
Affiliation(s)
- Liankui Han
- Department of Thoracic Surgery, Guizhou Provincial People's Hospital, Guizhou 550002, P.R. China
| | - Gang Xu
- Department of Thoracic Surgery, The Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou 563000, P.R. China
| | - Chuan Xu
- Department of Thoracic Surgery, Guizhou Provincial People's Hospital, Guizhou 550002, P.R. China
| | - Bo Liu
- Department of Thoracic Surgery, Guizhou Provincial People's Hospital, Guizhou 550002, P.R. China
| | - Di Liu
- Department of Thoracic Surgery, Guizhou Provincial People's Hospital, Guizhou 550002, P.R. China
| |
Collapse
|
38
|
Shi YX, Wang Y, Li X, Zhang W, Zhou HH, Yin JY, Liu ZQ. Genome-wide DNA methylation profiling reveals novel epigenetic signatures in squamous cell lung cancer. BMC Genomics 2017; 18:901. [PMID: 29169318 PMCID: PMC5701423 DOI: 10.1186/s12864-017-4223-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 10/17/2017] [Indexed: 11/15/2022] Open
Abstract
Background Epigenetic alterations are strongly associated with the development of cancer. The aim of this study was to identify epigenetic pattern in squamous cell lung cancer (LUSC) on a genome-wide scale. Results Here we performed DNA methylation profiling on 24 LUSC and paired non-tumor lung (NTL) tissues by Illumina Human Methylation 450 K BeadArrays, and identified 5214 differentially methylated probes. By integrating DNA methylation and mRNA expression data, 449 aberrantly methylated genes accompanied with altered expression were identified. Ingenuity Pathway analysis highlighted these genes which were closely related to the carcinogenesis of LUSC, such as ERK family, NFKB signaling pathway, Hedgehog signaling pathway, providing new clues for understanding the molecular mechanisms of LUSC pathogenesis. To verify the results of high-throughput screening, we used 56 paired independent tissues for clinical validation by pyrosequencing. Subsequently, another 343 tumor tissues from the Cancer Genome Atlas (TCGA) database were utilized for further validation. Then, we identified a panel of DNA methylation biomarkers (CLDN1, TP63, TBX5, TCF21, ADHFE1 and HNF1B) in LUSC. Furthermore, we performed receiver operating characteristics (ROC) analysis to assess the performance of biomarkers individually, suggesting that they could be suitable as potential diagnostic biomarkers for LUSC. Moreover, hierarchical clustering analysis of the DNA methylation data identified two tumor subgroups, one of which showed increased DNA methylation. Conclusions Collectively, these results suggest that DNA methylation plays critical roles in lung tumorigenesis and may potentially be proposed as a diagnostic biomarker. Trial registration ChiCTR-RCC-12002830 Date of registration: 2012–12-17. Electronic supplementary material The online version of this article (10.1186/s12864-017-4223-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yuan-Xiang Shi
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China
| | - Ying Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China
| | - Xi Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China.
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, 421001, People's Republic of China.
| |
Collapse
|
39
|
Gamerith G, Rainer J, Huber JM, Hackl H, Trajanoski Z, Koeck S, Lorenz E, Kern J, Kofler R, Kelm JM, Zwierzina H, Amann A. 3D-cultivation of NSCLC cell lines induce gene expression alterations of key cancer-associated pathways and mimic in-vivo conditions. Oncotarget 2017; 8:112647-112661. [PMID: 29348853 PMCID: PMC5762538 DOI: 10.18632/oncotarget.22636] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 10/02/2017] [Indexed: 12/11/2022] Open
Abstract
This work evaluated gene expression differences between a hanging-drop 3D NSCLC model and 2D cell cultures and their in-vivo relevance by comparison to patient-derived data from The Cancer Genome Atlas. Gene expression of 2D and 3D cultures for Colo699 and A549 were assessed using Affymetrix HuGene 1.0 ST gene chips. Biostatistical analyses tested for reproducibility, comparability and significant differences in gene expression profiles between cell lines, experiments and culture methods. The analyses revealed a high interassay correlation within specific culture systems proving a high validity. 979 genes were altered in A549 and 1106 in Colo699 cells due to 3D cultivation. The overlap of changed genes between the cell lines was small (149), but the involved pathways in the reactome and GO- analyses showed a high overlap with DNA methylation, cell cycle, SIRT1, PKN1 pathway, DNA repair and oxidative stress as well known cancer-associated representatives. Additional specific GSEA-analyses revealed changes in immunologic and endothelial cell proliferation pathways, whereas hypoxic, EMT and angiogenic pathways were downregulated. Gene enrichment analyses showed 3D-induced gene up-regulations in the cell lines 38 to be represented in in-vivo samples of NSCLC patients using data of The Cancer Genome Atlas. Thus, our 3D NSCLC model might provide a tool for early drug development and investigation of microenvironment-associated mechanisms. However, this work also highlights the need for further individualization and model adaption to address remaining challenges.
Collapse
Affiliation(s)
- Gabriele Gamerith
- Medical University of Innsbruck, Department of Internal Medicine V, 6020 Innsbruck, Austria.,Tyrolean Cancer Research Institute, 6020 Innsbruck, Austria
| | - Johannes Rainer
- Medical University of Innsbruck, Biocenter, Division of Molecular Pathophysiology, 6020 Innsbruck, Austria.,European Academy of Bolzano/Bozen (EURAC), Center for Biomedicine, 39100 Bolzano, Italy
| | - Julia M Huber
- Medical University of Innsbruck, Department of Internal Medicine V, 6020 Innsbruck, Austria.,Tyrolean Cancer Research Institute, 6020 Innsbruck, Austria.,Oncotyrol, Innsbruck, 6020 Innsbruck, Austria
| | - Hubert Hackl
- Medical University of Innsbruck, Biocenter, Division of Bioinformatics, 6020 Innsbruck, Austria
| | - Zlatko Trajanoski
- Medical University of Innsbruck, Biocenter, Division of Bioinformatics, 6020 Innsbruck, Austria
| | - Stefan Koeck
- Medical University of Innsbruck, Department of Internal Medicine V, 6020 Innsbruck, Austria.,Tyrolean Cancer Research Institute, 6020 Innsbruck, Austria
| | - Edith Lorenz
- Medical University of Innsbruck, Department of Internal Medicine V, 6020 Innsbruck, Austria.,Tyrolean Cancer Research Institute, 6020 Innsbruck, Austria
| | - Johann Kern
- Oncotyrol, Innsbruck, 6020 Innsbruck, Austria
| | - Reinhard Kofler
- Medical University of Innsbruck, Biocenter, Division of Molecular Pathophysiology, 6020 Innsbruck, Austria
| | | | - Heinz Zwierzina
- Medical University of Innsbruck, Department of Internal Medicine V, 6020 Innsbruck, Austria.,Tyrolean Cancer Research Institute, 6020 Innsbruck, Austria
| | - Arno Amann
- Medical University of Innsbruck, Department of Internal Medicine V, 6020 Innsbruck, Austria.,Tyrolean Cancer Research Institute, 6020 Innsbruck, Austria
| |
Collapse
|
40
|
Affiliation(s)
- Delphine Lissa
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, USA
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, USA
| |
Collapse
|
41
|
Evanno E, Godet J, Piccirilli N, Guilhot J, Milin S, Gombert JM, Fouchaq B, Roche J. Tri-methylation of H3K79 is decreased in TGF-β1-induced epithelial-to-mesenchymal transition in lung cancer. Clin Epigenetics 2017; 9:80. [PMID: 28804523 PMCID: PMC5549304 DOI: 10.1186/s13148-017-0380-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 07/31/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The epithelial-to-mesenchymal transition (EMT) enables epithelial cancer cells to acquire mesenchymal features and contributes to metastasis and resistance to treatment. This process involves epigenetic reprogramming for gene expression. We explored global histone modifications during TGF-β1-induced EMT in two non-small cell lung cancer (NSCLC) cell lines and tested different epigenetic treatment to modulate or partially reverse EMT. RESULTS Loss of classical epithelial markers and gain of mesenchymal markers were verified in A549 and H358 cell lines during TGF-β1-induced EMT. In addition, we noticed increased expression of the axonal guidance protein semaphorin 3C (SEMA3C) and PD-L1 (programmed death-ligand 1) involved in the inhibition of the immune system, suggesting that both SEMA3C and PD-L1 could be the new markers of TGF-β1-induced EMT. H3K79me3 and H2BK120me1 were decreased in A549 and H358 cell lines after a 48-h TGF-β1 treatment, as well as H2BK120ac in A549 cells. However, decreased H3K79me3 was not associated with expression of the histone methyltransferase DOT1L. Furthermore, H3K79me3 was decreased in tumors compared in normal tissues and not associated with cell proliferation. Associations of histone deacetylase inhibitor (SAHA) with DOT1L inhibitors (EPZ5676 or SGC0946) or BET bromodomain inhibitor (PFI-1) were efficient to partially reverse TGF-β1 effects by decreasing expression of PD-L1, SEMA3C, and its receptor neuropilin-2 (NRP2) and by increasing epithelial markers such as E-cadherin. CONCLUSION Histone methylation was modified during EMT, and combination of epigenetic compounds with conventional or targeted chemotherapy might contribute to reduce metastasis and to enhance clinical responses.
Collapse
Affiliation(s)
- Emilie Evanno
- Eurofins Cerep SA, Le Bois l’Evêque, F-86600 Celle L’Evescault, France
- Université de Poitiers, Laboratoire LNEC, F-86022 Poitiers, France
| | - Julie Godet
- CHU de Poitiers, Service d’Anatomie et de Cytologie Pathologiques, F-86021 Poitiers, France
| | | | - Joëlle Guilhot
- INSERM CIC 0802, CHU de Poitiers, F-86021 Poitiers, France
| | - Serge Milin
- CHU de Poitiers, Service d’Anatomie et de Cytologie Pathologiques, F-86021 Poitiers, France
| | - Jean Marc Gombert
- INSERM U1082, CHU de Poitiers, F-86021 Poitiers, France
- Service Immunologie, CHU de Poitiers, F-86021 Poitiers, France
| | - Benoit Fouchaq
- Eurofins Cerep SA, Le Bois l’Evêque, F-86600 Celle L’Evescault, France
| | - Joëlle Roche
- Laboratoire Ecologie et Biologie des Interactions (EBI), Université de Poitiers, UMR-CNRS 7267, F-86073 Poitiers, France
| |
Collapse
|
42
|
Roche J, Gemmill RM, Drabkin HA. Epigenetic Regulation of the Epithelial to Mesenchymal Transition in Lung Cancer. Cancers (Basel) 2017; 9:cancers9070072. [PMID: 28672805 PMCID: PMC5532608 DOI: 10.3390/cancers9070072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/17/2017] [Accepted: 06/17/2017] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. It is an aggressive and devastating cancer because of metastasis triggered by enhanced migration and invasion, and resistance to cytotoxic chemotherapy. The epithelial to mesenchymal transition (EMT) is a fundamental developmental process that is reactivated in wound healing and a variety of diseases including cancer where it promotes migration/invasion and metastasis, resistance to treatment, and generation and maintenance of cancer stem cells. The induction of EMT is associated with reprogramming of the epigenome. This review focuses on major mechanisms of epigenetic regulation mainly in lung cancer with recent data on EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit ), the catalytic subunit of the PRC2 (Polycomb Group PcG), that behaves as an oncogene in lung cancer associated with gene repression, non-coding RNAs and the epitranscriptome.
Collapse
Affiliation(s)
- Joëlle Roche
- Laboratoire Ecologie et Biologie des Interactions, Equipe SEVE, Université de Poitiers, UMR CNRS 7267, F-86073 Poitiers, France.
| | - Robert M Gemmill
- Division of Hematology-Oncology, Medical University of South Carolina, 39 Sabin St., MSC 635, Charleston, SC 29425, USA.
| | - Harry A Drabkin
- Division of Hematology-Oncology, Medical University of South Carolina, 39 Sabin St., MSC 635, Charleston, SC 29425, USA.
| |
Collapse
|
43
|
Liu C, Lv D, Li M, Zhang X, Sun G, Bai Y, Chang D. Hypermethylation of miRNA-589 promoter leads to upregulation of HDAC5 which promotes malignancy in non-small cell lung cancer. Int J Oncol 2017; 50:2079-2090. [DOI: 10.3892/ijo.2017.3967] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/20/2017] [Indexed: 11/06/2022] Open
|
44
|
Du J, Zhang L. Pathway deviation-based biomarker and multi-effect target identification in asbestos-related squamous cell carcinoma of the lung. Int J Mol Med 2017; 39:579-586. [PMID: 28204826 PMCID: PMC5360351 DOI: 10.3892/ijmm.2017.2878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 01/20/2017] [Indexed: 12/19/2022] Open
Abstract
Asbestos-related lung carcinoma is one of the most devastating occupational cancers, and effective techniques for early diagnosis are still lacking. In the present study, a systematic approach was applied to detect a potential biomarker for asbestos-related lung cancer (ARLC); in particular asbestos-related squamous cell carcinoma (ARLC-SCC). Microarray data (GSE23822) were retrieved from the Gene Expression Omnibus database, including 26 ARLC-SCCs and 30 non-asbestos-related squamous cell lung carcinomas (NARLC-SCCs). Differentially expressed genes (DEGs) were identified by the limma package, and then a protein-protein interaction (PPI) network was constructed according to the BioGRID and HPRD databases. A novel scoring approach integrating an expression deviation score and network degree of the gene was then proposed to weight the DEGs. Subsequently, the important genes were uploaded to DAVID for pathway enrichment analysis. Pathway correlation analysis was carried out using Spearman's rank correlation coefficient of the pathscore. In total, 1,333 DEGs, 391 upregulated and 942 downregulated, were obtained between the ARLC-SCCs and NARLC-SCCs. A total of 524 important genes for ARLC-SCC were significantly enriched in 22 KEGG pathways. Correlation analysis of these pathways showed that the pathway of SNARE interactions in vesicular transport was significantly correlated with 12 other pathways. Additionally, obvious correlations were found between multiple pathways by sharing cross-talk genes (EGFR, PRKX, PDGFB, PIK3R3, SLK, IGF1, CDC42 and PRKCA). On the whole, our data demonstrate that 8 cross-talk genes were found to bridge multiple ARLC-SCC-specific pathways, which may be used as candidate biomarkers and potential multi-effect targets. As these genes are involved in multiple pathways, it is possible that drugs targeting these genes may thus be able to influence multiple pathways simultaneously.
Collapse
Affiliation(s)
- Jiang Du
- Department of Thoracic Surgery, First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Lin Zhang
- Department of Thoracic Surgery, First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| |
Collapse
|
45
|
Zhang Y, Elgizouli M, Schöttker B, Holleczek B, Nieters A, Brenner H. Smoking-associated DNA methylation markers predict lung cancer incidence. Clin Epigenetics 2016; 8:127. [PMID: 27924164 PMCID: PMC5123284 DOI: 10.1186/s13148-016-0292-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022] Open
Abstract
Background Newly established blood DNA methylation markers that are strongly associated with smoking might open new avenues for lung cancer (LC) screening. We aimed to assess the performance of the top hits from previous epigenome-wide association studies in prediction of LC incidence. In a prospective nested case-control study, DNA methylation at AHRR (cg05575921), 6p21.33 (cg06126421), and F2RL3 (cg03636183) were measured by pyrosequencing in baseline whole blood samples of 143 incident LC cases identified during 11 years of follow-up and 457 age- and sex-matched controls without diagnosis of LC until the end of follow-up. The individual and joint associations of the 3 markers with LC risk were estimated by logistic regression, adjusted for potential confounders including smoking status and cigarette pack-years. The predictive performance was evaluated for both the individual markers and their combinations derived from multiple algorithms. Results Pronounced demethylation of all 3 markers was observed at baseline among cases compared to controls. Risk of developing LC increased with decreasing DNA methylation levels, with adjusted ORs (95% CI) of 15.86 (4.18–60.17), 8.12 (2.69–4.48), and 10.55 (3.44–32.31), respectively, for participants in the lowest quartile of AHRR, 6p21.33, and F2RL3 compared to participants in the highest 2 quartiles of each site among controls. The individual 3 markers exhibited similar accuracy in predicting LC incidence, with AUCs ranging from 0.79 to 0.81. Combination of the 3 markers did not improve the predictive performance (AUC = 0.80). The individual markers or their combination outperformed self-reported smoking exposure particularly in light smokers. No variation in risk prediction was identified with respect to age, follow-up time, and histological subtypes. Conclusions AHRR, 6p21.33, and F2RL3 methylation in blood DNA are predictive for LC development, which might be useful for identification of risk groups for further specific screening, such as CT examination. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0292-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Magdeldin Elgizouli
- Center for Chronic Immunodeficiency (CCI), Research Group Epidemiology, University Medical Center Freiburg, Freiburg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Alexandra Nieters
- Center for Chronic Immunodeficiency (CCI), Research Group Epidemiology, University Medical Center Freiburg, Freiburg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
46
|
Dong N, Shi L, Wang DC, Chen C, Wang X. Role of epigenetics in lung cancer heterogeneity and clinical implication. Semin Cell Dev Biol 2016; 64:18-25. [PMID: 27575638 DOI: 10.1016/j.semcdb.2016.08.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 08/24/2016] [Indexed: 12/15/2022]
Abstract
Lung cancer, as a highly heterogeneous disease, can be initiated and progressed through the interaction between permanent genetic mutations and dynamic epigenetic alterations. However, the mediating mechanisms of epigenetics in cancer heterogeneity remain unclear. The evolution of cancer, the existence of cancer stem cells (CSCs) and the phenomenon of epithelial-mesenchymal transition (EMT) have been reported to be involved in lung cancer heterogeneity. In this review, we briefly recap the definition of heterogeneity and concept of epigenetics, highlight the potential roles and mechanisms of epigenetic regulation in heterogeneity of lung cancer, and summarize the diagnostic and therapeutic implications of epigenetic alterations in lung cancer, especially the role of DNA methylation and histone acetylation. Deep understanding of epigenetic regulation in cancer heterogeneity is instrumental to the design of novel therapeutic approaches that target lung cancer.
Collapse
Affiliation(s)
- Nian Dong
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China
| | - Lin Shi
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics; Zhongshan Hospital Institute of Clinical Science of Fudan University, Shanghai, China
| | - Diane C Wang
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China
| | - Chengshui Chen
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China.
| | - Xiangdong Wang
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China; Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics; Zhongshan Hospital Institute of Clinical Science of Fudan University, Shanghai, China.
| |
Collapse
|
47
|
Zhang X, Gao L, Liu ZP, Jia S, Chen L. Uncovering Driver DNA Methylation Events in Nonsmoking Early Stage Lung Adenocarcinoma. Biomed Res Int 2016; 2016:2090286. [PMID: 27610367 DOI: 10.1155/2016/2090286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 01/04/2023]
Abstract
As smoking rates decrease, proportionally more cases with lung adenocarcinoma occur in never-smokers, while aberrant DNA methylation has been suggested to contribute to the tumorigenesis of lung adenocarcinoma. It is extremely difficult to distinguish which genes play key roles in tumorigenic processes via DNA methylation-mediated gene silencing from a large number of differentially methylated genes. By integrating gene expression and DNA methylation data, a pipeline combined with the differential network analysis is designed to uncover driver methylation genes and responsive modules, which demonstrate distinctive expressions and network topology in tumors with aberrant DNA methylation. Totally, 135 genes are recognized as candidate driver genes in early stage lung adenocarcinoma and top ranked 30 genes are recognized as driver methylation genes. Functional annotation and the differential network analysis indicate the roles of identified driver genes in tumorigenesis, while literature study reveals significant correlations of the top 30 genes with early stage lung adenocarcinoma in never-smokers. The analysis pipeline can also be employed in identification of driver epigenetic events for other cancers characterized by matched gene expression data and DNA methylation data.
Collapse
|
48
|
Drzewiecka H, Gałęcki B, Jarmołowska-Jurczyszyn D, Kluk A, Dyszkiewicz W, Jagodziński PP. Decreased expression of connective tissue growth factor in non-small cell lung cancer is associated with clinicopathological variables and can be restored by epigenetic modifiers. J Cancer Res Clin Oncol 2016; 142:1927-46. [PMID: 27393180 PMCID: PMC4978771 DOI: 10.1007/s00432-016-2195-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 06/18/2016] [Indexed: 01/27/2023]
Abstract
Purpose Recent studies indicated undisputed contribution of connective tissue growth factor (CTGF) in the development of many cancers, including non-small cell lung cancer (NSCLC). However, the functional role and regulation of CTGF expression during tumorigenesis remain elusive. Our goal was to determine CTGF transcript and protein levels in tumoral and matched control tissues from 98 NSCLC patients, to correlate the results with clinicopathological features and to investigate whether the CTGF expression can be epigenetically regulated in NSCLC. Methods We used quantitative PCR, Western blotting and immunohistochemistry to evaluate CTGF expression in lung cancerous and histopathologically unchanged tissues. We tested the impact of 5-Aza-2′-deoxycytidine (5-dAzaC) and trichostatin A (TSA) on CTGF transcript and protein levels in NSCLC cells (A549, Calu-1). DNA methylation status of the CTGF regulatory region was evaluated by bisulfite sequencing. The influence of 5-dAzaC and TSA on NSCLC cells viability and proliferation was monitored by the trypan blue assay. Results We found significantly decreased levels of CTGF mRNA and protein (both p < 0.0000001) in cancerous tissues of NSCLC patients. Down-regulation of CTGF occurred regardless of gender in all histological subtypes of NSCLC. Moreover, we showed that 5-dAzaC and TSA were able to restore CTGF mRNA and protein contents in NSCLC cells. However, no methylation within CTGF regulatory region was detected. Both compounds significantly reduced NSCLC cells proliferation. Conclusions Decreased expression of CTGF is a common feature in NSCLC; however, it can be restored by the chromatin-modifying agents such as 5-dAzaC or TSA and consequently restrain cancer development. Electronic supplementary material The online version of this article (doi:10.1007/s00432-016-2195-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hanna Drzewiecka
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Święcickiego 6 Street, 60-781, Poznan, Poland.
| | - Bartłomiej Gałęcki
- Department of Thoracic Surgery, Poznan University of Medical Sciences, Szamarzewskiego 62 Street, 60-569, Poznan, Poland
| | - Donata Jarmołowska-Jurczyszyn
- Department of Clinical Pathomorphology, Poznan University of Medical Sciences, Przybyszewskiego 49 Street, 60-355, Poznan, Poland
| | - Andrzej Kluk
- Department of Clinical Pathomorphology, Poznan University of Medical Sciences, Przybyszewskiego 49 Street, 60-355, Poznan, Poland
| | - Wojciech Dyszkiewicz
- Department of Thoracic Surgery, Poznan University of Medical Sciences, Szamarzewskiego 62 Street, 60-569, Poznan, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Święcickiego 6 Street, 60-781, Poznan, Poland
| |
Collapse
|
49
|
Abstract
Lung cancer remains the number one cause of cancer-related deaths worldwide with 221,200 estimated new cases and 158,040 estimated deaths in 2015. Approximately 80% of cases are non-small cell lung cancer (NSCLC). The diagnosis is usually made at an advanced stage where the prognosis is poor and therapeutic options are limited. The evolution of lung cancer is a multistep process involving genetic, epigenetic, and environmental factor interactions that result in the dysregulation of key oncogenes and tumor suppressor genes, culminating in activation of cancer-related signaling pathways. The past decade has witnessed the discovery of multiple molecular aberrations that drive lung cancer growth, among which are epidermal growth factor receptor (EGFR) mutations and translocations involving the anaplastic lymphoma kinase (ALK) gene. This has translated into therapeutic agent developments that target these molecular alterations. The absence of targetable mutations in 50% of NSCLC cases and targeted therapy resistance development underscores the importance for developing alternative therapeutic strategies for treating lung cancer. Among these strategies, pharmacologic modulation of the epigenome has been used to treat lung cancer. Epigenetics approaches may circumvent the problem of tumor heterogeneity by affecting the expression of multiple tumor suppression genes (TSGs), halting tumor growth and survival. Moreover, it may be effective for tumors that are not driven by currently recognized druggable mutations. This review summarizes the molecular pathology of lung cancer epigenetic aberrations and discusses current efforts to target the epigenome with different pharmacological approaches. Our main focus will be on hypomethylating agents, histone deacetylase (HDAC) inhibitors, microRNA modulations, and the role of novel epigenetic biomarkers. Last, we will address the challenges that face this old-new strategy in treating lung cancer.
Collapse
Affiliation(s)
- Junaid Ansari
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Rodney E Shackelford
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Hazem El-Osta
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| |
Collapse
|
50
|
Abstract
AXIN2, an important regulator in Wnt/β-catenin signaling pathway, takes part in regulating cell proliferation, cytometaplasia, migration, apoptosis and other important functions, has showed close relations with the development of liver cancer, colon cancer, lung cancer, breast cancer and so on. The epigenetic regulation provides new insights for further exploring the pathogenesis of tumor. In this paper, the roles of AXIN2 in tumorigenesis, AXIN2 methylation, ubiquitination and siRNA/RNA regulation will be reviewed.
Collapse
|