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Bahado-Singh RO, Radhakrishna U, Gordevičius J, Aydas B, Yilmaz A, Jafar F, Imam K, Maddens M, Challapalli K, Metpally RP, Berrettini WH, Crist RC, Graham SF, Vishweswaraiah S. Artificial Intelligence and Circulating Cell-Free DNA Methylation Profiling: Mechanism and Detection of Alzheimer's Disease. Cells 2022; 11:cells11111744. [PMID: 35681440 PMCID: PMC9179874 DOI: 10.3390/cells11111744] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Despite extensive efforts, significant gaps remain in our understanding of Alzheimer’s disease (AD) pathophysiology. Novel approaches using circulating cell-free DNA (cfDNA) have the potential to revolutionize our understanding of neurodegenerative disorders. Methods: We performed DNA methylation profiling of cfDNA from AD patients and compared them to cognitively normal controls. Six Artificial Intelligence (AI) platforms were utilized for the diagnosis of AD while enrichment analysis was used to elucidate the pathogenesis of AD. Results: A total of 3684 CpGs were significantly (adj. p-value < 0.05) differentially methylated in AD versus controls. All six AI algorithms achieved high predictive accuracy (AUC = 0.949−0.998) in an independent test group. As an example, Deep Learning (DL) achieved an AUC (95% CI) = 0.99 (0.95−1.0), with 94.5% sensitivity and specificity. Conclusion: We describe numerous epigenetically altered genes which were previously reported to be differentially expressed in the brain of AD sufferers. Genes identified by AI to be the best predictors of AD were either known to be expressed in the brain or have been previously linked to AD. We highlight enrichment in the Calcium signaling pathway, Glutamatergic synapse, Hedgehog signaling pathway, Axon guidance and Olfactory transduction in AD sufferers. To the best of our knowledge, this is the first reported genome-wide DNA methylation study using cfDNA to detect AD.
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Affiliation(s)
- Ray O. Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA; (R.O.B.-S.); (A.Y.); (S.F.G.)
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
- Correspondence: (U.R.); (S.V.); Tel.: +1-248-551-2574 (U.R.); +1-248-551-2569 (S.V.)
| | - Juozas Gordevičius
- Vugene, LLC, 625 Kenmoor Ave Suite 301 PMB 96578, Grand Rapids, MI 49546, USA;
| | - Buket Aydas
- Department of Care Management Analytics, Blue Cross Blue Shield of Michigan, Detroit, MI 48226, USA;
| | - Ali Yilmaz
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA; (R.O.B.-S.); (A.Y.); (S.F.G.)
- Department of Alzheimer’s Disease Research, Beaumont Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA
| | - Faryal Jafar
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Khaled Imam
- Department of Internal Medicine, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (K.I.); (M.M.)
| | - Michael Maddens
- Department of Internal Medicine, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (K.I.); (M.M.)
| | - Kshetra Challapalli
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
| | - Raghu P. Metpally
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA 17821, USA; (R.P.M.); (W.H.B.)
| | - Wade H. Berrettini
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA 17821, USA; (R.P.M.); (W.H.B.)
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Richard C. Crist
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Stewart F. Graham
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Royal Oak, MI 48309, USA; (R.O.B.-S.); (A.Y.); (S.F.G.)
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
- Department of Alzheimer’s Disease Research, Beaumont Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Beaumont Health, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (F.J.); (K.C.)
- Correspondence: (U.R.); (S.V.); Tel.: +1-248-551-2574 (U.R.); +1-248-551-2569 (S.V.)
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