Frontiers in Immunology (Feb 2024)
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches
- Anna Niarakis,
- Anna Niarakis,
- Marek Ostaszewski,
- Alexander Mazein,
- Inna Kuperstein,
- Inna Kuperstein,
- Inna Kuperstein,
- Martina Kutmon,
- Marc E. Gillespie,
- Marc E. Gillespie,
- Akira Funahashi,
- Marcio Luis Acencio,
- Ahmed Hemedan,
- Michael Aichem,
- Karsten Klein,
- Tobias Czauderna,
- Felicia Burtscher,
- Takahiro G. Yamada,
- Yusuke Hiki,
- Noriko F. Hiroi,
- Noriko F. Hiroi,
- Finterly Hu,
- Finterly Hu,
- Nhung Pham,
- Nhung Pham,
- Friederike Ehrhart,
- Egon L. Willighagen,
- Alberto Valdeolivas,
- Aurelien Dugourd,
- Francesco Messina,
- Marina Esteban-Medina,
- Marina Esteban-Medina,
- Maria Peña-Chilet,
- Maria Peña-Chilet,
- Maria Peña-Chilet,
- Kinza Rian,
- Sylvain Soliman,
- Sara Sadat Aghamiri,
- Bhanwar Lal Puniya,
- Aurélien Naldi,
- Tomáš Helikar,
- Vidisha Singh,
- Marco Fariñas Fernández,
- Viviam Bermudez,
- Eirini Tsirvouli,
- Arnau Montagud,
- Vincent Noël,
- Vincent Noël,
- Vincent Noël,
- Miguel Ponce-de-Leon,
- Dieter Maier,
- Angela Bauch,
- Benjamin M. Gyori,
- John A. Bachman,
- Augustin Luna,
- Augustin Luna,
- Janet Piñero,
- Janet Piñero,
- Laura I. Furlong,
- Laura I. Furlong,
- Irina Balaur,
- Adrien Rougny,
- Adrien Rougny,
- Yohan Jarosz,
- Rupert W. Overall,
- Robert Phair,
- Livia Perfetto,
- Lisa Matthews,
- Devasahayam Arokia Balaya Rex,
- Marija Orlic-Milacic,
- Luis Cristobal Monraz Gomez,
- Luis Cristobal Monraz Gomez,
- Luis Cristobal Monraz Gomez,
- Bertrand De Meulder,
- Jean Marie Ravel,
- Jean Marie Ravel,
- Jean Marie Ravel,
- Bijay Jassal,
- Venkata Satagopam,
- Venkata Satagopam,
- Guanming Wu,
- Martin Golebiewski,
- Piotr Gawron,
- Laurence Calzone,
- Laurence Calzone,
- Laurence Calzone,
- Jacques S. Beckmann,
- Chris T. Evelo,
- Peter D’Eustachio,
- Falk Schreiber,
- Falk Schreiber,
- Julio Saez-Rodriguez,
- Joaquin Dopazo,
- Joaquin Dopazo,
- Joaquin Dopazo,
- Joaquin Dopazo,
- Martin Kuiper,
- Alfonso Valencia,
- Alfonso Valencia,
- Olaf Wolkenhauer,
- Olaf Wolkenhauer,
- Hiroaki Kitano,
- Emmanuel Barillot,
- Emmanuel Barillot,
- Emmanuel Barillot,
- Charles Auffray,
- Rudi Balling,
- Reinhard Schneider,
- the COVID-19 Disease Map Community
Affiliations
- Anna Niarakis
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
- Anna Niarakis
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
- Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Inna Kuperstein
- Institut Curie, P.S.L. Research University, Paris, France
- Inna Kuperstein
- INSERM, Paris, France
- Inna Kuperstein
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
- Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Marc E. Gillespie
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Marc E. Gillespie
- St. John’s University, Queens, NY, United States
- Akira Funahashi
- 0Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
- Marcio Luis Acencio
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Ahmed Hemedan
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Michael Aichem
- 1Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Karsten Klein
- 1Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Tobias Czauderna
- 2Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
- Felicia Burtscher
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Takahiro G. Yamada
- 0Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
- Yusuke Hiki
- 3Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa, Japan
- Noriko F. Hiroi
- 4Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa, Japan
- Noriko F. Hiroi
- 5Keio University School of Medicine, Tokyo, Japan
- Finterly Hu
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Finterly Hu
- 6Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
- Nhung Pham
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Nhung Pham
- 6Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
- Friederike Ehrhart
- 6Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
- Egon L. Willighagen
- 6Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
- Alberto Valdeolivas
- 7Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
- Aurelien Dugourd
- 7Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
- Francesco Messina
- 8Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases’ Lazzaro Spallanzani’ - IRCCS, Rome, Italy
- Marina Esteban-Medina
- 9Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Marina Esteban-Medina
- 0Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Maria Peña-Chilet
- 9Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Maria Peña-Chilet
- 0Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Maria Peña-Chilet
- 1Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
- Kinza Rian
- 9Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Sylvain Soliman
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
- Sara Sadat Aghamiri
- 2Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
- Bhanwar Lal Puniya
- 2Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
- Aurélien Naldi
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
- Tomáš Helikar
- 2Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
- Vidisha Singh
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
- Marco Fariñas Fernández
- 3Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Viviam Bermudez
- 3Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Eirini Tsirvouli
- 3Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Arnau Montagud
- 4Barcelona Supercomputing Center (BSC.), Barcelona, Spain
- Vincent Noël
- Institut Curie, P.S.L. Research University, Paris, France
- Vincent Noël
- INSERM, Paris, France
- Vincent Noël
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
- Miguel Ponce-de-Leon
- 4Barcelona Supercomputing Center (BSC.), Barcelona, Spain
- Dieter Maier
- 5Labvantage-Biomax GmbH, Planegg, Germany
- Angela Bauch
- 5Labvantage-Biomax GmbH, Planegg, Germany
- Benjamin M. Gyori
- 6Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
- John A. Bachman
- 6Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
- Augustin Luna
- 7Computational Biology Branch, National Library of Medicine, Bethesda, MD, United States
- Augustin Luna
- 8Department of Systems Biology, Harvard Medical School, Boston, MA, United States
- Janet Piñero
- 9Medbioinformatics Solutions SL, Barcelona, Spain
- Janet Piñero
- 0Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Laura I. Furlong
- 9Medbioinformatics Solutions SL, Barcelona, Spain
- Laura I. Furlong
- 0Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Irina Balaur
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Adrien Rougny
- 1Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan
- Adrien Rougny
- 2Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan
- Yohan Jarosz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Rupert W. Overall
- 3Institute for Biology, Humboldt University of Berlin, Berlin, Germany
- Robert Phair
- 4Integrative Bioinformatics, Inc., Mountain View, CA, United States
- Livia Perfetto
- 5Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
- Lisa Matthews
- 6Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
- Devasahayam Arokia Balaya Rex
- 7Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Derlakatte, Mangalore, India
- Marija Orlic-Milacic
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Luis Cristobal Monraz Gomez
- Institut Curie, P.S.L. Research University, Paris, France
- Luis Cristobal Monraz Gomez
- INSERM, Paris, France
- Luis Cristobal Monraz Gomez
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
- Bertrand De Meulder
- 8Association E.I.S.B.M, Brignais, France
- Jean Marie Ravel
- Institut Curie, P.S.L. Research University, Paris, France
- Jean Marie Ravel
- INSERM, Paris, France
- Jean Marie Ravel
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
- Bijay Jassal
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Venkata Satagopam
- 9Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Guanming Wu
- 0Oregon Health Sciences University, Portland, OR, United States
- Martin Golebiewski
- 1Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Laurence Calzone
- Institut Curie, P.S.L. Research University, Paris, France
- Laurence Calzone
- INSERM, Paris, France
- Laurence Calzone
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
- Jacques S. Beckmann
- 2University of Lausanne, Lausanne, Switzerland
- Chris T. Evelo
- 6Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
- Peter D’Eustachio
- 6Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
- Falk Schreiber
- 1Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Falk Schreiber
- 3Faculty of Information Technology, Monash University, Clayton, Victoria, VIC, Australia
- Julio Saez-Rodriguez
- 7Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
- Joaquin Dopazo
- 9Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Joaquin Dopazo
- 0Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Joaquin Dopazo
- 1Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
- Joaquin Dopazo
- 4FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain
- Martin Kuiper
- 3Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Alfonso Valencia
- 4Barcelona Supercomputing Center (BSC.), Barcelona, Spain
- Alfonso Valencia
- 5I.C.R.E.A., Pg. Lluís Companys 23, Barcelona, Spain
- Olaf Wolkenhauer
- 6Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
- Olaf Wolkenhauer
- 7Leibniz Institute for Food Systems Biology, at the Technical University Munich, Munich, Germany
- Hiroaki Kitano
- 8Systems Biology Institute, Tokyo, Japan
- Emmanuel Barillot
- Institut Curie, P.S.L. Research University, Paris, France
- Emmanuel Barillot
- INSERM, Paris, France
- Emmanuel Barillot
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
- Charles Auffray
- 8Association E.I.S.B.M, Brignais, France
- Rudi Balling
- 9Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
- Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- the COVID-19 Disease Map Community
- 0FAIRDOMHub: https://fairdomhub.org/projects/190
- DOI
- https://doi.org/10.3389/fimmu.2023.1282859
- Journal volume & issue
-
Vol. 14
Abstract
IntroductionThe COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. MethodsExtensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors.ResultsResults revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. DiscussionThe key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.
Keywords
