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Blanot M, Casaroli-Marano RP, Mondéjar-Medrano J, Sallén T, Ramírez E, Segú-Vergés C, Artigas L. Aflibercept Off-Target Effects in Diabetic Macular Edema: An In Silico Modeling Approach. Int J Mol Sci 2024; 25:3621. [PMID: 38612432 PMCID: PMC11011561 DOI: 10.3390/ijms25073621] [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: 01/03/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
Intravitreal aflibercept injection (IAI) is a treatment for diabetic macular edema (DME), but its mechanism of action (MoA) has not been completely elucidated. Here, we aimed to explore IAI's MoA and its multi-target nature in DME pathophysiology with an in silico (computer simulation) disease model. We used the Therapeutic Performance Mapping System (Anaxomics Biotech property) to generate mathematical models based on the available scientific knowledge at the time of the study, describing the relationship between the modulation of vascular endothelial growth factor receptors (VEGFRs) by IAI and DME pathophysiological processes. We also undertook an enrichment analysis to explore the processes modulated by IAI, visualized the effectors' predicted protein activity, and specifically evaluated the role of VEGFR1 pathway inhibition on DME treatment. The models simulated the potential pathophysiology of DME and the likely IAI's MoA by inhibiting VEGFR1 and VEGFR2 signaling. The action of IAI through both signaling pathways modulated the identified pathophysiological processes associated with DME, with the strongest effects in angiogenesis, blood-retinal barrier alteration and permeability, and inflammation. VEGFR1 inhibition was essential to modulate inflammatory protein effectors. Given the role of VEGFR1 signaling on the modulation of inflammatory-related pathways, IAI may offer therapeutic advantages for DME through sustained VEGFR1 pathway inhibition.
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Affiliation(s)
- Morgane Blanot
- Anaxomics Biotech S.L., 08007 Barcelona, Spain; (M.B.); (E.R.); (C.S.-V.); (L.A.)
| | - Ricardo Pedro Casaroli-Marano
- Department of Surgery (FMCS), Universitat de Barcelona, 08007 Barcelona, Spain
- Hospital Clínic de Barcelona (IDIBAPS), Universitat de Barcelona, 08007 Barcelona, Spain
| | | | - Thaïs Sallén
- Bayer Hispania S.L., 08970 Sant Joan Despí, Spain; (J.M.-M.); (T.S.)
| | - Esther Ramírez
- Anaxomics Biotech S.L., 08007 Barcelona, Spain; (M.B.); (E.R.); (C.S.-V.); (L.A.)
| | - Cristina Segú-Vergés
- Anaxomics Biotech S.L., 08007 Barcelona, Spain; (M.B.); (E.R.); (C.S.-V.); (L.A.)
- Research Programme on Biomedical Informatics (GRIB), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08002 Barcelona, Spain
| | - Laura Artigas
- Anaxomics Biotech S.L., 08007 Barcelona, Spain; (M.B.); (E.R.); (C.S.-V.); (L.A.)
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Coto-Segura P, Segú-Vergés C, Martorell A, Moreno-Ramírez D, Jorba G, Junet V, Guerri F, Daura X, Oliva B, Cara C, Suárez-Magdalena O, Abraham S, Mas JM. A quantitative systems pharmacology model for certolizumab pegol treatment in moderate-to-severe psoriasis. Front Immunol 2023; 14:1212981. [PMID: 37809085 PMCID: PMC10552644 DOI: 10.3389/fimmu.2023.1212981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Background Psoriasis is a chronic immune-mediated inflammatory systemic disease with skin manifestations characterized by erythematous, scaly, itchy and/or painful plaques resulting from hyperproliferation of keratinocytes. Certolizumab pegol [CZP], a PEGylated antigen binding fragment of a humanized monoclonal antibody against TNF-alpha, is approved for the treatment of moderate-to-severe plaque psoriasis. Patients with psoriasis present clinical and molecular variability, affecting response to treatment. Herein, we utilized an in silico approach to model the effects of CZP in a virtual population (vPop) with moderate-to-severe psoriasis. Our proof-of-concept study aims to assess the performance of our model in generating a vPop and defining CZP response variability based on patient profiles. Methods We built a quantitative systems pharmacology (QSP) model of a clinical trial-like vPop with moderate-to-severe psoriasis treated with two dosing schemes of CZP (200 mg and 400 mg, both every two weeks for 16 weeks, starting with a loading dose of CZP 400 mg at weeks 0, 2, and 4). We applied different modelling approaches: (i) an algorithm to generate vPop according to reference population values and comorbidity frequencies in real-world populations; (ii) physiologically based pharmacokinetic (PBPK) models of CZP dosing schemes in each virtual patient; and (iii) systems biology-based models of the mechanism of action (MoA) of the drug. Results The combination of our different modelling approaches yielded a vPop distribution and a PBPK model that aligned with existing literature. Our systems biology and QSP models reproduced known biological and clinical activity, presenting outcomes correlating with clinical efficacy measures. We identified distinct clusters of virtual patients based on their psoriasis-related protein predicted activity when treated with CZP, which could help unravel differences in drug efficacy in diverse subpopulations. Moreover, our models revealed clusters of MoA solutions irrespective of the dosing regimen employed. Conclusion Our study provided patient specific QSP models that reproduced clinical and molecular efficacy features, supporting the use of computational methods as modelling strategy to explore drug response variability. This might shed light on the differences in drug efficacy in diverse subpopulations, especially useful in complex diseases such as psoriasis, through the generation of mechanistically based hypotheses.
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Affiliation(s)
- Pablo Coto-Segura
- Dermatology Department, Hospital Vital Alvarez-Buylla de Mieres, Asturias, Spain
| | - Cristina Segú-Vergés
- Anaxomics Biotech SL, Barcelona, Spain
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - David Moreno-Ramírez
- Dermatology Department, University Hospital Virgen Macarena, Andalusian Health Service, University of Seville, Seville, Spain
| | - Guillem Jorba
- Anaxomics Biotech SL, Barcelona, Spain
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Valentin Junet
- Anaxomics Biotech SL, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Filippo Guerri
- Anaxomics Biotech SL, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, Spain
| | - Baldomero Oliva
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | - Sonya Abraham
- National Heart and Lung Institute (NHLI), Faculty of Medicine, Imperial College, London, United Kingdom
- Medical Affairs, UCB Pharma, Brussels, Belgium
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Junet V, Matos‐Filipe P, García‐Illarramendi JM, Ramírez E, Oliva B, Farrés J, Daura X, Mas JM, Morales R. A decision support system based on artificial intelligence and systems biology for the simulation of pancreatic cancer patient status. CPT Pharmacometrics Syst Pharmacol 2023; 12:916-928. [PMID: 37002678 PMCID: PMC10349189 DOI: 10.1002/psp4.12961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/23/2023] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
Oncology treatments require continuous individual adjustment based on the measurement of multiple clinical parameters. Prediction tools exploiting the patterns present in the clinical data could be used to assist decision making and ease the burden associated to the interpretation of all these parameters. The goal of this study was to predict the evolution of patients with pancreatic cancer at their next visit using information routinely recorded in health records, providing a decision-support system for clinicians. We selected hematological variables as the visit's clinical outcomes, under the assumption that they can be predictive of the evolution of the patient. Multivariate models based on regression trees were generated to predict next-visit values for each of the clinical outcomes selected, based on the longitudinal clinical data as well as on molecular data sets streaming from in silico simulations of individual patient status at each visit. The models predict, with a mean prediction score (balanced accuracy) of 0.79, the evolution trends of eosinophils, leukocytes, monocytes, and platelets. Time span between visits and neutropenia were among the most common factors contributing to the predicted evolution. The inclusion of molecular variables from the systems-biology in silico simulations provided a molecular background for the observed variations in the selected outcome variables, mostly in relation to the regulation of hematopoiesis. In spite of its limitations, this study serves as a proof of concept for the application of next-visit prediction tools in real-world settings, even when available data sets are small.
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Affiliation(s)
- Valentin Junet
- Anaxomics Biotech SLBarcelonaSpain
- Institute of Biotechnology and BiomedicineUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Pedro Matos‐Filipe
- Anaxomics Biotech SLBarcelonaSpain
- Structural Bioinformatics (GRIB‐IMIM), Departament de Ciències Experimentals i de la SalutUniversitat Pompeu FabraBarcelonaSpain
| | - Juan Manuel García‐Illarramendi
- Anaxomics Biotech SLBarcelonaSpain
- Institute of Biotechnology and BiomedicineUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | | | - Baldo Oliva
- Structural Bioinformatics (GRIB‐IMIM), Departament de Ciències Experimentals i de la SalutUniversitat Pompeu FabraBarcelonaSpain
| | | | - Xavier Daura
- Institute of Biotechnology and BiomedicineUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
- Catalan Institution for Research and Advanced Studies (ICREA)BarcelonaSpain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER‐BBN)Instituto de Salud Carlos IIICerdanyola del VallèsSpain
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Gutiérrez-Casares JR, Segú-Vergés C, Sabate Chueca J, Pozo-Rubio T, Coma M, Montoto C, Quintero J. In silico evaluation of the role of lisdexamfetamine on attention-deficit/hyperactivity disorder common psychiatric comorbidities: mechanistic insights on binge eating disorder and depression. Front Neurosci 2023; 17:1118253. [PMID: 37457000 PMCID: PMC10347683 DOI: 10.3389/fnins.2023.1118253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a psychiatric condition well recognized in the pediatric population that can persist into adulthood. The vast majority of patients with ADHD present psychiatric comorbidities that have been suggested to share, to some extent, the pathophysiological mechanism of ADHD. Lisdexamfetamine (LDX) is a stimulant prodrug approved for treating ADHD and, in the US, also for binge eating disorder (BED). Herein, we evaluated, through a systems biology-based in silico method, the efficacy of a virtual model of LDX (vLDX) as ADHD treatment to improve five common ADHD psychiatric comorbidities in adults and children, and we explored the molecular mechanisms behind LDX's predicted efficacy. After the molecular characterization of vLDX and the comorbidities (anxiety, BED, bipolar disorder, depression, and tics disorder), we created a protein-protein interaction human network to which we applied artificial neural networks (ANN) algorithms. We also generated virtual populations of adults and children-adolescents totaling 2,600 individuals and obtained the predicted protein activity from Therapeutic Performance Mapping System models. The latter showed that ADHD molecular description shared 53% of its protein effectors with at least one studied psychiatric comorbidity. According to the ANN analysis, proteins targeted by vLDX are predicted to have a high probability of being related to BED and depression. In BED, vLDX was modeled to act upon neurotransmission and neuroplasticity regulators, and, in depression, vLDX regulated the hypothalamic-pituitary-adrenal axis, neuroinflammation, oxidative stress, and glutamatergic excitotoxicity. In conclusion, our modeling results, despite their limitations and although requiring in vitro or in vivo validation, could supplement the design of preclinical and potentially clinical studies that investigate treatment for patients with ADHD with psychiatric comorbidities, especially from a molecular point of view.
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Affiliation(s)
- José Ramón Gutiérrez-Casares
- Unidad Ambulatoria de Psiquiatría y Salud Mental de la Infancia, Niñez y Adolescencia, Hospital Perpetuo Socorro, Badajoz, Spain
| | - Cristina Segú-Vergés
- Anaxomics Biotech, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | | | - Carmen Montoto
- Department of Medical, Takeda Farmacéutica España, Madrid, Spain
| | - Javier Quintero
- Servicio de Psiquiatría, Hospital Universitario Infanta Leonor, Departamento de Medicina Legal, Patología y Psiquiatría, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
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Valls R, Wagg J, Paz-Priel I, Man G, Artigas L, Jaccard G, Coma M, Schmitt C. Application of systems biology to identify pharmacological mechanisms of thrombotic microangiopathy evoked by combined activated prothrombin complex concentrate and emicizumab. Sci Rep 2023; 13:10078. [PMID: 37344529 DOI: 10.1038/s41598-023-36891-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023] Open
Abstract
Emicizumab is a bispecific monoclonal antibody that substitutes for the function of missing or deficient factor VIII (FVIII) in people with hemophilia A (PwHA). Long-term safety and efficacy of emicizumab have been demonstrated in several clinical trials. Nevertheless, in the first of these, three cases of thrombotic microangiopathy (TMA) occurred in PwHA treated with emicizumab receiving high doses of activated prothrombin complex concentrate (aPCC), a bypassing agent used for treating breakthrough bleeds when FVIII neutralizing antibodies (inhibitors) make FVIII replacement ineffective. The aim of the present work is to offer a method to elucidate the pathophysiological and pharmacological mechanisms involved in this treatment-induced TMA. Systems biology and machine learning-based Therapeutic Performance Mapping System is a validated in silico technology that allowed us to construct models of potential mechanisms behind induced TMA. Two drug combinations were modeled and assessed: emicizumab plus aPCC and emicizumab plus recombinant activated factor VII (another bypassing agent). Our models showed that both combinations were related to activation of the coagulation cascade. However, mechanisms involved mainly in platelet activation and possibly in complement activation were detected only for emicizumab plus aPCC, potentially explaining the occurrence of TMA only in this combination.
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Affiliation(s)
| | - Jonathan Wagg
- Roche Innovation Center, Basel, Switzerland
- AC Immune SA, EPFL Innovation Park, Lausanne, Switzerland
| | - Ido Paz-Priel
- Genentech, Inc., South San Francisco, CA, USA
- Graphite Bio Inc., South San Francisco, CA, USA
| | - Gabriel Man
- Genentech, Inc., South San Francisco, CA, USA
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Gutiérrez-Casares JR, Quintero J, Segú-Vergés C, Rodríguez Monterde P, Pozo-Rubio T, Coma M, Montoto C. In silico clinical trial evaluating lisdexamfetamine's and methylphenidate's mechanism of action computational models in an attention-deficit/hyperactivity disorder virtual patients' population. Front Psychiatry 2023; 14:939650. [PMID: 37333910 PMCID: PMC10273406 DOI: 10.3389/fpsyt.2023.939650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 04/21/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction Attention-deficit/hyperactivity disorder (ADHD) is an impairing psychiatric condition with the stimulants, lisdexamfetamine (LDX), and methylphenidate (MPH), as the first lines pharmacological treatment. Methods Herein, we applied a novel in silico method to evaluate virtual LDX (vLDX) and vMPH as treatments for ADHD applying quantitative systems pharmacology (QSP) models. The objectives were to evaluate the model's output, considering the model characteristics and the information used to build them, to compare both virtual drugs' efficacy mechanisms, and to assess how demographic (age, body mass index, and sex) and clinical characteristics may affect vLDX's and vMPH's relative efficacies. Results and Discussion We molecularly characterized the drugs and pathologies based on a bibliographic search, and generated virtual populations of adults and children-adolescents totaling 2,600 individuals. For each virtual patient and virtual drug, we created physiologically based pharmacokinetic and QSP models applying the systems biology-based Therapeutic Performance Mapping System technology. The resulting models' predicted protein activity indicated that both virtual drugs modulated ADHD through similar mechanisms, albeit with some differences. vMPH induced several general synaptic, neurotransmitter, and nerve impulse-related processes, whereas vLDX seemed to modulate neural processes more specific to ADHD, such as GABAergic inhibitory synapses and regulation of the reward system. While both drugs' models were linked to an effect over neuroinflammation and altered neural viability, vLDX had a significant impact on neurotransmitter imbalance and vMPH on circadian system deregulation. Among demographic characteristics, age and body mass index affected the efficacy of both virtual treatments, although the effect was more marked for vLDX. Regarding comorbidities, only depression negatively impacted both virtual drugs' efficacy mechanisms and, while that of vLDX were more affected by the co-treatment of tic disorders, the efficacy mechanisms of vMPH were disturbed by wide-spectrum psychiatric drugs. Our in silico results suggested that both drugs could have similar efficacy mechanisms as ADHD treatment in adult and pediatric populations and allowed raising hypotheses for their differential impact in specific patient groups, although these results require prospective validation for clinical translatability.
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Affiliation(s)
- José Ramón Gutiérrez-Casares
- Unidad Ambulatoria de Psiquiatría y Salud Mental de la Infancia, Niñez y Adolescencia, Hospital Perpetuo Socorro, Badajoz, Spain
| | - Javier Quintero
- Servicio de Psiquiatría, Hospital Universitario Infanta Leonor, Universidad Complutense, Madrid, Spain
| | - Cristina Segú-Vergés
- Anaxomics Biotech, Barcelona, Spain
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | | | - Carmen Montoto
- Medical Department, Takeda Farmacéutica España, Madrid, Spain
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Gómez J, Artigas L, Valls R, Gervas-Arruga J. An in silico approach to identify early damage biomarker candidates in metachromatic leukodystrophy. Mol Genet Metab Rep 2023; 35:100974. [PMID: 37275681 PMCID: PMC10233284 DOI: 10.1016/j.ymgmr.2023.100974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 06/07/2023] Open
Abstract
Metachromatic leukodystrophy (MLD) is a rare, autosomal recessive lysosomal storage disease. Deficient activity of arylsulfatase A causes sulfatides to accumulate in cells of different tissues, including those in the central and peripheral nervous systems, leading to progressive demyelination and neurodegeneration. Although there is some association between specific arylsulfatase A alleles and disease severity, genotype-phenotype correlations are not fully understood. We aimed to identify biomarker candidates of early tissue damage in MLD using a modeling approach based on systems biology. A review of the literature was performed in an initial disease characterization step, allowing identification of pathophysiological processes involved in MLD and proteins relating to these processes. Three mathematical models were generated to simulate different stages of MLD at the molecular level: an early pro-inflammatory stage model (including only processes considered to be active in the early stages of disease), a pre-demyelination stage model (including additional processes that are active after some disease progression), and a demyelination stage model (in which all pathophysiological processes are active). The models evaluated 3457 proteins of interest, individually and by pairs through data mining techniques, applying five filters to prioritize biomarkers that could differentiate between the models. Sixteen potential biomarkers were identified, including effectors relating to mitochondrial dysfunction, remyelination, and neurodegeneration. The findings were corroborated in a gene expression data set from T lymphocytes of patients with MLD; all candidates formed combinations that were able to distinguish patients with MLD from controls, and all but one candidate distinguished late-infantile MLD from juvenile MLD as part of a combinatorial biomarker pair. In particular, pro-neuregulin-1 appeared as differential on all comparisons (patients with MLD vs controls and within clinical subtypes); casein kinase II subunit alpha was detected as a potential individual marker within clinical subtypes. These findings provide a panel of biomarker candidates suitable for experimental validation and highlight the utility of mathematical models to identify biomarker candidates of early tissue damage in MLD with a high degree of accuracy and sensitivity.
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Casadomé-Perales Á, Naya S, Fernández-Martínez E, Mille BG, Guerrero-Valero M, Peinado H, Guix FX, Dotti CG, Palomer E. Neuronal Prosurvival Role of Ceramide Synthase 2 by Olidogendrocyte-to-Neuron Extracellular Vesicle Transfer. Int J Mol Sci 2023; 24:ijms24065986. [PMID: 36983060 PMCID: PMC10052063 DOI: 10.3390/ijms24065986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Ageing is associated with notorious alterations in neurons, i.e., in gene expression, mitochondrial function, membrane degradation or intercellular communication. However, neurons live for the entire lifespan of the individual. One of the reasons why neurons remain functional in elderly people is survival mechanisms prevail over death mechanisms. While many signals are either pro-survival or pro-death, others can play both roles. Extracellular vesicles (EVs) can signal both pro-toxicity and survival. We used young and old animals, primary neuronal and oligodendrocyte cultures and neuroblastoma and oligodendrocytic lines. We analysed our samples using a combination of proteomics and artificial neural networks, biochemistry and immunofluorescence approaches. We found an age-dependent increase in ceramide synthase 2 (CerS2) in cortical EVs, expressed by oligodendrocytes. In addition, we show that CerS2 is present in neurons via the uptake of oligodendrocyte-derived EVs. Finally, we show that age-associated inflammation and metabolic stress favour CerS2 expression and that oligodendrocyte-derived EVs loaded with CerS2 lead to the expression of the antiapoptotic factor Bcl2 in inflammatory conditions. Our study shows that intercellular communication is altered in the ageing brain, which favours neuronal survival through the transfer of oligodendrocyte-derived EVs containing CerS2.
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Affiliation(s)
- Álvaro Casadomé-Perales
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, 28049 Madrid, Spain
| | - Sara Naya
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, 28049 Madrid, Spain
| | - Elisa Fernández-Martínez
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, 28049 Madrid, Spain
| | - Bea G Mille
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, 28049 Madrid, Spain
| | - Marta Guerrero-Valero
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, 28049 Madrid, Spain
| | - Héctor Peinado
- Microenvironment and Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Francesc X Guix
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, 28049 Madrid, Spain
- Department of Bioengineering, Institut Químic de Sarrià (IQS), Universitat Ramón Llull (URL), 08017 Barcelona, Spain
| | - Carlos G Dotti
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, 28049 Madrid, Spain
| | - Ernest Palomer
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, 28049 Madrid, Spain
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Artificial intelligence assessment of the potential of tocilizumab along with corticosteroids therapy for the management of COVID-19 evoked acute respiratory distress syndrome. PLoS One 2023; 18:e0280677. [PMID: 36791125 PMCID: PMC9931125 DOI: 10.1371/journal.pone.0280677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/05/2023] [Indexed: 02/16/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS), associated with high mortality rate, affects up to 67% of hospitalized COVID-19 patients. Early evidence indicated that the pathogenesis of COVID-19 evoked ARDS is, at least partially, mediated by hyperinflammatory cytokine storm in which interleukin 6 (IL-6) plays an essential role. The corticosteroid dexamethasone is an effective treatment for severe COVID-19 related ARDS. However, trials of other immunomodulatory therapies, including anti-IL6 agents such as tocilizumab and sarilumab, have shown limited evidence of benefit as monotherapy. But recently published large trials have reported added benefit of tocilizumab in combination with dexamethasone in severe COVID-19 related ARDS. In silico tools can be useful to shed light on the mechanisms evoked by SARS-CoV-2 infection and of the potential therapeutic approaches. Therapeutic performance mapping system (TPMS), based on systems biology and artificial intelligence, integrate available biological, pharmacological and medical knowledge to create mathematical models of the disease. This technology was used to identify the pharmacological mechanism of dexamethasone, with or without tocilizumab, in the management of COVID-19 evoked ARDS. The results showed that while dexamethasone would be addressing a wider range of pathological processes with low intensity, tocilizumab might provide a more direct and intense effect upon the cytokine storm. Based on this in silico study, we conclude that the use of tocilizumab alongside dexamethasone is predicted to induce a synergistic effect in dampening inflammation and subsequent pathological processes, supporting the beneficial effect of the combined therapy in critically ill patients. Future research will allow identifying the ideal subpopulation of patients that would benefit better from this combined treatment.
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Fernández-Carballido C, Sanchez-Piedra C, Valls R, Garg K, Sánchez-Alonso F, Artigas L, Mas JM, Jovaní V, Manrique S, Campos C, Freire M, Martínez-González O, Castrejón I, Perella C, Coma M, van der Horst-Bruinsma IE. Female Sex, Age, and Unfavorable Response to Tumor Necrosis Factor Inhibitors in Patients With Axial Spondyloarthritis: Results of Statistical and Artificial Intelligence-Based Data Analyses of a National Multicenter Prospective Registry. Arthritis Care Res (Hoboken) 2023; 75:115-124. [PMID: 36278846 DOI: 10.1002/acr.25048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Real-world studies are needed to identify factors associated with response to biologic therapies in patients with axial spondyloarthritis (SpA). The objective was to assess sex differences in response to tumor necrosis factor inhibitors (TNFi) and to explore possible risk factors associated with TNFi efficacy. METHODS A total of 969 patients with axial SpA (315 females, 654 males) enrolled in the BIOBADASER registry (2000-2019) who initiated a TNFi (first, second, or further lines) were studied. Statistical and artificial intelligence (AI)-based data analyses were used to explore the association of sex differences and other factors to TNFi response, using the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), to calculate the BASDAI50, with an improvement of at least 50% of the BASDAI score, and using the Ankylosing Spondylitis Disease Activity Score, calculated using the C-reactive protein level (ASDAS-CRP). RESULTS Females had a lower probability of reaching a BASDAI50 response with a first line TNFi treatment at the second year of follow-up (P = 0.018) and a lesser reduction of the ASDAS-CRP at this time point. The logistic regression model showed lower BASDAI50 responses to TNFi in females (P = 0.05). Other factors, such as older age (P = 0.004), were associated with unfavorable responses. The AI data analyses reinforced the idea that age at the beginning of the treatment was the main factor associated with an unfavorable response. The combination of age with other clinical characteristics (female sex or cardiovascular risk factors and events) potentially contributed to an unfavorable response to TNFi. CONCLUSION In this national multicenter registry, female sex was associated with less response to a first-line TNFi by the second year of follow-up. A higher age at the start of the TNFi was the main factor associated with an unfavorable response to TNFi.
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Affiliation(s)
| | - Carlos Sanchez-Piedra
- Health Technology Assessment Agency of Carlos III Institute of Health, Madrid, Spain
| | | | | | | | | | | | - Vega Jovaní
- Hospital General Universitario Dr. Balmis, Alicante, Spain
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11
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Segú-Vergés C, Gómez J, Terradas-Montana P, Artigas L, Smeets S, Ferrer M, Savic S. Unveiling chronic spontaneous urticaria pathophysiology through systems biology. J Allergy Clin Immunol 2022; 151:1005-1014. [PMID: 36587849 DOI: 10.1016/j.jaci.2022.12.809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/06/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Chronic spontaneous urticaria (CSU) is a rare, heterogeneous, severely debilitating, and often poorly controlled skin disease resulting in an itchy eruption that can be persistent. Antihistamines and omalizumab, an anti-IgE mAb, are the only licensed therapies. Although CSU pathogenesis is not yet fully understood, mast cell activation through the IgE:high-affinity IgE receptor (FcεRI) axis appears central to the disease process. OBJECTIVE We sought to model CSU pathophysiology and identify in silico the mechanism of action of different CSU therapeutic strategies currently in use or under development. METHODS Therapeutic performance mapping system technology, based on systems biology and machine learning, was used to create a CSU interactome validated with gene expression data from patients with CSU and a CSU model that was used to evaluate CSU pathophysiology and the mechanism of action of different therapeutic strategies. RESULTS Our models reflect the known role of mast cell activation as a central process of CSU pathophysiology, as well as recognized roles for different therapeutic strategies in this and other innate and adaptive immune processes. They also allow determining similarities and differences between them; anti-IgE and Bruton tyrosine kinase inhibitors play a more direct role in mast cell biology through abrogation of FcεRI signaling activity, whereas anti-interleukins and anti-Siglec-8 have a role in adaptive immunity modulation. CONCLUSION In silico CSU models reproduced known CSU and therapeutic strategies features. Our results could help advance understanding of therapeutic mechanisms of action and further advance treatment research by patient profile.
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Affiliation(s)
- Cristina Segú-Vergés
- Anaxomics Biotech, Barcelona, Spain; Research Programme on Biomedical Informatics, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | | | | | - Marta Ferrer
- Department of Allergy and Clinical Immunology, Clínica Universidad de Navarra, Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra, 3Cooperative Research Network Health Oriented, Pamplona, Spain
| | - Sinisa Savic
- Department of Clinical Immunology and Allergy, Leeds Teaching Hospital NHS Trust, Leeds, United Kingdom.
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12
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Segú-Vergés C, Caño S, Calderón-Gómez E, Bartra H, Sardon T, Kaveri S, Terencio J. Systems biology and artificial intelligence analysis highlights the pleiotropic effect of IVIg therapy in autoimmune diseases with a predominant role on B cells and complement system. Front Immunol 2022; 13:901872. [PMID: 36248801 PMCID: PMC9563374 DOI: 10.3389/fimmu.2022.901872] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/31/2022] [Indexed: 11/26/2022] Open
Abstract
Intravenous immunoglobulin (IVIg) is used as treatment for several autoimmune and inflammatory conditions, but its specific mechanisms are not fully understood. Herein, we aimed to evaluate, using systems biology and artificial intelligence techniques, the differences in the pathophysiological pathways of autoimmune and inflammatory conditions that show diverse responses to IVIg treatment. We also intended to determine the targets of IVIg involved in the best treatment response of the evaluated diseases. Our selection and classification of diseases was based on a previously published systematic review, and we performed the disease characterization through manual curation of the literature. Furthermore, we undertook the mechanistic evaluation with artificial neural networks and pathway enrichment analyses. A set of 26 diseases was selected, classified, and compared. Our results indicated that diseases clearly benefiting from IVIg treatment were mainly characterized by deregulated processes in B cells and the complement system. Indeed, our results show that proteins related to B-cell and complement system pathways, which are targeted by IVIg, are involved in the clinical response. In addition, targets related to other immune processes may also play an important role in the IVIg response, supporting its wide range of actions through several mechanisms. Although B-cell responses and complement system have a key role in diseases benefiting from IVIg, protein targets involved in such processes are not necessarily the same in those diseases. Therefore, IVIg appeared to have a pleiotropic effect that may involve the collaborative participation of several proteins. This broad spectrum of targets and 'non-specificity' of IVIg could be key to its efficacy in very different diseases.
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Affiliation(s)
| | - Silvia Caño
- Grifols Innovation and New Technologies (GIANT) Ltd., Dublin, Ireland
| | | | - Helena Bartra
- Health Department, Anaxomics Biotech, Barcelona, Spain
| | - Teresa Sardon
- Health Department, Anaxomics Biotech, Barcelona, Spain
| | - Srini Kaveri
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - José Terencio
- Grifols Innovation and New Technologies (GIANT) Ltd., Dublin, Ireland
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Bozkurt B, Nair AP, Misra A, Scott CZ, Mahar JH, Fedson S. Neprilysin Inhibitors in Heart Failure: The Science, Mechanism of Action, Clinical Studies, and Unanswered Questions. JACC. BASIC TO TRANSLATIONAL SCIENCE 2022; 8:88-105. [PMID: 36777165 PMCID: PMC9911324 DOI: 10.1016/j.jacbts.2022.05.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022]
Abstract
This article provides a contemporary review and a new perspective on the role of neprilysin inhibition in heart failure (HF) in the context of recent clinical trials and addresses potential mechanisms and unanswered questions in certain HF patient populations. Neprilysin is an endopeptidase that cleaves a variety of peptides such as natriuretic peptides, bradykinin, adrenomedullin, substance P, angiotensin I and II, and endothelin. It has a broad role in cardiovascular, renal, pulmonary, gastrointestinal, endocrine, and neurologic functions. The combined angiotensin receptor and neprilysin inhibitor (ARNi) has been developed with an intent to increase vasodilatory natriuretic peptides and prevent counterregulatory activation of the angiotensin system. ARNi therapy is very effective in reducing the risks of death and hospitalization for HF in patients with HF and New York Heart Association functional class II to III symptoms, but studies failed to show any benefits with ARNi when compared with angiotensin-converting enzyme inhibitors or angiotensin receptor blocker in patients with advanced HF with reduced ejection fraction or in patients following myocardial infarction with left ventricular dysfunction but without HF. These raise the questions about whether the enzymatic breakdown of natriuretic peptides may not be a very effective solution in advanced HF patients when there is downstream blunting of the response to natriuretic peptides or among post-myocardial infarction patients in the absence of HF when there may not be a need for increased natriuretic peptide availability. Furthermore, there is a need for additional studies to determine the long-term effects of ARNi on albuminuria, obesity, glycemic control and lipid profile, blood pressure, and cognitive function in patients with HF.
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Key Words
- ACE, angiotensin-converting enzyme
- ANP, atrial natriuretic peptide
- ARB, angiotensin receptor blocker
- ARN, angiotensin receptor–neprilysin
- ARNi
- Aβ, amyloid beta
- BNP, brain natriuretic peptide
- BP, blood pressure
- CSF, cerebrospinal fluid
- EF, ejection fraction
- FDA, U.S. Food and Drug Administration
- GFR, glomerular filtration rate
- HF, heart failure
- HFpEF, heart failure with preserved ejection fraction
- HFrEF, heart failure with reduced ejection fraction
- LV, left ventricular
- LVEF, left ventricular ejection fraction
- MI, myocardial infarction
- NEP inhibitor
- NT-proBNP, N-terminal pro–brain natriuretic peptide
- NYHA, New York Heart Association
- PDE, phosphodiesterase
- RAAS, renin-angiotensin-aldosterone system
- UACR, urinary albumin/creatine ratio
- angiotensin receptor–neprilysin inhibitor
- cGMP, cyclic guanosine monophosphate
- eGFR, estimated glomerular filtration rate
- heart failure
- neprilysin
- neprilysin inhibitor
- sacubitril
- sacubitril/valsartan
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Affiliation(s)
- Biykem Bozkurt
- Winters Center for Heart Failure Research, Cardiovascular Research Institute, Baylor College of Medicine, DeBakey Veterans Affairs Medical Center, Houston Texas, USA
- Cardiology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston Texas, USA
- Address for correspondence: Dr Biykem Bozkurt, MEDVAMC, 2002 Holcombe Boulevard, Houston, Texas, 77030, USA.
| | - Ajith P. Nair
- Cardiology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Arunima Misra
- Cardiology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston Texas, USA
| | - Claire Z. Scott
- Cardiology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Jamal H. Mahar
- Cardiology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Savitri Fedson
- Cardiology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston Texas, USA
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Identification of the Potential Molecular Mechanisms Linking RUNX1 Activity with Nonalcoholic Fatty Liver Disease, by Means of Systems Biology. Biomedicines 2022; 10:biomedicines10061315. [PMID: 35740337 PMCID: PMC9219880 DOI: 10.3390/biomedicines10061315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/24/2022] [Accepted: 06/01/2022] [Indexed: 12/10/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most prevalent chronic hepatic disease; nevertheless, no definitive diagnostic method exists yet, apart from invasive liver biopsy, and nor is there a specific approved treatment. Runt-related transcription factor 1 (RUNX1) plays a major role in angiogenesis and inflammation; however, its link with NAFLD is unclear as controversial results have been reported. Thus, the objective of this work was to determine the proteins involved in the molecular mechanisms between RUNX1 and NAFLD, by means of systems biology. First, a mathematical model that simulates NAFLD pathophysiology was generated by analyzing Anaxomics databases and reviewing available scientific literature. Artificial neural networks established NAFLD pathophysiological processes functionally related to RUNX1: hepatic insulin resistance, lipotoxicity, and hepatic injury-liver fibrosis. Our study indicated that RUNX1 might have a high relationship with hepatic injury-liver fibrosis, and a medium relationship with lipotoxicity and insulin resistance motives. Additionally, we found five RUNX1-regulated proteins with a direct involvement in NAFLD motives, which were NFκB1, NFκB2, TNF, ADIPOQ, and IL-6. In conclusion, we suggested a relationship between RUNX1 and NAFLD since RUNX1 seems to regulate NAFLD molecular pathways, posing it as a potential therapeutic target of NAFLD, although more studies in this field are needed.
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15
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Data mining analyses for precision medicine in acromegaly: a proof of concept. Sci Rep 2022; 12:8979. [PMID: 35643771 PMCID: PMC9148300 DOI: 10.1038/s41598-022-12955-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/13/2022] [Indexed: 11/21/2022] Open
Abstract
Predicting which acromegaly patients could benefit from somatostatin receptor ligands (SRL) is a must for personalized medicine. Although many biomarkers linked to SRL response have been identified, there is no consensus criterion on how to assign this pharmacologic treatment according to biomarker levels. Our aim is to provide better predictive tools for an accurate acromegaly patient stratification regarding the ability to respond to SRL. We took advantage of a multicenter study of 71 acromegaly patients and we used advanced mathematical modelling to predict SRL response combining molecular and clinical information. Different models of patient stratification were obtained, with a much higher accuracy when the studied cohort is fragmented according to relevant clinical characteristics. Considering all the models, a patient stratification based on the extrasellar growth of the tumor, sex, age and the expression of E-cadherin, GHRL, IN1-GHRL, DRD2, SSTR5 and PEBP1 is proposed, with accuracies that stand between 71 to 95%. In conclusion, the use of data mining could be very useful for implementation of personalized medicine in acromegaly through an interdisciplinary work between computer science, mathematics, biology and medicine. This new methodology opens a door to more precise and personalized medicine for acromegaly patients.
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García-Consuegra I, Asensio-Peña S, Garrido-Moraga R, Pinós T, Domínguez-González C, Santalla A, Nogales-Gadea G, Serrano-Lorenzo P, Andreu AL, Arenas J, Zugaza JL, Lucia A, Martín MA. Identification of Potential Muscle Biomarkers in McArdle Disease: Insights from Muscle Proteome Analysis. Int J Mol Sci 2022; 23:4650. [PMID: 35563042 PMCID: PMC9100117 DOI: 10.3390/ijms23094650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/03/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
Glycogen storage disease type V (GSDV, McArdle disease) is a rare genetic myopathy caused by deficiency of the muscle isoform of glycogen phosphorylase (PYGM). This results in a block in the use of muscle glycogen as an energetic substrate, with subsequent exercise intolerance. The pathobiology of GSDV is still not fully understood, especially with regard to some features such as persistent muscle damage (i.e., even without prior exercise). We aimed at identifying potential muscle protein biomarkers of GSDV by analyzing the muscle proteome and the molecular networks associated with muscle dysfunction in these patients. Muscle biopsies from eight patients and eight healthy controls showing none of the features of McArdle disease, such as frequent contractures and persistent muscle damage, were studied by quantitative protein expression using isobaric tags for relative and absolute quantitation (iTRAQ) followed by artificial neuronal networks (ANNs) and topology analysis. Protein candidate validation was performed by Western blot. Several proteins predominantly involved in the process of muscle contraction and/or calcium homeostasis, such as myosin, sarcoplasmic/endoplasmic reticulum calcium ATPase 1, tropomyosin alpha-1 chain, troponin isoforms, and alpha-actinin-3, showed significantly lower expression levels in the muscle of GSDV patients. These proteins could be potential biomarkers of the persistent muscle damage in the absence of prior exertion reported in GSDV patients. Further studies are needed to elucidate the molecular mechanisms by which PYGM controls the expression of these proteins.
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Affiliation(s)
- Inés García-Consuegra
- Mitochondrial and Neuromuscular Disorders Group, Hospital 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain; (I.G.-C.); (S.A.-P.); (R.G.-M.); (C.D.-G.); (P.S.-L.); (J.A.); (A.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain;
| | - Sara Asensio-Peña
- Mitochondrial and Neuromuscular Disorders Group, Hospital 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain; (I.G.-C.); (S.A.-P.); (R.G.-M.); (C.D.-G.); (P.S.-L.); (J.A.); (A.L.)
| | - Rocío Garrido-Moraga
- Mitochondrial and Neuromuscular Disorders Group, Hospital 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain; (I.G.-C.); (S.A.-P.); (R.G.-M.); (C.D.-G.); (P.S.-L.); (J.A.); (A.L.)
| | - Tomàs Pinós
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain;
- Mitochondrial and Neuromuscular Disorders Unit, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Cristina Domínguez-González
- Mitochondrial and Neuromuscular Disorders Group, Hospital 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain; (I.G.-C.); (S.A.-P.); (R.G.-M.); (C.D.-G.); (P.S.-L.); (J.A.); (A.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain;
| | - Alfredo Santalla
- Department of Computer and Sport Sciences, Universidad Pablo de Olavide, 41013 Sevilla, Spain;
| | - Gisela Nogales-Gadea
- Grup de Recerca en Malalties Neuromusculars i Neuropediàtriques, Department of Neurosciences, Institut d’Investigacio en Ciencies de la Salut Germans Trias i Pujol i Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Barcelona, Spain;
| | - Pablo Serrano-Lorenzo
- Mitochondrial and Neuromuscular Disorders Group, Hospital 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain; (I.G.-C.); (S.A.-P.); (R.G.-M.); (C.D.-G.); (P.S.-L.); (J.A.); (A.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain;
| | - Antoni L. Andreu
- EATRIS, European Infrastructure for Translational Medicine, 1019 Amsterdam, The Netherlands;
| | - Joaquín Arenas
- Mitochondrial and Neuromuscular Disorders Group, Hospital 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain; (I.G.-C.); (S.A.-P.); (R.G.-M.); (C.D.-G.); (P.S.-L.); (J.A.); (A.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain;
| | - José L. Zugaza
- Achucarro Basque Center for Neuroscience, Science Park of the UPV/EHU, and Department of Genetics, Physical Anthropology, and Animal Physiology, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Spain;
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Alejandro Lucia
- Mitochondrial and Neuromuscular Disorders Group, Hospital 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain; (I.G.-C.); (S.A.-P.); (R.G.-M.); (C.D.-G.); (P.S.-L.); (J.A.); (A.L.)
- Faculty of Sport Sciences, Universidad Europea de Madrid, 28670 Madrid, Spain
| | - Miguel A. Martín
- Mitochondrial and Neuromuscular Disorders Group, Hospital 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain; (I.G.-C.); (S.A.-P.); (R.G.-M.); (C.D.-G.); (P.S.-L.); (J.A.); (A.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain;
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Simats A, Ramiro L, Valls R, de Ramón H, García-Rodríguez P, Orset C, Artigas L, Sardon T, Rosell A, Montaner J. Ceruletide and Alpha-1 Antitrypsin as a Novel Combination Therapy for Ischemic Stroke. Neurotherapeutics 2022; 19:513-527. [PMID: 35226340 PMCID: PMC9226209 DOI: 10.1007/s13311-022-01203-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2022] [Indexed: 12/29/2022] Open
Abstract
Ischemic stroke is a primary cause of morbidity and mortality worldwide. Beyond the approved thrombolytic therapies, there is no effective treatment to mitigate its progression. Drug repositioning combinational therapies are becoming promising approaches to identify new uses of existing drugs to synergically target multiple disease-response mechanisms underlying complex pathologies. Here, we used a systems biology-based approach based on artificial intelligence and pattern recognition tools to generate in silico mathematical models mimicking the ischemic stroke pathology. Combinational treatments were acquired by screening these models with more than 5 million two-by-two combinations of drugs. A drug combination (CA) formed by ceruletide and alpha-1 antitrypsin showing a predicted value of neuroprotection of 92% was evaluated for their synergic neuroprotective effects in a mouse pre-clinical stroke model. The administration of both drugs in combination was safe and effective in reducing by 39.42% the infarct volume 24 h after cerebral ischemia. This neuroprotection was not observed when drugs were given individually. Importantly, potential incompatibilities of the drug combination with tPA thrombolysis were discarded in vitro and in vivo by using a mouse thromboembolic stroke model with t-PA-induced reperfusion, revealing an improvement in the forepaw strength 72 h after stroke in CA-treated mice. Finally, we identified the predicted mechanisms of action of ceruletide and alpha-1 antitrypsin and we demonstrated that CA modulates EGFR and ANGPT-1 levels in circulation within the acute phase after stroke. In conclusion, we have identified a promising combinational treatment with neuroprotective effects for the treatment of ischemic stroke.
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Affiliation(s)
- Alba Simats
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, Barcelona, 08035, Spain
| | - Laura Ramiro
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, Barcelona, 08035, Spain
| | | | - Helena de Ramón
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, Barcelona, 08035, Spain
| | - Paula García-Rodríguez
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, Barcelona, 08035, Spain
| | - Cyrille Orset
- Inserm UMR-S U1237, Physiopathology and Imaging of Neurological Disorders, Université Caen-Normandie, GIP Cyceron, Caen, France
| | | | | | - Anna Rosell
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, Barcelona, 08035, Spain
| | - Joan Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, Barcelona, 08035, Spain.
- Stroke Research Program, Institute of Biomedicine of Seville, IBiS/Hospital Universitario Virgen del Rocío/CSIC, University of Seville, Seville, Spain.
- Department of Neurology, Hospital Universitario Virgen Macarena, Seville, Spain.
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Durán I, Castellano D, Puente J, Martín-Couce L, Bello E, Anido U, Mas JM, Costa L. Exploring the synergistic effects of cabozantinib and a programmed cell death protein 1 inhibitor in metastatic renal cell carcinoma with machine learning. Oncotarget 2022; 13:237-256. [PMID: 35106125 PMCID: PMC8794707 DOI: 10.18632/oncotarget.28183] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022] Open
Abstract
Clinical evidence supports the combination of cabozantinib with an immune checkpoint inhibitor for the treatment of metastatic clear cell renal cell carcinoma (mccRCC) and suggests a synergistic antitumour activity of this combination. Nevertheless, the biological basis of this synergy is not fully characterized. We studied the mechanisms underpinning the potential synergism of cabozantinib combined with a PD1 inhibitor in mccRCC and delved into cabozantinib monotherapy properties supporting its role to partner these combinations. To model physiological drug action, we used a machine learning-based technology known as Therapeutic Performance Mapping Systems, applying two approaches: Artificial Neural Networks and Sampling Methods. We found that the combined therapy was predicted to exert a wide therapeutic action in the tumour and the microenvironment. Cabozantinib may enhance the effects of PD1 inhibitors on immunosurveillance by modulating the innate and adaptive immune system, through the inhibition of VEGF-VEGFR and Gas6-AXL/TYRO3/MER (TAM) axes, while the PD1 inhibitors may boost the antiangiogenic and pro-apoptotic effects of cabozantinib by modulating angiogenesis and T-cell cytotoxicity. Cabozantinib alone was predicted to restore cellular adhesion and hamper tumour proliferation and invasion. These data provide a biological rationale and further support for cabozantinib plus PD1 inhibitor combination and may guide future nonclinical and clinical research.
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Affiliation(s)
- Ignacio Durán
- Medical Oncology Department, University Hospital Marqués de Valdecilla, IDIVAL, Santander, Spain
| | - Daniel Castellano
- Medical Oncology Department, University Hospital 12 de Octubre, Madrid, Spain
| | - Javier Puente
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), CIBERONC, Madrid, Spain
| | - Lidia Martín-Couce
- IPSEN, Planta 7, Torre Realia, L’hospitalet de Llobregat, Barcelona, Spain
| | - Esther Bello
- IPSEN, Planta 7, Torre Realia, L’hospitalet de Llobregat, Barcelona, Spain
| | - Urbano Anido
- Department of Medical Oncology, University Clinic Hospital of Santiago, Health Research Institute (IDIS), ONCOMET, Santiago de Compostela, Spain
| | | | - Luis Costa
- Oncology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
- Instituto de Medicina Molecular-João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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Peck RW, Holstein SA, van der Graaf PH. BIA 10-2474: Some Lessons are Clear but Important Questions Remain Unanswered. Clin Pharmacol Ther 2022; 111:343-345. [PMID: 35007339 DOI: 10.1002/cpt.2495] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Richard W Peck
- Pharma Research and Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Sarah A Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
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20
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Domingo S, Solé C, Moliné T, Ferrer B, Cortés-Hernández J. Thalidomide Exerts Anti-Inflammatory Effects in Cutaneous Lupus by Inhibiting the IRF4/NF-ҡB and AMPK1/mTOR Pathways. Biomedicines 2021; 9:biomedicines9121857. [PMID: 34944673 PMCID: PMC8698478 DOI: 10.3390/biomedicines9121857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
Thalidomide is effective in patients with refractory cutaneous lupus erythematosus (CLE). However, the mechanism of action is not completely understood, and its use is limited by its potential, severe side-effects. Immune cell subset analysis in thalidomide’s CLE responder patients showed a reduction of circulating and tissue cytotoxic T-cells with an increase of iNKT cells and a shift towards a Th2 response. We conducted an RNA-sequencing study using CLE skin biopsies performing a Therapeutic Performance Mapping System (TMPS) analysis in order to generate a predictive model of its mechanism of action and to identify new potential therapeutic targets. Integrating RNA-seq data, public databases, and literature, TMPS analysis generated mathematical models which predicted that thalidomide acts via two CRBN-CRL4A- (CRL4CRBN) dependent pathways: IRF4/NF-ҡB and AMPK1/mTOR. Skin biopsies showed a significant reduction of IRF4 and mTOR in post-treatment samples by immunofluorescence. In vitro experiments confirmed the effect of thalidomide downregulating IRF4 in PBMCs and mTOR in keratinocytes, which converged in an NF-ҡB reduction that led to a resolution of the inflammatory lesion. These results emphasize the anti-inflammatory role of thalidomide in CLE treatment, providing novel molecular targets for the development of new therapies that could avoid thalidomide’s side effects while maintaining its efficacy.
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Affiliation(s)
- Sandra Domingo
- Lupus Unit, Rheumatology Departament, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autonoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
| | - Cristina Solé
- Lupus Unit, Rheumatology Departament, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autonoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
- Correspondence: ; Tel.: +34-93-489-4045
| | - Teresa Moliné
- Department of Pathology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (T.M.); (B.F.)
| | - Berta Ferrer
- Department of Pathology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (T.M.); (B.F.)
| | - Josefina Cortés-Hernández
- Lupus Unit, Rheumatology Departament, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autonoma de Barcelona, 08035 Barcelona, Spain; (S.D.); (J.C.-H.)
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21
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Gutiérrez-Casares JR, Quintero J, Jorba G, Junet V, Martínez V, Pozo-Rubio T, Oliva B, Daura X, Mas JM, Montoto C. Methods to Develop an in silico Clinical Trial: Computational Head-to-Head Comparison of Lisdexamfetamine and Methylphenidate. Front Psychiatry 2021; 12:741170. [PMID: 34803764 PMCID: PMC8595241 DOI: 10.3389/fpsyt.2021.741170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Regulatory agencies encourage computer modeling and simulation to reduce the time and cost of clinical trials. Although still not classified in formal guidelines, system biology-based models represent a powerful tool for generating hypotheses with great molecular detail. Herein, we have applied a mechanistic head-to-head in silico clinical trial (ISCT) between two treatments for attention-deficit/hyperactivity disorder, to wit lisdexamfetamine (LDX) and methylphenidate (MPH). The ISCT was generated through three phases comprising (i) the molecular characterization of drugs and pathologies, (ii) the generation of adult and children virtual populations (vPOPs) totaling 2,600 individuals and the creation of physiologically based pharmacokinetic (PBPK) and quantitative systems pharmacology (QSP) models, and (iii) data analysis with artificial intelligence methods. The characteristics of our vPOPs were in close agreement with real reference populations extracted from clinical trials, as did our PBPK models with in vivo parameters. The mechanisms of action of LDX and MPH were obtained from QSP models combining PBPK modeling of dosing schemes and systems biology-based modeling technology, i.e., therapeutic performance mapping system. The step-by-step process described here to undertake a head-to-head ISCT would allow obtaining mechanistic conclusions that could be extrapolated or used for predictions to a certain extent at the clinical level. Altogether, these computational techniques are proven an excellent tool for hypothesis-generation and would help reach a personalized medicine.
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Affiliation(s)
- José Ramón Gutiérrez-Casares
- Unidad Ambulatoria de Psiquiatría y Salud Mental de la Infancia, Niñez y Adolescencia, Hospital Perpetuo Socorro, Badajoz, Spain
| | - Javier Quintero
- Servicio de Psiquiatría, Hospital Universitario Infanta Leonor, Universidad Complutense, Madrid, Spain
| | - Guillem Jorba
- Anaxomics Biotech, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Valentin Junet
- Anaxomics Biotech, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | | | - Baldomero Oliva
- Research Programme on Biomedical Informatics (GRIB), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | | | - Carmen Montoto
- Medical Department, Takeda Farmacéutica España, Madrid, Spain
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22
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Prasad K, Kumar V. Artificial intelligence-driven drug repurposing and structural biology for SARS-CoV-2. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100042. [PMID: 34870150 PMCID: PMC8317454 DOI: 10.1016/j.crphar.2021.100042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
It has been said that COVID-19 is a generational challenge in many ways. But, at the same time, it becomes a catalyst for collective action, innovation, and discovery. Realizing the full potential of artificial intelligence (AI) for structure determination of unknown proteins and drug discovery are some of these innovations. Potential applications of AI include predicting the structure of the infectious proteins, identifying drugs that may be effective in targeting these proteins, and proposing new chemical compounds for further testing as potential drugs. AI and machine learning (ML) allow for rapid drug development including repurposing existing drugs. Algorithms were used to search for novel or approved antiviral drugs capable of inhibiting SARS-CoV-2. This paper presents a survey of AI and ML methods being used in various biochemistry of SARS-CoV-2, from structure to drug development, in the fight against the deadly COVID-19 pandemic. It is envisioned that this study will provide AI/ML researchers and the wider community an overview of the current status of AI applications particularly in structural biology, drug repurposing, and development, and motivate researchers in harnessing AI potentials in the fight against COVID-19.
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Affiliation(s)
- Kartikay Prasad
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP, 201303, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP, 201303, India
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23
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Lozano ML, Segú-Vergés C, Coma M, Álvarez-Roman MT, González-Porras JR, Gutiérrez L, Valcárcel D, Butta N. Elucidating the Mechanism of Action of the Attributed Immunomodulatory Role of Eltrombopag in Primary Immune Thrombocytopenia: An In Silico Approach. Int J Mol Sci 2021; 22:ijms22136907. [PMID: 34199099 PMCID: PMC8269123 DOI: 10.3390/ijms22136907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
Eltrombopag is a thrombopoietin receptor (MPL) agonist approved for the treatment of primary immune thrombocytopenia (ITP). Recent evidence shows that some patients may sustain platelet counts following eltrombopag discontinuation. The systemic immunomodulatory response that resolves ITP in some patients could result from an increase in platelet mass, caused either by the direct action of eltrombopag on megakaryocytes through MPL stimulation, or potential MPL-independent actions on other cell types. To uncover the possible mechanisms of action of eltrombopag, in silico analyses were performed, including a systems biology-based approach, a therapeutic performance mapping system, and structural analyses. Through manual curation of the available bibliography, 56 key proteins were identified and integrated into the ITP interactome analysis. Mathematical models (94.92% mean accuracy) were obtained to elucidate potential MPL-dependent pathways in non-megakaryocytic cell subtypes. In addition to the effects on megakaryocytes and platelet numbers, the results were consistent with MPL-mediated effects on other cells, which could involve interferon-gamma, transforming growth factor-beta, peroxisome proliferator-activated receptor-gamma, and forkhead box protein P3 pathways. Structural analyses indicated that effects on three apoptosis-related proteins (BCL2L1, BCL2, BAX) from the Bcl-2 family may be off-target effects of eltrombopag. In conclusion, this study proposes new hypotheses regarding the immunomodulatory functions of eltrombopag in patients with ITP.
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MESH Headings
- Benzoates/chemistry
- Benzoates/pharmacology
- Benzoates/therapeutic use
- Biomarkers
- Disease Management
- Disease Susceptibility
- Humans
- Hydrazines/chemistry
- Hydrazines/pharmacology
- Hydrazines/therapeutic use
- Immunomodulation/drug effects
- Models, Biological
- Models, Molecular
- Molecular Targeted Therapy/methods
- Protein Interaction Mapping
- Protein Interaction Maps
- Purpura, Thrombocytopenic, Idiopathic/drug therapy
- Purpura, Thrombocytopenic, Idiopathic/etiology
- Purpura, Thrombocytopenic, Idiopathic/metabolism
- Pyrazoles/chemistry
- Pyrazoles/pharmacology
- Pyrazoles/therapeutic use
- Receptors, Thrombopoietin/antagonists & inhibitors
- Receptors, Thrombopoietin/chemistry
- Receptors, Thrombopoietin/metabolism
- Signal Transduction/drug effects
- Structure-Activity Relationship
- T-Lymphocytes/drug effects
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Treatment Outcome
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Affiliation(s)
- Maria L. Lozano
- Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, 30007 Murcia, Spain
- Correspondence: (M.L.L.); (N.B.)
| | - Cristina Segú-Vergés
- Anaxomics Biotech S.L., Diputació 237, 1°, 1, 08007 Barcelona, Spain; (C.S.-V.); (M.C.)
| | - Mireia Coma
- Anaxomics Biotech S.L., Diputació 237, 1°, 1, 08007 Barcelona, Spain; (C.S.-V.); (M.C.)
| | - María T. Álvarez-Roman
- Unidad de Trombosis y Hemostasia, Servicio de Hematología, Hospital Universitario La Paz, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Paseo de la Castellana 261, 28046 Madrid, Spain;
| | - José R. González-Porras
- Unidad de Hemostasia y Trombosis, Servicio de Hematología, Hospital Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), Paseo de San Vicente, 58-182, 37007 Salamanca, Spain;
| | - Laura Gutiérrez
- Grupo de Investigación en Plaquetas, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Departamento de Medicina, Universidad de Oviedo, 33071 Oviedo, Spain;
| | - David Valcárcel
- Servicio Hematología, Vall d´Hebron Insitute of Oncology (VHIO), Hospital Univesitario Vall d’Hebron, Universitat Autònoma de Barcelona, Centro Cellex, Natzaret, 115-117, 08035 Barcelona, Spain;
| | - Nora Butta
- Instituto de Investigación HospitaUniversitario La Paz (IdiPAZ), Paseo de la Castellana 261, 28046 Madrid, Spain
- Correspondence: (M.L.L.); (N.B.)
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24
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Matorras R, Valls R, Azkargorta M, Burgos J, Rabanal A, Elortza F, Mas JM, Sardon T. Proteomics based drug repositioning applied to improve in vitro fertilization implantation: an artificial intelligence model. Syst Biol Reprod Med 2021; 67:281-297. [PMID: 34126818 DOI: 10.1080/19396368.2021.1928792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Embryo implantation is one of the most inefficient steps in assisted reproduction, so the identifying drugs with a potential clinical application to improve it has a strong interest. This work applies artificial intelligence and systems biology-based mathematical modeling strategies to unveil potential treatments by computationally analyzing and integrating available molecular and clinical data from patients. The mathematical models of embryo implantation computationally generated here simulate the molecular networks underneath this biological process. Once generated, these models were analyzed in order to identify potential repositioned drugs (drugs already used for other indications) able to improve embryo implantation by modulating the molecular pathways involved. Interestingly, the repositioning analysis has identified drugs considering two endpoints: (1) drugs able to modulate the activity of proteins whose role in embryo implantation is already bibliographically acknowledged, and (2) drugs that modulate key proteins in embryo implantation previously predicted through a mechanistic analysis of the mathematical models. This second approach increases the scope open for examination and potential novelty of the repositioning strategy. As a result, a list of 23 drug candidates to improve embryo implantation after IVF was identified by the mathematical models. This list includes many of the compounds already tested for this purpose, which reinforces the predictive capacity of our approach, together with novel repositioned candidates (e.g., Infliximab, Polaprezinc, and Amrinone). In conclusion, the present study exploits existing molecular and clinical information to offer new hypotheses regarding molecular mechanisms in embryo implantation and therapeutic candidates to improve it. This information will be very useful to guide future research.Abbreviations: IVF: in vitro fertilization; EI: Embryo implantation; TPMS: Therapeutic Performance Mapping System; MM: mathematical models; ANN: Artificial Neuronal Networks; TNFα: tumour necrosis factor factor-alpha; HSPs: heat shock proteins; VEGF: vascular endothelial growth factor; PPARA: peroxisome proliferator activated receptor-α PXR: pregnane X receptor; TTR: transthyretin; BED: Biological Effectors Database; MLP: multilayer perceptron.
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Affiliation(s)
- Roberto Matorras
- Department of Obstetrics and Gynecology, University of the Basque Country, Bilbao, Spain.,IVIRMA Bilbao, Bilbao, Spain
| | | | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Jorge Burgos
- Biocruces Bizkaia Health Research Institute. Osakidetza. Cruces University Hospital, University of the Basque Country, Bilbao, Spain
| | - Aintzane Rabanal
- Department of Obstetrics and Gynecology, University of the Basque Country, Bilbao, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
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25
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Segú-Vergés C, Coma M, Kessel C, Smeets S, Foell D, Aldea A. Application of systems biology-based in silico tools to optimize treatment strategy identification in Still's disease. Arthritis Res Ther 2021; 23:126. [PMID: 33892792 PMCID: PMC8063416 DOI: 10.1186/s13075-021-02507-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 04/07/2021] [Indexed: 01/06/2023] Open
Abstract
Background Systemic juvenile idiopathic arthritis (sJIA) and adult-onset Still’s disease (AOSD) are manifestations of an autoinflammatory disorder with complex pathophysiology and significant morbidity, together also termed Still’s disease. The objective of the current study is to set in silico models based on systems biology and investigate the optimal treat-to-target strategy for Still’s disease as a proof-of-concept of the modeling approach. Methods Molecular characteristics of Still’s disease and data on biological inhibitors of interleukin (IL)-1 (anakinra, canakinumab), IL-6 (tocilizumab, sarilumab), and glucocorticoids as well as conventional disease-modifying anti-rheumatic drugs (DMARDs, methotrexate) were used to construct in silico mechanisms of action (MoA) models by means of Therapeutic Performance Mapping System (TPMS) technology. TPMS combines artificial neuronal networks, sampling-based methods, and artificial intelligence. Model outcomes were validated with published expression data from sJIA patients. Results Biologicals demonstrated more pathophysiology-directed efficiency than non-biological drugs. IL-1 blockade mainly acts on proteins implicated in the innate immune system, while IL-6 signaling blockade has a weaker effect on innate immunity and rather affects adaptive immune mechanisms. The MoA models showed that in the autoinflammatory/systemic phases of Still’s disease, in which the innate immunity plays a pivotal role, the IL-1β-neutralizing antibody canakinumab is more efficient than the IL-6 receptor-inhibiting antibody tocilizumab. MoA models reproduced 67% of the information obtained from expression data. Conclusions Systems biology-based modeling supported the preferred use of biologics as an immunomodulatory treatment strategy for Still’s disease. Our results reinforce the role for IL-1 blockade on innate immunity regulation, which is critical in systemic autoinflammatory diseases. This further encourages early use on Still’s disease IL-1 blockade to prevent the development of disease or drug-related complications. Further analysis at the clinical level will validate the findings and help determining the timeframe of the window of opportunity for canakinumab treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-021-02507-w.
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Affiliation(s)
- Cristina Segú-Vergés
- Anaxomics Biotech, Carrer Diputació 237, 1°, 1ª, 08007, Barcelona, Catalonia, Spain
| | - Mireia Coma
- Anaxomics Biotech, Carrer Diputació 237, 1°, 1ª, 08007, Barcelona, Catalonia, Spain
| | - Christoph Kessel
- Department of Pediatric Rheumatology & Immunology, University Children's Hospital, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Serge Smeets
- Novartis, Haaksbergweg, 1101 BX, Amsterdam, The Netherlands
| | - Dirk Foell
- Department of Pediatric Rheumatology & Immunology, University Children's Hospital, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Anna Aldea
- Novartis, Gran Via de les Corts Catalanes, 764, 08013, Barcelona, Catalonia, Spain.
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26
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Carcereny E, Fernández-Nistal A, López A, Montoto C, Naves A, Segú-Vergés C, Coma M, Jorba G, Oliva B, Mas JM. Head to head evaluation of second generation ALK inhibitors brigatinib and alectinib as first-line treatment for ALK+ NSCLC using an in silico systems biology-based approach. Oncotarget 2021; 12:316-332. [PMID: 33659043 PMCID: PMC7899557 DOI: 10.18632/oncotarget.27875] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
Around 3-7% of patients with non-small cell lung cancer (NSCLC), which represent 85% of diagnosed lung cancers, have a rearrangement in the ALK gene that produces an abnormal activity of the ALK protein cell signaling pathway. The developed ALK tyrosine kinase inhibitors (TKIs), such as crizotinib, ceritinib, alectinib, brigatinib and lorlatinb present good performance treating ALK+ NSCLC, although all patients invariably develop resistance due to ALK secondary mutations or bypass mechanisms. In the present study, we compare the potential differences between brigatinib and alectinib's mechanisms of action as first-line treatment for ALK+ NSCLC in a systems biology-based in silico setting. Therapeutic performance mapping system (TPMS) technology was used to characterize the mechanisms of action of brigatinib and alectinib and the impact of potential resistances and drug interferences with concomitant treatments. The analyses indicate that brigatinib and alectinib affect cell growth, apoptosis and immune evasion through ALK inhibition. However, brigatinib seems to achieve a more diverse downstream effect due to a broader cancer-related kinase target spectrum. Brigatinib also shows a robust effect over invasiveness and central nervous system metastasis-related mechanisms, whereas alectinib seems to have a greater impact on the immune evasion mechanism. Based on this in silico head to head study, we conclude that brigatinib shows a predicted efficacy similar to alectinib and could be a good candidate in a first-line setting against ALK+ NSCLC. Future investigation involving clinical studies will be needed to confirm these findings. These in silico systems biology-based models could be applied for exploring other unanswered questions.
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Affiliation(s)
- Enric Carcereny
- Catalan Institute of Oncology B-ARGO Group, Hospital Germans Trias i Pujol, Badalona, Spain
| | | | | | | | | | | | | | - Guillem Jorba
- Anaxomics Biotech, Barcelona, Spain
- Structural Bioinformatics (GRIB-IMIM), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Baldomero Oliva
- Structural Bioinformatics (GRIB-IMIM), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
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27
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Neurohumoral, cardiac and inflammatory markers in the evaluation of heart failure severity and progression. JOURNAL OF GERIATRIC CARDIOLOGY : JGC 2021; 18:47-66. [PMID: 33613659 PMCID: PMC7868913 DOI: 10.11909/j.issn.1671-5411.2021.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Heart failure is common in adult population, accounting for substantial morbidity and mortality worldwide. The main risk factors for heart failure are coronary artery disease, hypertension, obesity, diabetes mellitus, chronic pulmonary diseases, family history of cardiovascular diseases, cardiotoxic therapy. The main factor associated with poor outcome of these patients is constant progression of heart failure. In the current review we present evidence on the role of established and candidate neurohumoral biomarkers for heart failure progression management and diagnostics. A growing number of biomarkers have been proposed as potentially useful in heart failure patients, but not one of them still resembles the characteristics of the “ideal biomarker.” A single marker will hardly perform well for screening, diagnostic, prognostic, and therapeutic management purposes. Moreover, the pathophysiological and clinical significance of biomarkers may depend on the presentation, stage, and severity of the disease. The authors cover main classification of heart failure phenotypes, based on the measurement of left ventricular ejection fraction, including heart failure with preserved ejection fraction, heart failure with reduced ejection fraction, and the recently proposed category heart failure with mid-range ejection fraction. One could envisage specific sets of biomarker with different performances in heart failure progression with different left ventricular ejection fraction especially as concerns prediction of the future course of the disease and of left ventricular adverse/reverse remodeling. This article is intended to provide an overview of basic and additional mechanisms of heart failure progression will contribute to a more comprehensive knowledge of the disease pathogenesis.
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28
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Gimenez N, Tripathi R, Giró A, Rosich L, López-Guerra M, López-Oreja I, Playa-Albinyana H, Arenas F, Mas JM, Pérez-Galán P, Delgado J, Campo E, Farrés J, Colomer D. Systems biology drug screening identifies statins as enhancers of current therapies in chronic lymphocytic leukemia. Sci Rep 2020; 10:22153. [PMID: 33335123 PMCID: PMC7746765 DOI: 10.1038/s41598-020-78315-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a B lymphoid malignancy highly dependent on the microenvironment. Despite new targeted therapies such as ibrutinib and venetoclax, disease progression and relapse remain an issue. CLL cell interactions with the supportive tissue microenvironment play a critical role in disease pathogenesis. We used a platform for drug discovery based on systems biology and artificial intelligence, to identify drugs targeting key proteins described to have a role in the microenvironment. The selected compounds were screened in CLL cell lines in the presence of stromal cells to mimic the microenvironment and validated the best candidates in primary CLL cells. Our results showed that the commercial drug simvastatin was the most effective and selective out of the tested compounds. Simvastatin decreased CLL cell survival and proliferation as well as cell adhesion. Importantly, this drug enhanced the antitumor effect of venetoclax and ibrutinib. We proposed that systems biology approaches combined with pharmacological screening could help to find new drugs for CLL treatment and to predict new combinations with current therapies. Our results highlight the possibility of repurposing widely used drugs such as statins to target the microenvironment and to improve the efficacy of ibrutinib or venetoclax in CLL cells.
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Affiliation(s)
- Neus Gimenez
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Anaxomics Biotech, Barcelona, Spain
| | - Rupal Tripathi
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ariadna Giró
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Laia Rosich
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Mònica López-Guerra
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Irene López-Oreja
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Heribert Playa-Albinyana
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Fabian Arenas
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | | | - Patricia Pérez-Galán
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Microenvironment in Lymphoma Pathogenesis and Therapy Group, IDIBAPS, Barcelona, Spain
| | - Julio Delgado
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Department of Hematology, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Elias Campo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clinic, IDIBAPS, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | | | - Dolors Colomer
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain. .,Hematopathology Unit, Department of Pathology, Hospital Clinic, IDIBAPS, Barcelona, Spain. .,University of Barcelona, Barcelona, Spain.
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29
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Artigas L, Coma M, Matos-Filipe P, Aguirre-Plans J, Farrés J, Valls R, Fernandez-Fuentes N, de la Haba-Rodriguez J, Olvera A, Barbera J, Morales R, Oliva B, Mas JM. In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm. PLoS One 2020; 15:e0240149. [PMID: 33006999 PMCID: PMC7531795 DOI: 10.1371/journal.pone.0240149] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023] Open
Abstract
From January 2020, COVID-19 is spreading around the world producing serious respiratory symptoms in infected patients that in some cases can be complicated by the severe acute respiratory syndrome, sepsis and septic shock, multiorgan failure, including acute kidney injury and cardiac injury. Cost and time efficient approaches to reduce the burthen of the disease are needed. To find potential COVID-19 treatments among the whole arsenal of existing drugs, we combined system biology and artificial intelligence-based approaches. The drug combination of pirfenidone and melatonin has been identified as a candidate treatment that may contribute to reduce the virus infection. Starting from different drug targets the effect of the drugs converges on human proteins with a known role in SARS-CoV-2 infection cycle. Simultaneously, GUILDify v2.0 web server has been used as an alternative method to corroborate the effect of pirfenidone and melatonin against the infection of SARS-CoV-2. We have also predicted a potential therapeutic effect of the drug combination over the respiratory associated pathology, thus tackling at the same time two important issues in COVID-19. These evidences, together with the fact that from a medical point of view both drugs are considered safe and can be combined with the current standard of care treatments for COVID-19 makes this combination very attractive for treating patients at stage II, non-severe symptomatic patients with the presence of virus and those patients who are at risk of developing severe pulmonary complications.
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Affiliation(s)
| | | | - Pedro Matos-Filipe
- Anaxomics Biotech, Barcelona, Spain
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Science, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Joaquim Aguirre-Plans
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Science, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | | | | | - Narcis Fernandez-Fuentes
- Department of Biosciences, U Science Tech, Universitat de Vic—Universitat Central de Catalunya, Vic, Catalonia, Spain
| | - Juan de la Haba-Rodriguez
- Maimonides Biomedical Research Institute, Reina Sofia Hospital, University of Cordoba, Cordoba, Spain
| | - Alex Olvera
- Institut de Recerca de la Sida—IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona (Barcelona), Spain
| | - Jose Barbera
- Servicio de Medicina interna—Unidad de Infecciosas, La Mancha—Centro Hospital, Alcázar de San Juan, Spain
| | - Rafael Morales
- Servicio de Medicina interna—Unidad de Infecciosas, La Mancha—Centro Hospital, Alcázar de San Juan, Spain
| | - Baldo Oliva
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Science, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
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30
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Gallizioli M, Miró-Mur F, Otxoa-de-Amezaga A, Cugota R, Salas-Perdomo A, Justicia C, Brait VH, Ruiz-Jaén F, Arbaizar-Rovirosa M, Pedragosa J, Bonfill-Teixidor E, Gelderblom M, Magnus T, Cano E, Del Fresno C, Sancho D, Planas AM. Dendritic Cells and Microglia Have Non-redundant Functions in the Inflamed Brain with Protective Effects of Type 1 cDCs. Cell Rep 2020; 33:108291. [PMID: 33086061 PMCID: PMC7578563 DOI: 10.1016/j.celrep.2020.108291] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/02/2020] [Accepted: 09/29/2020] [Indexed: 01/14/2023] Open
Abstract
Brain CD11c+ cells share features with microglia and dendritic cells (DCs). Sterile inflammation increases brain CD11c+ cells, but their phenotype, origin, and functions remain largely unknown. We report that, after cerebral ischemia, microglia attract DCs to the inflamed brain, and astroglia produce Flt3 ligand, supporting development and expansion of CD11c+ cells. CD11c+ cells in the inflamed brain are a complex population derived from proliferating microglia and infiltrating DCs, including a major subset of OX40L+ conventional cDC2, and also cDC1, plasmacytoid, and monocyte-derived DCs. Despite sharing certain morphological features and markers, CD11c+ microglia and DCs display differential expression of pattern recognition receptors and chemokine receptors. DCs excel CD11c- and CD11c+ microglia in the capacity to present antigen through MHCI and MHCII. Of note, cDC1s protect from brain injury after ischemia. We thus reveal aspects of the dynamics and functions of brain DCs in the regulation of inflammation and immunity.
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Affiliation(s)
- Mattia Gallizioli
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain; Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Francesc Miró-Mur
- Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain; Fundació Clínic, Barcelona 08036, Spain
| | - Amaia Otxoa-de-Amezaga
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain; Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Roger Cugota
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain
| | - Angélica Salas-Perdomo
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain; Fundació Clínic, Barcelona 08036, Spain
| | - Carles Justicia
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain; Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Vanessa H Brait
- Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Francisca Ruiz-Jaén
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain; Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Maria Arbaizar-Rovirosa
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain; Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Jordi Pedragosa
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain; Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Ester Bonfill-Teixidor
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain
| | - Mathias Gelderblom
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Tim Magnus
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Eva Cano
- Neuroinflammation Unit, Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III, Majadahonda, Madrid 28222, Spain
| | - Carlos Del Fresno
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - David Sancho
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Anna M Planas
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08036, Spain; Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain.
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31
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Moncunill G, Scholzen A, Mpina M, Nhabomba A, Hounkpatin AB, Osaba L, Valls R, Campo JJ, Sanz H, Jairoce C, Williams NA, Pasini EM, Arteta D, Maynou J, Palacios L, Duran-Frigola M, Aponte JJ, Kocken CHM, Agnandji ST, Mas JM, Mordmüller B, Daubenberger C, Sauerwein R, Dobaño C. Antigen-stimulated PBMC transcriptional protective signatures for malaria immunization. Sci Transl Med 2020; 12:12/543/eaay8924. [DOI: 10.1126/scitranslmed.aay8924] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/26/2019] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
Identifying immune correlates of protection and mechanisms of immunity accelerates and streamlines the development of vaccines. RTS,S/AS01E, the most clinically advanced malaria vaccine, has moderate efficacy in African children. In contrast, immunization with sporozoites under antimalarial chemoprophylaxis (CPS immunization) can provide 100% sterile protection in naïve adults. We used systems biology approaches to identifying correlates of vaccine-induced immunity based on transcriptomes of peripheral blood mononuclear cells from individuals immunized with RTS,S/AS01E or chemoattenuated sporozoites stimulated with parasite antigens in vitro. Specifically, we used samples of individuals from two age cohorts and three African countries participating in an RTS,S/AS01E pediatric phase 3 trial and malaria-naïve individuals participating in a CPS trial. We identified both preimmunization and postimmunization transcriptomic signatures correlating with protection. Signatures were validated in independent children and infants from the RTS,S/AS01E phase 3 trial and individuals from an independent CPS trial with high accuracies (>70%). Transcription modules revealed interferon, NF-κB, Toll-like receptor (TLR), and monocyte-related signatures associated with protection. Preimmunization signatures suggest that priming the immune system before vaccination could potentially improve vaccine immunogenicity and efficacy. Last, signatures of protection could be useful to determine efficacy in clinical trials, accelerating vaccine candidate testing. Nevertheless, signatures should be tested more extensively across multiple cohorts and trials to demonstrate their universal predictive capacity.
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Affiliation(s)
- Gemma Moncunill
- ISGlobal, Hospital Clínic–Universitat de Barcelona, E-08036 Barcelona, Catalonia, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Rua 12, Cambeve, Vila de Manhiça, CP 1929 Maputo, Mozambique
| | - Anja Scholzen
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, Netherlands
| | - Maximillian Mpina
- Ifakara Health Institute, Bagamoyo Research and Training Centre. P.O. Box 74, Bagamoyo, Tanzania
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Augusto Nhabomba
- Centro de Investigação em Saúde de Manhiça (CISM), Rua 12, Cambeve, Vila de Manhiça, CP 1929 Maputo, Mozambique
| | - Aurore Bouyoukou Hounkpatin
- Centre de Recherches Médicales de Lambaréné (CERMEL), BP 242 Lambaréné, Gabon
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Wilhelmstraße 27, D-72074 Tübingen, Germany
| | - Lourdes Osaba
- Progenika Biopharma. A Grifols Company, S.A., 48160 Derio, Vizcaya, Spain
| | | | - Joseph J. Campo
- ISGlobal, Hospital Clínic–Universitat de Barcelona, E-08036 Barcelona, Catalonia, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Rua 12, Cambeve, Vila de Manhiça, CP 1929 Maputo, Mozambique
| | - Hèctor Sanz
- ISGlobal, Hospital Clínic–Universitat de Barcelona, E-08036 Barcelona, Catalonia, Spain
| | - Chenjerai Jairoce
- Centro de Investigação em Saúde de Manhiça (CISM), Rua 12, Cambeve, Vila de Manhiça, CP 1929 Maputo, Mozambique
| | - Nana Aba Williams
- ISGlobal, Hospital Clínic–Universitat de Barcelona, E-08036 Barcelona, Catalonia, Spain
| | - Erica M. Pasini
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - David Arteta
- Progenika Biopharma. A Grifols Company, S.A., 48160 Derio, Vizcaya, Spain
| | - Joan Maynou
- Progenika Biopharma. A Grifols Company, S.A., 48160 Derio, Vizcaya, Spain
| | - Lourdes Palacios
- Progenika Biopharma. A Grifols Company, S.A., 48160 Derio, Vizcaya, Spain
| | - Miquel Duran-Frigola
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain
| | - John J. Aponte
- ISGlobal, Hospital Clínic–Universitat de Barcelona, E-08036 Barcelona, Catalonia, Spain
| | - Clemens H. M. Kocken
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Selidji Todagbe Agnandji
- Centre de Recherches Médicales de Lambaréné (CERMEL), BP 242 Lambaréné, Gabon
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Wilhelmstraße 27, D-72074 Tübingen, Germany
| | | | - Benjamin Mordmüller
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Wilhelmstraße 27, D-72074 Tübingen, Germany
| | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Robert Sauerwein
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, Netherlands
| | - Carlota Dobaño
- ISGlobal, Hospital Clínic–Universitat de Barcelona, E-08036 Barcelona, Catalonia, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Rua 12, Cambeve, Vila de Manhiça, CP 1929 Maputo, Mozambique
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32
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Villalba A, Rodriguez-Fernandez S, Perna-Barrull D, Ampudia RM, Gomez-Muñoz L, Pujol-Autonell I, Aguilera E, Coma M, Cano-Sarabia M, Vázquez F, Verdaguer J, Vives-Pi M. Repurposed Analog of GLP-1 Ameliorates Hyperglycemia in Type 1 Diabetic Mice Through Pancreatic Cell Reprogramming. Front Endocrinol (Lausanne) 2020; 11:258. [PMID: 32477262 PMCID: PMC7237704 DOI: 10.3389/fendo.2020.00258] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022] Open
Abstract
Type 1 diabetes is an autoimmune disease caused by the destruction of the insulin-producing β-cells. An ideal immunotherapy should combine the blockade of the autoimmune response with the recovery of functional target cell mass. With the aim to develop new therapies for type 1 diabetes that could contribute to β-cell mass restoration, a drug repositioning analysis based on systems biology was performed to identify the β-cell regenerative potential of commercially available compounds. Drug repositioning is a strategy used for identifying new uses for approved drugs that are outside the scope of the medical indication. A list of 28 non-synonymous repurposed drug candidates was obtained, and 16 were selected as diabetes mellitus type 1 treatment candidates regarding pancreatic β-cell regeneration. Drugs with poor safety profile were further filtered out. Lastly, we selected liraglutide for its predictive efficacy values for neogenesis, transdifferentiation of α-cells, and/or replication of pre-existing β-cells. Liraglutide is an analog of glucagon-like peptide-1, a drug used in patients with type 2 diabetes. Liraglutide was tested in immunodeficient NOD-Scid IL2rg-/- (NSG) mice with type 1 diabetes. Liraglutide significantly improved the blood glucose levels in diabetic NSG mice. During the treatment, a significant increase in β-cell mass was observed due to a boost in β-cell number. Both parameters were reduced after withdrawal. Interestingly, islet bihormonal glucagon+insulin+ cells and insulin+ ductal cells arose during treatment. In vitro experiments showed an increase of insulin and glucagon gene expression in islets cultured with liraglutide in normoglycemia conditions. These results point to β-cell replacement, including transdifferentiation and neogenesis, as aiding factors and support the role of liraglutide in β-cell mass restoration in type 1 diabetes. Understanding the mechanism of action of this drug could have potential clinical relevance in this autoimmune disease.
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Affiliation(s)
- Adrian Villalba
- Immunology Section, Germans Trias i Pujol Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Silvia Rodriguez-Fernandez
- Immunology Section, Germans Trias i Pujol Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - David Perna-Barrull
- Immunology Section, Germans Trias i Pujol Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Rosa-Maria Ampudia
- Immunology Section, Germans Trias i Pujol Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Laia Gomez-Muñoz
- Immunology Section, Germans Trias i Pujol Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Irma Pujol-Autonell
- Immunology Section, Germans Trias i Pujol Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Eva Aguilera
- Endocrinology Section, Germans Trias i Pujol Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | | | - Mary Cano-Sarabia
- Catalan Institute of Nanoscience and Nanotechnology, CSIC and The Barcelona Institute of Science and Technology, Bellaterra, Spain
| | - Federico Vázquez
- Endocrinology Section, Germans Trias i Pujol Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Joan Verdaguer
- Immunology Unit, Department of Experimental Medicine, Faculty of Medicine, IRBLleida, University of Lleida, Lleida, Spain
- CIBER of Diabetes and Associated Metabolic Disease (CIBERDEM), ISCIII, Madrid, Spain
| | - Marta Vives-Pi
- Immunology Section, Germans Trias i Pujol Research Institute, Autonomous University of Barcelona, Badalona, Spain
- CIBER of Diabetes and Associated Metabolic Disease (CIBERDEM), ISCIII, Madrid, Spain
- *Correspondence: Marta Vives-Pi
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