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Zhang JD, Xue C, Kolachalama VB, Donald WA. Interpretable Machine Learning on Metabolomics Data Reveals Biomarkers for Parkinson's Disease. ACS CENTRAL SCIENCE 2023; 9:1035-1045. [PMID: 37252351 PMCID: PMC10214508 DOI: 10.1021/acscentsci.2c01468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Indexed: 05/31/2023]
Abstract
The use of machine learning (ML) with metabolomics provides opportunities for the early diagnosis of disease. However, the accuracy of ML and extent of information obtained from metabolomics can be limited owing to challenges associated with interpreting disease prediction models and analyzing many chemical features with abundances that are correlated and "noisy". Here, we report an interpretable neural network (NN) framework to accurately predict disease and identify significant biomarkers using whole metabolomics data sets without a priori feature selection. The performance of the NN approach for predicting Parkinson's disease (PD) from blood plasma metabolomics data is significantly higher than other ML methods with a mean area under the curve of >0.995. PD-specific markers that predate clinical PD diagnosis and contribute significantly to early disease prediction were identified including an exogenous polyfluoroalkyl substance. It is anticipated that this accurate and interpretable NN-based approach can improve diagnostic performance for many diseases using metabolomics and other untargeted 'omics methods.
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Affiliation(s)
- J. Diana Zhang
- School
of Chemistry, University of New South Wales, Sydney 2052, Australia
- Department
of Medicine, Boston University School of
Medicine, Boston, Massachusetts 02118, United States
| | - Chonghua Xue
- Department
of Medicine, Boston University School of
Medicine, Boston, Massachusetts 02118, United States
| | - Vijaya B. Kolachalama
- Department
of Medicine, Boston University School of
Medicine, Boston, Massachusetts 02118, United States
- Department
of Computer Science and Faculty of Computing & Data Sciences, Boston University, Boston, Massachusetts 02215, United States
| | - William A. Donald
- School
of Chemistry, University of New South Wales, Sydney 2052, Australia
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Viswanathan A, Zhurina A, Assoah B, Paakkunainen A, Musa A, Kute D, Saravanan KM, Yli-Harja O, Candeias NR, Kandhavelu M. Decane-1,2-diol derivatives as potential antitumor agents for the treatment of glioblastoma. Eur J Pharmacol 2018; 837:105-116. [PMID: 30179612 DOI: 10.1016/j.ejphar.2018.08.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 12/20/2022]
Abstract
Glioblastoma remains the most common and aggressive type of malignant brain tumor among adults thus, considerable attention has been given to discovery of novel anti-tumor drugs for its treatment. This study reports the synthesis of a series of twelve novel decane-1,2-diol derivatives and evaluation of its anti-tumor activity in mammalian glioblastoma cell lines, U87 and LN229. Starting from decane-1,2-diol, several derivatives were prepared using a diversity oriented synthesis approach through which a small library composed of esters, silyl ethers, sulfonates, sulfites, sulfates, ketals, and phosphonates was built. The decane-1,2-diol ditosylated derivative, DBT, found to have higher cytotoxicity than the standard drug cisplatin, has IC50 value of 52 µM in U87 and 270 µM in LN229. Migration analysis of U87 cell line treated with the DBT indicated its ability to effectively suppress proliferation during initial hours of treatment and decrease anti-proliferative property over time. Additionally, DBT was assessed for its role in apoptosis, oxidative stress and caspase 3/7 activation in U87. Interestingly, our experiments indicated that its cytotoxicity is independent of Reactive oxygen species induced caspase 3/7 activity. The compound also exhibited caspase independent apoptosis activity in U87. DBT treatment led to G1/S cell cycle arrest and apoptosis induction of glioma cell lines. In addition, we identified 1533 genes with significant changes at the transcriptional level, in response to DBT. A molecular docking study accounting for the interaction of DBT with NMDA receptor disclosed several hydrogen bonds and charged residue interactions with 17 amino acids, which might be the basis of the DBT cytotoxicity observed. We conclude that this molecule exerts its cytotoxicity via caspase 3/7 independent pathways in glioblastoma cells. Concisely, simple decane-1,2-diol derivatives might serve as scaffolds for the development of effective anti-glioblastoma agents.
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Affiliation(s)
- Anisha Viswanathan
- Molecular Signaling Lab, Computational Systems Biology Research Group, BioMediTech and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland
| | - Anastasia Zhurina
- Molecular Signaling Lab, Computational Systems Biology Research Group, BioMediTech and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland
| | - Benedicta Assoah
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, 33101 Tampere, Finland
| | - Aleksi Paakkunainen
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, 33101 Tampere, Finland
| | - Aliyu Musa
- Predictive Medicine and Data Analytics Lab, Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland
| | - Dinesh Kute
- Molecular Signaling Lab, Computational Systems Biology Research Group, BioMediTech and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland
| | - Konda Mani Saravanan
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Chennai 600025, India
| | - Olli Yli-Harja
- Molecular Signaling Lab, Computational Systems Biology Research Group, BioMediTech and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland; Institute for Systems Biology, 1441N 34th Street, Seattle, WA 98103-8904, USA
| | - Nuno R Candeias
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, 33101 Tampere, Finland.
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Computational Systems Biology Research Group, BioMediTech and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland.
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Chen YQ, Zhong SM, Liu ST, Gao F, Li F, Zhao Y, Sun XH, Miao Y, Wang Z. Neuroprotective effect of 5ɑ-androst-3β,5,6β-triol on retinal ganglion cells in a rat chronic ocular hypertension model. Neurosci Lett 2017; 660:90-95. [PMID: 28919536 DOI: 10.1016/j.neulet.2017.09.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/21/2017] [Accepted: 09/11/2017] [Indexed: 01/01/2023]
Abstract
Previous studies have demonstrated that 5ɑ-androst-3β,5,6β-triol (Triol), a synthesized steroid compound, showed notable neuroprotective effect in cultured cortical neurons. In the present study, we explored whether and how Triol have neuroprotective effect on retinal ganglion cells (RGCs) in a chronic ocular hypertension (COH) rat model. COH model was produced by injecting superparamagnetic iron oxide micro-beads into the anterior chamber, and Triol was administrated (4.8μg/100g, i.p., once daily for 4 weeks). Immunohistochemistry experiments showed that in whole flat-mounted COH retinas, the number of CTB-labeled survival RGCs was progressively reduced, while TUNEL-positive signals were significantly increased from 1 to 4 weeks after the micro-bead injection. Triol administration significantly attenuated the reduction in the number of CTB-labeled RGCs, and partially reduced the increased number of TUNEL-positive signals in COH retinas. Furthermore, Triol administration partially reduced the levels of malondialdehyde (MDA) and reactive oxygen species (ROS), and significantly rescued the activities of mitochondrial respiratory chain complex (MRCC) I/II/III in COH retinas. Our results suggest that Triol prevents RGCs from apoptotic death in COH retinas by reducing the lipid peroxidation and enhancing the activities of MRCCs.
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Affiliation(s)
- Yan-Qiu Chen
- Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Shu-Min Zhong
- Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Shu-Ting Liu
- Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Feng Gao
- Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China; Department of Ophthalmology at Eye & ENT Hospital, Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200031, China
| | - Fang Li
- Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Yuan Zhao
- Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China; Department of Ophthalmology at Eye & ENT Hospital, Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200031, China
| | - Xing-Huai Sun
- Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China; Department of Ophthalmology at Eye & ENT Hospital, Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200031, China
| | - Yanying Miao
- Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China.
| | - Zhongfeng Wang
- Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China; Department of Ophthalmology at Eye & ENT Hospital, Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200031, China.
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Bansal R, Singh R. Exploring the potential of natural and synthetic neuroprotective steroids against neurodegenerative disorders: A literature review. Med Res Rev 2017; 38:1126-1158. [PMID: 28697282 DOI: 10.1002/med.21458] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/01/2017] [Accepted: 06/20/2017] [Indexed: 12/18/2022]
Abstract
Neurodegeneration is a complex process, which leads to progressive brain damage due to loss of neurons. Despite exhaustive research, the cause of neuronal loss in various degenerative disorders is not entirely understood. Neuroprotective steroids constitute an important line of attack, which could play a major role against the common mechanisms associated with various neurodegenerative disorders like Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Natural endogenous steroids induce the neuroprotection by protecting the nerve cells from neuronal injury through multiple mechanisms, therefore the structural modifications of the endogenous steroids could be helpful in the generation of new therapeutically useful neuroprotective agents. The review article will keep the readers apprised of the detailed description of natural as well as synthetic neuroprotective steroids from the medicinal chemistry point of view, which would be helpful in drug discovery efforts aimed toward neurodegenerative diseases.
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Affiliation(s)
- Ranju Bansal
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Ranjit Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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