1
|
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] [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
|
2
|
Li P, Liu S, Du L, Mohseni G, Zhang Y, Wang C. Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer. Clin Epigenetics 2022; 14:118. [PMID: 36153611 PMCID: PMC9509651 DOI: 10.1186/s13148-022-01337-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/16/2022] [Indexed: 11/27/2022] Open
Abstract
Lung cancer (LC) is the main cause of cancer-related mortality. Most LC patients are diagnosed in an advanced stage when the symptoms are obvious, and the prognosis is quite poor. Although low-dose computed tomography (LDCT) is a routine clinical examination for early detection of LC, the false-positive rate is over 90%. As one of the intensely studied epigenetic modifications, DNA methylation plays a key role in various diseases, including cancer and other diseases. Hypermethylation in tumor suppressor genes or hypomethylation in oncogenes is an important event in tumorigenesis. Remarkably, DNA methylation usually occurs in the very early stage of malignant tumors. Thus, DNA methylation analysis may provide some useful information about the early detection of LC. In recent years, liquid biopsy has developed rapidly. Liquid biopsy can detect and monitor both primary and metastatic malignant tumors and can reflect tumor heterogeneity. Moreover, it is a minimally invasive procedure, and it causes less pain for patients. This review summarized various liquid biopsies based on DNA methylation for LC. At first, we briefly discussed some emerging technologies for DNA methylation analysis. Subsequently, we outlined cell-free DNA (cfDNA), sputum, bronchoalveolar lavage fluid, bronchial aspirates, and bronchial washings DNA methylation-based liquid biopsy for the early detection of LC. Finally, the prognostic value of DNA methylation in cfDNA and sputum and the diagnostic value of other DNA methylation-based liquid biopsies for LC were also analyzed.
Collapse
|
3
|
Cai D, Ma X, Guo H, Zhang H, Bian A, Yu H, Cheng W. Prognostic value of p16, p53, and pcna in sarcoma and an evaluation of immune infiltration. J Orthop Surg Res 2022; 17:305. [PMID: 35689249 PMCID: PMC9185979 DOI: 10.1186/s13018-022-03193-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/26/2022] [Indexed: 12/22/2022] Open
Abstract
Background p16, p53, and proliferating cell nuclear antigen (pcna) genes play significant roles in many chromatin modifications and have been found to be highly expressed in a variety of tumor tissues. Therefore, they have been used as target genes for some tumor therapies. However, the differential expressions of the p16, p53, and pcna genes in human sarcomas and their effects on prognosis have not been widely reported. Methods The Oncomine dataset was used to analyze the transcription levels of p16, p53, and pcna genes, and the gene expression profile interactive analysis (GEPIA) dataset was used to analyze the differential expressions of p16, p53, and pcna. The expression levels of p16, p53, and pcna were further analyzed by Western Blotting. GEPIA and Kaplan–Meier analyses were used to analyze the prognostic value of p16, p53, and pcna. Furthermore, p16, p53, and pcna gene mutations and their association with overall survival (OS) and disease-free survival (DFS) were analyzed using cBioPortal datasets. In addition, genes co-expressed with p16, p53, and pcna were analyzed using Oncomine. The DAVID dataset was used to analyze the functional enrichment of p16, p53, pcna, and their co-expressed genes by Gene Ontology (GO) and Metascape were used to construct a network map. Finally, the immune cell infiltration of p16, p53, and pcna in patients with sarcoma was reported by Tumor Immune Estimation Resource (TIMER). Results p16, p53, and pcna were up-regulated in human sarcoma tissues and almost all sarcoma cell lines. Western Blotting showed that the expression of p16, p53, and pcna was elevated in osteosarcoma cell lines. The expression of pcna was correlated with OS, the expression of p16, p53, and pcna was correlated with relapse-free survival, and the genetic mutation of p16 was negatively correlated with OS and DFS. We also found that p16, p53, and pcna genes were positively/negatively correlated with immune cell infiltration in sarcoma. Conclusions The results of this study showed that p16, p53, and pcna can significantly affect the survival and immune status of sarcoma patients. Therefore, p16, p53, and pcna could be used as potential biomarkers of prognosis and immune infiltration in human sarcoma and provide a possible therapeutic target for sarcoma.
Collapse
Affiliation(s)
- Dechao Cai
- Department of Orthopedics, The Second Hospital of Anhui Medical University, 678 Furong Road, Hefei, 230601, China
| | - Xiao Ma
- Department of Orthopedics, The Second Hospital of Anhui Medical University, 678 Furong Road, Hefei, 230601, China
| | - Huihui Guo
- Department of Orthopedics, The Second Hospital of Anhui Medical University, 678 Furong Road, Hefei, 230601, China
| | - Haotian Zhang
- Department of Orthopedics, The Second Hospital of Anhui Medical University, 678 Furong Road, Hefei, 230601, China
| | - Ashuai Bian
- Department of Orthopedics, The Second Hospital of Anhui Medical University, 678 Furong Road, Hefei, 230601, China
| | - Haoran Yu
- Department of Orthopedics, The Second Hospital of Anhui Medical University, 678 Furong Road, Hefei, 230601, China
| | - Wendan Cheng
- Department of Orthopedics, The Second Hospital of Anhui Medical University, 678 Furong Road, Hefei, 230601, China.
| |
Collapse
|
4
|
Brunetti M, Panagopoulos I, Micci F, Davidson B. MGMT
promoter methylation is a rare epigenetic change in malignant effusions. Cytopathology 2019; 31:12-15. [DOI: 10.1111/cyt.12782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/10/2019] [Accepted: 10/26/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Marta Brunetti
- Section for Cancer CytogeneticsInstitute for Cancer Genetics and InformaticsThe Norwegian Radium HospitalOslo University Hospital Oslo Norway
- Department of PathologyNorwegian Radium HospitalOslo University Hospital Oslo Norway
- Institute of Clinical MedicineFaculty of MedicineUniversity of Oslo Oslo Norway
| | - Ioannis Panagopoulos
- Section for Cancer CytogeneticsInstitute for Cancer Genetics and InformaticsThe Norwegian Radium HospitalOslo University Hospital Oslo Norway
| | - Francesca Micci
- Section for Cancer CytogeneticsInstitute for Cancer Genetics and InformaticsThe Norwegian Radium HospitalOslo University Hospital Oslo Norway
| | - Ben Davidson
- Department of PathologyNorwegian Radium HospitalOslo University Hospital Oslo Norway
- Institute of Clinical MedicineFaculty of MedicineUniversity of Oslo Oslo Norway
| |
Collapse
|
5
|
Ooki A, Maleki Z, Tsay JCJ, Goparaju C, Brait M, Turaga N, Nam HS, Rom WN, Pass HI, Sidransky D, Guerrero-Preston R, Hoque MO. A Panel of Novel Detection and Prognostic Methylated DNA Markers in Primary Non-Small Cell Lung Cancer and Serum DNA. Clin Cancer Res 2017; 23:7141-7152. [PMID: 28855354 DOI: 10.1158/1078-0432.ccr-17-1222] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/26/2017] [Accepted: 08/23/2017] [Indexed: 11/16/2022]
Abstract
Purpose: To establish a novel panel of cancer-specific methylated genes for cancer detection and prognostic stratification of early-stage non-small cell lung cancer (NSCLC).Experimental Design: Identification of differentially methylated regions (DMR) was performed with bumphunter on "The Cancer Genome Atlas (TCGA)" dataset, and clinical utility was assessed using quantitative methylation-specific PCR assay in multiple sets of primary NSCLC and body fluids that included serum, pleural effusion, and ascites samples.Results: A methylation panel of 6 genes (CDO1, HOXA9, AJAP1, PTGDR, UNCX, and MARCH11) was selected from TCGA dataset. Promoter methylation of the gene panel was detected in 92.2% (83/90) of the training cohort with a specificity of 72.0% (18/25) and in 93.0% (40/43) of an independent cohort of stage IA primary NSCLC. In serum samples from the later 43 stage IA subjects and population-matched 42 control subjects, the gene panel yielded a sensitivity of 72.1% (31/41) and specificity of 71.4% (30/42). Similar diagnostic accuracy was observed in pleural effusion and ascites samples. A prognostic risk category based on the methylation status of CDO1, HOXA9, PTGDR, and AJAP1 refined the risk stratification for outcomes as an independent prognostic factor for an early-stage disease. Moreover, the paralog group for HOXA9, predominantly overexpressed in subjects with HOXA9 methylation, showed poor outcomes.Conclusions: Promoter methylation of a panel of 6 genes has potential for use as a biomarker for early cancer detection and to predict prognosis at the time of diagnosis. Clin Cancer Res; 23(22); 7141-52. ©2017 AACR.
Collapse
Affiliation(s)
- Akira Ooki
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Zahra Maleki
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Jun-Chieh J Tsay
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, New York
| | - Chandra Goparaju
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Langone Medical Center, New York University of Medicine, New York, New York
| | - Mariana Brait
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Nitesh Turaga
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Hae-Seong Nam
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Division of Pulmonology, Department of Internal Medicine, Inha University School of Medicine, Incheon, South Korea
| | - William N Rom
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, New York
| | - Harvey I Pass
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Langone Medical Center, New York University of Medicine, New York, New York
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Rafael Guerrero-Preston
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland. .,Department of Oncology, Johns Hopkins University, Baltimore, Maryland.,Department of Obstetrics and Gynecology, University of Puerto Rico, San Juan, Puerto Rico
| | - Mohammad Obaidul Hoque
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland. .,Department of Oncology, Johns Hopkins University, Baltimore, Maryland.,Department of Urology, Johns Hopkins University, Baltimore, Maryland
| |
Collapse
|
6
|
Diagnostic value of tumor markers for lung adenocarcinoma-associated malignant pleural effusion: a validation study and meta-analysis. Int J Clin Oncol 2016; 22:283-290. [DOI: 10.1007/s10147-016-1073-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/02/2016] [Indexed: 12/30/2022]
|
7
|
Szpechcinski A, Rudzinski P, Kupis W, Langfort R, Orlowski T, Chorostowska-Wynimko J. Plasma cell-free DNA levels and integrity in patients with chest radiological findings: NSCLC versus benign lung nodules. Cancer Lett 2016; 374:202-7. [DOI: 10.1016/j.canlet.2016.02.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/27/2016] [Accepted: 02/01/2016] [Indexed: 12/11/2022]
|
8
|
Pousada G, Baloira A, Valverde D. Methylation Analysis of the BMPR2 Gene Promoter Region in Patients With Pulmonary Arterial Hypertension. Arch Bronconeumol 2015; 52:293-8. [PMID: 26654628 DOI: 10.1016/j.arbres.2015.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 09/25/2015] [Accepted: 10/15/2015] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Pulmonary arterial hypertension is characterizated by obstruction of the pulmonary arteries. The gene mainly related to pathology is the bone morphogenetic protein receptor type II (BMPR2). The aim of this study was to analyze the methylation pattern of the BMPR2 promoter region in patients and controls. METHODS We used Methyl Primer Express(®) v.1.0 and MatInspector softwares to analyze this region. Genomic DNA obtained from the peripheral blood of patients and controls was modified with sodium bisulphite. Methylation was analyzed using methylation-specific PCR. DNA treated with CpG methyltransferase was used as a positive control for methylation and H1299 cell culture DNA was used as positive control for gene expression. RESULTS We identified a CpG island, which may have been methylated, in the BMPR2 promoter region, in addition to NIT-2 (global-acting regulatory protein), sex-determining region Y) and heat shock factor transcription factor binding sites. We found no evidence of methylation in patients and controls. No methylated CpG sites were identified in H1299 cells expressing the BMPR2 gene. CONCLUSIONS The BMPR2 promoter region is the most suitable for study because of the high number of transcription factor binding sites that could alter gene function. No evidence of methylation was detected in this region in patients and controls.
Collapse
Affiliation(s)
- Guillermo Pousada
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, España; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, España
| | - Adolfo Baloira
- Servicio de Neumología, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, España
| | - Diana Valverde
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, España; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, España.
| |
Collapse
|
9
|
Chen C, Hua H, Han C, Cheng Y, Cheng Y, Wang Z, Bao J. Prognosis value of MGMT promoter methylation for patients with lung cancer: a meta-analysis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:11560-11564. [PMID: 26617891 PMCID: PMC4637707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/20/2015] [Indexed: 06/05/2023]
Abstract
The role of MGMT promoter methylation in lung cancer (LC) remains controversial. To clarify the association of MGMT promoter methylation with survival in LC, we performed a meta-analysis of the literature with meta-analysis. Trials were selected for further analysis if they provided an independent assessment of MGMT promoter methylation in LC and reported the survival data in the context of MGMT promoter methylation status. Subgroup analyses were conducted according to the study characteristic. A total of 9 trials, which comprised 859 patients, were included in the meta-analysis. The combined hazard ratio (HR) of 1.27 [95% CI 0.88-1.82; test for heterogeneity P = 0.027] suggests that MGMT promoter methylation has none impact on patient survival. In Stage I-III or younger populations, a significant association was found for MGMT promoter methylation in the prognosis of LC. In addition, the heterogeneity disappeared when the analysis was restricted to Stage I-III LC. Our analysis indicates that MGMT promoter methylation in stage I-III or younger patients was significantly correlated with wore survival. Further study is needed to determine these specific subgroups of LC patients.
Collapse
Affiliation(s)
- Chao Chen
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Nanjing Traditional Chinese Medcine University Jiangyin 214400, China
| | - Haiqing Hua
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Nanjing Traditional Chinese Medcine University Jiangyin 214400, China
| | - Chenglong Han
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Nanjing Traditional Chinese Medcine University Jiangyin 214400, China
| | - Yuan Cheng
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Nanjing Traditional Chinese Medcine University Jiangyin 214400, China
| | - Yin Cheng
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Nanjing Traditional Chinese Medcine University Jiangyin 214400, China
| | - Zhen Wang
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Nanjing Traditional Chinese Medcine University Jiangyin 214400, China
| | - Jutao Bao
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Nanjing Traditional Chinese Medcine University Jiangyin 214400, China
| |
Collapse
|
10
|
Li W, Deng J, Tang JX. Combined effects methylation of FHIT, RASSF1A and RARβ genes on non-small cell lung cancer in the Chinese population. Asian Pac J Cancer Prev 2015; 15:5233-7. [PMID: 25040980 DOI: 10.7314/apjcp.2014.15.13.5233] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Epigenetic modifications of tumour suppressor genes are involved in all kinds of human cancer. Aberrant promoter methylation is also considered to play an essential role in development of lung cancer, but the pathogenesis remains unclear.We collected the data of 112 subjects, including 56 diagnosed patients with lung cancer and 56 controls without cancer. Methylation of the FHIT, RASSF1A and RAR-β genes in DNA from all samples and the corresponding gene methylation status were assessed using the methylation-specific polymerase chain reaction (PCR, MSP). The results showed that the total frequency of separate gene methylation was significantly higher in lung cancer compared with controls (33.9-85.7 vs 0 %) (p<0.01).Similar outcomes were obtained from the aberrant methylation of combinations of any two or three genes (p<0.01). There was a tendency that the frequency of combinations of any two or three genes was higher in stage I+II than that in stage III+IV with lung cancer. However, no significant difference was found across various clinical stages and clinic pathological gradings of lung cancer (p>0.05).These observations suggest that there is a significant association of promoter methylation of individual genes with lung cancer risk, and that aberrant methylation of combination of any two or three genes may be associated with clinical stage in lung cancer patients and involved in the initiation of lung cancer tumorigenesis. Methylation of FHIT, RASSF1A and RARβ genes may be related to progression of lung oncogenesis.
Collapse
Affiliation(s)
- Wen Li
- Key Laboratory of Green Packaging and Application of Biological Nanotechnology of Hunan Province, Hunan University of Technology, ZhuZhou, Hunan Province, China E-mail :
| | | | | |
Collapse
|