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Li C, Hou I, Ma M, Wang G, Bai Y, Liu X. Orthogonal analysis of variants in APOE gene using in-silico approaches reveals novel disrupting variants. FRONTIERS IN BIOINFORMATICS 2023; 3:1122559. [PMID: 37091907 PMCID: PMC10117898 DOI: 10.3389/fbinf.2023.1122559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Introduction: Alzheimer’s disease (AD) is one of the most prominent medical conditions in the world. Understanding the genetic component of the disease can greatly advance our knowledge regarding its progression, treatment and prognosis. Single amino-acid variants (SAVs) in the APOE gene have been widely investigated as a risk factor for AD Studies, including genome-wide association studies, meta-analysis based studies, and in-vivo animal studies, were carried out to investigate the functional importance and pathogenesis potential of APOE SAVs. However, given the high cost of such large-scale or experimental studies, there are only a handful of variants being reported that have definite explanations. The recent development of in-silico analytical approaches, especially large-scale deep learning models, has opened new opportunities for us to probe the structural and functional importance of APOE variants extensively.Method: In this study, we are taking an ensemble approach that simultaneously uses large-scale protein sequence-based models, including Evolutionary Scale Model and AlphaFold, together with a few in-silico functional prediction web services to investigate the known and possibly disease-causing SAVs in APOE and evaluate their likelihood of being functional and structurally disruptive.Results: As a result, using an ensemble approach with little to no prior field-specific knowledge, we reported 5 SAVs in APOE gene to be potentially disruptive, one of which (C112R) was classificed by previous studies as a key risk factor for AD.Discussion: Our study provided a novel framework to analyze and prioritize the functional and structural importance of SAVs for future experimental and functional validation.
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Affiliation(s)
- Chang Li
- USF Genomics and College of Public Health, University of South Florida, Tampa, FL, United States
- *Correspondence: Chang Li, ; Yongsheng Bai, ; Xiaoming Liu,
| | - Ian Hou
- The John Cooper School, The Woodlands, TX, United States
| | - Mingjia Ma
- Novi High School, Novi, MI, United States
| | - Grace Wang
- Del Norte High School, San Diego, CA, United States
| | - Yongsheng Bai
- Next-Gen Intelligent Science Training, Ann Arbor, MI, United States
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States
- *Correspondence: Chang Li, ; Yongsheng Bai, ; Xiaoming Liu,
| | - Xiaoming Liu
- USF Genomics and College of Public Health, University of South Florida, Tampa, FL, United States
- *Correspondence: Chang Li, ; Yongsheng Bai, ; Xiaoming Liu,
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Cross interactions between Apolipoprotein E and amyloid proteins in neurodegenerative diseases. Comput Struct Biotechnol J 2023; 21:1189-1204. [PMID: 36817952 PMCID: PMC9932299 DOI: 10.1016/j.csbj.2023.01.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
Three common Apolipoprotein E isoforms, ApoE2, ApoE3, and ApoE4, are key regulators of lipid homeostasis, among other functions. Apolipoprotein E can interact with amyloid proteins. The isoforms differ by one or two residues at positions 112 and 158, and possess distinct structural conformations and functions, leading to isoform-specific roles in amyloid-based neurodegenerative diseases. Over 30 different amyloid proteins have been found to share similar characteristics of structure and toxicity, suggesting a common interactome. The molecular and genetic interactions of ApoE with amyloid proteins have been extensively studied in neurodegenerative diseases, but have not yet been well connected and clarified. Here we summarize essential features of the interactions between ApoE and different amyloid proteins, identify gaps in the understanding of the interactome and propose the general interaction mechanism between ApoE isoforms and amyloid proteins. Perhaps more importantly, this review outlines what we can learn from the interactome of ApoE and amyloid proteins; that is the need to see both ApoE and amyloid proteins as a basis to understand neurodegenerative diseases.
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Pandit S. 1 H, 15 N and 13 C chemical shift assignments of the N-terminal domain of the two isoforms of the human apolipoprotein E. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:191-196. [PMID: 35451799 DOI: 10.1007/s12104-022-10078-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Apolipoprotein E (ApoE) is one of the major lipid transporters in humans. It is also implicated in pathological conditions like Alzheimer's and cardiovascular diseases. The N-terminal domain of ApoE binds low-density lipoprotein receptors (LDLR) while the C-terminal domain binds to the lipid. I report the backbone and aliphatic side-chain NMR chemical shifts of the N-terminal domain of two isoforms of ApoE, namely ApoE3 NTD (BMRB No. 51,122) and ApoE4 NTD (BMRB No. 51,123) at pH 3.5 (20 °C).
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Affiliation(s)
- Subhendu Pandit
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, 500107, Hyderabad, India.
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Choudhuri S. Toxicological Implications of Biological Heterogeneity. Int J Toxicol 2022; 41:132-142. [PMID: 35311363 DOI: 10.1177/10915818211066492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
From a micro to macro scale of biological organization, macromolecular diversity and biological heterogeneity are fundamental properties of biological systems. Heterogeneity may result from genetic, epigenetic, and non-genetic characteristics (e.g., tissue microenvironment). Macromolecular diversity and biological heterogeneity are tolerated as long as the sustenance and propagation of life are not disrupted. They also provide the raw materials for microevolutionary changes that may help organisms adapt to new selection pressures arising from the environment. Sequence evolution, functional divergence, and positive selection of gene and promoter dosage play a major role in the evolution of life's diversity including complex metabolic networks, which is ultimately reflected in changes in the allele frequency over time. Robustness in evolvable biological systems is conferred by functional redundancy that is often created by macromolecular diversity and biological heterogeneity. The ability to investigate biological macromolecules at an increasingly finer level has uncovered a wealth of information in this regard. Therefore, the dynamics of biological complexity should be taken into consideration in biomedical research.
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Affiliation(s)
- Supratim Choudhuri
- Division of Food Ingredients, Office of Food Additive Safety, US Food and Drug Administration, College Park, MD, USA
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