1
|
Philibert R, Moody J, Philibert W, Dogan MV, Hoffman EA. The Reversion of the Epigenetic Signature of Coronary Heart Disease in Response to Smoking Cessation. Genes (Basel) 2023; 14:1233. [PMID: 37372412 PMCID: PMC10297911 DOI: 10.3390/genes14061233] [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: 05/15/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Coronary heart disease (CHD) is the leading cause of death worldwide. However, current diagnostic tools for CHD, such as coronary computed tomography angiography (CCTA), are poorly suited for monitoring treatment response. Recently, we have introduced an artificial-intelligence-guided integrated genetic-epigenetic test for CHD whose core consists of six assays that determine methylation in pathways known to moderate the pathogenesis of CHD. However, whether methylation at these six loci is sufficiently dynamic to guide CHD treatment response is unknown. To test that hypothesis, we examined the relationship of changes in these six loci to changes in cg05575921, a generally accepted marker of smoking intensity, using DNA from a cohort of 39 subjects undergoing a 90-day smoking cessation intervention and methylation-sensitive digital PCR (MSdPCR). We found that changes in epigenetic smoking intensity were significantly associated with reversion of the CHD-associated methylation signature at five of the six MSdPCR predictor sites: cg03725309, cg12586707, cg04988978, cg17901584, and cg21161138. We conclude that methylation-based approaches could be a scalable method for assessing the clinical effectiveness of CHD interventions, and that further studies to understand the responsiveness of these epigenetic measures to other forms of CHD treatment are in order.
Collapse
Affiliation(s)
- Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.M.); (W.P.)
- Cardio Diagnostics Inc., Chicago, IL 60642, USA;
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA;
| | - Joanna Moody
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.M.); (W.P.)
| | - Willem Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.M.); (W.P.)
| | - Meeshanthini V. Dogan
- Cardio Diagnostics Inc., Chicago, IL 60642, USA;
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA;
| | - Eric A. Hoffman
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA;
- Department of Radiology, University of Iowa, Iowa City, IA 52242, USA
| |
Collapse
|
2
|
Cheruba E, Viswanathan R, Wong PM, Womersley HJ, Han S, Tay B, Lau Y, Gan A, Poon PSY, Skanderup A, Ng SB, Chok AY, Chong DQ, Tan IB, Cheow LF. Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients. SCIENCE ADVANCES 2022; 8:eabn4030. [PMID: 36083902 PMCID: PMC9462700 DOI: 10.1126/sciadv.abn4030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 07/22/2022] [Indexed: 06/01/2023]
Abstract
Genome-wide analysis of cell-free DNA methylation profile is a promising approach for sensitive and specific detection of many cancers. However, scaling such assays for clinical translation is impractical because of the high cost of whole-genome bisulfite sequencing. We show that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbors most of the cancer-specific methylation signature. Here, we report on the simple and effective heat enrichment of CpG-rich regions for bisulfite sequencing (Heatrich-BS) platform that allows for focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable accurate tumor burden estimation and quantitative tracking of colorectal cancer patient's response to treatment at much reduced sequencing cost suitable for frequent monitoring. We also show tumor epigenetic subtyping using Heatrich-BS, which could enable patient stratification. Heatrich-BS holds great potential for highly scalable screening and monitoring of cancer using liquid biopsy.
Collapse
Affiliation(s)
- Elsie Cheruba
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Ramya Viswanathan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Pui-Mun Wong
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Howard John Womersley
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Shuting Han
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Brenda Tay
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Yiting Lau
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Anna Gan
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Polly S. Y. Poon
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Anders Skanderup
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Sarah B. Ng
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Aik Yong Chok
- Department of Colorectal Surgery, Singapore General Hospital, Singapore 169608, Singapore
| | - Dawn Qingqing Chong
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Iain Beehuat Tan
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| |
Collapse
|
3
|
Dogan MV, Knight S, Dogan TK, Knowlton KU, Philibert R. External validation of integrated genetic-epigenetic biomarkers for predicting incident coronary heart disease. Epigenomics 2021; 13:1095-1112. [PMID: 34148365 PMCID: PMC8356680 DOI: 10.2217/epi-2021-0123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/07/2021] [Indexed: 12/27/2022] Open
Abstract
Aim: The Framingham Risk Score (FRS) and atherosclerotic cardiovascular disease (ASCVD) Pooled Cohort Equation (PCE) for predicting risk for incident coronary heart disease (CHD) work poorly. To improve risk stratification for CHD, we developed a novel integrated genetic-epigenetic tool. Materials & methods: Using machine learning techniques and datasets from the Framingham Heart Study (FHS) and Intermountain Healthcare (IM), we developed and validated an integrated genetic-epigenetic model for predicting 3-year incident CHD. Results: Our approach was more sensitive than FRS and PCE and had high generalizability across cohorts. It performed with sensitivity/specificity of 79/75% in the FHS test set and 75/72% in the IM set. The sensitivity/specificity was 15/93% in FHS and 31/89% in IM for FRS, and sensitivity/specificity was 41/74% in FHS and 69/55% in IM for PCE. Conclusion: The use of our tool in a clinical setting could better identify patients at high risk for a heart attack.
Collapse
Affiliation(s)
- Meeshanthini V Dogan
- Cardio Diagnostics, Inc., Coralville, IA 52241, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Stacey Knight
- Intermountain Heart Institute, Intermountain Healthcare, Salt Lake City, UT 84103, USA
- Department of Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Kirk U Knowlton
- Intermountain Heart Institute, Intermountain Healthcare, Salt Lake City, UT 84103, USA
| | - Robert Philibert
- Cardio Diagnostics, Inc., Coralville, IA 52241, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA
| |
Collapse
|