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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [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: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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Philibert R, Dogan TK, Knight S, Ahmad F, Lau S, Miles G, Knowlton KU, Dogan MV. Validation of an Integrated Genetic-Epigenetic Test for the Assessment of Coronary Heart Disease. J Am Heart Assoc 2023; 12:e030934. [PMID: 37982274 PMCID: PMC10727271 DOI: 10.1161/jaha.123.030934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/16/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Coronary heart disease (CHD) is the leading cause of death in the world. Unfortunately, many of the key diagnostic tools for CHD are insensitive, invasive, and costly; require significant specialized infrastructure investments; and do not provide information to guide postdiagnosis therapy. In prior work using data from the Framingham Heart Study, we provided in silico evidence that integrated genetic-epigenetic tools may provide a new avenue for assessing CHD. METHODS AND RESULTS In this communication, we use an improved machine learning approach and data from 2 additional cohorts, totaling 449 cases and 2067 controls, to develop a better model for ascertaining symptomatic CHD. Using the DNA from the 2 new cohorts, we translate and validate the in silico findings into an artificial intelligence-guided, clinically implementable method that uses input from 6 methylation-sensitive digital polymerase chain reaction and 10 genotyping assays. Using this method, the overall average area under the curve, sensitivity, and specificity in the 3 test cohorts is 82%, 79%, and 76%, respectively. Analysis of targeted cytosine-phospho-guanine loci shows that they map to key risk pathways involved in atherosclerosis that suggest specific therapeutic approaches. CONCLUSIONS We conclude that this scalable integrated genetic-epigenetic approach is useful for the diagnosis of symptomatic CHD, performs favorably as compared with many existing methods, and may provide personalized insight to CHD therapy. Furthermore, given the dynamic nature of DNA methylation and the ease of methylation-sensitive digital polymerase chain reaction methodologies, these findings may pave a pathway for precision epigenetic approaches for monitoring CHD treatment response.
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Affiliation(s)
- Robert Philibert
- Cardio Diagnostics IncChicagoILUSA
- Department of PsychiatryUniversity of IowaIowa CityIAUSA
- Department of Biomedical EngineeringUniversity of IowaIowa CityIAUSA
| | | | - Stacey Knight
- Intermountain Heart Institute, Intermountain HealthcareSalt Lake CityUTUSA
- Department of Internal MedicineUniversity of UtahSalt Lake CityUTUSA
| | - Ferhaan Ahmad
- Division of Cardiovascular Medicine, Department of Internal MedicineUniversity of IowaIowa CityIAUSA
| | - Stanley Lau
- Southern California Heart CentersSan GabrielCAUSA
| | - George Miles
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
| | - Kirk U. Knowlton
- Intermountain Heart Institute, Intermountain HealthcareSalt Lake CityUTUSA
| | - Meeshanthini V. Dogan
- Cardio Diagnostics IncChicagoILUSA
- Department of Biomedical EngineeringUniversity of IowaIowa CityIAUSA
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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] [Grants] [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
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Philibert R, Hoffman RM. Assessing Our Will to Change. Chest 2023; 163:1360-1361. [PMID: 37295878 DOI: 10.1016/j.chest.2023.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 06/12/2023] Open
Affiliation(s)
- Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA; Behavioral Diagnostics LLC, Coralville, IA.
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Jacobsen KK, Kobylecki CJ, Skov-Jeppesen SM, Bojesen SE. Development and validation of a simple general population lung cancer risk model including AHRR-methylation. Lung Cancer 2023; 181:107229. [PMID: 37150141 DOI: 10.1016/j.lungcan.2023.107229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/09/2023]
Abstract
INTRODUCTION Screening reduces lung cancer mortality of high-risk populations. Currently proposed screening eligibility criteria only identify half of those individuals, who later develop lung cancer. This study aimed to develop and validate a sensitive and simple model for predicting 10-year lung cancer risk. METHODS Using the 1991-94 examination of The Copenhagen City Heart Study in Denmark, 6,820 former or current smokers from the general population were followed for lung cancer within 10 years after examination. Logistic regression of baseline variables (age, sex, education, chronic obstructive pulmonary disease, family history of lung cancer, smoking status and cumulative smoking, secondhand smoking, occupational exposures to dust and fume, body mass index, lung function, plasma C-reactive protein, and AHRR(cg05575921) methylation) identified the best predictive model. The model was validated among 3,740 former or current smokers from the 2001-03 examination, also followed for 10 years. A simple risk chart was developed with Poisson regression. RESULTS Age, sex, education, smoking status, cumulative smoking, and AHRR(cg05575921) methylation identified 65 of 88 individuals who developed lung cancer in the validation cohort. The highest risk group, consisting of less educated men aged >65 with current smoking status and cumulative smoking >20 pack-years, had absolute 10-year risks varying from 4% to 16% by AHRR(cg05575921) methylation. CONCLUSION A simple risk chart including age, sex, education, smoking status, cumulative smoking, and AHRR(cg05575921) methylation, identifies individuals with 10-year lung cancer risk from below 1% to 16%. Including AHRR(cg05575921) methylation in the eligibility criteria for screening identifies smokers who would benefit the most from screening.
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Affiliation(s)
- Katja Kemp Jacobsen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, Copenhagen, Denmark
| | - Camilla Jannie Kobylecki
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Sune Moeller Skov-Jeppesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Stig Egil Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark; The Copenhagen City Heart Study, Copenhagen University Hospital, Frederiksberg and Bispebjerg Hospital, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Long JD, Gehlsen MP, Moody J, Weeks G, Philibert R. Predictors of Smoking in Older Adults and an Epigenetic Validation of Self-Report. Genes (Basel) 2022; 14:genes14010025. [PMID: 36672765 PMCID: PMC9912258 DOI: 10.3390/genes14010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
There are several established predictors of smoking, but it is unknown if these predictors operate similarly for young and old smokers. We examined clinical data from the National Lung Screening Trial (NLST) to determine the predictive ability of gender, body mass index (BMI), marital status, and race on smoking behavior, with emphasis on gender interactions. In addition, we validated the self-report of smoking behaviors for a subgroup that had available epigenetic data in the form of cg05575921 methylation. Participants were N=9572 current or former smokers from the NLST biofluids database, age 55-74, minimum of 30 pack years, and mostly White. A subgroup of N=3084 who had DNA were used for the self-report validation analysis. The predictor analysis was based on the larger group and used penalized logistic regression to predict the self-report of being a former or current smoker at baseline. Cg05575921 methylation showed a moderate ability to discriminate among former and current smokers, AUC = 0.85 (95% confidence interval = [0.83, 0.86]). The final selected variables for the prediction model were BMI, gender, BMI by gender, age, divorced (vs. married), education, and race. The gender by BMI interaction was such that males had a higher probability of current smoking for lower BMI, but this switched to females having higher current smoking for overweight to obese. There is evidence that the self-reported smoking behavior in NLST is moderately accurate. The results of the primary analysis are consistent with the general smoking literature, and our results provide additional specificity regarding the gender by BMI interaction. Body weight issues might play a role in smoking cessation for older established smokers in a similar manner as younger smokers. It could be that women have less success with cessation when their BMI increases.
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Affiliation(s)
- Jeffrey D. Long
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA 52242, USA; (J.D.L.); (J.M.); (G.W.)
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa, IA 52242, USA
| | - Michael P. Gehlsen
- South Saint Paul Public Schools, 104 5th Ave. S, South Saint Paul, MN 55075, USA;
| | - Joanna Moody
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA 52242, USA; (J.D.L.); (J.M.); (G.W.)
| | - Gracie Weeks
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA 52242, USA; (J.D.L.); (J.M.); (G.W.)
| | - Robert Philibert
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA 52242, USA; (J.D.L.); (J.M.); (G.W.)
- Behavioral Diagnostics LLC, 2500 Crosspark Rd., Suite W245, Coralville, IA 53341, USA
- Department of Biomedical Engineering, University of Iowa, Iowa, IA 52242, USA
- Correspondence:
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