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Monti F, Stewart D, Surendra A, Alecu I, Nguyen-Tran T, Bennett SAL, Čuperlović-Culf M. Signed distance correlation (SiDCo): an online implementation of distance correlation and partial distance correlation for data-driven network analysis. Bioinformatics 2023; 39:7151065. [PMID: 37137236 PMCID: PMC10353719 DOI: 10.1093/bioinformatics/btad210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/09/2023] [Accepted: 05/01/2023] [Indexed: 05/05/2023] Open
Abstract
MOTIVATION There is a need for easily accessible implementations that measure the strength of both linear and non-linear relationships between metabolites in biological systems as an approach for data-driven network development. While multiple tools implement linear Pearson and Spearman methods, there are no such tools that assess distance correlation. RESULTS We present here SIgned Distance COrrelation (SiDCo). SiDCo is a GUI-platform for calculation of distance correlation in omics data, measuring linear and non-linear dependences between variables, as well as correlation between vectors of different lengths, e.g., different sample sizes. By combining the sign of the overall trend from Pearson's correlation with distance correlation values, we further provide a novel signed distance correlation of particular use in metabolomic and lipidomic analyses. Distance correlations can be selected as one-to-one or one-to-all correlations, showing relationships between each feature and all other features one at a time or in combination. Additionally, we implement partial distance correlation, calculated using the Gaussian Graphical model approach adapted to distance covariance. Our platform provides an easy-to-use software implementation that can be applied to the investigation of any dataset. AVAILABILITY The SiDCo software application is freely available at https://complimet.ca/sidco. SUPPLEMENTARY INFORMATION Supplementary help pages are provided at https://complimet.ca/sidco. Supplementary Material shows an example of an application of SiDCo in metabolomics.
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Affiliation(s)
- Francesco Monti
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Ontario Canada
- Neural Regeneration Laboratory and India Taylor Lipidomic Research Platform, Ottawa, Ontario Canada
| | - David Stewart
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Ontario Canada
- Neural Regeneration Laboratory and India Taylor Lipidomic Research Platform, Ottawa, Ontario Canada
| | - Anuradha Surendra
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Ontario Canada
- Neural Regeneration Laboratory and India Taylor Lipidomic Research Platform, Ottawa, Ontario Canada
| | - Irina Alecu
- Neural Regeneration Laboratory and India Taylor Lipidomic Research Platform, Ottawa, Ontario Canada
- Department of Biochemistry, Microbiology, and Immunology and Ottawa Institute of Systems Biology, Ottawa, Ontario Canada
| | - Thao Nguyen-Tran
- Neural Regeneration Laboratory and India Taylor Lipidomic Research Platform, Ottawa, Ontario Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario Canada
| | - Steffany A L Bennett
- Neural Regeneration Laboratory and India Taylor Lipidomic Research Platform, Ottawa, Ontario Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario Canada
| | - Miroslava Čuperlović-Culf
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Ontario Canada
- Department of Biochemistry, Microbiology, and Immunology and Ottawa Institute of Systems Biology, Ottawa, Ontario Canada
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Hashimoto-Roth E, Surendra A, Lavallée-Adam M, Bennett SAL, Čuperlović-Culf M. METAbolomics data Balancing with Over-sampling Algorithms (META-BOA): an online resource for addressing class imbalance. Bioinformatics 2022; 38:5326-5327. [PMID: 36222566 DOI: 10.1093/bioinformatics/btac649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/04/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Class imbalance, or unequal sample sizes between classes, is an increasing concern in machine learning for metabolomic and lipidomic data mining, which can result in overfitting for the over-represented class. Numerous methods have been developed for handling class imbalance, but they are not readily accessible to users with limited computational experience. Moreover, there is no resource that enables users to easily evaluate the effect of different over-sampling algorithms. RESULTS METAbolomics data Balancing with Over-sampling Algorithms (META-BOA) is a web-based application that enables users to select between four different methods for class balancing, followed by data visualization and classification of the sample to observe the augmentation effects. META-BOA outputs a newly balanced dataset, generating additional samples in the minority class, according to the user's choice of Synthetic Minority Over-sampling Technique (SMOTE), Borderline-SMOTE (BSMOTE), Adaptive Synthetic (ADASYN) or Random Over-Sampling Examples (ROSE). To present the effect of over-sampling on the data META-BOA further displays both principal component analysis and t-distributed stochastic neighbor embedding visualization of data pre- and post-over-sampling. Random forest classification is utilized to compare sample classification in both the original and balanced datasets, enabling users to select the most appropriate method for their further analyses. AVAILABILITY AND IMPLEMENTATION META-BOA is available at https://complimet.ca/meta-boa. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emily Hashimoto-Roth
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Ottawa, ON, Canada.,Neural Regeneration Laboratory and India Taylor Lipidomic Research Platform, Ottawa, ON K1H 8M5, Canada
| | - Anuradha Surendra
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Ottawa, ON, Canada
| | - Steffany A L Bennett
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Ottawa, ON, Canada.,Neural Regeneration Laboratory and India Taylor Lipidomic Research Platform, Ottawa, ON K1H 8M5, Canada.,Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Miroslava Čuperlović-Culf
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Ottawa, ON, Canada.,Neural Regeneration Laboratory and India Taylor Lipidomic Research Platform, Ottawa, ON K1H 8M5, Canada.,Digital Technologies Research Centre, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada
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Shao X, Vishweswaraiah S, Čuperlović-Culf M, Yilmaz A, Greenwood CMT, Surendra A, McGuinness B, Passmore P, Kehoe PG, Maddens ME, Bennett SAL, Green BD, Radhakrishna U, Graham SF. Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential. Commun Biol 2022; 5:1279. [PMID: 36418427 PMCID: PMC9684551 DOI: 10.1038/s42003-022-03965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
Dementia with Lewy bodies (DLB) is a common form of dementia with known genetic and environmental interactions. However, the underlying epigenetic mechanisms which reflect these gene-environment interactions are poorly studied. Herein, we measure genome-wide DNA methylation profiles of post-mortem brain tissue (Broadmann area 7) from 15 pathologically confirmed DLB brains and compare them with 16 cognitively normal controls using Illumina MethylationEPIC arrays. We identify 17 significantly differentially methylated CpGs (DMCs) and 17 differentially methylated regions (DMRs) between the groups. The DMCs are mainly located at the CpG islands, promoter and first exon regions. Genes associated with the DMCs are linked to "Parkinson's disease" and "metabolic pathway", as well as the diseases of "severe intellectual disability" and "mood disorders". Overall, our study highlights previously unreported DMCs offering insights into DLB pathogenesis with the possibility that some of these could be used as biomarkers of DLB in the future.
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Affiliation(s)
- Xiaojian Shao
- grid.24433.320000 0004 0449 7958National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Sangeetha Vishweswaraiah
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA
| | - Miroslava Čuperlović-Culf
- grid.24433.320000 0004 0449 7958National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada ,grid.28046.380000 0001 2182 2255Ottawa Institute of Systems Biology, Ottawa, Ontario Canada ,grid.28046.380000 0001 2182 2255Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Ali Yilmaz
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
| | - Celia M. T. Greenwood
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Canada ,grid.14709.3b0000 0004 1936 8649Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
| | - Anuradha Surendra
- grid.24433.320000 0004 0449 7958National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Bernadette McGuinness
- grid.4777.30000 0004 0374 7521Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Peter Passmore
- grid.4777.30000 0004 0374 7521Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Patrick G. Kehoe
- grid.5337.20000 0004 1936 7603Dementia Research Group, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael E. Maddens
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
| | - Steffany A. L. Bennett
- grid.28046.380000 0001 2182 2255Ottawa Institute of Systems Biology, Ottawa, Ontario Canada ,grid.28046.380000 0001 2182 2255Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Brian D. Green
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, Northern Ireland, UK
| | - Uppala Radhakrishna
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
| | - Stewart F. Graham
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
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Čuperlović-Culf M, Khieu NH, Surendra A, Hewitt M, Charlebois C, Sandhu JK. Analysis and Simulation of Glioblastoma Cell Lines-Derived Extracellular Vesicles Metabolome. Metabolites 2020; 10:E88. [PMID: 32131411 PMCID: PMC7142482 DOI: 10.3390/metabo10030088] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/24/2020] [Accepted: 02/28/2020] [Indexed: 12/30/2022] Open
Abstract
Glioblastoma (GBM) is one of the most aggressive cancers of the central nervous system. Despite current advances in non-invasive imaging and the advent of novel therapeutic modalities, patient survival remains very low. There is a critical need for the development of effective biomarkers for GBM diagnosis and therapeutic monitoring. Extracellular vesicles (EVs) produced by GBM tumors have been shown to play an important role in cellular communication and modulation of the tumor microenvironment. As GBM-derived EVs contain specific "molecular signatures" of their parental cells and are able to transmigrate across the blood-brain barrier into biofluids such as the blood and cerebrospinal fluid (CSF), they are considered as a valuable source of potential diagnostic biomarkers. Given the relatively harsh extracellular environment of blood and CSF, EVs have to endure and adapt to different conditions. The ability of EVs to adjust and function depends on their lipid bilayer, metabolic content and enzymes and transport proteins. The knowledge of EVs metabolic characteristics and adaptability is essential for their utilization as diagnostic and therapeutic tools. The main aim of this study was to determine the metabolome of small EVs or exosomes derived from different GBM cells and compare to the metabolic profile of their parental cells using NMR spectroscopy. In addition, a possible flux of metabolic processes in GBM-derived EVs was simulated using constraint-based modeling from published proteomics information. Our results showed a clear difference between the metabolic profiles of GBM cells, EVs and media. Machine learning analysis of EV metabolomics, as well as flux simulation, supports the notion of active metabolism within EVs, including enzymatic reactions and the transfer of metabolites through the EV membrane. These results are discussed in the context of novel GBM diagnostics and therapeutic monitoring.
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Affiliation(s)
- Miroslava Čuperlović-Culf
- Digital Technologies Research Centre, Bldg-M50, 1200 Montreal Road, National Research Council Canada, Ottawa, ON K1A0R6, Canada;
| | - Nam H. Khieu
- Human Health Therapeutics Research Centre, Bldg-M54, 1200 Montreal Road, National Research Council Canada, Ottawa, ON K1A0R6, Canada; (N.H.K.); (M.H.); (C.C.)
| | - Anuradha Surendra
- Digital Technologies Research Centre, Bldg-M50, 1200 Montreal Road, National Research Council Canada, Ottawa, ON K1A0R6, Canada;
| | - Melissa Hewitt
- Human Health Therapeutics Research Centre, Bldg-M54, 1200 Montreal Road, National Research Council Canada, Ottawa, ON K1A0R6, Canada; (N.H.K.); (M.H.); (C.C.)
| | - Claudie Charlebois
- Human Health Therapeutics Research Centre, Bldg-M54, 1200 Montreal Road, National Research Council Canada, Ottawa, ON K1A0R6, Canada; (N.H.K.); (M.H.); (C.C.)
| | - Jagdeep K. Sandhu
- Human Health Therapeutics Research Centre, Bldg-M54, 1200 Montreal Road, National Research Council Canada, Ottawa, ON K1A0R6, Canada; (N.H.K.); (M.H.); (C.C.)
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Culf AS, Yin H, Monro S, Ghosh A, Barnett DA, Ouellette RJ, Čuperlović-Culf M, McFarland SA. A spectroscopic study of substituted anthranilic acids as sensitive environmental probes for detecting cancer cells. Bioorg Med Chem 2016; 24:929-37. [DOI: 10.1016/j.bmc.2015.12.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/18/2015] [Accepted: 12/27/2015] [Indexed: 10/22/2022]
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Culf AS, Čuperlović-Culf M, Ouellette RJ, Decken A. Metal-Free, Acid-Catalyzed ortho-Directed Synthesis of Anthranilic Acid Derivatives Using Carbodiimides. Org Lett 2015; 17:2744-7. [DOI: 10.1021/acs.orglett.5b01160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrian S. Culf
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
| | | | | | - Andreas Decken
- Department of Chemistry, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
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Culf AS, Čuperlović-Culf M, Léger DA, Decken A. Correction to Small Head-to-Tail Macrocyclic α-Peptoids. Org Lett 2014. [DOI: 10.1021/ol502281r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
A convenient and efficient methodology for the head-to-tail macrocyclization of small 3-mer, 4-mer, and 5-mer α-peptoid acids (9-, 12-, and 15-atom N-substituted glycine oligomers) is described. The cyclic trimer has a ccc amide sequence in the crystal structure, whereas the tetramer has ctct and the pentamer has ttccc stereochemistry. NMR analysis reveals rigid structures in solution. These synthetic macrocycles may prove useful in medicinal and materials applications.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute , 35 Providence Street, Moncton, NB E1C 8X3, Canada
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Doiron J, Soultan AH, Richard R, Touré MM, Picot N, Richard R, Čuperlović-Culf M, Robichaud GA, Touaibia M. Synthesis and structure–activity relationship of 1- and 2-substituted-1,2,3-triazole letrozole-based analogues as aromatase inhibitors. Eur J Med Chem 2011; 46:4010-24. [DOI: 10.1016/j.ejmech.2011.05.074] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 05/30/2011] [Accepted: 05/31/2011] [Indexed: 11/28/2022]
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Čuperlović-Culf M, Barnett DA, Culf AS, Chute I. Cell culture metabolomics: applications and future directions. Drug Discov Today 2010; 15:610-21. [DOI: 10.1016/j.drudis.2010.06.012] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 05/18/2010] [Accepted: 06/23/2010] [Indexed: 01/20/2023]
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Culf AS, Werner-Zwanziger U, Robertson KN, Chen B, Čuperlović-Culf M, Barnett DA, Ouellette RJ. Polymeric and polymer-ligated spirobicyclic zwitterionic Janovsky complexes. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.03.136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Blacquiere JM, Sicora O, Vogels CM, Čuperlović-Culf M, Decken A, Ouellette RJ, Westcott SA. Dihydropyrimidinones containing boronic acids. CAN J CHEM 2005. [DOI: 10.1139/v05-211] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The addition of formylphenylboronic acid derivatives to urea and ethyl acetoacetate proceeds in the absence of an additional Lewis acid catalyst to give the corresponding dihydropyrimidinones (Biginelli products) in good yields. Novel boron-containing dihydropyrimidinones have been investigated for their ability to act as anticancer agents against the breast cancer cell line MCF7.Key words: anticancer, Biginelli compounds, boronic acids, breast cancer, dihydropyrimidinones.
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