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Tan MS, Cheah PL, Chin AV, Looi LM, Chang SW. A review on omics-based biomarkers discovery for Alzheimer's disease from the bioinformatics perspectives: Statistical approach vs machine learning approach. Comput Biol Med 2021; 139:104947. [PMID: 34678481 DOI: 10.1016/j.compbiomed.2021.104947] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 12/26/2022]
Abstract
Alzheimer's Disease (AD) is a neurodegenerative disease that affects cognition and is the most common cause of dementia in the elderly. As the number of elderly individuals increases globally, the incidence and prevalence of AD are expected to increase. At present, AD is diagnosed clinically, according to accepted criteria. The essential elements in the diagnosis of AD include a patients history, a physical examination and neuropsychological testing, in addition to appropriate investigations such as neuroimaging. The omics-based approach is an emerging field of study that may not only aid in the diagnosis of AD but also facilitate the exploration of factors that influence the development of the disease. Omics techniques, including genomics, transcriptomics, proteomics and metabolomics, may reveal the pathways that lead to neuronal death and identify biomolecular markers associated with AD. This will further facilitate an understanding of AD neuropathology. In this review, omics-based approaches that were implemented in studies on AD were assessed from a bioinformatics perspective. Current state-of-the-art statistical and machine learning approaches used in the single omics analysis of AD were compared based on correlations of variants, differential expression, functional analysis and network analysis. This was followed by a review of the approaches used in the integration and analysis of multi-omics of AD. The strengths and limitations of multi-omics analysis methods were explored and the issues and challenges associated with omics studies of AD were highlighted. Lastly, future studies in this area of research were justified.
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Affiliation(s)
- Mei Sze Tan
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Phaik-Leng Cheah
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ai-Vyrn Chin
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Siow-Wee Chang
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
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Tan MA, Zakharova E, An SSA. Diaportheone A Analogues Instigate a Neuroprotective Effect by Protecting Neuroblastoma SH-SY5Y Cells from Oxidative Stress. BIOLOGY 2021; 10:biology10030199. [PMID: 33807686 PMCID: PMC8002093 DOI: 10.3390/biology10030199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/17/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) remains an incurable neurodegenerative illness. Oxidative stress resulting in the formation of reactive oxygen species (ROS) and the abnormal deposition of amyloid-beta (Aβ) are the major pathological hallmarks associated with AD. In search for small molecules targeting multiple pathways of AD and of no known molecular targets, the neuroprotective effects of the synthetic chromones diaportheone A1 and diaportheone A2, analogues of the natural product diaportheone A, were investigated. Chromones are heterocyclic compounds bearing the benzoannelated γ-pyrone moiety and were regarded as an important class of organic molecules due to their diverse pharmacological activities. The influence of the compounds on the inhibition of Aβ aggregation was determined by Thioflavin T (ThT) assay, and the cell viability, ROS, and mitochondrial membrane potential were evaluated with human neuroblastoma SH-SY5Y cells. Results showed that both compounds inhibited the Aβ aggregation at 80.41% and 73.68% for diaportheone A1 and diaportheone A2, respectively. Increased cell viabilities were observed from the protection by both compounds using Aβ- or H2O2-induced SH-SY5Y cells. Both compounds also reduced the intracellular ROS level in Aβ- or H2O2-induced SH-SY5Y cells at 10 and 20 μM concentrations, and increased the mitochondrial membrane potentials in Aβ-induced SH-SY5Y cells at 20 μM concentration. Molecular docking experiments using the Aβ protein models 2MXU and 2BEG also indicated a good agreement with the experimental data. The results demonstrated for the first time the oxidative stress effects associated with the chromones diaportheone A1 and diaportheone A2 as potential neuroprotective therapeutic agents against AD.
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Affiliation(s)
- Mario A. Tan
- Department of Bionano Technology, Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujung-gu, Seongnam-si 461-701, Korea
- College of Science and Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana, Manila 1015, Philippines
- Correspondence: (M.A.T.); (S.S.A.A.); Tel.: +63-2-7314031 (M.A.T.); +82-31-7508755 (S.S.A.A.)
| | - Elena Zakharova
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland;
| | - Seong Soo A. An
- Department of Bionano Technology, Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujung-gu, Seongnam-si 461-701, Korea
- Correspondence: (M.A.T.); (S.S.A.A.); Tel.: +63-2-7314031 (M.A.T.); +82-31-7508755 (S.S.A.A.)
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3
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Duits FH, Wesenhagen KEJ, Ekblad L, Wolters E, Willemse EAJ, Scheltens P, van der Flier WM, Teunissen CE, Visser PJ, Tijms BM. Four subgroups based on tau levels in Alzheimer's disease observed in two independent cohorts. Alzheimers Res Ther 2021; 13:2. [PMID: 33397464 PMCID: PMC7780683 DOI: 10.1186/s13195-020-00713-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/22/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND As Alzheimer's disease (AD) pathology presents decades before dementia manifests, unbiased biomarker cut-points may more closely reflect presence of pathology than clinically defined cut-points. Currently, unbiased cerebrospinal fluid (CSF) tau cut-points are lacking. METHODS We investigated CSF t-tau and p-tau cut-points across the clinical spectrum using Gaussian mixture modelling, in two independent cohorts (Amsterdam Dementia Cohort and ADNI). RESULTS Individuals with normal cognition (NC) (total n = 1111), mild cognitive impairment (MCI) (total n = 1213) and Alzheimer's disease dementia (AD) (total n = 1524) were included. In both cohorts, four CSF t- and p-tau distributions and three corresponding cut-points were identified. Increasingly high tau subgroups were characterized by steeper MMSE decline and higher progression risk to AD (cohort/platform-dependent HR, t-tau 1.9-21.3; p-tau 2.2-9.5). LIMITATIONS The number of subjects in some subgroups and subanalyses was small, especially in the highest tau subgroup and in tau PET analyses. CONCLUSIONS In two independent cohorts, t-tau and p-tau levels showed four subgroups. Increasingly high tau subgroups were associated with faster clinical decline, suggesting our approach may aid in more precise prognoses.
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Affiliation(s)
- Flora H Duits
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Kirsten E J Wesenhagen
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Laura Ekblad
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Turku PET Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Emma Wolters
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Radiology & Nuclear Medicine, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Eline A J Willemse
- Department of Clinical Chemistry, Neurochemistry Laboratory, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Philip Scheltens
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Wiesje M van der Flier
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Epidemiology and Biostatistics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Department of Clinical Chemistry, Neurochemistry Laboratory, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Pieter Jelle Visser
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Alzheimer Center Limburg, Department of Psychiatry & Neuropsychology, School of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Betty M Tijms
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
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Zhou X, Li YYT, Fu AKY, Ip NY. Polygenic Score Models for Alzheimer's Disease: From Research to Clinical Applications. Front Neurosci 2021; 15:650220. [PMID: 33854414 PMCID: PMC8039467 DOI: 10.3389/fnins.2021.650220] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
The high prevalence of Alzheimer's disease (AD) among the elderly population and its lack of effective treatments make this disease a critical threat to human health. Recent epidemiological and genetics studies have revealed the polygenic nature of the disease, which is possibly explainable by a polygenic score model that considers multiple genetic risks. Here, we systemically review the rationale and methods used to construct polygenic score models for studying AD. We also discuss the associations of polygenic risk scores (PRSs) with clinical outcomes, brain imaging findings, and biochemical biomarkers from both the brain and peripheral system. Finally, we discuss the possibility of incorporating polygenic score models into research and clinical practice along with potential challenges.
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Affiliation(s)
- Xiaopu Zhou
- Division of Life Science, State Key Laboratory of Molecular Neuroscience and Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen–Hong Kong Institute of Brain Science, Shenzhen, China
| | - Yolanda Y. T. Li
- Division of Life Science, State Key Laboratory of Molecular Neuroscience and Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Amy K. Y. Fu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience and Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen–Hong Kong Institute of Brain Science, Shenzhen, China
| | - Nancy Y. Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience and Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen–Hong Kong Institute of Brain Science, Shenzhen, China
- *Correspondence: Nancy Y. Ip,
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Berger M, Cooter M, Roesler AS, Chung S, Park J, Modliszewski JL, VanDusen KW, Thompson JW, Moseley A, Devinney MJ, Smani S, Hall A, Cai V, Browndyke JN, Lutz MW, Corcoran DL. APOE4 Copy Number-Dependent Proteomic Changes in the Cerebrospinal Fluid. J Alzheimers Dis 2020; 79:511-530. [PMID: 33337362 PMCID: PMC7902966 DOI: 10.3233/jad-200747] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background: APOE4 has been hypothesized to increase Alzheimer’s disease risk by increasing neuroinflammation, though the specific neuroinflammatory pathways involved are unclear. Objective: Characterize cerebrospinal fluid (CSF) proteomic changes related to APOE4 copy number. Methods: We analyzed targeted proteomic data from ADNI CSF samples using a linear regression model adjusting for age, sex, and APOE4 copy number, and additional linear models also adjusting for AD clinical status or for CSF Aβ, tau, or p-tau levels. False discovery rate was used to correct for multiple comparisons correction. Results: Increasing APOE4 copy number was associated with a significant decrease in a CRP peptide level across all five models (q < 0.05 for each), and with significant increases in ALDOA, CH3L1 (YKL-40), and FABPH peptide levels (q < 0.05 for each) except when controlling for AD clinical status or neurodegeneration biomarkers (i.e., CSF tau or p-tau). In all models except the one controlling for CSF Aβ levels, though not statistically significant, there was a consistent inverse direction of association between APOE4 copy number and the levels of all 24 peptides from all 8 different complement proteins measured. The odds of this happening by chance for 24 unrelated peptides would be less than 1 in 16 million. Conclusion: Increasing APOE4 copy number was associated with decreased CSF CRP levels across all models, and increased CSF ALDOA, CH3L1, and FABH levels when controlling for CSF Aβ levels. Increased APOE4 copy number may also be associated with decreased CSF complement pathway protein levels, a hypothesis for investigation in future studies.
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Affiliation(s)
- Miles Berger
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Center for Cognitive Neuroscience, Duke Institute for Brain Sciences, Durham, NC, USA.,Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC, USA
| | - Mary Cooter
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Alexander S Roesler
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Stacey Chung
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - John Park
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | | | - Keith W VanDusen
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - J Will Thompson
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Arthur Moseley
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Michael J Devinney
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Shayan Smani
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Ashley Hall
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Victor Cai
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Jeffrey N Browndyke
- Center for Cognitive Neuroscience, Duke Institute for Brain Sciences, Durham, NC, USA.,Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC, USA.,Department of Psychiatry & Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
| | - Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - David L Corcoran
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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Neuroprotective potential of the oxindole alkaloids isomitraphylline and mitraphylline in human neuroblastoma SH-SY5Y cells. 3 Biotech 2020; 10:517. [PMID: 33194521 DOI: 10.1007/s13205-020-02535-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
The purified oxindole alkaloids, isomitraphylline and mitraphylline from Uncaria perrottetii, revealed their ability to break amyloid aggregates in vitro suggesting their therapeutic potentials in Alzheimer's disease (AD). Thioflavin-T assay for assessing amyloid-beta (Aβ) aggregation of these alkaloids exhibited inhibitions at 60.321% ± 2.61 (50 μM) for isomitraphylline and 43.17% ± 3.48 (50 μM) for mitraphylline. Neuroprotective effects were elaborated against Aβ-induced SH-SY5Y cells at 20 μM and 10 μM for isomitraphylline, and 20 μM for mitraphylline. In addition, both alkaloids attenuated and protected the H2O2-induced SH-SY5Y cell cytotoxicity at 20 μM. The intracellular ROS levels of SH-SY5Y cells from H2O2-induced oxidative stress were reduced at 20 μM and 10 μM, and the mitochondrial membrane potentials of Aβ-induced SH-SY5Y cells were protected at 20 μM. The overall results suggested the potentials of both alkaloids to target certain pathological biomarkers of AD and could be further investigated as therapeutic or preventive drug leads against AD.
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