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Tang X, Guo R, Mo Z, Fu W, Qian X. Causality-driven candidate identification for reliable DNA methylation biomarker discovery. Nat Commun 2025; 16:680. [PMID: 39814752 PMCID: PMC11735613 DOI: 10.1038/s41467-025-56054-y] [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: 06/28/2024] [Accepted: 01/06/2025] [Indexed: 01/18/2025] Open
Abstract
Despite vast data support in DNA methylation (DNAm) biomarker discovery to facilitate health-care research, this field faces huge resource barriers due to preliminary unreliable candidates and the consequent compensations using expensive experiments. The underlying challenges lie in the confounding factors, especially measurement noise and individual characteristics. To achieve reliable identification of a candidate pool for DNAm biomarker discovery, we propose a Causality-driven Deep Regularization framework to reinforce correlations that are suggestive of causality with disease. It integrates causal thinking, deep learning, and biological priors to handle non-causal confounding factors, through a contrastive scheme and a spatial-relation regularization that reduces interferences from individual characteristics and noises, respectively. The comprehensive reliability of the proposed method was verified by simulations and applications involving various human diseases, sample origins, and sequencing technologies, highlighting its universal biomedical significance. Overall, this study offers a causal-deep-learning-based perspective with a compatible tool to identify reliable DNAm biomarker candidates, promoting resource-efficient biomarker discovery.
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Affiliation(s)
- Xinlu Tang
- The Medical Image and Health Informatics Lab, the School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Guo
- The Medical Image and Health Informatics Lab, the School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhanfeng Mo
- College of Computing and Data Science, Nanyang Technological University, Singapore, Singapore
| | - Wenli Fu
- The Medical Image and Health Informatics Lab, the School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaohua Qian
- The Medical Image and Health Informatics Lab, the School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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Glaesser D, Iwig M. Increased molar ratio of free fatty acids to albumin in blood as cause and early biomarker for the development of cataracts and Alzheimer's disease. Exp Eye Res 2024; 243:109888. [PMID: 38583754 DOI: 10.1016/j.exer.2024.109888] [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: 10/25/2023] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Cataracts and Alzheimer's disease (AD) are closely linked and are associated with aging and with systemic diseases that increase the molar ratio of free fatty acids to albumin (mFAR) in the blood. From the results of our earlier studies on the development of senile cataracts and from results recently published in the literature on the pathogenesis of Alzheimer's disease, we suggest that there is a common lipotoxic cascade for both diseases, explaining the strong connection between aging, an elevated mFAR in the blood, cataract formation, and AD. Long-chain free fatty acids (FFA) are transported in the blood as FFA/albumin complexes. In young people, vascular albumin barriers in the eyes and brain, very similar in their structure and effect, reduce the FFA/albumin complex concentration from around 650 μmol/l in the blood to 1-3 μmol/l in the aqueous humour of the eyes as well as in the cerebrospinal fluid of the brain. At such low concentrations the fatty acid uptake of the target cells - lens epithelial and brain cells - rises with increasing FFA/albumin complex concentrations, especially when the fatty acid load of albumin molecules is mFAR>1. At higher albumin concentrations, for instance in blood plasma or the interstitial tissue spaces, the fatty acid uptake of the target cells becomes increasingly independent of the FFA/albumin complex concentration and is mainly a function of the mFAR (Richieri et al., 1993). In the blood plasma of young people, the mFAR is normally below 1.0. In people over 40 years old, aging increases the mFAR by decreasing the plasma concentration of albumin and enhancing the plasma concentrations of FFA. The increase in the mFAR in association with C6-unsaturated FFA are risk factors for the vascular albumin barriers (Hennig et al., 1984). Damage to the vascular albumin barrier in the eyes and brain increases the concentration of FFA/albumin complex in the aqueous humour as well as in the cerebrospinal fluid, leading to mitochondrial dysfunction and the death of lens epithelial and brain cells, the development of cataracts, and AD. An age-dependent increase in the concentration of FFA/albumin complex has been found in the aqueous humour of 177 cataract patients, correlating with the mitochondria-mediated apoptotic death of lens epithelial cells, lens opacification and cataracts (Iwig et al., 2004). Mitochondrial dysfunction is also an early crucial event in Alzheimer's pathology, closely connected with the generation of amyloid beta peptides (Leuner et al., 2012). Very recently, amyloid beta production has also been confirmed in the lenses of Alzheimer's patients, causing cataracts (Moncaster et al., 2022). In view of this, we propose that there is a common lipotoxic cascade for senile cataract formation and senile AD, initiated by aging and/or systemic diseases, leading to an mFAR>1 in the blood.
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Affiliation(s)
- Dietmar Glaesser
- Institute of Physiological Chemistry, Martin-Luther-University Halle-Wittenberg, D-06097, Halle, Germany.
| | - Martin Iwig
- Institute of Physiological Chemistry, Martin-Luther-University Halle-Wittenberg, D-06097, Halle, Germany
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Sarangi S, Minaeva O, Ledoux DM, Parsons DS, Moncaster JA, Black CA, Hollander J, Tripodis Y, Clark JI, Hunter DG, Goldstein LE. In vivo quasi-elastic light scattering detects molecular changes in the lenses of adolescents with Down syndrome. Exp Eye Res 2024; 241:109818. [PMID: 38422787 DOI: 10.1016/j.exer.2024.109818] [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: 05/24/2023] [Revised: 12/08/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
Down syndrome (DS) is the most common chromosomal disorder in humans. DS is associated with increased prevalence of several ocular sequelae, including characteristic blue-dot cerulean cataract. DS is accompanied by age-dependent accumulation of Alzheimer's disease (AD) amyloid-β (Aβ) peptides and amyloid pathology in the brain and comorbid early-onset Aβ amyloidopathy and colocalizing cataracts in the lens. Quasi-elastic light scattering (QLS) is an established optical technique that noninvasively measures changes in protein size distributions in the human lens in vivo. In this cross-sectional study, lenticular QLS correlation time was decreased in adolescent subjects with DS compared to age-matched control subjects. Clinical QLS was consistent with alterations in relative particle hydrodynamic radius in lenses of adolescents with DS. These correlative results suggest that noninvasive QLS can be used to evaluate molecular changes in the lenses of individuals with DS.
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Affiliation(s)
- Srikant Sarangi
- Molecular Aging & Development Laboratory, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; Boston University Photonics Center, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Olga Minaeva
- Molecular Aging & Development Laboratory, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; Boston University Photonics Center, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Boston University Alzheimer's Disease Research Center, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; Department of Ophthalmology, Boston Children's Hospital, Boston, MA, USA
| | - Danielle M Ledoux
- Department of Ophthalmology, Boston Children's Hospital, Boston, MA, USA; Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Douglas S Parsons
- Molecular Aging & Development Laboratory, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; Boston University Photonics Center, Boston University, Boston, MA, USA
| | - Juliet A Moncaster
- Molecular Aging & Development Laboratory, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; Boston University Photonics Center, Boston University, Boston, MA, USA; Boston University Alzheimer's Disease Research Center, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Caitlin A Black
- Department of Ophthalmology, Boston Children's Hospital, Boston, MA, USA
| | - Jeffrey Hollander
- Department of Ophthalmology, Boston Children's Hospital, Boston, MA, USA
| | - Yorghos Tripodis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - John I Clark
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - David G Hunter
- Department of Ophthalmology, Boston Children's Hospital, Boston, MA, USA; Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Lee E Goldstein
- Molecular Aging & Development Laboratory, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; Boston University Photonics Center, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Boston University Alzheimer's Disease Research Center, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
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