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Andersen A, Milefchik E, Papworth E, Penaluna B, Dawes K, Moody J, Weeks G, Froehlich E, deBlois K, Long JD, Philibert R. ZSCAN25 methylation predicts seizures and severe alcohol withdrawal syndrome. Epigenetics 2024; 19:2298057. [PMID: 38166538 PMCID: PMC10766392 DOI: 10.1080/15592294.2023.2298057] [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: 08/26/2023] [Accepted: 12/11/2023] [Indexed: 01/04/2024] Open
Abstract
Currently, clinicians use their judgement and indices such as the Prediction of Alcohol Withdrawal Syndrome Scale (PAWSS) to determine whether patients are admitted to hospitals for consideration of withdrawal syndrome (AWS). However, only a fraction of those admitted will experience severe AWS. Previously, we and others have shown that epigenetic indices, such as the Alcohol T-Score (ATS), can quantify recent alcohol consumption. However, whether these or other alcohol biomarkers, such as carbohydrate deficient transferrin (CDT), could identify those at risk for severe AWS is unknown. To determine this, we first conducted genome-wide DNA methylation analyses of subjects entering and exiting alcohol treatment to identify loci whose methylation quickly reverted as a function of abstinence. We then tested whether methylation at a rapidly reverting locus, cg07375256, or other existing metrics including PAWSS scores, CDT levels, or ATS, could predict outcome in 125 subjects admitted for consideration of AWS. We found that PAWSS did not significantly predict severe AWS nor seizures. However, methylation at cg07375256 (ZSCAN25) and CDT strongly predicted severe AWS with ATS (p < 0.007) and cg07375256 (p < 6 × 10-5) methylation also predicting AWS associated seizures. We conclude that epigenetic methods can predict those likely to experience severe AWS and that the use of these or similar Precision Epigenetic approaches could better guide AWS management.
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Affiliation(s)
- Allan Andersen
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emily Milefchik
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emma Papworth
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Brandan Penaluna
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Behavioral Diagnostics LLC, Coralville, IA, USA
| | - Joanna Moody
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Gracie Weeks
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ellyse Froehlich
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Kaitlyn deBlois
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Jeffrey D Long
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Department of Biostatistics, University of Iowa, Iowa City, IA, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Behavioral Diagnostics LLC, Coralville, IA, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA
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Frisvold D, Dogan M, Dogan T, Abdullahi K, Koep T, Philibert R. The Use of Precision Epigenetic Methods for the Diagnosis and Care of Stable Coronary Heart Disease Reduces Healthcare Costs. Adv Ther 2024; 41:2367-2380. [PMID: 38662186 DOI: 10.1007/s12325-024-02860-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
INTRODUCTION The cost of secondary prevention of coronary heart disease (CHD) is continuing to increase, with a substantial portion of this acceleration being driven by the expense of confirmatory diagnostic testing. Conceivably, newly developed precision epigenetic technologies could drive down these costs. However, at the current time, their impact on overall expense for CHD care is poorly understood. We hypothesized that the use of a newly developed, highly sensitive, and specific epigenetic test, PrecisionCHD, could decrease the costs of secondary prevention. METHODS To test this hypothesis, we constructed a budget impact analysis using a cost calculation model that examined the effects of substituting PrecisionCHD for conventional CHD diagnostic tests on the expenses of the initial evaluation and first year of care of stable CHD using a 1-year time horizon with no discounting. RESULTS The model projected that for a commercial insurer with one million members, full adoption of PrecisionCHD as the primary method of initial CHD assessment would save approximately $113.6 million dollars in the initial year. CONCLUSION These analyses support the use of precision epigenetic methods as part of the initial diagnosis and care of stable CHD and can meaningfully reduce cost. Real-world pilots to test the reliability of these analyses are indicated.
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Affiliation(s)
- David Frisvold
- Department of Economics, University of Iowa, Iowa City, IA, 52242, USA
| | | | - Timur Dogan
- Cardio Diagnostics Inc, Chicago, IL, 60654, USA
| | | | - Tyler Koep
- Cardio Diagnostics Inc, Chicago, IL, 60654, USA
| | - Robert Philibert
- Cardio Diagnostics Inc, Chicago, IL, 60654, USA.
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA.
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Bartemes KR, Gochanour BR, Routman DM, Ma DJ, Doering KA, Burger KN, Foote PH, Taylor WR, Mahoney DW, Berger CK, Cao X, Then SS, Haller TJ, Larish AM, Moore EJ, Garcia JJ, Graham RP, Bakkum-Gamez JN, Kisiel JB, Van Abel KM. Assessing the capacity of methylated DNA markers of cervical squamous cell carcinoma to discriminate oropharyngeal squamous cell carcinoma in human papillomavirus mediated disease. Oral Oncol 2023; 146:106568. [PMID: 37717549 PMCID: PMC10591712 DOI: 10.1016/j.oraloncology.2023.106568] [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: 06/02/2023] [Revised: 08/11/2023] [Accepted: 09/06/2023] [Indexed: 09/19/2023]
Abstract
OBJECTIVE Early identification of human papillomavirus associated oropharyngeal squamous cell carcinoma (HPV(+)OPSCC) is challenging and novel biomarkers are needed. We hypothesized that a panel of methylated DNA markers (MDMs) found in HPV(+) cervical squamous cell carcinoma (CSCC) will have similar discrimination in HPV(+)OPSCC tissues. MATERIALS AND METHODS Formalin-fixed, paraffin-embedded tissues were obtained from patients with primary HPV(+)OPSCC or HPV(+)CSCC; control tissues included normal oropharynx palatine tonsil (NOP) and cervix (NCS). Using a methylation-specific polymerase chain reaction, 21 previously validated cervical MDMs were evaluated on tissue-extracted DNA. Discrimination between case and control cervical and oropharynx tissue was assessed using area under the curve (AUC). RESULTS 34 HPV(+)OPSCC, 36 HPV(+)CSCC, 26 NOP, and 24 NCS patients met inclusion criteria. Within HPV(+)CSCC, 18/21 (86%) of MDMs achieved an AUC ≥ 0.9 and all MDMs exhibited better than chance classifications relative to control cervical tissue (all p < 0.001). In contrast, within HPV(+)OPSCC only 5/21 (24%) MDMs achieved an AUC ≥ 0.90 but 19/21 (90%) exhibited better than chance classifications relative to control tonsil tissue (all p < 0.001). Overall, 13/21 MDMs had statistically significant lower AUCs in the oropharyngeal cohort compared to the cervical cohort, and only 1 MDM exhibited a statistically significant increase in AUC. CONCLUSIONS Previously validated MDMs exhibited robust performance in independent HPV(+)CSCC patients. However, most of these MDMs exhibited higher discrimination for HPV(+)CSCC than for HPV(+)OPSCC. This suggests that each SCC subtype requires a unique set of MDMs for optimal discrimination. Future studies are necessary to establish an MDM panel for HPV(+)OPSCC.
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Affiliation(s)
- Kathleen R Bartemes
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, MN, USA
| | | | | | - Daniel J Ma
- Department of Radiation Oncology, Rochester, MN, USA
| | | | - Kelli N Burger
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | | | - Douglas W Mahoney
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - Xiaoming Cao
- Department of Gastroenterology, Rochester, MN, USA
| | - Sara S Then
- Department of Gastroenterology, Rochester, MN, USA
| | - Travis J Haller
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, MN, USA
| | - Alyssa M Larish
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
| | - Eric J Moore
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, MN, USA
| | - Joaquin J Garcia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rondell P Graham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Kathryn M Van Abel
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, MN, USA.
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Protsenko E, Wolkowitz OM, Yaffe K. Associations of stress and stress-related psychiatric disorders with GrimAge acceleration: review and suggestions for future work. Transl Psychiatry 2023; 13:142. [PMID: 37130894 PMCID: PMC10154294 DOI: 10.1038/s41398-023-02360-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 05/04/2023] Open
Abstract
The notion of "biological aging" as distinct from chronological aging has been of increasing interest in psychiatry, and many studies have explored associations of stress and psychiatric illness with accelerated biological aging. The "epigenetic clocks" are one avenue of this research, wherein "biological age" is estimated using DNA methylation data from specific CpG dinucleotide sites within the human genome. Many iterations of the epigenetic clocks have been developed, but the GrimAge clock continues to stand out for its ability to predict morbidity and mortality. Several studies have now explored associations of stress, PTSD, and MDD with GrimAge acceleration (GrimAA). While stress, PTSD, and MDD are distinct psychiatric entities, they may share common mechanisms underlying accelerated biological aging. Yet, no one has offered a review of the evidence on associations of stress and stress-related psychopathology with GrimAA. In this review, we identify nine publications on associations of stress, PTSD, and MDD with GrimAA. We find that results are mixed both within and across each of these exposures. However, we also find that analytic methods - and specifically, the choice of covariates - vary widely between studies. To address this, we draw upon popular methods from the field of clinical epidemiology to offer (1) a systematic framework for covariate selection, and (2) an approach to results reporting that facilitates analytic consensus. Although covariate selection will differ by the research question, we encourage researchers to consider adjustment for tobacco, alcohol use, physical activity, race, sex, adult socioeconomic status, medical comorbidity, and blood cell composition.
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Affiliation(s)
- Ekaterina Protsenko
- Department of Psychiatry, Stanford University School of Medicine, Palo Alto, CA, USA.
- Department Epidemiology & Biostatistics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA.
| | - Owen M Wolkowitz
- Weill Institute for Neurosciences and Department of Psychiatry and Behavioral Sciences, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Kristine Yaffe
- Department Epidemiology & Biostatistics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Weill Institute for Neurosciences and Department of Psychiatry and Behavioral Sciences, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
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Epigenetic and Proteomic Biomarkers of Elevated Alcohol Use Predict Epigenetic Aging and Cell-Type variation Better Than Self-Report. Genes (Basel) 2022; 13:genes13101888. [PMID: 36292773 PMCID: PMC9601579 DOI: 10.3390/genes13101888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/12/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022] Open
Abstract
Excessive alcohol consumption (EAC) has a generally accepted effect on morbidity and mortality, outcomes thought to be reflected in measures of epigenetic aging (EA). As the association of self-reported EAC with EA has not been consistent with these expectations, underscoring the need for readily employable non-self-report tools for accurately assessing and monitoring the contribution of EAC to accelerated EA, newly developed alcohol consumption DNA methylation indices, such as the Alcohol T Score (ATS) and Methyl DetectR (MDR), may be helpful. To test that hypothesis, we used these new indices along with the carbohydrate deficient transferrin (CDT), concurrent as well as past self-reports of EAC, and well-established measures of cigarette smoking to examine the relationship of EAC to both accelerated EA and immune cell counts in a cohort of 437 young Black American adults. We found that MDR, CDT, and ATS were intercorrelated, even after controlling for gender and cotinine effects. Correlations between EA and self-reported EAC were low or non-significant, replicating prior research, whereas correlations with non-self-report indices were significant and more substantial. Comparing non-self-report indices showed that the ATS predicted more than four times as much variance in EA, CDT4 cells and B-cells as for both the MDR and CDT, and better predicted indices of accelerated EA. We conclude that each of the non-self-report indices have differing predictive capacities with respect to key alcohol-related health outcomes, and that the ATS may be particularly useful for clinicians seeking to understand and prevent accelerated EA. The results also underscore the likelihood of substantial underestimates of problematic use when self-report is used and a reduction in correlations with EA and variance in cell-types.
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Beach SRH, Klopack ET, Carter SE, Philibert RA, Simons RL, Gibbons FX, Ong ML, Gerrard M, Lei MK. Do Loneliness and Per Capita Income Combine to Increase the Pace of Biological Aging for Black Adults across Late Middle Age? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13421. [PMID: 36294002 PMCID: PMC9602511 DOI: 10.3390/ijerph192013421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
In a sample of 685 late middle-aged Black adults (M age at 2019 = 57.17 years), we examined the effects of loneliness and per capita income on accelerated aging using a newly developed DNA-methylation based index: the DunedinPACE. First, using linear, mixed effects regression in a growth curve framework, we found that change in DunedinPACE was dependent on age, with a linear model best fitting the data (b = 0.004, p < 0.001), indicating that average pace of change increased among older participants. A quadratic effect was also tested, but was non-significant. Beyond the effect of age, both change in loneliness (b = 0.009, p < 0.05) and change in per capita income (b = -0.016, p < 0.001) were significantly associated with change in DunedinPACE across an 11-year period, accounting for significant between person variability observed in the unconditional model. Including non-self-report indices of smoking and alcohol use did not reduce the association of loneliness or per capita income with DunedinPACE. However, change in smoking was strongly associated with change in DunedinPACE such that those reducing their smoking aged less rapidly than those continuing to smoke. In addition, both loneliness and per capita income were associated with DunedinPACE after controlling for variation in cell-types.
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Affiliation(s)
- Steven R. H. Beach
- Center for Family Research, The University of Georgia, Athens, GA 30602, USA
- Department of Psychology, The University of Georgia, Athens, GA 30602, USA
| | - Eric T. Klopack
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90007, USA
| | - Sierra E. Carter
- Department of Psychology, Georgia State University, Atlanta, GA 30302, USA
| | | | - Ronald L. Simons
- Department of Sociology, The University of Georgia, Athens, GA 30602, USA
| | - Frederick X. Gibbons
- Department of Psychological Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Mei Ling Ong
- Center for Family Research, The University of Georgia, Athens, GA 30602, USA
| | - Meg Gerrard
- Department of Psychological Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Man-Kit Lei
- Department of Sociology, The University of Georgia, Athens, GA 30602, USA
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