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Zhao Y, Zhang S, Xu J, Yu Y, Peng G, Cannistraci CV, Han JDJ. Spatial Reconstruction of Oligo and Single Cells by De Novo Coalescent Embedding of Transcriptomic Networks. Adv Sci (Weinh) 2023:e2206307. [PMID: 37323105 PMCID: PMC10369275 DOI: 10.1002/advs.202206307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/18/2023] [Indexed: 06/17/2023]
Abstract
Single cell RNA-seq (scRNA-seq) profiles conceal temporal and spatial tissue developmental information. De novo reconstruction of single cell temporal trajectory has been fairly addressed, but reverse engineering single cell 3D spatial tissue organization is hitherto landmark based, and de novo spatial reconstruction is a compelling computational open problem. Here it is shown that a proposed algorithm for de novo coalescent embedding (D-CE) of oligo/single cell transcriptomic networks can help to address this problem. Relying on the spatial information encoded in the expression patterns of genes, it is found that D-CE of cell-cell association transcriptomic networks, by preserving mesoscale network organization, captures spatial domains, identifies spatially expressed genes, reconstructs cell samples' 3D spatial distribution, and uncovers spatial domains and markers necessary for understanding the design principles on spatial organization and pattern formation. Comparison to the novoSpaRC and CSOmap (the only available de novo 3D spatial reconstruction methods) on 14 datasets and 497 reconstructions, reveals a significantly superior performance of D-CE.
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Affiliation(s)
- Yuxuan Zhao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, P. R. China
| | - Shiqiang Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, P. R. China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, P. R. China
| | - Jian Xu
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, P. R. China
| | - Yangyang Yu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, P. R. China
| | - Guangdun Peng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, P. R. China
- Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, 510530, P. R. China
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47-49, 01307, Dresden, Germany
| | - Carlo Vittorio Cannistraci
- Center for Complex Network Intelligence (CCNI), Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Physics, Department of Computer Science, Department of Biomedical Engineering, Tsinghua University, 60 Chengfu Road, Beijing, 100084, P. R. China
- Center for Systems Biology Dresden (CSBD) Pfotenhauerstr, 108, 01307, Dresden, Germany
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, P. R. China
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Cackett L, Cannistraci CV, Meier S, Ferrandi P, Pěnčík A, Gehring C, Novák O, Ingle RA, Donaldson L. Salt-Specific Gene Expression Reveals Elevated Auxin Levels in Arabidopsis thaliana Plants Grown Under Saline Conditions. Front Plant Sci 2022; 13:804716. [PMID: 35222469 PMCID: PMC8866861 DOI: 10.3389/fpls.2022.804716] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Soil salinization is increasing globally, driving a reduction in crop yields that threatens food security. Salinity stress reduces plant growth by exerting two stresses on plants: rapid shoot ion-independent effects which are largely osmotic and delayed ionic effects that are specific to salinity stress. In this study we set out to delineate the osmotic from the ionic effects of salinity stress. Arabidopsis thaliana plants were germinated and grown for two weeks in media supplemented with 50, 75, 100, or 125 mM NaCl (that imposes both an ionic and osmotic stress) or iso-osmolar concentrations (100, 150, 200, or 250 mM) of sorbitol, that imposes only an osmotic stress. A subsequent transcriptional analysis was performed to identify sets of genes that are differentially expressed in plants grown in (1) NaCl or (2) sorbitol compared to controls. A comparison of the gene sets identified genes that are differentially expressed under both challenge conditions (osmotic genes) and genes that are only differentially expressed in plants grown on NaCl (ionic genes, hereafter referred to as salt-specific genes). A pathway analysis of the osmotic and salt-specific gene lists revealed that distinct biological processes are modulated during growth under the two conditions. The list of salt-specific genes was enriched in the gene ontology (GO) term "response to auxin." Quantification of the predominant auxin, indole-3-acetic acid (IAA) and IAA biosynthetic intermediates revealed that IAA levels are elevated in a salt-specific manner through increased IAA biosynthesis. Furthermore, the expression of NITRILASE 2 (NIT2), which hydrolyses indole-3-acetonitile (IAN) into IAA, increased in a salt-specific manner. Overexpression of NIT2 resulted in increased IAA levels, improved Na:K ratios and enhanced survival and growth of Arabidopsis under saline conditions. Overall, our data suggest that auxin is involved in maintaining growth during the ionic stress imposed by saline conditions.
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Affiliation(s)
- Lee Cackett
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, South Africa
| | - Carlo Vittorio Cannistraci
- Center for Complex Network Intelligence, Tsinghua Laboratory of Brain and Intelligence, Department of Computer Science, Tsinghua University, Beijing, China
- Center for Complex Network Intelligence, Tsinghua Laboratory of Brain and Intelligence, Department of Biomedical Engineering, Tsinghua University, Beijing, China
- Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Stuart Meier
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, South Africa
| | - Paul Ferrandi
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czechia
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czechia
| | - Robert A. Ingle
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, South Africa
| | - Lara Donaldson
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
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Nishi M, Ogata T, Kobayakawa K, Kobayakawa R, Matsuo T, Cannistraci CV, Tomita S, Taminishi S, Suga T, Kitani T, Higuchi Y, Sakamoto A, Tsuji Y, Soga T, Matoba S. Energy-sparing by 2-methyl-2-thiazoline protects heart from ischaemia/reperfusion injury. ESC Heart Fail 2021; 9:428-441. [PMID: 34854235 PMCID: PMC8787978 DOI: 10.1002/ehf2.13732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/10/2021] [Revised: 10/13/2021] [Accepted: 11/11/2021] [Indexed: 11/06/2022] Open
Abstract
AIMS Cardiac ischaemia/reperfusion (I/R) injury remains a critical issue in the therapeutic management of ischaemic heart failure. Although mild hypothermia has a protective effect on cardiac I/R injury, more rapid and safe methods that can obtain similar results to hypothermia therapy are required. 2-Methyl-2-thiazoline (2MT), an innate fear inducer, causes mild hypothermia resulting in resistance to critical hypoxia in cutaneous or cerebral I/R injury. The aim of this study is to demonstrate the protective effect of systemically administered 2MT on cardiac I/R injury and to elucidate the mechanism underlying this effect. METHODS AND RESULTS A single subcutaneous injection of 2MT (50 mg/kg) was given prior to reperfusion of the I/R injured 10 week-old male mouse heart and its efficacy was evaluated 24 h after the ligation of the left anterior descending coronary artery. 2MT preserved left ventricular systolic function following I/R injury (ejection fraction, %: control 37.9 ± 6.7, 2MT 54.1 ± 6.4, P < 0.01). 2MT also decreased infarct size (infarct size/ischaemic area at risk, %: control 48.3 ± 12.1, 2MT 25.6 ± 4.2, P < 0.05) and serum cardiac troponin levels (ng/mL: control 8.9 ± 1.1, 2MT 1.9 ± 0.1, P < 0.01) after I/R. Moreover, 2MT reduced the oxidative stress-exposed area within the heart (%: control 25.3 ± 4.7, 2MT 10.8 ± 1.4, P < 0.01). These results were supported by microarray analysis of the mouse hearts. 2MT induced a transient, mild decrease in core body temperature (°C: -2.4 ± 1.4), which gradually recovered over several hours. Metabolome analysis of the mouse hearts suggested that 2MT minimized energy metabolism towards suppressing oxidative stress. Furthermore, 18F-fluorodeoxyglucose-positron emission tomography/computed tomography imaging revealed that 2MT reduced the activity of brown adipose tissue (standardized uptake value: control 24.3 ± 6.4, 2MT 18.4 ± 5.8, P < 0.05). 2MT also inhibited mitochondrial respiration and glycolysis in rat cardiomyoblasts. CONCLUSIONS We identified the cardioprotective effect of systemically administered 2MT on cardiac I/R injury by sparing energy metabolism with reversible hypothermia. Our results highlight the potential of drug-induced hypothermia therapy as an adjunct to coronary intervention in severe ischaemic heart disease.
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Affiliation(s)
- Masahiro Nishi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Takehiro Ogata
- Department of Pathology and Cell Regulation, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Ko Kobayakawa
- Functional Neuroscience Lab, Kansai Medical University, Hirakata, Japan
| | - Reiko Kobayakawa
- Functional Neuroscience Lab, Kansai Medical University, Hirakata, Japan
| | - Tomohiko Matsuo
- Functional Neuroscience Lab, Kansai Medical University, Hirakata, Japan
| | - Carlo Vittorio Cannistraci
- Center for Complex Network Intelligence (CCNI), Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Computer Science, Department of Biomedical Engineering, Tsinghua University, China.,Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Shinya Tomita
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shunta Taminishi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaomi Suga
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomoya Kitani
- 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
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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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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Cannistraci CV, Valsecchi MG, Capua I. Age-sex population adjusted analysis of disease severity in epidemics as a tool to devise public health policies for COVID-19. Sci Rep 2021; 11:11787. [PMID: 34083555 PMCID: PMC8175671 DOI: 10.1038/s41598-021-89615-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/28/2021] [Indexed: 11/08/2022] Open
Abstract
Governments continue to update social intervention strategies to contain COVID-19 infections. However, investigation of COVID-19 severity indicators across the population might help to design more precise strategies, balancing the need to keep people safe and to reduce the socio-economic burden of generalized restriction precedures. Here, we propose a method for age-sex population-adjusted analysis of disease severity in epidemics that has the advantage to use simple and repeatable variables, which are daily or weekly available. This allows to monitor the effect of public health policies in short term, and to repeat these calculations over time to surveille epidemic dynamics and impact. Our method can help to define a risk-categorization of likeliness to develop a severe COVID-19 disease which requires intensive care or is indicative of a higher risk of dying. Indeed, analysis of suitable open-access COVID-19 data in three European countries indicates that individuals in the 0-40 age interval and females under 60 are significantly less likely to develop a severe condition and die, whereas males equal or above 60 are more likely at risk of severe disease and death. Hence, a combination of age-adaptive and sex-balanced guidelines for social interventions could represent key public health management tools for policymakers.
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Affiliation(s)
- Carlo Vittorio Cannistraci
- Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Biomedical Engineering, Tsinghua University, 160 Chengfu Rd., SanCaiTang Building, Haidian District, Beijing, 100084, China.
- 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.
| | - Maria Grazia Valsecchi
- Bicocca Center of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Ilaria Capua
- One Health Center of Excellence, University of Florida, Gainesville, FL, USA.
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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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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJ, Rackham OJ, Rizzu P, Martinez DFS, Sandelin A, Sanjana P, Semple CA, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest AR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJ, Shin JW, Carninci P. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020. [DOI: 10.1101/gr.270330.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Eisenhofer G, Durán C, Cannistraci CV, Peitzsch M, Williams TA, Riester A, Burrello J, Buffolo F, Prejbisz A, Beuschlein F, Januszewicz A, Mulatero P, Lenders JWM, Reincke M. Use of Steroid Profiling Combined With Machine Learning for Identification and Subtype Classification in Primary Aldosteronism. JAMA Netw Open 2020; 3:e2016209. [PMID: 32990741 PMCID: PMC7525346 DOI: 10.1001/jamanetworkopen.2020.16209] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
IMPORTANCE Most patients with primary aldosteronism, a major cause of secondary hypertension, are not identified or appropriately treated because of difficulties in diagnosis and subtype classification. Applications of artificial intelligence combined with mass spectrometry-based steroid profiling could address this problem. OBJECTIVE To assess whether plasma steroid profiling combined with machine learning might facilitate diagnosis and treatment stratification of primary aldosteronism, particularly for patients with unilateral adenomas due to pathogenic KCNJ5 sequence variants. DESIGN, SETTING, AND PARTICIPANTS This diagnostic study was conducted at multiple tertiary care referral centers. Steroid profiles were measured from June 2013 to March 2017 in 462 patients tested for primary aldosteronism and 201 patients with hypertension. Data analyses were performed from September 2018 to August 2019. MAIN OUTCOMES AND MEASURES The aldosterone to renin ratio and saline infusion tests were used to diagnose primary aldosteronism. Subtyping was done by adrenal venous sampling and follow-up of patients who underwent adrenalectomy. Statistical tests and machine-learning algorithms were applied to plasma steroid profiles. Areas under receiver operating characteristic curves, sensitivity, specificity, and other diagnostic performance measures were calculated. RESULTS Primary aldosteronism was confirmed in 273 patients (165 men [60%]; mean [SD] age, 51 [10] years), including 134 with bilateral disease and 139 with unilateral adenomas (58 with and 81 without somatic KCNJ5 sequence variants). Plasma steroid profiles varied according to disease subtype and were particularly distinctive in patients with adenomas due to KCNJ5 variants, who showed better rates of biochemical cure after adrenalectomy than other patients. Among patients tested for primary aldosteronism, a selection of 8 steroids in combination with the aldosterone to renin ratio showed improved effectiveness for diagnosis over either strategy alone. In contrast, the steroid profile alone showed superior performance over the aldosterone to renin ratio for identifying unilateral disease, particularly adenomas due to KCNJ5 variants. Among 632 patients included in the analysis, machine learning-designed combinatorial marker profiles of 7 steroids alone both predicted primary aldosteronism in 1 step and subtyped patients with unilateral adenomas due to KCNJ5 variants at diagnostic sensitivities of 69% (95% CI, 68%-71%) and 85% (95% CI, 81%-88%), respectively, and at specificities of 94% (95% CI, 93%-94%) and 97% (95% CI, 97%-98%), respectively. The validation series yielded comparable diagnostic performance. CONCLUSIONS AND RELEVANCE Machine learning-designed combinatorial plasma steroid profiles may facilitate both screening for primary aldosteronism and identification of patients with unilateral adenomas due to pathogenic KCNJ5 variants, who are most likely to show benefit from surgical intervention.
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Affiliation(s)
- Graeme Eisenhofer
- Department of Internal Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Center for Systems Biology Dresden, Department of Physics, Technische Universität Dresden, Dresden, Germany
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Center for Systems Biology Dresden, Department of Physics, Technische Universität Dresden, Dresden, Germany
- Center for Complex Network Intelligence Laboratory at the Tsinghua Laboratory of Brain and Intelligence, Department of Bioengineering, Tsinghua University, Beijing, China
| | - Mirko Peitzsch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Tracy Ann Williams
- Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Turin, Turin, Italy
- Medizinische Klinik und Poliklinik IV, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anna Riester
- Medizinische Klinik und Poliklinik IV, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacopo Burrello
- Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Fabrizio Buffolo
- Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Felix Beuschlein
- Medizinische Klinik und Poliklinik IV, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Endocrinology, Diabetology, and Clinical Nutrition, UniversitätsSpital Zürich, Zürich, Switzerland
| | | | - Paolo Mulatero
- Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Jacques W. M. Lenders
- Department of Internal Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
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9
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJF, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020; 30:1060-1072. [PMID: 32718982 PMCID: PMC7397864 DOI: 10.1101/gr.254219.119] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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: 07/12/2019] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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Affiliation(s)
- Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yari Ciani
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | | | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Leonie Roos
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrük Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Ivan V Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Christopher JF Cameron
- School of Computer Science, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
| | - 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 01062, Germany.,Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Bioengineering, Tsinghua University, Beijing 100084, China
| | - Ryan Cardenas
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Howard Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California 94305, USA
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich 8093, Switzerland
| | - Alexander Favorov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Diego Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome 00179, Italy
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lusy Handoko
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Hasegawa
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Norihito Hayatsu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Peter Heutink
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Eddie L Imada
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Bogumil Kaczkowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Aditi Kanhere
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Emily Kawabata
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Tsugumi Kawashima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - S Thomas Kelly
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Miki Kojima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Anton Kratz
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Mariola Kurowska-Stolarska
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, Scotland G12 8QQ, United Kingdom
| | - Andrew Tae Jun Kwon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jeffrey Leek
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Fernando López-Redondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shiori Maeda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Vsevolod J Makeev
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuhiro R Nitta
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yukihiko Noro
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Denis Paquette
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Callum J C Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Patrizia Rizzu
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | | | - Albin Sandelin
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Pillay Sanjana
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Colin A M Semple
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Martin S Taylor
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Malte Thodberg
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Vidisha Tripathi
- National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roberto Verardo
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ilya E Vorontsov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chinatsu Yamamoto
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Robert S Young
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08002, Spain
| | | | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen N-5008, Norway
| | - Claudio Schneider
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.,Department of Medicine and Consorzio Interuniversitario Biotecnologie p.zle Kolbe 1 University of Udine, Udine 33100, Italy
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
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10
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Xu M, Pan Q, Muscoloni A, Xia H, Cannistraci CV. Modular gateway-ness connectivity and structural core organization in maritime network science. Nat Commun 2020; 11:2849. [PMID: 32503974 PMCID: PMC7275034 DOI: 10.1038/s41467-020-16619-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 09/28/2018] [Accepted: 04/20/2020] [Indexed: 11/25/2022] Open
Abstract
Around 80% of global trade by volume is transported by sea, and thus the maritime transportation system is fundamental to the world economy. To better exploit new international shipping routes, we need to understand the current ones and their complex systems association with international trade. We investigate the structure of the global liner shipping network (GLSN), finding it is an economic small-world network with a trade-off between high transportation efficiency and low wiring cost. To enhance understanding of this trade-off, we examine the modular segregation of the GLSN; we study provincial-, connector-hub ports and propose the definition of gateway-hub ports, using three respective structural measures. The gateway-hub structural-core organization seems a salient property of the GLSN, which proves importantly associated to network integration and function in realizing the cargo transportation of international trade. This finding offers new insights into the GLSN’s structural organization complexity and its relevance to international trade. It is crucial to understand the evolving structure of global liner shipping system. Here the authors unveiled the architecture of a recent global liner shipping network (GLSN) and show that the structure of global liner shipping system has evolved to be self-organized with a trade-off between high transportation efficiency and low wiring cost and ports’ gateway-ness is most highly associated with ports’ economic performance.
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Affiliation(s)
- Mengqiao Xu
- School of Economics and Management, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian City, Liaoning Province, 116024, China.
| | - Qian Pan
- School of Economics and Management, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian City, Liaoning Province, 116024, China
| | - Alessandro Muscoloni
- 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. Tatzberg 47/49, 01307, Dresden, Germany
| | - Haoxiang Xia
- School of Economics and Management, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian City, Liaoning Province, 116024, China.
| | - 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. Tatzberg 47/49, 01307, Dresden, Germany. .,Center for Complex Network Intelligence (CCNI), Tsinghua Laboratory of Brain and Intelligence (THBI), Tsinghua University. 160 Chengfu Rd., SanCaiTang Building, Haidian District, Beijing, 100084, China.
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11
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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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12
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Durán C, Daminelli S, Thomas JM, Haupt VJ, Schroeder M, Cannistraci CV. Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory. Brief Bioinform 2019; 19:1183-1202. [PMID: 28453640 PMCID: PMC6291778 DOI: 10.1093/bib/bbx041] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Indexed: 01/03/2023] Open
Abstract
The bipartite network representation of the drug–target interactions (DTIs) in a biosystem enhances understanding of the drugs’ multifaceted action modes, suggests therapeutic switching for approved drugs and unveils possible side effects. As experimental testing of DTIs is costly and time-consuming, computational predictors are of great aid. Here, for the first time, state-of-the-art DTI supervised predictors custom-made in network biology were compared—using standard and innovative validation frameworks—with unsupervised pure topological-based models designed for general-purpose link prediction in bipartite networks. Surprisingly, our results show that the bipartite topology alone, if adequately exploited by means of the recently proposed local-community-paradigm (LCP) theory—initially detected in brain-network topological self-organization and afterwards generalized to any complex network—is able to suggest highly reliable predictions, with comparable performance with the state-of-the-art-supervised methods that exploit additional (non-topological, for instance biochemical) DTI knowledge. Furthermore, a detailed analysis of the novel predictions revealed that each class of methods prioritizes distinct true interactions; hence, combining methodologies based on diverse principles represents a promising strategy to improve drug–target discovery. To conclude, this study promotes the power of bio-inspired computing, demonstrating that simple unsupervised rules inspired by principles of topological self-organization and adaptiveness arising during learning in living intelligent systems (like the brain) can efficiently equal perform complicated algorithms based on advanced, supervised and knowledge-based engineering.
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Affiliation(s)
| | - Simone Daminelli
- Corresponding authors: Carlo Cannistraci, Biomedical Cybernetics Group at Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden (TUD), Tatzberg 47-49, 01307 Dresden, Germany, Tel.: +49 (0)351 463 40080; E-mail: ; Simone Daminelli, Bioinformatics Group at Biotechnology Center (BIOTEC), Center of Molecular Cellular Bioengineering (CMCB), TUD, Tatzberg 47-49, 01307 Dresden, Germany, Tel.: +49 (0)351 463 40060; E-mail: ; Michael Schroeder, Bioinformatics Group at Biotechnology Center (BIOTEC), Center of Molecular and Cellular Bioengineering (CMCB), TUD Tatzberg 47-49, 01307 Dresden, Germany, Tel.: +49 (0)351 463 40062; E-mail:
| | | | | | - Michael Schroeder
- Corresponding authors: Carlo Cannistraci, Biomedical Cybernetics Group at Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden (TUD), Tatzberg 47-49, 01307 Dresden, Germany, Tel.: +49 (0)351 463 40080; E-mail: ; Simone Daminelli, Bioinformatics Group at Biotechnology Center (BIOTEC), Center of Molecular Cellular Bioengineering (CMCB), TUD, Tatzberg 47-49, 01307 Dresden, Germany, Tel.: +49 (0)351 463 40060; E-mail: ; Michael Schroeder, Bioinformatics Group at Biotechnology Center (BIOTEC), Center of Molecular and Cellular Bioengineering (CMCB), TUD Tatzberg 47-49, 01307 Dresden, Germany, Tel.: +49 (0)351 463 40062; E-mail:
| | - Carlo Vittorio Cannistraci
- Corresponding authors: Carlo Cannistraci, Biomedical Cybernetics Group at Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden (TUD), Tatzberg 47-49, 01307 Dresden, Germany, Tel.: +49 (0)351 463 40080; E-mail: ; Simone Daminelli, Bioinformatics Group at Biotechnology Center (BIOTEC), Center of Molecular Cellular Bioengineering (CMCB), TUD, Tatzberg 47-49, 01307 Dresden, Germany, Tel.: +49 (0)351 463 40060; E-mail: ; Michael Schroeder, Bioinformatics Group at Biotechnology Center (BIOTEC), Center of Molecular and Cellular Bioengineering (CMCB), TUD Tatzberg 47-49, 01307 Dresden, Germany, Tel.: +49 (0)351 463 40062; E-mail:
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13
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Poser SW, Otto O, Arps-Forker C, Ge Y, Herbig M, Andree C, Gruetzmann K, Adasme MF, Stodolak S, Nikolakopoulou P, Park DM, Mcintyre A, Lesche M, Dahl A, Lennig P, Bornstein SR, Schroeck E, Klink B, Leker RR, Bickle M, Chrousos GP, Schroeder M, Cannistraci CV, Guck J, Androutsellis-Theotokis A. Controlling distinct signaling states in cultured cancer cells provides a new platform for drug discovery. FASEB J 2019; 33:9235-9249. [PMID: 31145643 DOI: 10.1096/fj.201802603rr] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer cells can switch between signaling pathways to regulate growth under different conditions. In the tumor microenvironment, this likely helps them evade therapies that target specific pathways. We must identify all possible states and utilize them in drug screening programs. One such state is characterized by expression of the transcription factor Hairy and Enhancer of Split 3 (HES3) and sensitivity to HES3 knockdown, and it can be modeled in vitro. Here, we cultured 3 primary human brain cancer cell lines under 3 different culture conditions that maintain low, medium, and high HES3 expression and characterized gene regulation and mechanical phenotype in these states. We assessed gene expression regulation following HES3 knockdown in the HES3-high conditions. We then employed a commonly used human brain tumor cell line to screen Food and Drug Administration (FDA)-approved compounds that specifically target the HES3-high state. We report that cells from multiple patients behave similarly when placed under distinct culture conditions. We identified 37 FDA-approved compounds that specifically kill cancer cells in the high-HES3-expression conditions. Our work reveals a novel signaling state in cancer, biomarkers, a strategy to identify treatments against it, and a set of putative drugs for potential repurposing.-Poser, S. W., Otto, O., Arps-Forker, C., Ge, Y., Herbig, M., Andree, C., Gruetzmann, K., Adasme, M. F., Stodolak, S., Nikolakopoulou, P., Park, D. M., Mcintyre, A., Lesche, M., Dahl, A., Lennig, P., Bornstein, S. R., Schroeck, E., Klink, B., Leker, R. R., Bickle, M., Chrousos, G. P., Schroeder, M., Cannistraci, C. V., Guck, J., Androutsellis-Theotokis, A. Controlling distinct signaling states in cultured cancer cells provides a new platform for drug discovery.
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Affiliation(s)
- Steven W Poser
- Department of Internal Medicine III, Technische Universität Dresden, Dresden, Germany
| | - Oliver Otto
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
| | - Carina Arps-Forker
- Department of Internal Medicine III, Technische Universität Dresden, Dresden, Germany
| | - Yan Ge
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany.,Biomedical Cybernetics Group, Department of Physics, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Technische Universität Dresden, Dresden, Germany
| | - Maik Herbig
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
| | - Cordula Andree
- Technology Development Studio, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Konrad Gruetzmann
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melissa F Adasme
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
| | - Szymon Stodolak
- Division of Cancer and Stem Cells, University of Nottingham, Nottingham, United Kingdom
| | | | - Deric M Park
- Department of Neurology, Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois, USA.,Innate Repair, London, United Kingdom
| | - Alan Mcintyre
- Division of Cancer and Stem Cells, University of Nottingham, Nottingham, United Kingdom
| | - Mathias Lesche
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany.,Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Andreas Dahl
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany.,Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Petra Lennig
- B - CUBE Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Stefan R Bornstein
- Department of Internal Medicine III, Technische Universität Dresden, Dresden, Germany.,Innate Repair, London, United Kingdom
| | - Evelin Schroeck
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany.,Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Barbara Klink
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany.,Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ronen R Leker
- Stroke Unit, Department of Neurology, Stroke Center and the Peritz and Chantal Sheinberg Cerebrovascular Research Laboratory, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Marc Bickle
- Technology Development Studio, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - George P Chrousos
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Athens, Greece.,Aghia Sophia Children's Hospital, Athens, Greece
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Department of Physics, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Technische Universität Dresden, Dresden, Germany.,Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi Bonino Pulejo, Messina, Italy
| | - Jochen Guck
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
| | - Andreas Androutsellis-Theotokis
- Department of Internal Medicine III, Technische Universität Dresden, Dresden, Germany.,Division of Cancer and Stem Cells, University of Nottingham, Nottingham, United Kingdom.,Innate Repair, London, United Kingdom.,Center for Regenerative Therapies Dresden, Dresden, Germany
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14
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Onesto V, Villani M, Narducci R, Malara N, Imbrogno A, Allione M, Costa N, Coppedè N, Zappettini A, Cannistraci CV, Cancedda L, Amato F, Di Fabrizio E, Gentile F. Cortical-like mini-columns of neuronal cells on zinc oxide nanowire surfaces. Sci Rep 2019; 9:4021. [PMID: 30858456 PMCID: PMC6411964 DOI: 10.1038/s41598-019-40548-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 10/26/2018] [Accepted: 02/18/2019] [Indexed: 11/25/2022] Open
Abstract
A long-standing goal of neuroscience is a theory that explains the formation of the minicolumns in the cerebral cortex. Minicolumns are the elementary computational units of the mature neocortex. Here, we use zinc oxide nanowires with controlled topography as substrates for neural-cell growth. We observe that neuronal cells form networks where the networks characteristics exhibit a high sensitivity to the topography of the nanowires. For certain values of nanowires density and fractal dimension, neuronal networks express small world attributes, with enhanced information flows. We observe that neurons in these networks congregate in superclusters of approximately 200 neurons. We demonstrate that this number is not coincidental: the maximum number of cells in a supercluster is limited by the competition between the binding energy between cells, adhesion to the substrate, and the kinetic energy of the system. Since cortical minicolumns have similar size, similar anatomical and topological characteristics of neuronal superclusters on nanowires surfaces, we conjecture that the formation of cortical minicolumns is likewise guided by the interplay between energy minimization, information optimization and topology. For the first time, we provide a clear account of the mechanisms of formation of the minicolumns in the brain.
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Affiliation(s)
- V Onesto
- Center for Advanced Biomaterials for HealthCare, Istituto Italiano di Tecnologia, 80125, Naples, Italy.,Department of Experimental and Clinical Medicine, University of Magna Graecia, 88100, Catanzaro, Italy
| | - M Villani
- IMEM-CNR Parco Area delle Scienze 37/A, 43124, Parma, Italy
| | - R Narducci
- Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - N Malara
- Department of Experimental and Clinical Medicine, University of Magna Graecia, 88100, Catanzaro, Italy
| | - A Imbrogno
- Tyndall National Institute, Cork, T12 R5CP, Ireland
| | - M Allione
- PSE division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - N Costa
- Health Department, University of Magna Graecia, 88100, Catanzaro, Italy
| | - N Coppedè
- IMEM-CNR Parco Area delle Scienze 37/A, 43124, Parma, Italy
| | - A Zappettini
- IMEM-CNR Parco Area delle Scienze 37/A, 43124, Parma, Italy
| | - C 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
| | - L Cancedda
- Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.,Dulbecco Telethon Institute, Rome, Italy
| | - F Amato
- Department of Electrical Engineering and Information Technology, University Federico II, Naples, Italy
| | - Enzo Di Fabrizio
- PSE division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - F Gentile
- Department of Electrical Engineering and Information Technology, University Federico II, Naples, Italy.
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15
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Zanardi A, Conti A, Cremonesi M, D'Adamo P, Gilberti E, Apostoli P, Cannistraci CV, Piperno A, David S, Alessio M. Ceruloplasmin replacement therapy ameliorates neurological symptoms in a preclinical model of aceruloplasminemia. EMBO Mol Med 2019; 10:91-106. [PMID: 29183916 PMCID: PMC5760856 DOI: 10.15252/emmm.201708361] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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] [Indexed: 12/21/2022] Open
Abstract
Aceruloplasminemia is a monogenic disease caused by mutations in the ceruloplasmin gene that result in loss of protein ferroxidase activity. Ceruloplasmin plays a role in iron homeostasis, and its activity impairment leads to iron accumulation in liver, pancreas, and brain. Iron deposition promotes diabetes, retinal degeneration, and progressive neurodegeneration. Current therapies mainly based on iron chelation, partially control systemic iron deposition but are ineffective on neurodegeneration. We investigated the potential of ceruloplasmin replacement therapy in reducing the neurological pathology in the ceruloplasmin-knockout (CpKO) mouse model of aceruloplasminemia. CpKO mice were intraperitoneal administered for 2 months with human ceruloplasmin that was able to enter the brain inducing replacement of the protein levels and rescue of ferroxidase activity. Ceruloplasmin-treated mice showed amelioration of motor incoordination that was associated with diminished loss of Purkinje neurons and reduced brain iron deposition, in particular in the choroid plexus. Computational analysis showed that ceruloplasmin-treated CpKO mice share a similar pattern with wild-type animals, highlighting the efficacy of the therapy. These data suggest that enzyme replacement therapy may be a promising strategy for the treatment of aceruloplasminemia.
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Affiliation(s)
- Alan Zanardi
- Proteome Biochemistry, Division of Genetics and Cell Biology, IRCCS-San Raffaele Scientific Institute, Milan, Italy
| | - Antonio Conti
- Proteome Biochemistry, Division of Genetics and Cell Biology, IRCCS-San Raffaele Scientific Institute, Milan, Italy
| | - Marco Cremonesi
- Proteome Biochemistry, Division of Genetics and Cell Biology, IRCCS-San Raffaele Scientific Institute, Milan, Italy
| | - Patrizia D'Adamo
- Molecular Genetics of Intellectual Disabilities, Division of Neuroscience, IRCCS-San Raffaele Scientific Institute, Milan, Italy
| | - Enrica Gilberti
- Unit of Occupational Health and Industrial Hygiene, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Pietro Apostoli
- Unit of Occupational Health and Industrial Hygiene, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Dresden, Germany.,Brain Bio-Inspired Computation (BBC) Lab, IRCCS Centro Neurolesi "Bonino Pulejo", Messina, Italy
| | - Alberto Piperno
- School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy.,Centre for Diagnosis and Treatment of Hemochromatosis, ASST-S.Gerardo Hospital, Monza, Italy
| | - Samuel David
- Center for Research in Neuroscience, The Research Institute of The McGill University Health Center, Montreal, QC, Canada
| | - Massimo Alessio
- Proteome Biochemistry, Division of Genetics and Cell Biology, IRCCS-San Raffaele Scientific Institute, Milan, Italy
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16
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Cannistraci CV. Modelling Self-Organization in Complex Networks Via a Brain-Inspired Network Automata Theory Improves Link Reliability in Protein Interactomes. Sci Rep 2018; 8:15760. [PMID: 30361555 PMCID: PMC6202355 DOI: 10.1038/s41598-018-33576-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 09/24/2018] [Indexed: 01/14/2023] Open
Abstract
Protein interactomes are epitomes of incomplete and noisy networks. Methods for assessing link-reliability using exclusively topology are valuable in network biology, and their investigation facilitates the general understanding of topological mechanisms and models to draw and correct complex network connectivity. Here, I revise and extend the local-community-paradigm (LCP). Initially detected in brain-network topological self-organization and afterward generalized to any complex network, the LCP is a theory to model local-topology-dependent link-growth in complex networks using network automata. Four novel LCP-models are compared versus baseline local-topology-models. It emerges that the reliability of an interaction between two proteins is higher: (i) if their common neighbours are isolated in a complex (local-community) that has low tendency to interact with other external proteins; (ii) if they have a low propensity to link with other proteins external to the local-community. These two rules are mathematically combined in C1*: a proposed mechanistic model that, in fact, outperforms the others. This theoretical study elucidates basic topological rules behind self-organization principia of protein interactomes and offers the conceptual basis to extend this theory to any class of complex networks. The link-reliability improvement, based on the mere topology, can impact many applied domains such as systems biology and network medicine.
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Affiliation(s)
- Carlo Vittorio 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, Italy.
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17
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Naganathan SR, Fürthauer S, Rodriguez J, Fievet BT, Jülicher F, Ahringer J, Cannistraci CV, Grill SW. Morphogenetic degeneracies in the actomyosin cortex. eLife 2018; 7:37677. [PMID: 30346273 PMCID: PMC6226289 DOI: 10.7554/elife.37677] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 04/18/2018] [Accepted: 10/16/2018] [Indexed: 01/07/2023] Open
Abstract
One of the great challenges in biology is to understand the mechanisms by which morphogenetic processes arise from molecular activities. We investigated this problem in the context of actomyosin-based cortical flow in C. elegans zygotes, where large-scale flows emerge from the collective action of actomyosin filaments and actin binding proteins (ABPs). Large-scale flow dynamics can be captured by active gel theory by considering force balances and conservation laws in the actomyosin cortex. However, which molecular activities contribute to flow dynamics and large-scale physical properties such as viscosity and active torque is largely unknown. By performing a candidate RNAi screen of ABPs and actomyosin regulators we demonstrate that perturbing distinct molecular processes can lead to similar flow phenotypes. This is indicative for a ‘morphogenetic degeneracy’ where multiple molecular processes contribute to the same large-scale physical property. We speculate that morphogenetic degeneracies contribute to the robustness of bulk biological matter in development.
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Affiliation(s)
| | - Sebastian Fürthauer
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Computational Biology, Flatiron Institute, New York, United States
| | - Josana Rodriguez
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom.,Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, United Kingdom
| | - Bruno Thomas Fievet
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, United Kingdom
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Julie Ahringer
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, United Kingdom
| | - Carlo Vittorio Cannistraci
- BIOTEC, Technische Universität Dresden, Dresden, Germany.,Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi "Bonino Pulejo", Messina, Italy
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,BIOTEC, Technische Universität Dresden, Dresden, Germany
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18
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Abstract
Omic sciences coupled with novel computational approaches such as machine intelligence offer completely new approaches to major depressive disorder (MDD) research. The complexity of MDD's pathophysiology is being integrated into studies examining MDD's biology within the omic fields. Lipidomics, as a late-comer among other omic fields, is increasingly being recognized in psychiatric research because it has allowed the investigation of global lipid perturbations in patients suffering from MDD and indicated a crucial role of specific patterns of lipid alterations in the development and progression of MDD. Combinatorial lipid-markers with high classification power are being developed in order to assist MDD diagnosis, while rodent models of depression reveal lipidome changes and thereby unveil novel treatment targets for depression. In this systematic review, we provide an overview of current breakthroughs and future trends in the field of lipidomics in MDD research and thereby paving the way for precision medicine in MDD.
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Affiliation(s)
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, TU Dresden, Dresden, Germany
- Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi “Bonino Pulejo”, Messina, Italy
| | | | - Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, TU Dresden, Dresden, Germany
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19
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Cannistraci CV, Nieminen T, Nishi M, Khachigian LM, Viikilä J, Laine M, Cianflone D, Maseri A, Yeo KK, Bhindi R, Ammirati E. "Summer Shift": A Potential Effect of Sunshine on the Time Onset of ST-Elevation Acute Myocardial Infarction. J Am Heart Assoc 2018; 7:JAHA.117.006878. [PMID: 29626152 PMCID: PMC6015398 DOI: 10.1161/jaha.117.006878] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 12/22/2022]
Abstract
Background ST‐elevation acute myocardial infarction (STEMI) represents one of the leading causes of death. The time of STEMI onset has a circadian rhythm with a peak during diurnal hours, and the occurrence of STEMI follows a seasonal pattern with a salient peak of cases in the winter months and a marked reduction of cases in the summer months. Scholars investigated the reason behind the winter peak, suggesting that environmental and climatic factors concur in STEMI pathogenesis, but no studies have investigated whether the circadian rhythm is modified with the seasonal pattern, in particular during the summer reduction in STEMI occurrence. Methods and Results Here, we provide a multiethnic and multination epidemiological study (from both hemispheres at different latitudes, n=2270 cases) that investigates whether the circadian variation of STEMI onset is altered in the summer season. The main finding is that the difference between numbers of diurnal (6:00 to 18:00) and nocturnal (18:00 to 6:00) STEMI is markedly decreased in the summer season, and this is a prodrome of a complex mechanism according to which the circadian rhythm of STEMI time onset seems season dependent. Conclusions The “summer shift” of STEMI to the nocturnal interval is consistent across different populations, and the sunshine duration (a measure related to cloudiness and solar irradiance) underpins this season‐dependent circadian perturbation. Vitamin D, which in our results seems correlated with this summer shift, is also primarily regulated by the sunshine duration, and future studies should investigate their joint role in the mechanisms of STEMI etiogenesis.
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Affiliation(s)
- Carlo Vittorio 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, Dresden, Germany .,Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi "Bonino Pulejo", Messina, Italy
| | - Tuomo Nieminen
- Internal Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.,South Karelia Central Hospital, Lappeenranta, Finland
| | - Masahiro Nishi
- Department of Cardiology, Omihachiman Community Medical Center, Omihachiman, Japan
| | - Levon M Khachigian
- Vascular Biology and Translational Research, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Juho Viikilä
- Cardiology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Mika Laine
- Cardiology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | | | | | | | | | - Enrico Ammirati
- De Gasperis Cardio Center, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
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20
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Álvarez-Fernández SM, Barbariga M, Cannizzaro L, Cannistraci CV, Hurley L, Zanardi A, Conti A, Sanvito F, Innocenzi A, Pecorelli N, Braga M, Alessio M. Serological immune response against ADAM10 pro-domain is associated with favourable prognosis in stage III colorectal cancer patients. Oncotarget 2018; 7:80059-80076. [PMID: 27517630 PMCID: PMC5346771 DOI: 10.18632/oncotarget.11181] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 04/12/2016] [Accepted: 07/10/2016] [Indexed: 02/07/2023] Open
Abstract
A humoral immune response against aberrant tumor proteins can be elicited in cancer patients, resulting in the production of auto-antibodies (Abs). By serological proteome analysis we identified the surface membrane protein ADAM10, a metalloproteinase that has a role in epithelial-tumor progression and invasion, as a target of the immune response in colorectal cancer (Crc). A screening carried out on the purified protein using testing cohorts of sera (Crc patients n = 57; control subjects n = 39) and validation cohorts of sera (Crc patients n = 49; control subjects n = 52) indicated that anti-ADAM10 auto-Abs were significantly induced in a large group (74%) of colon cancer patients, in particular in patients at stage II and III of the disease. Interestingly, in Crc patients classified as stage III disease, the presence of anti-ADAM10 auto-Abs in the sera was associated with a favourable follow-up with a significant shifting of the recurrence-free survival median time from 23 to 55 months. Even though the ADAM10 protein was expressed in Crc regardless the presence of auto-Abs, the immature/non-functional isoform of ADAM10 was highly expressed in the tumor of anti-ADAM10-positive patients and was the isoform targeted by the auto-Abs. In conclusion, the presence of anti-ADAM10 auto-Abs seems to reflect the increased tumor expression of the immunogenic immature-ADAM10 in a group of Crc patients, and is associated with a favourable prognosis in patients at stage III of the disease.
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Affiliation(s)
| | - Marco Barbariga
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, Milan, Italy.,Translational Neurology group, Wallenberg Neuroscience Center, BMC, Lund, Sweden
| | - Luca Cannizzaro
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, Milan, Italy.,Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Laura Hurley
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, Milan, Italy.,Wayne State University, School of Medicine, Cancer Biology PhD Program, Detroit, Michigan, USA
| | - Alan Zanardi
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, Milan, Italy
| | - Antonio Conti
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, Milan, Italy
| | | | - Anna Innocenzi
- Pathology, IRCCS-San Raffaele Scientific Institute, Milan, Italy
| | - Nicolò Pecorelli
- Department of Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Marco Braga
- Department of Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Massimo Alessio
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, Milan, Italy
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21
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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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22
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Liu X, Wang W, He D, Jiao P, Jin D, Cannistraci CV. Semi-supervised community detection based on non-negative matrix factorization with node popularity. Inf Sci (N Y) 2017. [DOI: 10.1016/j.ins.2016.11.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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23
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Narula V, Zippo AG, Muscoloni A, Biella GEM, Cannistraci CV. Can local-community-paradigm and epitopological learning enhance our understanding of how local brain connectivity is able to process, learn and memorize chronic pain? Appl Netw Sci 2017; 2:28. [PMID: 30443582 PMCID: PMC6214247 DOI: 10.1007/s41109-017-0048-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/07/2017] [Indexed: 05/15/2023]
Abstract
The mystery behind the origin of the pain and the difficulty to propose methodologies for its quantitative characterization fascinated philosophers (and then scientists) from the dawn of our modern society. Nowadays, studying patterns of information flow in mesoscale activity of brain networks is a valuable strategy to offer answers in computational neuroscience. In this paper, complex network analysis was performed on the time-varying brain functional connectomes of a rat model of persistent peripheral neuropathic pain, obtained by means of local field potential and spike train analysis. A wide range of topological network measures (14 in total, the code is publicly released at: https://github.com/biomedical-cybernetics/topological_measures_wide_analysis) was employed to quantitatively investigate the rewiring mechanisms of the brain regions responsible for development and upkeep of pain along time, from three hours to 16 days after nerve injury. The time trend (across the days) of each network measure was correlated with a behavioural test for rat pain, and surprisingly we found that the rewiring mechanisms associated with two local topological measure, the local-community-paradigm and the power-lawness, showed very high statistical correlations (higher than 0.9, being the maximum value 1) with the behavioural test. We also disclosed clear functional connectivity patterns that emerged in association with chronic pain in the primary somatosensory cortex (S1) and ventral posterolateral (VPL) nuclei of thalamus. This study represents a pioneering attempt to exploit network science models in order to elucidate the mechanisms of brain region re-wiring and engram formations that are associated with chronic pain in mammalians. We conclude that the local-community-paradigm is a model of complex network organization that triggers a local learning rule, which seems associated to processing, learning and memorization of chronic pain in the brain functional connectivity. This rule is based exclusively on the network topology, hence was named epitopological learning.
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Affiliation(s)
- Vaibhav Narula
- 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, Dresden, Germany
| | - Antonio Giuliano Zippo
- Institute of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche, Segrate, Milan, Italy
| | - Alessandro Muscoloni
- 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, Dresden, Germany
| | - Gabriele Eliseo M. Biella
- Institute of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche, Segrate, Milan, Italy
| | - Carlo Vittorio 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, Dresden, Germany
- Brain bio-inspired computatiing (BBC) lab, IRCCS Centro Neurolesi “Bonino Pulejo”, Messina, Italy
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24
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Abstract
One of the critical steps in two-dimensional electrophoresis (2-DE) image pre-processing is the denoising, that might aggressively affect either spot detection or pixel-based methods. The Median Modified Wiener Filter (MMWF), a new nonlinear adaptive spatial filter, resulted to be a good denoising approach to use in practice with 2-DE. MMWF is suitable for global denoising, and contemporary for the removal of spikes and Gaussian noise, being its best setting invariant on the type of noise. The second critical step rises because of the fact that 2-DE gel images may contain high levels of background, generated by the laboratory experimental procedures, that must be subtracted for accurate measurements of the proteomic optical density signals. Here we discuss an efficient mathematical method for background estimation, that is suitable to work even before the 2-DE image spot detection, and it is based on the 3D mathematical morphology (3DMM) theory.
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Affiliation(s)
- Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.
| | - Massimo Alessio
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milan, Italy.
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25
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Alessio M, Cannistraci CV. Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data. Methods Mol Biol 2016; 1384:289-298. [PMID: 26611421 DOI: 10.1007/978-1-4939-3255-9_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dimensionality reduction is largely and successfully employed for the visualization and discrimination of patterns, hidden in multidimensional proteomics datasets. Principal component analysis (PCA), which is the preferred approach for linear dimensionality reduction, may present serious limitations, in particular when samples are nonlinearly related, as often occurs in several two-dimensional electrophoresis (2-DE) datasets. An aggravating factor is that PCA robustness is impaired when the number of samples is small in comparison to the number of proteomic features, and this is the case in high-dimensional proteomic datasets, including 2-DE ones. Here, we describe the use of a nonlinear unsupervised learning machine for dimensionality reduction called minimum curvilinear embedding (MCE) that was successfully applied to different biological samples datasets. In particular, we provide an example where we directly compare MCE performance with that of PCA in disclosing neuropathic pain patterns, hidden in a multidimensional proteomic dataset.
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Affiliation(s)
- Massimo Alessio
- Proteome Biochemistry, IRCCS-San Raffaele Scientific Institute, Milan, Italy.
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.
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26
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Cannistraci CV, Alanis-Lobato G, Ravasi T. Erratum: From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks. Sci Rep 2015; 5:9794. [PMID: 26194002 PMCID: PMC4508526 DOI: 10.1038/srep09794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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27
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Cannistraci CV, Abbas A, Gao X. Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra. Sci Rep 2015; 5:8017. [PMID: 25619991 PMCID: PMC4306135 DOI: 10.1038/srep08017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/29/2014] [Indexed: 11/21/2022] Open
Abstract
Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet's performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.
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Affiliation(s)
- Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Ahmed Abbas
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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28
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Abstract
MOTIVATION Most functions within the cell emerge thanks to protein-protein interactions (PPIs), yet experimental determination of PPIs is both expensive and time-consuming. PPI networks present significant levels of noise and incompleteness. Predicting interactions using only PPI-network topology (topological prediction) is difficult but essential when prior biological knowledge is absent or unreliable. METHODS Network embedding emphasizes the relations between network proteins embedded in a low-dimensional space, in which protein pairs that are closer to each other represent good candidate interactions. To achieve network denoising, which boosts prediction performance, we first applied minimum curvilinear embedding (MCE), and then adopted shortest path (SP) in the reduced space to assign likelihood scores to candidate interactions. Furthermore, we introduce (i) a new valid variation of MCE, named non-centred MCE (ncMCE); (ii) two automatic strategies for selecting the appropriate embedding dimension; and (iii) two new randomized procedures for evaluating predictions. RESULTS We compared our method against several unsupervised and supervisedly tuned embedding approaches and node neighbourhood techniques. Despite its computational simplicity, ncMCE-SP was the overall leader, outperforming the current methods in topological link prediction. CONCLUSION Minimum curvilinearity is a valuable non-linear framework that we successfully applied to the embedding of protein networks for the unsupervised prediction of novel PPIs. The rationale for our approach is that biological and evolutionary information is imprinted in the non-linear patterns hidden behind the protein network topology, and can be exploited for predicting new protein links. The predicted PPIs represent good candidates for testing in high-throughput experiments or for exploitation in systems biology tools such as those used for network-based inference and prediction of disease-related functional modules. AVAILABILITY https://sites.google.com/site/carlovittoriocannistraci/home. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Carlo Vittorio Cannistraci
- Integrative Systems Biology Laboratory, Biological and Environmental Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
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29
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Cannistraci CV, Alanis-Lobato G, Ravasi T. From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks. Sci Rep 2013; 3:1613. [PMID: 23563395 PMCID: PMC3619147 DOI: 10.1038/srep01613] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [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: 02/04/2013] [Accepted: 02/20/2013] [Indexed: 12/17/2022] Open
Abstract
Growth and remodelling impact the network topology of complex systems, yet a general theory explaining how new links arise between existing nodes has been lacking, and little is known about the topological properties that facilitate link-prediction. Here we investigate the extent to which the connectivity evolution of a network might be predicted by mere topological features. We show how a link/community-based strategy triggers substantial prediction improvements because it accounts for the singular topology of several real networks organised in multiple local communities - a tendency here named local-community-paradigm (LCP). We observe that LCP networks are mainly formed by weak interactions and characterise heterogeneous and dynamic systems that use self-organisation as a major adaptation strategy. These systems seem designed for global delivery of information and processing via multiple local modules. Conversely, non-LCP networks have steady architectures formed by strong interactions, and seem designed for systems in which information/energy storage is crucial.
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Affiliation(s)
- Carlo Vittorio Cannistraci
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
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30
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Alanis-Lobato G, Cannistraci CV, Ravasi T. Exploitation of genetic interaction network topology for the prediction of epistatic behavior. Genomics 2013; 102:202-8. [PMID: 23892246 DOI: 10.1016/j.ygeno.2013.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 06/24/2013] [Accepted: 07/17/2013] [Indexed: 11/30/2022]
Abstract
Genetic interaction (GI) detection impacts the understanding of human disease and the ability to design personalized treatment. The mapping of every GI in most organisms is far from complete due to the combinatorial amount of gene deletions and knockdowns required. Computational techniques to predict new interactions based only on network topology have been developed in network science but never applied to GI networks. We show that topological prediction of GIs is possible with high precision and propose a graph dissimilarity index that is able to provide robust prediction in both dense and sparse networks. Computational prediction of GIs is a strong tool to aid high-throughput GI determination. The dissimilarity index we propose in this article is able to attain precise predictions that reduce the universe of candidate GIs to test in the lab.
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Affiliation(s)
- Gregorio Alanis-Lobato
- Integrative Systems Biology Lab, Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia; Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
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31
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Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M. Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. ACTA ACUST UNITED AC 2010; 26:i531-9. [PMID: 20823318 PMCID: PMC2935424 DOI: 10.1093/bioinformatics/btq376] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [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] [Indexed: 11/13/2022]
Abstract
MOTIVATION Nonlinear small datasets, which are characterized by low numbers of samples and very high numbers of measures, occur frequently in computational biology, and pose problems in their investigation. Unsupervised hybrid-two-phase (H2P) procedures-specifically dimension reduction (DR), coupled with clustering-provide valuable assistance, not only for unsupervised data classification, but also for visualization of the patterns hidden in high-dimensional feature space. METHODS 'Minimum Curvilinearity' (MC) is a principle that-for small datasets-suggests the approximation of curvilinear sample distances in the feature space by pair-wise distances over their minimum spanning tree (MST), and thus avoids the introduction of any tuning parameter. MC is used to design two novel forms of nonlinear machine learning (NML): Minimum Curvilinear embedding (MCE) for DR, and Minimum Curvilinear affinity propagation (MCAP) for clustering. RESULTS Compared with several other unsupervised and supervised algorithms, MCE and MCAP, whether individually or combined in H2P, overcome the limits of classical approaches. High performance was attained in the visualization and classification of: (i) pain patients (proteomic measurements) in peripheral neuropathy; (ii) human organ tissues (genomic transcription factor measurements) on the basis of their embryological origin. CONCLUSION MC provides a valuable framework to estimate nonlinear distances in small datasets. Its extension to large datasets is prefigured for novel NMLs. Classification of neuropathic pain by proteomic profiles offers new insights for future molecular and systems biology characterization of pain. Improvements in tissue embryological classification refine results obtained in an earlier study, and suggest a possible reinterpretation of skin attribution as mesodermal. AVAILABILITY https://sites.google.com/site/carlovittoriocannistraci/home.
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Affiliation(s)
- Carlo Vittorio Cannistraci
- Computational Bioscience Research Center, Division of Chemical and Life Sciences and Engineering, King Abdullah University for Science and Technology (KAUST), Jeddah, Kingdom of Saudi Arabia.
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32
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Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest ARR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 2010; 140:744-52. [PMID: 20211142 DOI: 10.1016/j.cell.2010.01.044] [Citation(s) in RCA: 546] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 09/22/2009] [Accepted: 01/25/2010] [Indexed: 01/04/2023]
Abstract
Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.
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Affiliation(s)
- Timothy Ravasi
- The FANTOM Consortium, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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