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Calado CRC. Bridging the gap between target-based and phenotypic-based drug discovery. Expert Opin Drug Discov 2024; 19:789-798. [PMID: 38747562 DOI: 10.1080/17460441.2024.2355330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
INTRODUCTION The unparalleled progress in science of the last decades has brought a better understanding of the molecular mechanisms of diseases. This promoted drug discovery processes based on a target approach. However, despite the high promises associated, a critical decrease in the number of first-in-class drugs has been observed. AREAS COVERED This review analyses the challenges, advances, and opportunities associated with the main strategies of the drug discovery process, i.e. based on a rational target approach and on an empirical phenotypic approach. This review also evaluates how the gap between these two crossroads can be bridged toward a more efficient drug discovery process. EXPERT OPINION The critical lack of knowledge of the complex biological networks is leading to targets not relevant for the clinical context or to drugs that present undesired adverse effects. The phenotypic systems designed by considering available molecular mechanisms can mitigate these knowledge gaps. Associated with the expansion of the chemical space and other technologies, these designs can lead to more efficient drug discoveries. Technological and scientific knowledge should also be applied to identify, as early as possible, both drug targets and mechanisms of action, leading to a more efficient drug discovery pipeline.
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Affiliation(s)
- Cecília R C Calado
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
- iBB - Institute for Bioengineering and Biosciences, i4HB - The Associate Laboratory Institute for Health and Bioeconomy, IST - Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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2
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Falkovich R, Danielson EW, Perez de Arce K, Wamhoff EC, Strother J, Lapteva AP, Sheng M, Cottrell JR, Bathe M. A synaptic molecular dependency network in knockdown of autism- and schizophrenia-associated genes revealed by multiplexed imaging. Cell Rep 2023; 42:112430. [PMID: 37099425 DOI: 10.1016/j.celrep.2023.112430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/29/2023] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
The complex functions of neuronal synapses depend on their tightly interconnected protein network, and their dysregulation is implicated in the pathogenesis of autism spectrum disorders and schizophrenia. However, it remains unclear how synaptic molecular networks are altered biochemically in these disorders. Here, we apply multiplexed imaging to probe the effects of RNAi knockdown of 16 autism- and schizophrenia-associated genes on the simultaneous joint distribution of 10 synaptic proteins, observing several protein composition phenotypes associated with these risk genes. We apply Bayesian network analysis to infer hierarchical dependencies among eight excitatory synaptic proteins, yielding predictive relationships that can only be accessed with single-synapse, multiprotein measurements performed simultaneously in situ. Finally, we find that central features of the network are affected similarly across several distinct gene knockdowns. These results offer insight into the convergent molecular etiology of these widespread disorders and provide a general framework to probe subcellular molecular networks.
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Affiliation(s)
- Reuven Falkovich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric W Danielson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karen Perez de Arce
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eike-C Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Juliana Strother
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna P Lapteva
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Morgan Sheng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey R Cottrell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School Initiative for RNA Medicine, Harvard University, Cambridge, MA, USA.
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3
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Cordella F, Ferrucci L, D’Antoni C, Ghirga S, Brighi C, Soloperto A, Gigante Y, Ragozzino D, Bezzi P, Di Angelantonio S. Human iPSC-Derived Cortical Neurons Display Homeostatic Plasticity. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111884. [PMID: 36431019 PMCID: PMC9696876 DOI: 10.3390/life12111884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
Maintaining the excitability of neurons and circuits is fundamental for healthy brain functions. The global compensatory increase in excitatory synaptic strength, in response to decreased activity, is one of the main homeostatic mechanisms responsible for such regulation. This type of plasticity has been extensively characterized in rodents in vivo and in vitro, but few data exist on human neurons maturation. We have generated an in vitro cortical model system, based on differentiated human-induced pluripotent stem cells, chronically treated with tetrodotoxin, to investigate homeostatic plasticity at different developmental stages. Our findings highlight the presence of homeostatic plasticity in human cortical networks and show that the changes in synaptic strength are due to both pre- and post-synaptic mechanisms. Pre-synaptic plasticity involves the potentiation of neurotransmitter release machinery, associated to an increase in synaptic vesicle proteins expression. At the post-synaptic level, we report an increase in the expression of post-synaptic density proteins, involved in glutamatergic receptor anchoring. These results extend our understanding of neuronal homeostasis and reveal the developmental regulation of its expression in human cortical networks. Since induced pluripotent stem cell-derived neurons can be obtained from patients with neurodevelopmental and neurodegenerative diseases, our platform offers a versatile model for assessing human neural plasticity under physiological and pathological conditions.
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Affiliation(s)
- Federica Cordella
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Laura Ferrucci
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
| | - Chiara D’Antoni
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Silvia Ghirga
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Carlo Brighi
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- CrestOptics S.p.A., Via di Torre Rossa 66, 00165 Rome, Italy
| | - Alessandro Soloperto
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Ylenia Gigante
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- D-Tails s.r.l., Via di Torre Rossa 66, 00165 Rome, Italy
| | - Davide Ragozzino
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
- Santa Lucia Foundation, European Center for Brain Research, 00143 Rome, Italy
| | - Paola Bezzi
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
- Department of Fundamental Neurosciences, University of Lausanne, 1015 Lausanne, Switzerland
- Correspondence: or (P.B.); or (S.D.A.)
| | - Silvia Di Angelantonio
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- D-Tails s.r.l., Via di Torre Rossa 66, 00165 Rome, Italy
- Correspondence: or (P.B.); or (S.D.A.)
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4
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Garcia G, Pinto S, Ferreira S, Lopes D, Serrador MJ, Fernandes A, Vaz AR, de Mendonça A, Edenhofer F, Malm T, Koistinaho J, Brites D. Emerging Role of miR-21-5p in Neuron-Glia Dysregulation and Exosome Transfer Using Multiple Models of Alzheimer's Disease. Cells 2022; 11:3377. [PMID: 36359774 PMCID: PMC9655962 DOI: 10.3390/cells11213377] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 08/25/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder associated with neuron-glia dysfunction and dysregulated miRNAs. We previously reported upregulated miR-124/miR-21 in AD neurons and their exosomes. However, their glial distribution, phenotypic alterations and exosomal spread are scarcely documented. Here, we show glial cell activation and miR-21 overexpression in mouse organotypic hippocampal slices transplanted with SH-SY5Y cells expressing the human APP695 Swedish mutation. The upregulation of miR-21 only in the CSF from a small series of mild cognitive impairment (MCI) AD patients, but not in non-AD MCI individuals, supports its discriminatory potential. Microglia, neurons, and astrocytes differentiated from the same induced pluripotent stem cells from PSEN1ΔE9 AD patients all showed miR-21 elevation. In AD neurons, miR-124/miR-21 overexpression was recapitulated in their exosomes. In AD microglia, the upregulation of iNOS and miR-21/miR-146a supports their activation. AD astrocytes manifested a restrained inflammatory profile, with high miR-21 but low miR-155 and depleted exosomal miRNAs. Their immunostimulation with C1q + IL-1α + TNF-α induced morphological alterations and increased S100B, inflammatory transcripts, sAPPβ, cytokine release and exosomal miR-21. PPARα, a target of miR-21, was found to be repressed in all models, except in neurons, likely due to concomitant miR-125b elevation. The data from these AD models highlight miR-21 as a promising biomarker and a disease-modifying target to be further explored.
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Affiliation(s)
- Gonçalo Garcia
- Neuroinflammation, Signaling and Neuroregeneration Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Sara Pinto
- Neuroinflammation, Signaling and Neuroregeneration Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Sofia Ferreira
- Neuroinflammation, Signaling and Neuroregeneration Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Daniela Lopes
- Neuroinflammation, Signaling and Neuroregeneration Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Maria João Serrador
- Neuroinflammation, Signaling and Neuroregeneration Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Adelaide Fernandes
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Central Nervous System, Blood and Peripheral Inflammation Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Ana Rita Vaz
- Neuroinflammation, Signaling and Neuroregeneration Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | | | - Frank Edenhofer
- Department of Genomics, Stem Cell Biology and Regenerative Medicine, Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jari Koistinaho
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
- Neuroscience Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Dora Brites
- Neuroinflammation, Signaling and Neuroregeneration Lab, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
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5
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Mitrečić D, Hribljan V, Jagečić D, Isaković J, Lamberto F, Horánszky A, Zana M, Foldes G, Zavan B, Pivoriūnas A, Martinez S, Mazzini L, Radenovic L, Milasin J, Chachques JC, Buzanska L, Song MS, Dinnyés A. Regenerative Neurology and Regenerative Cardiology: Shared Hurdles and Achievements. Int J Mol Sci 2022; 23:855. [PMID: 35055039 PMCID: PMC8776151 DOI: 10.3390/ijms23020855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/24/2021] [Accepted: 01/09/2022] [Indexed: 02/05/2023] Open
Abstract
From the first success in cultivation of cells in vitro, it became clear that developing cell and/or tissue specific cultures would open a myriad of new opportunities for medical research. Expertise in various in vitro models has been developing over decades, so nowadays we benefit from highly specific in vitro systems imitating every organ of the human body. Moreover, obtaining sufficient number of standardized cells allows for cell transplantation approach with the goal of improving the regeneration of injured/disease affected tissue. However, different cell types bring different needs and place various types of hurdles on the path of regenerative neurology and regenerative cardiology. In this review, written by European experts gathered in Cost European action dedicated to neurology and cardiology-Bioneca, we present the experience acquired by working on two rather different organs: the brain and the heart. When taken into account that diseases of these two organs, mostly ischemic in their nature (stroke and heart infarction), bring by far the largest burden of the medical systems around Europe, it is not surprising that in vitro models of nervous and heart muscle tissue were in the focus of biomedical research in the last decades. In this review we describe and discuss hurdles which still impair further progress of regenerative neurology and cardiology and we detect those ones which are common to both fields and some, which are field-specific. With the goal to elucidate strategies which might be shared between regenerative neurology and cardiology we discuss methodological solutions which can help each of the fields to accelerate their development.
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Affiliation(s)
- Dinko Mitrečić
- Laboratory for Stem Cells, Croatian Institute for Brain Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
- Department of Histology and Embryology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Valentina Hribljan
- Laboratory for Stem Cells, Croatian Institute for Brain Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
- Department of Histology and Embryology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Denis Jagečić
- Laboratory for Stem Cells, Croatian Institute for Brain Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
- Department of Histology and Embryology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | | | - Federica Lamberto
- BioTalentum Ltd., Aulich Lajos Str. 26, 2100 Gordillo, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, Páter Károly Str. 1, 2100 Godollo, Hungary
| | - Alex Horánszky
- BioTalentum Ltd., Aulich Lajos Str. 26, 2100 Gordillo, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, Páter Károly Str. 1, 2100 Godollo, Hungary
| | - Melinda Zana
- BioTalentum Ltd., Aulich Lajos Str. 26, 2100 Gordillo, Hungary
| | - Gabor Foldes
- Heart and Vascular Center, Semmelweis University, 1122 Budapest, Hungary
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK
| | - Barbara Zavan
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Augustas Pivoriūnas
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, LT-01102 Vilnius, Lithuania
| | - Salvador Martinez
- Instituto de Neurociencias UMH-CSIC, 03550 San Juan de Alicante, Spain
| | - Letizia Mazzini
- ALS Center, Department of Neurology, Maggiore della Carità Hospital, University of Piemonte Orientale, 28100 Novara, Italy
| | - Lidija Radenovic
- Center for Laser Microscopy, Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia
| | - Jelena Milasin
- Laboratory for Stem Cell Research, School of Dental Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Juan Carlos Chachques
- Laboratory of Biosurgical Research, Pompidou Hospital, University of Paris, 75006 Paris, France
| | - Leonora Buzanska
- Department of Stem Cell Bioengineering, Mossakowski Medical Research Institute Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Min Suk Song
- Omnion Research International Ltd., 10000 Zagreb, Croatia
| | - András Dinnyés
- BioTalentum Ltd., Aulich Lajos Str. 26, 2100 Gordillo, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, Páter Károly Str. 1, 2100 Godollo, Hungary
- HCEMM-USZ Stem Cell Research Group, Department of Cell Biology and Molecular Medicine, University of Szeged, 6720 Szeged, Hungary
- College of Life Sciences, Sichuan University, Chengdu 610064, China
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6
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Giacomelli E, Vahsen BF, Calder EL, Xu Y, Scaber J, Gray E, Dafinca R, Talbot K, Studer L. Human stem cell models of neurodegeneration: From basic science of amyotrophic lateral sclerosis to clinical translation. Cell Stem Cell 2022; 29:11-35. [PMID: 34995492 PMCID: PMC8785905 DOI: 10.1016/j.stem.2021.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Neurodegenerative diseases are characterized by progressive cell loss leading to disruption of the structure and function of the central nervous system. Amyotrophic lateral sclerosis (ALS) was among the first of these disorders modeled in patient-specific iPSCs, and recent findings have translated into some of the earliest iPSC-inspired clinical trials. Focusing on ALS as an example, we evaluate the status of modeling neurodegenerative diseases using iPSCs, including methods for deriving and using disease-relevant neuronal and glial lineages. We further highlight the remaining challenges in exploiting the full potential of iPSC technology for understanding and potentially treating neurodegenerative diseases such as ALS.
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Affiliation(s)
- Elisa Giacomelli
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Björn F Vahsen
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Elizabeth L Calder
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Yinyan Xu
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK; Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Jakub Scaber
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Elizabeth Gray
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ruxandra Dafinca
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Kevin Talbot
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
| | - Lorenz Studer
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA.
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