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Ge Y, Rosendahl P, Duran C, Topfner N, Ciucci S, Guck J, Cannistraci CV. Cell Mechanics Based Computational Classification of Red Blood Cells Via Machine Intelligence Applied to Morpho-Rheological Markers. IEEE/ACM Trans Comput Biol Bioinform 2021; 18:1405-1415. [PMID: 31670675 DOI: 10.1109/tcbb.2019.2945762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite fluorescent cell-labelling being widely employed in biomedical studies, some of its drawbacks are inevitable, with unsuitable fluorescent probes or probes inducing a functional change being the main limitations. Consequently, the demand for and development of label-free methodologies to classify cells is strong and its impact on precision medicine is relevant. Towards this end, high-throughput techniques for cell mechanical phenotyping have been proposed to get a multidimensional biophysical characterization of single cells. With this motivation, our goal here is to investigate the extent to which an unsupervised machine learning methodology, which is applied exclusively on morpho-rheological markers obtained by real-time deformability and fluorescence cytometry (RT-FDC), can address the difficult task of providing label-free discrimination of reticulocytes from mature red blood cells. We focused on this problem, since the characterization of reticulocytes (their percentage and cellular features) in the blood is vital in multiple human disease conditions, especially bone-marrow disorders such as anemia and leukemia. Our approach reports promising label-free results in the classification of reticulocytes from mature red blood cells, and it represents a step forward in the development of high-throughput morpho-rheological-based methodologies for the computational categorization of single cells. Besides, our methodology can be an alternative but also a complementary method to integrate with existing cell-labelling techniques.
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Durán C, Ciucci S, Palladini A, Ijaz UZ, Zippo AG, Sterbini FP, Masucci L, Cammarota G, Ianiro G, Spuul P, Schroeder M, Grill SW, Parsons BN, Pritchard DM, Posteraro B, Sanguinetti M, Gasbarrini G, Gasbarrini A, Cannistraci CV. Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome. Nat Commun 2021; 12:1926. [PMID: 33771992 PMCID: PMC7997970 DOI: 10.1038/s41467-021-22135-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/24/2021] [Indexed: 12/11/2022] Open
Abstract
The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.
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Affiliation(s)
- Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Alessandra Palladini
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden, Helmholtz Zentrum Munchen, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Umer Z Ijaz
- Department of Infrastructure and Environment University of Glasgow, School of Engineering, Glasgow, UK
| | - Antonio G Zippo
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche, Milan, Italy
| | | | - Luca Masucci
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Cammarota
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianluca Ianiro
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Pirjo Spuul
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Stephan W Grill
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Bryony N Parsons
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - D Mark Pritchard
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Department of Gastroenterology, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | - Brunella Posteraro
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Giovanni Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonio Gasbarrini
- Internal Medicine and Gastroenterology Unit, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany.
- Center for Complex Network Intelligence (CCNI) at Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Biomedical Engineering, Tsinghua University, Beijing, China.
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Nishi M, Ogata T, Cannistraci CV, Ciucci S, Nakanishi N, Higuchi Y, Sakamoto A, Tsuji Y, Mizushima K, Matoba S. Systems Network Genomic Analysis Reveals Cardioprotective Effect of MURC/Cavin-4 Deletion Against Ischemia/Reperfusion Injury. J Am Heart Assoc 2019; 8:e012047. [PMID: 31364493 PMCID: PMC6761664 DOI: 10.1161/jaha.119.012047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background Ischemia/reperfusion (I/R) injury is a critical issue in the development of treatment strategies for ischemic heart disease. MURC (muscle‐restricted coiled‐coil protein)/Cavin‐4 (caveolae‐associated protein 4), which is a component of caveolae, is involved in the pathophysiology of dilated cardiomyopathy and cardiac hypertrophy. However, the role of MURC in cardiac I/R injury remains unknown. Methods and Results The systems network genomic analysis based on PC‐corr network inference on microarray data between wild‐type and MURC knockout mouse hearts predicted a network of discriminating genes associated with reactive oxygen species. To demonstrate the prediction, we analyzed I/R‐injured mouse hearts. MURC deletion decreased infarct size and preserved heart contraction with reactive oxygen species–related molecule EGR1 (early growth response protein 1) and DDIT4 (DNA‐damage‐inducible transcript 4) suppression in I/R‐injured hearts. Because PC‐corr network inference integrated with a protein–protein interaction network prediction also showed that MURC is involved in the apoptotic pathway, we confirmed the upregulation of STAT3 (signal transducer and activator of transcription 3) and BCL2 (B‐cell lymphoma 2) and the inactivation of caspase 3 in I/R‐injured hearts of MURC knockout mice compared with those of wild‐type mice. STAT3 inhibitor canceled the cardioprotective effect of MURC deletion in I/R‐injured hearts. In cardiomyocytes exposed to hydrogen peroxide, MURC overexpression promoted apoptosis and MURC knockdown inhibited apoptosis. STAT3 inhibitor canceled the antiapoptotic effect of MURC knockdown in cardiomyocytes. Conclusions Our findings, obtained by prediction from systems network genomic analysis followed by experimental validation, suggested that MURC modulates cardiac I/R injury through the regulation of reactive oxygen species–induced cell death and STAT3‐meditated antiapoptosis. Functional inhibition of MURC may be effective in reducing cardiac I/R injury.
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Affiliation(s)
- Masahiro Nishi
- Department of Cardiovascular Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Takehiro Ogata
- Department of Cardiovascular Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan.,Department of Pathology and Cell Regulation Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC) Center for Molecular and Cellular Bioengineering (CMCB) Center for Systems Biology Dresden Department of Physics Technische Universität Dresden Dresden Germany.,Tsinghua Laboratory of Brain and Intelligence Tsinghua University Beijing China
| | - Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC) Center for Molecular and Cellular Bioengineering (CMCB) Center for Systems Biology Dresden Department of Physics Technische Universität Dresden Dresden Germany
| | - Naohiko Nakanishi
- Department of Cardiovascular Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Yusuke Higuchi
- Department of Cardiovascular Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Akira Sakamoto
- Department of Cardiovascular Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Yumika Tsuji
- Department of Cardiovascular Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Katsura Mizushima
- Department of Molecular Gastroenterology and Hepatology Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
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Miendlarzewska EA, Ciucci S, Cannistraci CV, Bavelier D, Schwartz S. Reward-enhanced encoding improves relearning of forgotten associations. Sci Rep 2018; 8:8557. [PMID: 29867116 PMCID: PMC5986818 DOI: 10.1038/s41598-018-26929-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/18/2018] [Indexed: 12/16/2022] Open
Abstract
Research on human memory has shown that monetary incentives can enhance hippocampal memory consolidation and thereby protect memory traces from forgetting. However, it is not known whether initial reward may facilitate the recovery of already forgotten memories weeks after learning. Here, we investigated the influence of monetary reward on later relearning. Nineteen healthy human participants learned object-location associations, for half of which we offered money. Six weeks later, most of these associations had been forgotten as measured by a test of declarative memory. Yet, relearning in the absence of any reward was faster for the originally rewarded associations. Thus, associative memories encoded in a state of monetary reward motivation may persist in a latent form despite the failure to retrieve them explicitly. Alternatively, such facilitation could be analogous to the renewal effect observed in animal conditioning, whereby a reward-associated cue can reinstate anticipatory arousal, which would in turn modulate relearning. This finding has important implications for learning and education, suggesting that even when learned information is no longer accessible via explicit retrieval, the enduring effects of a past prospect of reward could facilitate its recovery.
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Affiliation(s)
- Ewa A Miendlarzewska
- Department of Neuroscience, University of Geneva, Geneva, Switzerland. .,Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland. .,Geneva Finance Research Institute, University of Geneva, Geneva, Switzerland.
| | - Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.,Lipotype GmbH, Tatzberg 47, 01307, Dresden, Germany
| | - Carlo V Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.,Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi "Bonino Pulejo", Messina, 98124, Italy
| | - Daphne Bavelier
- Psychology Section, FPSE, University of Geneva, Geneva, Switzerland.,Brain & Cognitive Sciences, University of Rochester, Rochester, NY, United States
| | - Sophie Schwartz
- Department of Neuroscience, University of Geneva, Geneva, Switzerland. .,Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland. .,Geneva Neuroscience Center, University of Geneva, Geneva, Switzerland.
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5
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Ciucci S, Ge Y, Durán C, Palladini A, Jiménez-Jiménez V, Martínez-Sánchez LM, Wang Y, Sales S, Shevchenko A, Poser SW, Herbig M, Otto O, Androutsellis-Theotokis A, Guck J, Gerl MJ, Cannistraci CV. Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies. Sci Rep 2017; 7:43946. [PMID: 28287094 PMCID: PMC5347127 DOI: 10.1038/srep43946] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/06/2017] [Indexed: 01/08/2023] Open
Abstract
Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation. Biologists and medical researchers often prefer effective methods that offer an immediate interpretation to complicated algorithms that in principle promise an improvement but in practice are difficult to be applied and interpreted. Here we present PC-corr: a simple algorithm that associates to any PCA segregation a discriminative network of features. Such network can be inspected in search of functional modules useful in the definition of combinatorial and multiscale biomarkers from multifaceted omic data in systems and precision biomedicine. We offer proofs of PC-corr efficacy on lipidomic, metagenomic, developmental genomic, population genetic, cancer promoteromic and cancer stem-cell mechanomic data. Finally, PC-corr is a general functional network inference approach that can be easily adopted for big data exploration in computer science and analysis of complex systems in physics.
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Affiliation(s)
- Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Lipotype GmbH, Tatzberg 47, 01307 Dresden, Germany
| | - Yan Ge
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Alessandra Palladini
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.,Lipotype GmbH, Tatzberg 47, 01307 Dresden, Germany.,Membrane Biochemistry Group, DZD Paul Langerhans Institute, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Víctor Jiménez-Jiménez
- Integrin Signalling Group, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Luisa María Martínez-Sánchez
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Yuting Wang
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrstraße 108, 01307 Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Susanne Sales
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrstraße 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrstraße 108, 01307 Dresden, Germany
| | - Steven W Poser
- Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstr.74, 01307 Dresden, Germany
| | - Maik Herbig
- Cellular Machines Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Oliver Otto
- Cellular Machines Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Andreas Androutsellis-Theotokis
- Center for Regenerative Therapies Dresden (CRTD), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany.,Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstr.74, 01307 Dresden, Germany.,Department of Stem Cell Biology, Centre for Biomolecular Sciences, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Jochen Guck
- Cellular Machines Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | | | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
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