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Peng Y, Ernani V, Liu D, Guo Q, Hopps M, Cappelleri JC, Gupta R, de Andrade M, Chen J, Yi ES, Yang P. Lung adenocarcinoma patients with ROS1-rearranged tumors by sex and smoking intensity. Heliyon 2024; 10:e28285. [PMID: 38560203 PMCID: PMC10981064 DOI: 10.1016/j.heliyon.2024.e28285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Background ROS1 rearrangements (ROS1+) define a distinct molecular subset of lung adenocarcinomas. ROS1 + tumors are known to occur more in never-smokers, but the frequency and outcome of ROS1 positivity by sex and smoking intensity are not clearly documented. Patients and methods This patient cohort study included all never- (<100 cigarettes lifetime) and light- (100 cigarettes-20 pack-years) smokers, and a sample of heavy-smokers. ROS1 + rates by sex and smoking intensity were compared within and beyond our study. Survival outcomes were analyzed using Kaplan-Meier curves and Cox proportional hazards models. Results Of the 571 total patients, ROS1 + was detected in 24 (4.2%): 6.4% in men and 3.0% in women; 5.1% in never-, 5.7% in light-, and 1.8% in heavy-smokers (P=0.05). Among the 209 stage IIIB-IV patients, men had much higher ROS1 + rate (11.1%) not only than women (1.7%, P=0.004) in our study, but also than men (0.4%-1.8%) in 8 published studies (Ps = 0.0019-0.0001). ROS1+ rates were similar between never- (9.3%) and light-smokers (8.1%) and significantly lower in heavy-smokers (1.2%, P=0.017), a finding confirmed by 6 published studies (Ps = 0.041-0.0001). Overall survival of ROS1 + patients were significantly better than the ROS1- (P=0.023) mainly due to targeted therapy. Among patients who exhibited resistance to crizotinib, follow-up treatment of entrectinib and lorlatinib showed remarkable survival benefits. Conclusions The ROS1 + rates were higher in men than in women, and similar in never- and light-smokers, more pronounced in stage IIIB-IV patients. Newer-generation ALK/ROS1-targeted drugs showed efficacy in a cohort of crizotinib resistant ROS1 + patients. These results, when validated, could assist efficiently accruing ROS1 + patients.
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Affiliation(s)
- Yanmei Peng
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, AZ, 85259, USA
- Department of Oncology, Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, 102400, China
| | - Vinicius Ernani
- Division of Hematology and Medical Oncology, Department of Medicine, Mayo Clinic, AZ, 85054, USA
| | - Dan Liu
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, AZ, 85259, USA
- Division of Pulmonary & Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610064, China
| | - Qian Guo
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, AZ, 85259, USA
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Markay Hopps
- Vaccine R&D, Pfizer Inc, New York, NY, 10017, USA
| | | | - Ruchi Gupta
- Division of Biostatistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Mariza de Andrade
- Division of Biostatistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jun Chen
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, AZ, 85259, USA
- The Second Affiliated Hospital of Dalian Medical University, Shahekou District, Dalian, 116023, China
| | - Eunhee S. Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ping Yang
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, AZ, 85259, USA
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Chang YP, Tsai YH, Chen YM, Huang KT, Lee CP, Hsu PY, Chen HC, Lin MC, Chen YC. Upregulated microRNA-125b-5p in patients with asthma-COPD overlap mediates oxidative stress and late apoptosis via targeting IL6R/TRIAP1 signaling. Respir Res 2024; 25:64. [PMID: 38302925 PMCID: PMC10835813 DOI: 10.1186/s12931-024-02703-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/24/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Among patients with chronic obstructive pulmonary disease (COPD), some have features of both asthma and COPD-a condition categorized as asthma-COPD overlap (ACO). Our aim was to determine whether asthma- or COPD-related microRNAs (miRNAs) play a role in the pathogenesis of ACO. METHODS A total of 22 healthy subjects and 27 patients with ACO were enrolled. We selected 6 miRNAs that were found to correlate with COPD and asthma. The expression of miRNAs and target genes was analyzed using quantitative reverse-transcriptase polymerase chain reaction. Cell apoptosis and intracellular reactive oxygen species production were evaluated using flow cytometry. In vitro human monocytic THP-1 cells and primary normal human bronchial epithelial (NHBE) cells under stimuli with cigarette smoke extract (CSE) or ovalbumin (OVA) allergen or both were used to verify the clinical findings. RESULTS We identified the upregulation of miR-125b-5p in patients with ACO and in THP-1 cells stimulated with CSE plus OVA allergen. We selected 16 genes related to the miR-125b-5p pathway and found that IL6R and TRIAP1 were both downregulated in patients with ACO and in THP-1 cells stimulated with CSE plus OVA. The percentage of late apoptotic cells increased in the THP-1 cell culture model when stimulated with CSE plus OVA, and the effect was reversed by transfection with miR-125b-5p small interfering RNA (siRNA). The percentage of reactive oxygen species-producing cells increased in the NHBE cell culture model when stimulated with CSE plus OVA, and the effect was reversed by transfection with miR-125b-5p siRNA. In NHBE cells, siRNA transfection reversed the upregulation of STAT3 under CSE+OVA stimulation. CONCLUSIONS Our study revealed that upregulation of miR-125b-5p in patients with ACO mediated late apoptosis in THP-1 cells and oxidative stress in NHBE cells via targeting IL6R and TRIAP1. STAT3 expression was also regulated by miR-125b-5p.
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Affiliation(s)
- Yu-Ping Chang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.)
| | - Yi-Hsuan Tsai
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.)
| | - Yu-Mu Chen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.)
| | - Kuo-Tung Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.)
| | - Chiu-Ping Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.)
| | - Po-Yuan Hsu
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.)
| | - Hung-Chen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.)
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.).
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.).
| | - Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.).
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, No. 123, Dapi Rd., Niaosong Dist., Kaohsiung, 83301, Taiwan (R.O.C.).
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Carreras-Gallo N, Dwaraka VB, Cáceres A, Smith R, Mendez TL, Went H, Gonzalez JR. Impact of tobacco, alcohol, and marijuana on genome-wide DNA methylation and its relationship with hypertension. Epigenetics 2023; 18:2214392. [PMID: 37216580 DOI: 10.1080/15592294.2023.2214392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/13/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Tobacco, alcohol, and marijuana consumption is an important public health problem because of their high use worldwide and their association with the risk of mortality and many health conditions, such as hypertension, which is the commonest risk factor for death throughout the world. A likely pathway of action of substance consumption leading to persistent hypertension is DNA methylation. Here, we evaluated the effects of tobacco, alcohol, and marijuana on DNA methylation in the same cohort (N = 3,424). Three epigenome-wide association studies (EWAS) were assessed in whole blood using the InfiniumHumanMethylationEPIC BeadChip. We also evaluated the mediation of the top CpG sites in the association between substance consumption and hypertension. Our analyses showed 2,569 CpG sites differentially methylated by alcohol drinking and 528 by tobacco smoking. We did not find significant associations with marijuana consumption after correcting for multiple comparisons. We found 61 genes overlapping between alcohol and tobacco that were enriched in biological processes involved in the nervous and cardiovascular systems. In the mediation analysis, we found 66 CpG sites that significantly mediated the effect of alcohol consumption on hypertension. The top alcohol-related CpG site (cg06690548, P-value = 5.9·10-83) mapped to SLC7A11 strongly mediated 70.5% of the effect of alcohol consumption on hypertension (P-value = 0.006). Our findings suggest that DNA methylation should be considered for new targets in hypertension prevention and management, particularly concerning alcohol consumption. Our data also encourage further research into the use of methylation in blood to study the neurological and cardiovascular effects of substance consumption.
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Affiliation(s)
| | | | - Alejandro Cáceres
- Epidemiology, Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Mathematics, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya, Barcelona, Spain
| | | | | | | | - Juan R Gonzalez
- Epidemiology, Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Mathematics, Universitat Autònoma de Barcelona, Barcelona, Spain
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Mahmoodi M, Karami F, Abdollahi H, Giahi N, Divsalar K, Honarmand A, Modarressi MH. Promoter Methylation of Two HOXA9 and NISCH Genes in Opium Users. ADDICTION & HEALTH 2023; 15:87-92. [PMID: 37560396 PMCID: PMC10408764 DOI: 10.34172/ahj.2023.1356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/03/2022] [Indexed: 08/11/2023]
Abstract
BACKGROUND Opiate abuse has been critically increased in the world, especially in Iran. Owing to the association of opiate use with multiple human cancers and neurological disorders, seeking for genetic and epigenetic effects of opium can pave the way for early diagnosis of major health defects in addicted users. Accordingly, the present study aimed to determine the methylation status of the promoter of two genes, which are actively involved in neurodevelopment and cancer evolution. METHODS DNA was isolated from peripheral blood of 28 opium abusers and 19 healthy controls and then subjected to sonication. Sonicated DNAs undergone methylated DNA immunoprecipitation-real time polymerase chain reaction (MeDIP-Real Time PCR) using specific primer pairs designed for HOXA9 and NISCH genes. Obtained data were analyzed using SPSS software. FINDINGS HOXA9 and NISCH genes were found to be significantly methylated in addicted users compared to controls (P<0.001) which was significantly associated with the mean of the age regarding HOXA9 gene (P=0.002). Neither opium amount nor duration or route of using was associated with the methylation status of HOXA9 or NISCH genes. CONCLUSION Hypermethylation of HOXA9 and NISCH genes as tumor suppressor in opium-addicted individuals can be considered as confirmatory evidence for carcinogenesis of opium. Further studies are required to figure out the role of epigenetic alterations in cancer evolution among opium users.
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Affiliation(s)
- Majid Mahmoodi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Karami
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
- Department of Medical Genetics, Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamidreza Abdollahi
- Department of Medical Genetics, Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Navidreza Giahi
- Akhtar Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kouros Divsalar
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Amin Honarmand
- Department of Emergency Medicine, Afzalipour Hospital, Kerman University of Medical Sciences, Kerman, Iran
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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.
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Houda A, Peter Michael J, Romeo M, Mohamad Eid H. Smoking and Its Consequences on Male and Female Reproductive Health. Stud Fam Plann 2022. [DOI: 10.5772/intechopen.104941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Smoking contributes to the death of around one in 10 adults worldwide. Specifically, cigarettes are known to contain around 4000 toxins and chemicals that are hazardous in nature. The negative effects of smoking on human health and interest in smoking-related diseases have a long history. Among these concerns are the harmful effects of smoking on reproductive health. Thirteen percent of female infertility is due to smoking. Female smoking can lead to gamete mutagenesis, early loss of reproductive function, and thus advance the time to menopause. It has been also associated with ectopic pregnancy and spontaneous abortion. Even when it comes to assisted reproductive technologies cycles, smokers require more cycles, almost double the number of cycles needed to conceive as non-smokers. Male smoking is shown to be correlated with poorer semen parameters and sperm DNA fragmentation. Not only active smokers but also passive smokers, when excessively exposed to smoking, can have reproductive problems comparable to those seen in smokers. In this book chapter, we will approach the effect of tobacco, especially tobacco smoking, on male and female reproductive health. This aims to take a preventive approach to infertility by discouraging smoking and helping to eliminate exposure to tobacco smoke in both women and men.
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Zhao X, Chen L, Wu J, You J, Hong Q, Ye F. Transcription factor KLF15 inhibits the proliferation and migration of gastric cancer cells via regulating the TFAP2A-AS1/NISCH axis. Biol Direct 2021; 16:21. [PMID: 34727954 PMCID: PMC8565027 DOI: 10.1186/s13062-021-00300-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recently, overwhelming evidence supports that long noncoding RNAs (lncRNAs) play crucial roles in the occurrence and progression of tumors. However, the role and mechanism of lncRNA TFAP2A-AS1 in human gastric cancer (GC) remains unclear. Thus, the biological role and regulatory mechanisms of TFAP2A-AS1 in GC were explored. METHODS Quantitative real-time PCR (qPCR) was applied to detect gene expression. Western blot was used to measure protein expression. Cell proliferation and migration were determined by functional assays. Fluorescence in situ hybridization (FISH) assays were performed to determine the subcellular distribution of TFAP2A-AS1 in GC. Mechanism investigations were conducted to explore the downstream genes of TFAP2A-AS1 and the upstream transcription factor of TFAP2A-AS1 in GC cells. RESULTS TFAP2A-AS1 inhibits the proliferation and migration of GC cells. In the downstream regulation mechanism, miR-3657 was verified as the downstream gene of TFAP2A-AS1 and NISCH as the target of miR-3657. NISCH also suppresses cell proliferation and migration in GC. In the upstream regulation mechanism, transcription factor KLF15 positively mediates TFAP2A-AS1 to suppress GC cell proliferation and migration. CONCLUSION KLF15-mediated TFAP2A-AS1 hampers cell proliferation and migration in GC via miR-3657/NISCH axis.
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Affiliation(s)
- Xin Zhao
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of clinical Medicine,, Fujian Medical University, No. 55 Zhenhai Road, Siming District, Xiamen, Fujian, China
| | - Linlin Chen
- Department of Gastroenterology, Xiangya Hospital of Centre-South University, Changsha, Hunan, China
| | - Jingxun Wu
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of clinical Medicine,, Fujian Medical University, No. 55 Zhenhai Road, Siming District, Xiamen, Fujian, China
| | - Jun You
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of clinical Medicine,, Fujian Medical University, No. 55 Zhenhai Road, Siming District, Xiamen, Fujian, China
| | - Qingqi Hong
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of clinical Medicine,, Fujian Medical University, No. 55 Zhenhai Road, Siming District, Xiamen, Fujian, China
| | - Feng Ye
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of clinical Medicine,, Fujian Medical University, No. 55 Zhenhai Road, Siming District, Xiamen, Fujian, China.
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Malapelle U, Pisapia P, Addeo A, Arrieta O, Bellosillo B, Cardona AF, Cristofanilli M, De Miguel-Perez D, Denninghoff V, Durán I, Jantus-Lewintre E, Nuzzo PV, O'Byrne K, Pauwels P, Pickering EM, Raez LE, Russo A, Serrano MJ, Gandara DR, Troncone G, Rolfo C. Liquid biopsy from research to clinical practice: focus on non-small cell lung cancer. Expert Rev Mol Diagn 2021; 21:1165-1178. [PMID: 34570988 DOI: 10.1080/14737159.2021.1985468] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION In the current era of personalized medicine, liquid biopsy has acquired a relevant importance in patient management of advanced stage non-small cell lung cancer (NSCLC). As a matter of fact, liquid biopsy may supplant the problem of inadequate tissue for molecular testing. The term 'liquid biopsy' refers to a number of different biological fluids, but is most clearly associated with plasma-related platforms. It must be taken into account that pre-analytical processing and the selection of the appropriate technology according to the clinical context may condition the results obtained. In addition, novel clinical applications beyond the evaluation of the molecular status of predictive biomarkers are currently under investigation. AREAS COVERED This review summarizes the available evidence on pre-analytical issues and different clinical applications of liquid biopsies in NSCLC patients. EXPERT OPINION Liquid biopsy should be considered not only as a valid alternative but as complementary to tissue-based molecular approaches. Careful attention should be paid to the optimization and standardization of all phases of liquid biopsy samples management in order to determine a significant improvement in either sensitivity or specificity, while significant reducing the number of 'false negative' or 'false positive' molecular results.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Alfredo Addeo
- Oncology Department, University Hospital Geneva, Geneva, Switzerland
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), México City, México
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Del Mar, Barcelona, Spain.,Department of Pathology, Ciberonc, Madrid, Spain
| | - Andres F Cardona
- Department of Oncology, Clinical and Translational Oncology Group, Clínica Del Country, Bogotá, Colombia.,Department of Oncology, Foundation for Clinical and Applied Cancer Research (Ficmac), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-g/oncolgroup), Universidad el Bosque, Bogotá, Colombia
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Diego De Miguel-Perez
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Valeria Denninghoff
- Department of Pathology, University of Buenos Aires - National Council for Scientific and Technical Research (Conicet), Buenos Aires, Argentina
| | - Ignacio Durán
- Department of Oncology, Hospital Universitario Marques de Valdecilla, IDIVAL, Santander, Spain
| | - Eloísa Jantus-Lewintre
- Department of Pathology, Ciberonc, Madrid, Spain.,Molecular Oncology Laboratory, Fundación Para La Investigación Del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,Department of Biotechnology, Universitat Politècnica De València, Valencia, Spain
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ken O'Byrne
- Medical Oncology, Princess Alexandra Hospital, Queensland University of Technology, Brisbane City, Australia
| | - Patrick Pauwels
- Center for Oncological Research Antwerp (Core), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (Uantwerp), Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Edward M Pickering
- Divison of Pulmonary and Critical Care Medicine, Section of Interventional Pulmonology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Luis E Raez
- Thoracic Oncology Program, Memorial Cancer Institute/Memorial Health Care System, Florida International University, Miami, FL, USA
| | - Alessandro Russo
- Department of Oncology, Medical Oncology Unit, A.O. Papardo, Messina, Italy
| | - Maria José Serrano
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain
| | - David R Gandara
- Department of Internal Medicine, UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
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Farooq M, Herman JG. Noninvasive Diagnostics for Early Detection of Lung Cancer: Challenges and Potential with a Focus on Changes in DNA Methylation. Cancer Epidemiol Biomarkers Prev 2020; 29:2416-2422. [PMID: 33148791 DOI: 10.1158/1055-9965.epi-20-0704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/20/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022] Open
Abstract
Lung cancer remains the leading cause of cancer deaths in the United States and the world. Early detection of this disease can reduce mortality, as demonstrated for low-dose computed tomography (LDCT) screening. However, there remains a need for improvements in lung cancer detection to complement LDCT screening and to increase adoption of screening. Molecular changes in the tumor, and the patient's response to the presence of the tumor, have been examined as potential biomarkers for diagnosing lung cancer. There are significant challenges to developing an effective biomarker with sufficient sensitivity and specificity for the early detection of lung cancer, particularly the detection of circulating tumor DNA, which is present in very small quantities. We will review approaches to develop biomarkers for the early detection of lung cancer, with special consideration to detection of rare tumor events, focus on the use of DNA methylation-based detection in plasma and sputum, and discuss the promise and challenges of lung cancer early detection. Plasma-based detection of lung cancer DNA methylation may provide a simple cost-effective method for the early detection of lung cancer.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Maria Farooq
- Department of Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - James G Herman
- Department of Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania. .,UPMC Hillman Comprehensive Cancer Center, Pittsburgh, Pennsylvania
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Kaur G, Begum R, Thota S, Batra S. A systematic review of smoking-related epigenetic alterations. Arch Toxicol 2019; 93:2715-2740. [PMID: 31555878 DOI: 10.1007/s00204-019-02562-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023]
Abstract
The aim of this study is to provide a systematic review of the known epigenetic alterations caused by cigarette smoke; establish an evidence-based perspective of their clinical value for screening, diagnosis, and treatment of smoke-related disorders; and discuss the challenges and ethical concerns associated with epigenetic studies. A well-defined, reproducible search strategy was employed to identify relevant literature (clinical, cellular, and animal-based) between 2000 and 2019 based on AMSTAR guidelines. A total of 80 studies were identified that reported alterations in DNA methylation, histone modifications, and miRNA expression following exposure to cigarette smoke. Changes in DNA methylation were most extensively documented for genes including AHRR, F2RL3, DAPK, and p16 after exposure to cigarette smoke. Likewise, miR16, miR21, miR146, and miR222 were identified to be differentially expressed in smokers and exhibit potential as biomarkers for determining susceptibility to COPD. We also identified 22 studies highlighting the transgenerational effects of maternal and paternal smoking on offspring. This systematic review lists the epigenetic events/alterations known to occur in response to cigarette smoke exposure and identifies the major genes and miRNAs that are potential targets for translational research in associated pathologies. Importantly, the limitations and ethical concerns related to epigenetic studies are also highlighted, as are the effects on the ability to address specific questions associated with exposure to tobacco/cigarette smoke. In the future, improved interpretation of epigenetic signatures will lead to their increased use as biomarkers and/or in drug development.
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Affiliation(s)
- Gagandeep Kaur
- Laboratory of Pulmonary Immuno-toxicology, Department of Environmental Toxicology, 129 Health Research Centre, Southern University and A&M College, Baton Rouge, LA, 70813, USA
| | - Rizwana Begum
- Laboratory of Pulmonary Immuno-toxicology, Department of Environmental Toxicology, 129 Health Research Centre, Southern University and A&M College, Baton Rouge, LA, 70813, USA
| | - Shilpa Thota
- Laboratory of Pulmonary Immuno-toxicology, Department of Environmental Toxicology, 129 Health Research Centre, Southern University and A&M College, Baton Rouge, LA, 70813, USA
| | - Sanjay Batra
- Laboratory of Pulmonary Immuno-toxicology, Department of Environmental Toxicology, 129 Health Research Centre, Southern University and A&M College, Baton Rouge, LA, 70813, USA.
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11
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Freudenheim JL, Shields PG, Song MA, Smiraglia D. DNA Methylation and Smoking: Implications for Understanding Effects of Electronic Cigarettes. CURR EPIDEMIOL REP 2019. [DOI: 10.1007/s40471-019-00191-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Li L, Fu K, Zhou W, Snyder M. Applying circulating tumor DNA methylation in the diagnosis of lung cancer. PRECISION CLINICAL MEDICINE 2019; 2:45-56. [PMID: 35694699 PMCID: PMC8985769 DOI: 10.1093/pcmedi/pbz003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/17/2019] [Accepted: 03/14/2019] [Indexed: 02/05/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Low dose computed tomography (LDCT) is commonly used for disease screening, with identified candidate cancerous regions further diagnosed using tissue biopsy. However, existing techniques are all invasive and unavoidably cause multiple complications. In contrast, liquid biopsy is a noninvasive, ideal surrogate for tissue biopsy that can identify circulating tumor DNA (ctDNA) containing tumorigenic signatures. It has been successfully implemented to assist treatment decisions and disease outcome prediction. ctDNA methylation, a type of lipid biopsy that profiles critical epigenetic alterations occurring during carcinogenesis, has gained increasing attention. Indeed, aberrant ctDNA methylation occurs at early stages in lung malignancy and therefore can be used as an alternative for the early diagnosis of lung cancer. In this review, we give a brief synopsis of the biological basis and detecting techniques of ctDNA methylation. We then summarize the latest progress in use of ctDNA methylation as a diagnosis biomarker. Lastly, we discuss the major issues that limit application of ctDNA methylation in the clinic, and propose possible solutions to enhance its usage.
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Affiliation(s)
- Lei Li
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, 37 Guoxuexiang, Chengdu, China
| | - Kai Fu
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
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Lozano MD, Echeveste JI, Abengozar M, Mejías LD, Idoate MA, Calvo A, de Andrea CE. Cytology Smears in the Era of Molecular Biomarkers in Non-Small Cell Lung Cancer: Doing More With Less. Arch Pathol Lab Med 2019; 142:291-298. [PMID: 29494220 DOI: 10.5858/arpa.2017-0208-ra] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - The rapid advances in targeted therapies in non-small cell lung cancer (NSCLC) make the optimization and implementation of cytology specimens for molecular testing a priority. Up to 70% of patients with NSCLC are diagnosed at advanced stages and tissue biopsies often cannot be taken. Although cytology samples provide high-quality material for molecular testing, molecular cytopathology is not yet well known or widely used. OBJECTIVE - To report the many advances in molecular cytopathology and the suitability and utility of cytology samples in molecular and genetic testing of NSCLC. DATA SOURCES - Data sources comprised published peer-reviewed literature and personal experience of the authors. CONCLUSIONS - Molecular testing can be performed on cytologic specimens, especially on direct smears. Rapid on-site evaluation by cytopathologists has improved the adequacy and the management of cytology samples for molecular testing. Mutational profiling of NSCLC using next-generation sequencing can be performed on cytology samples from very small amounts of DNA. Fluorescence in situ hybridization assays on cytology specimens, including stained direct smear, offer some distinct advantages over their histologic counterpart, and are used to detect ALK and ROS1 rearrangements in NSCLC. Cytology specimens allow assessment of the entire tumor cell nucleus, avoiding signal loss from truncation artifacts. The use of cytology samples for assessing programmed death ligand-1 protein expression is currently being developed. Protocols for bisulfite conversion and DNA droplet digital polymerase chain reaction assays have been optimized for cytology smear to investigate aberrant DNA methylation of several NSCLC-related genes.
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Affiliation(s)
| | | | | | | | | | | | - Carlos E de Andrea
- From the Department of Pathology, Clínica Universidad de Navarra, (Drs Lozano, Echeveste, Abengozar, Mejías, Idoate, and de Andrea), IDISNA and Program in Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA) (Dr Calvo), and the Department of Histology and Pathology (Drs Calvo and de Andrea), University of Navarra, Pamplona, Spain
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14
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Abstract
Cell-free DNA can be evaluated for the epigenetic component. Epigenetic alterations consist of changes in gene functions that do not involve changes in DNA sequence. The mainly studied epigenetic alteration is DNA methylation occurring at CpG islands in the promoter regions for which several literature data showed clinical relevance. This chapter is an overview of the epigenetic alterations detected in cell-free DNA.
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15
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16
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Franczak C, Filhine-Tressarieu P, Broséus J, Gilson P, Merlin JL, Harlé A. Clinical Interest of Circulating Tumor DNA in Oncology. Arch Med Res 2018; 49:297-305. [PMID: 30414710 DOI: 10.1016/j.arcmed.2018.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/25/2018] [Indexed: 12/18/2022]
Abstract
Genetic alterations in tumors, as predictor of response to targeted-therapies or as prognostic markers, are clinically relevant to determine adequate therapeutic management. Tumor biopsy is currently the golden standard for somatic alterations assessment, but this approach is invasive and does not consider tumor heterogeneity. In various body fluids like plasma, somatic mutations have been identified. Circulating tumor DNA (ctDNA) holds promises in tumor burden monitoring or malignancies early detection. Since allele frequencies of circulating somatic mutations are low, highly sensitive novel assays have been developed to allow the investigation of the tumor genome, leading to the emergence of the "liquid biopsy" concept. Despite these technological advances, other assays for identifying intratumor and intermetastases heterogeneity need to be developed. Before being applied to clinic, ctDNA analyses need to be harmonized and validated with well-powered, well-designed studies. One of the primary prerequisite to incorporation of ctDNA analysis in the follow-up strategy of malignancies is the checking of the concordance with golden standard detection methods, imaging, circulating proteins and biopsy. This review focuses on the clinical interest of ctDNA in solid tumors and hematological malignancies.
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Affiliation(s)
- Claire Franczak
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandœuvre-lès-Nancy, France
| | | | - Julien Broséus
- Inserm U954, Faculté de Médecine de Nancy, Université de Lorraine, Vandœuvre-lès-Nancy, France; Service d'Hématologie Biologique, Pôle Laboratoires, Centre Hospitalier Régional et Universitaire de Nancy, Vandœuvre-lès-Nancy, France
| | - Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Jean-Louis Merlin
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Alexandre Harlé
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France.
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17
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Vera-Puente O, Rodriguez-Antolin C, Salgado-Figueroa A, Michalska P, Pernia O, Reid BM, Rosas R, Garcia-Guede A, SacristÁn S, Jimenez J, Esteban-Rodriguez I, Martin ME, Sellers TA, León R, Gonzalez VÍM, De Castro J, Ibanez de Caceres I. MAFG is a potential therapeutic target to restore chemosensitivity in cisplatin-resistant cancer cells by increasing reactive oxygen species. Transl Res 2018; 200:1-17. [PMID: 30053382 PMCID: PMC7787305 DOI: 10.1016/j.trsl.2018.06.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/06/2018] [Accepted: 06/17/2018] [Indexed: 02/05/2023]
Abstract
Adjuvant chemotherapy for solid tumors based on platinum-derived compounds such as cisplatin is the treatment of choice in most cases. Cisplatin triggers signaling pathways that lead to cell death, but it also induces changes in tumor cells that modify the therapeutic response, thereby leading to cisplatin resistance. We have recently reported that microRNA-7 is silenced by DNA methylation and is involved in the resistance to platinum in cancer cells through the action of the musculoaponeurotic fibrosarcoma oncogene family, protein G (MAFG). In the present study, we first confirm the miR-7 epigenetic regulation of MAFG in 44 normal- and/or tumor-paired samples in non-small-cell lung cancer (NSCLC). We also provide translational evidence of the role of MAFG and the clinical outcome in NSCLC by the interrogation of two extensive in silico databases of 2019 patients. Moreover, we propose that MAFG-mediated resistance could be conferred due to lower reactive oxygen species production after cisplatin exposure. We developed specifically selected aptamers against MAFG, with high sensitivity to detect the protein at a nuclear level probed by aptacytochemistry and histochemistry analyses. The inhibition of MAFG activity through the action of the specific aptamer apMAFG6F increased the levels of reactive oxygen species production and the sensitivity to cisplatin. We report first the specific nuclear identification of MAFG as a novel detection method for diagnosis in NSCLC, and then we report that MAFG modulates the redox response and confers cell protection against free radicals generated after platinum administration, thus also being a promising therapeutic target.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/pharmacology
- Carcinoma, Non-Small-Cell Lung/diagnosis
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Cell Line, Tumor
- Cisplatin/therapeutic use
- Cloning, Molecular
- DNA Methylation
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/physiology
- Epigenesis, Genetic/genetics
- Gene Expression
- Gene Silencing
- HEK293 Cells
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- MafG Transcription Factor/antagonists & inhibitors
- MafG Transcription Factor/genetics
- MafG Transcription Factor/physiology
- MicroRNAs/genetics
- MicroRNAs/physiology
- Oxidation-Reduction
- Prognosis
- Reactive Oxygen Species/metabolism
- Repressor Proteins/antagonists & inhibitors
- Repressor Proteins/genetics
- Repressor Proteins/physiology
- Sequence Analysis, DNA
- Transfection
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Affiliation(s)
- Olga Vera-Puente
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Ana Salgado-Figueroa
- Department of Biochemistry Research, Laboratory of Aptamers, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Patrycja Michalska
- Biomedical Research Foundation of University Hospital La Princesa, Madrid, Spain; Institute Teófilo Hernando and Department of Pharmacology and Therapeutics, Autonomous University of Madrid, Madrid, Spain
| | - Olga Pernia
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Brett M Reid
- Department of Cancer Epidemiology, MOFFITT Cancer Center, Tampa, Florida
| | - RocÍo Rosas
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Alvaro Garcia-Guede
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Silvia SacristÁn
- Department of Biochemistry Research, Laboratory of Aptamers, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Julia Jimenez
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Isabel Esteban-Rodriguez
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain; Department of Pathology, La Paz University Hospital, Madrid, Spain
| | - M Elena Martin
- Department of Biochemistry Research, Laboratory of Aptamers, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Thomas A Sellers
- Department of Cancer Epidemiology, MOFFITT Cancer Center, Tampa, Florida
| | - Rafael León
- Biomedical Research Foundation of University Hospital La Princesa, Madrid, Spain; Institute Teófilo Hernando and Department of Pharmacology and Therapeutics, Autonomous University of Madrid, Madrid, Spain
| | - VÍctor M Gonzalez
- Department of Biochemistry Research, Laboratory of Aptamers, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Javier De Castro
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Inmaculada Ibanez de Caceres
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain.
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18
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Krishnamurthy K, Mishra TK, Saxena A, Daga MK, Khurana N, Masroor M, Jamatia E. Evaluating NISCH and CDH1 Promoter Hypermethylation in Nonsmokers, Cancer Free Smokers and Lung Cancer Patients: A Case Control Study. Indian J Clin Biochem 2018; 34:458-464. [PMID: 31686733 DOI: 10.1007/s12291-018-0767-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/09/2018] [Indexed: 11/26/2022]
Abstract
Lung cancer has very high mortality due to late stage diagnosis not amenable to curative resection. Cancer specific methylation patterns of tumor suppressor genes may precede precursor lesions of lung cancer. Our aim was to evaluate the promoter hypermethylation of tumor suppressor gene NISCH and CDH1 in cfDNA from plasma of lung cancer patients and its possible correlation with smoking status and various clinicopathological parameters. Forty histopathologically confirmed lung cancer cases, thirty smoker and thirty nonsmoker controls were enrolled. Plasma cfDNA was extracted and subjected to bisulfite treatment followed by MS-PCR. Serum nischarin levels were estimated by ELISA. The frequency of promoter hypermethylation of NISCH and CDH1 was significantly higher in lung cancer patients as compared to lifelong non-smoker controls (p < 0.05). It did not vary with smoking status among cancer cases. No significant association was found with staging or histological grading. NISCH methylation was found to be significantly higher among smoker controls. Pack years and packs per day were significantly higher in the methylated group. Serum nischarin levels showed no significant association with NISCH methylation or clinicopathological variables. NISCH is highly methylated in both high risk smoker controls as well as cancerousnon-smokers and may mark the convergence of varied etiologies of lung cancer. Hence NISCH and CDH1 are highly methylated in plasma cfDNA of lung cancer patients.
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Affiliation(s)
- Kritika Krishnamurthy
- 1Department of Biochemistry, Maulana Azad Medical College, 2 Bahadur Shah Zafar Marg, New Delhi, India
| | - T K Mishra
- 1Department of Biochemistry, Maulana Azad Medical College, 2 Bahadur Shah Zafar Marg, New Delhi, India
| | - Alpana Saxena
- 1Department of Biochemistry, Maulana Azad Medical College, 2 Bahadur Shah Zafar Marg, New Delhi, India
| | - M K Daga
- 2Department of Medicine, Maulana Azad Medical College, 2 Bahadur Shah Zafar Marg, New Delhi, India
| | - Nita Khurana
- 3Department of Pathology, Maulana Azad Medical College, 2 Bahadur Shah Zafar Marg, New Delhi, India
| | - Mirza Masroor
- 1Department of Biochemistry, Maulana Azad Medical College, 2 Bahadur Shah Zafar Marg, New Delhi, India
| | - Elvia Jamatia
- 1Department of Biochemistry, Maulana Azad Medical College, 2 Bahadur Shah Zafar Marg, New Delhi, India
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19
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Wan M, Bennett BD, Pittman GS, Campbell MR, Reynolds LM, Porter DK, Crowl CL, Wang X, Su D, Englert NA, Thompson IJ, Liu Y, Bell DA. Identification of Smoking-Associated Differentially Methylated Regions Using Reduced Representation Bisulfite Sequencing and Cell type-Specific Enhancer Activation and Gene Expression. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:047015. [PMID: 29706059 PMCID: PMC6071796 DOI: 10.1289/ehp2395] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Cigarette smoke is a causal factor in cancers and cardiovascular disease. Smoking-associated differentially methylated regions (SM-DMRs) have been observed in disease studies, but the causal link between altered DNA methylation and transcriptional change is obscure. OBJECTIVE Our objectives were to finely resolve SM-DMRs and to interrogate the mechanistic link between SM-DMRs and altered transcription of enhancer noncoding RNA (eRNA) and mRNA in human circulating monocytes. METHOD We integrated SM-DMRs identified by reduced representation bisulfite sequencing (RRBS) of circulating CD14+ monocyte DNA collected from two independent human studies [n=38 from Clinical Research Unit (CRU) and n=55 from the Multi-Ethnic Study of Atherosclerosis (MESA), about half of whom were active smokers] with gene expression for protein-coding genes and noncoding RNAs measured by RT-PCR or RNA sequencing. Candidate SM-DMRs were compared with RRBS of purified CD4+ T cells, CD8+ T cells, CD15+ granulocytes, CD19+ B cells, and CD56+ NK cells (n=19 females, CRU). DMRs were validated using pyrosequencing or bisulfite amplicon sequencing in up to 85 CRU volunteers, who also provided saliva DNA. RESULTS RRBS identified monocyte SM-DMRs frequently located in putative gene regulatory regions. The most significant monocyte DMR occurred at a poised enhancer in the aryl-hydrocarbon receptor repressor gene (AHRR) and it was also detected in both granulocytes and saliva DNA. To our knowledge, we identify for the first time that SM-DMRs in or near AHRR, C5orf55-EXOC-AS, and SASH1 were associated with increased noncoding eRNA as well as mRNA in monocytes. Functionally, the AHRR SM-DMR appeared to up-regulate AHRR mRNA through activating the AHRR enhancer, as suggested by increased eRNA in the monocytes, but not granulocytes, from smokers compared with nonsmokers. CONCLUSIONS Our findings suggest that AHRR SM-DMR up-regulates AHRR mRNA in a monocyte-specific manner by activating the AHRR enhancer. Cell type-specific activation of enhancers at SM-DMRs may represent a mechanism driving smoking-related disease. https://doi.org/10.1289/EHP2395.
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Affiliation(s)
- Ma Wan
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Brian D Bennett
- Integrative Bioinformatics Support Group, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina, USA
| | - Gary S Pittman
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Michelle R Campbell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Lindsay M Reynolds
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Devin K Porter
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Christopher L Crowl
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Xuting Wang
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Dan Su
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Neal A Englert
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Isabel J Thompson
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Douglas A Bell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
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20
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Marczylo EL, Jacobs MN, Gant TW. Environmentally induced epigenetic toxicity: potential public health concerns. Crit Rev Toxicol 2016; 46:676-700. [PMID: 27278298 PMCID: PMC5030620 DOI: 10.1080/10408444.2016.1175417] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Throughout our lives, epigenetic processes shape our development and enable us to adapt to a constantly changing environment. Identifying and understanding environmentally induced epigenetic change(s) that may lead to adverse outcomes is vital for protecting public health. This review, therefore, examines the present understanding of epigenetic mechanisms involved in the mammalian life cycle, evaluates the current evidence for environmentally induced epigenetic toxicity in human cohorts and rodent models and highlights the research considerations and implications of this emerging knowledge for public health and regulatory toxicology. Many hundreds of studies have investigated such toxicity, yet relatively few have demonstrated a mechanistic association among specific environmental exposures, epigenetic changes and adverse health outcomes in human epidemiological cohorts and/or rodent models. While this small body of evidence is largely composed of exploratory in vivo high-dose range studies, it does set a precedent for the existence of environmentally induced epigenetic toxicity. Consequently, there is worldwide recognition of this phenomenon, and discussion on how to both guide further scientific research towards a greater mechanistic understanding of environmentally induced epigenetic toxicity in humans, and translate relevant research outcomes into appropriate regulatory policies for effective public health protection.
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Affiliation(s)
- Emma L Marczylo
- a Toxicology Department, CRCE, PHE, Chilton , Oxfordshire , UK
| | - Miriam N Jacobs
- a Toxicology Department, CRCE, PHE, Chilton , Oxfordshire , UK
| | - Timothy W Gant
- a Toxicology Department, CRCE, PHE, Chilton , Oxfordshire , UK
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21
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Warton K, Samimi G. Methylation of cell-free circulating DNA in the diagnosis of cancer. Front Mol Biosci 2015; 2:13. [PMID: 25988180 PMCID: PMC4428375 DOI: 10.3389/fmolb.2015.00013] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/07/2015] [Indexed: 01/04/2023] Open
Abstract
A range of molecular alterations found in tumor cells, such as DNA mutations and DNA methylation, is reflected in cell-free circulating DNA (circDNA) released from the tumor into the blood, thereby making circDNA an ideal candidate for the basis of a blood-based cancer diagnosis test. In many cancer types, mutations driving tumor development and progression are present in a wide range of oncogenes and tumor suppressor genes. However, even when a gene is consistently mutated in a particular cancer, the mutations can be spread over very large regions of its sequence, making evaluation difficult. This diversity of sequence changes in tumor DNA presents a challenge for the development of blood tests based on DNA mutations for cancer diagnosis. Unlike mutations, DNA methylation that can be consistently measured, as it tends to occur in specific regions of the DNA called CpG islands. Since DNA methylation is reflected within circDNA, detection of tumor-specific DNA methylation in patient plasma is a feasible approach for the development of a blood-based test. Aberrant circDNA methylation has been described in most cancer types and is actively being investigated for clinical applications. A commercial blood test for colorectal cancer based on the methylation of the SEPT9 promoter region in circDNA is under review for approval by the Federal Drug Administration (FDA) for clinical use. In this paper, we review the state of research in circDNA methylation as an application for blood-based diagnostic tests in colorectal, breast, lung, pancreatic and ovarian cancers, and we consider some of the future directions and challenges in this field. There are a number of potential circDNA biomarkers currently under investigation, and experience with SEPT9 shows that the time to clinical translation can be relatively rapid, supporting the promise of circDNA as a biomarker.
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Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Goli Samimi
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
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22
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Besingi W, Johansson A. Smoke-related DNA methylation changes in the etiology of human disease. Hum Mol Genet 2013; 23:2290-7. [PMID: 24334605 DOI: 10.1093/hmg/ddt621] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Exposure to environmental and lifestyle factors, such as cigarette smoking, affect the epigenome and might mediate risk for diseases and cancers. We have performed a genome-wide DNA methylation study to determine the effect of smoke and snuff (smokeless tobacco) on DNA methylation. A total of 95 sites were differentially methylated [false discovery rate (FDR) q-values < 0.05] in smokers and a subset of the differentially methylated loci were also differentially expressed in smokers. We found no sites, neither any biological functions nor molecular processes enriched for smoke-less tobacco-related differential DNA methylation. This suggests that methylation changes are not caused by the basic components of the tobacco but from its burnt products. Instead, we see a clear enrichment (FDR q-value < 0.05) for genes, including CPOX, CDKN1A and PTK2, involved in response to arsenic-containing substance, which agrees with smoke containing small amounts of arsenic. A large number of biological functions and molecular processes with links to disease conditions are also enriched (FDR q-value < 0.05) for smoke-related DNA methylation changes. These include 'insulin receptor binding', and 'negative regulation of glucose import' which are associated with diabetes, 'positive regulation of interleukin-6-mediated signaling pathway', 'regulation of T-helper 2 cell differentiation', 'positive regulation of interleukin-13 production' which are associated with the immune system and 'sertoli cell fate commitment' which is important for male fertility. Since type 2 diabetes, repressed immune system and infertility have previously been associated with smoking, our results suggest that this might be mediated by DNA methylation changes.
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Affiliation(s)
- Welisane Besingi
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory
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DNA methylation in complex disease: Applications in nursing research, practice, and policy. Nurs Outlook 2013; 61:235-241.e4. [DOI: 10.1016/j.outlook.2013.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/23/2013] [Accepted: 04/28/2013] [Indexed: 12/31/2022]
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