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Fang F, Andersen AM, Philibert R, Hancock DB. Epigenetic biomarkers for smoking cessation. ADDICTION NEUROSCIENCE 2023; 6:100079. [PMID: 37123087 PMCID: PMC10136056 DOI: 10.1016/j.addicn.2023.100079] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cigarette smoking has been associated with epigenetic alterations that may be reversible upon cessation. As the most-studied epigenetic modification, DNA methylation is strongly associated with smoking exposure, providing a potential mechanism that links smoking to adverse health outcomes. Here, we reviewed the reversibility of DNA methylation in accessible peripheral tissues, mainly blood, in relation to cigarette smoking cessation and the utility of DNA methylation as a biomarker signature to differentiate current, former, and never smokers and to quantify time since cessation. We summarized thousands of differentially methylated Cytosine-Guanine (CpG) dinucleotides and regions associated with smoking cessation from candidate gene and epigenome-wide association studies, as well as the prediction accuracy of the multi-CpG predictors for smoking status. Overall, there is robust evidence for DNA methylation signature of cigarette smoking cessation. However, there are still gaps to fill, including (1) cell-type heterogeneity in measuring blood DNA methylation; (2) underrepresentation of non-European ancestry populations; (3) limited longitudinal data to quantitatively measure DNA methylation after smoking cessation over time; and (4) limited data to study the impact of smoking cessation on other epigenetic features, noncoding RNAs, and histone modifications. Epigenetic machinery provides promising biomarkers that can improve success in smoking cessation in the clinical setting. To achieve this goal, larger and more-diverse samples with longitudinal measures of a broader spectrum of epigenetic marks will be essential to developing a robust DNA methylation biomarker assay, followed by meeting validation requirements for the assay before being implemented as a clinically useful tool.
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Affiliation(s)
- Fang Fang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
| | - Allan M. Andersen
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
- Behavioral Diagnostics LLC, 2500 Crosspark Rd, Coralville, IA 52241, USA
- Department of Biomedical Engineering, 5601 Seamans Center for the Engineering Arts and Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Dana B. Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
- Corresponding author. (D.B. Hancock)
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Hypomethylation of AHRR (cg05575921) Is Related to Smoking Status in the Mexican Mestizo Population. Genes (Basel) 2021; 12:genes12081276. [PMID: 34440450 PMCID: PMC8391630 DOI: 10.3390/genes12081276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022] Open
Abstract
Tobacco smoking results in a multifactorial disease involving environmental and genetic factors; epigenome-wide association studies (EWAS) show changes in DNA methylation levels due to cigarette consumption, partially reversible upon tobacco smoking cessation. Therefore, methylation levels could predict smoking status. This study aimed to evaluate the DNA methylation level of cg05575921 (AHRR) and cg23771366 (PRSS23) and their correlation with lung function variables, cigarette consumption, and nicotine addiction in the Mexican smoking population. We included 114 non-smokers (NS) and 102 current tobacco smokers (TS); we then further subclassified them as heavy smokers (HS) (n = 53) and light smokers (LS) (n = 49). We used restriction enzymes (MspI/HpaII) and qPCR to determine the DNA methylation level. We observed significant hypomethylation of cg05575921 in smokers compared to NS (p = 0.003); further analysis found a difference between HS and NS (p = 0.02). We did not observe differences between other groups or a positive correlation between methylation levels and age, BMI, cigarette consumption, nicotine addiction, or lung function. In conclusion, the cg05575921 site of AHRR is significantly hypomethylated in Mexican smokers, especially in HS (≥20 cigarettes per day).
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Khoruddin NA, Noorizhab MN, Teh LK, Mohd Yusof FZ, Salleh MZ. Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays. Sci Rep 2021; 11:16158. [PMID: 34373545 PMCID: PMC8352870 DOI: 10.1038/s41598-021-95618-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most common genetic variations for various complex human diseases, including cancers. Genome-wide association studies (GWAS) have identified numerous SNPs that increase cancer risks, such as breast cancer, colorectal cancer, and leukemia. These SNPs were cataloged for scientific use. However, GWAS are often conducted on certain populations in which the Orang Asli and Malays were not included. Therefore, we have developed a bioinformatic pipeline to mine the whole-genome sequence databases of the Orang Asli and Malays to determine the presence of pathogenic SNPs that might increase the risks of cancers among them. Five different in silico tools, SIFT, PROVEAN, Poly-Phen-2, Condel, and PANTHER, were used to predict and assess the functional impacts of the SNPs. Out of the 80 cancer-related nsSNPs from the GWAS dataset, 52 nsSNPs were found among the Orang Asli and Malays. They were further analyzed using the bioinformatic pipeline to identify the pathogenic variants. Three nsSNPs; rs1126809 (TYR), rs10936600 (LRRC34), and rs757978 (FARP2), were found as the most damaging cancer pathogenic variants. These mutations alter the protein interface and change the allosteric sites of the respective proteins. As TYR, LRRC34, and FARP2 genes play important roles in numerous cellular processes such as cell proliferation, differentiation, growth, and cell survival; therefore, any impairment on the protein function could be involved in the development of cancer. rs1126809, rs10936600, and rs757978 are the important pathogenic variants that increase the risks of cancers among the Orang Asli and Malays. The roles and impacts of these variants in cancers will require further investigations using in vitro cancer models.
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Affiliation(s)
- Nurul Ain Khoruddin
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd NurFakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Farida Zuraina Mohd Yusof
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
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Vecchini Rodríguez CM, Escalona Meléndez Y, Flores-Otero J. Cannabinoid Receptors and Ligands: Lessons from CNS Disorders and the Quest for Novel Treatment Venues. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1297:43-64. [PMID: 33537936 PMCID: PMC8502072 DOI: 10.1007/978-3-030-61663-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The potential use of cannabinoids for therapeutic purposes is at the forefront of cannabinoid research which aims to develop innovative strategies to prevent, manage and treat a broad spectrum of human diseases. This chapter briefly reviews the pivotal role of the endocannabinoid system in modulating the central nervous system and its roles on neurodegenerative diseases and brain disorders. Ligand-induced modulation of cannabinoid 1 and 2 receptors to modulate immune response, decrease neurodegeneration and pain are aspects that are also discussed.
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Affiliation(s)
- Clara M Vecchini Rodríguez
- Department of Anatomy and Neurobiology, University of Puerto Rico School of Medicine, San Juan, PR, USA
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, USA
| | | | - Jacqueline Flores-Otero
- Department of Anatomy and Neurobiology, University of Puerto Rico School of Medicine, San Juan, PR, USA.
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, USA.
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Davagdorj K, Pham VH, Theera-Umpon N, Ryu KH. XGBoost-Based Framework for Smoking-Induced Noncommunicable Disease Prediction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17186513. [PMID: 32906777 PMCID: PMC7558165 DOI: 10.3390/ijerph17186513] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/28/2020] [Accepted: 09/05/2020] [Indexed: 12/23/2022]
Abstract
Smoking-induced noncommunicable diseases (SiNCDs) have become a significant threat to public health and cause of death globally. In the last decade, numerous studies have been proposed using artificial intelligence techniques to predict the risk of developing SiNCDs. However, determining the most significant features and developing interpretable models are rather challenging in such systems. In this study, we propose an efficient extreme gradient boosting (XGBoost) based framework incorporated with the hybrid feature selection (HFS) method for SiNCDs prediction among the general population in South Korea and the United States. Initially, HFS is performed in three stages: (I) significant features are selected by t-test and chi-square test; (II) multicollinearity analysis serves to obtain dissimilar features; (III) final selection of best representative features is done based on least absolute shrinkage and selection operator (LASSO). Then, selected features are fed into the XGBoost predictive model. The experimental results show that our proposed model outperforms several existing baseline models. In addition, the proposed model also provides important features in order to enhance the interpretability of the SiNCDs prediction model. Consequently, the XGBoost based framework is expected to contribute for early diagnosis and prevention of the SiNCDs in public health concerns.
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Affiliation(s)
- Khishigsuren Davagdorj
- Database and Bioinformatics Laboratory, College of Electrical and Computer Engineering, Chungbuk National University, Cheongju 28644, Korea;
| | - Van Huy Pham
- Faculty of Information Technology, Ton Duc Thang University, Ho Chi Minh 700000, Vietnam;
| | - Nipon Theera-Umpon
- Department of Electrical Engineering, Faculty of Engineering, Chiang Mai University, Chiang Mai 50200, Thailand;
- Biomedical Engineering Institute, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Keun Ho Ryu
- Faculty of Information Technology, Ton Duc Thang University, Ho Chi Minh 700000, Vietnam;
- Biomedical Engineering Institute, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: ; Tel.: +82-10-4930-1500
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Ibrahim BA, Al-Humaish S, Al-Obaide MAI. Tobacco Smoking, Lung Cancer, and Therapy in Iraq: Current Perspective. Front Public Health 2018; 6:311. [PMID: 30416993 PMCID: PMC6212484 DOI: 10.3389/fpubh.2018.00311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 10/09/2018] [Indexed: 01/16/2023] Open
Abstract
Tobacco smoking is a research topic of high interest to the public health in Iraq. Although Iraq is a country with a high percentage of smokers, we noticed the dearth of adequate studies and programs to deal with this problem. The percentage of smokers exceed 30% of the population and smoking problem becomes a permanent habit in adults and young people. The problems associated with tobacco smoking behavior related to individuals' post-traumatic stress disorder following post-war conflicts, and the social and cultural environment. The health consequences of tobacco smoking can harm almost every organ in the body, and there are reports confirmed the tobacco smoking is a high-risk factor for lung cancer and other diseases. The relative risk of lung cancer increases with increasing duration and intensity of smoking. Also, smoking associated with bladder, prostate, and head and neck cancers, in addition to respiratory diseases. Intervention efforts should focus on reducing the prevalence of cigarette smoking, introduce effective treatments for cancer and quit smoking. In this perspective article, we present our viewpoint and three scenarios to deal with the problem of tobacco smoking in Iraq. We recommend introducing educational, health and legislative policies for quitting smoking and using effective treatments for cancer.
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