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1
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Mangelinck A, Molitor E, Marchiq I, Alaoui L, Bouaziz M, Andrade-Pereira R, Darville H, Becht E, Lefebvre C. The combined use of scRNA-seq and network propagation highlights key features of pan-cancer Tumor-Infiltrating T cells. PLoS One 2024; 19:e0315980. [PMID: 39729479 DOI: 10.1371/journal.pone.0315980] [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: 06/17/2024] [Accepted: 12/03/2024] [Indexed: 12/29/2024] Open
Abstract
Improving the selectivity and effectiveness of drugs represents a crucial issue for future therapeutic developments in immuno-oncology. Traditional bulk transcriptomics faces limitations in this context for the early phase of target discovery as resulting gene expression levels represent the average measure from multiple cell populations. Alternatively, single cell RNA sequencing can dive into unique cell populations transcriptome, facilitating the identification of specific targets. Here, we generated Tumor-Infiltrating regulatory T cells (TI-Tregs) and exhausted T cells (Tex) gene signatures from a single cell RNA-seq pan-cancer T cell atlas. To overcome noise and sparsity inherent to single cell transcriptomics, we then propagated the gene signatures by diffusion in a protein-protein interaction network using the Patrimony high-throughput computing platform. This methodology enabled the refining of signatures by rescoring genes based on their biological connectivity and shed light not only on processes characteristics of TI-Treg and Tex development and functions but also on their immunometabolic specificities. The combined use of single cell transcriptomics and network propagation may thus represent an innovative and effective methodology for the characterization of cell populations of interest and eventually the development of new therapeutic strategies in immuno-oncology.
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Affiliation(s)
| | - Elodie Molitor
- Lincoln, Research & Development, Boulogne-Billancourt, France
| | | | - Lamine Alaoui
- Servier, Research & Development, Gif-sur-Yvette, France
| | | | | | | | - Etienne Becht
- Servier, Research & Development, Gif-sur-Yvette, France
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2
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Moingeon P. Harnessing the power of AI-based models to accelerate drug discovery against immune diseases. Expert Rev Clin Immunol 2024; 20:1135-1138. [PMID: 38932714 DOI: 10.1080/1744666x.2024.2373915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Affiliation(s)
- Philippe Moingeon
- Servier Research Institute, Paris-Saclay University, Gif-sur-Yvette, France
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3
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Nery GB, de Araujo CAR, da Silva GB, Bittar H, Bordallo VP, Amaral JB, Hardt M, Marti L, Birbrair A, Jimenez M, Bastos MF, Nali LHS, Longo PL, Laurentino GC, Bachi ALL, Heller D. Impact of social distancing from the COVID-19 pandemic on the immuno-inflammatory response of older adults. BMC Geriatr 2024; 24:99. [PMID: 38273281 PMCID: PMC10811891 DOI: 10.1186/s12877-024-04699-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Older adults, as the population considered at increased risk for severe COVID-19, were the most impacted by social isolation. Thus, this study aimed to assess the salivary immune/inflammatory response of older adults before and during the COVID-19 pandemic. METHODS A cohort of 11 older adults (mean age 66.8 ± 6.1) was followed at three different time points: before (S1) and after 6 (S2) and 20 months (S3) of the beginning of the COVID-19 pandemic in Brazil. Unstimulated saliva samples were obtained to assess the levels of antibodies (secretory IgA, IgG and IgM) by ELISA and cytokines (IL-2, IL-5, IL-6, IL-8 and IL-10, TSLP, IFN-γ, TNF-α) by multiplex analysis. Significant differences were evaluated using the Kruskal-Wallis test with Dunn's post-test. RESULTS None volunteer presented periodontal disease or caries. All volunteers received at least two doses of the COVID-19 vaccines after S2 and before S3. A tendency to increase salivary levels of SIgA and IgM at S2 and of IgG at S3 were observed compared to the values found at S1 and S2. Significantly decreased levels of IL-2 and IL-5 were found at S2 and S3 (p < 0.001) time points. Lower levels of IFN-γ were found at S2 as compared to the values observed at S1 (p < 0.01). A significant decrease in the IFN-γ/IL-10 ratio was found at S2 (p < 0.01). When assessing the Th1/Th2 ratios, a significant decrease was found in the IFN-γ/TSLP ratio at S2 (p < 0.001) and S3 (p < 0.001) when compared to the values at S1. In addition, a significant increase was observed in the TNF-α/IL-5 ratio at S2 (p < 0.001) and S3 (p < 0.001) in comparison to the values at S1. In a similar way, an increase in the TNF-α/IL-6 ratio (Fig. 5E) was observed at S3 (p < 0.001) when compared to the values at S1. CONCLUSIONS Overall, this study provides valuable insights into the impact of COVID-19-induced social isolation on immune/inflammatory responses in the upper airway mucosa, particularly those present in oral cavity, of older adults. It demonstrates that a controlled shift in Th1 and Th2 immune responses, both during infection and post-vaccination, can create favorable conditions to combat viral infections without exacerbating the immune response or worsening the pathology.
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Affiliation(s)
- Giulia Beletato Nery
- Post Graduate Program in Dentistry, Cruzeiro Do Sul University, São Paulo, Brazil
| | | | | | - Helena Bittar
- Post Graduate Program in Dentistry, Cruzeiro Do Sul University, São Paulo, Brazil
| | | | - Jônatas B Amaral
- Department of Otorhinolaryngology, ENT Lab, Federal University of Sao Paulo (UNIFESP), São Paulo, Brazil
| | - Markus Hardt
- Center for Salivary Diagnostics, The Forsyth Institute, Cambridge, MA, USA
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Luciana Marti
- Experimental Research, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Alexander Birbrair
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Manuel Jimenez
- Departamento de Didáctica de La Educación Física y Salud, Universidad Internacional de La Rioja, Logroño, Spain
| | - Marta Ferreira Bastos
- Postgraduate Program in Aging Sciences, São Judas Tadeu University, São Paulo, Brazil
| | - Luiz Henrique Silva Nali
- Department of Otorhinolaryngology, ENT Lab, Federal University of Sao Paulo (UNIFESP), São Paulo, Brazil
- Post-Graduate Program in Health Science, Santo Amaro University (UNISA), Santo Amaro, Brazil
| | | | | | - André L L Bachi
- Department of Otorhinolaryngology, ENT Lab, Federal University of Sao Paulo (UNIFESP), São Paulo, Brazil.
- Post-Graduate Program in Health Science, Santo Amaro University (UNISA), Santo Amaro, Brazil.
| | - Debora Heller
- Post Graduate Program in Dentistry, Cruzeiro Do Sul University, São Paulo, Brazil.
- Experimental Research, Hospital Israelita Albert Einstein, São Paulo, Brazil.
- Department of Periodontology, UT Health San Antonio, San Antonio, TX, USA.
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4
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Blaudin de Thé FX, Baudier C, Andrade Pereira R, Lefebvre C, Moingeon P. Transforming drug discovery with a high-throughput AI-powered platform: A 5-year experience with Patrimony. Drug Discov Today 2023; 28:103772. [PMID: 37717933 DOI: 10.1016/j.drudis.2023.103772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
High-throughput computational platforms are being established to accelerate drug discovery. Servier launched the Patrimony platform to harness computational sciences and artificial intelligence (AI) to integrate massive multimodal data from internal and external sources. Patrimony has enabled researchers to prioritize therapeutic targets based on a deep understanding of the pathophysiology of immuno-inflammatory diseases. Herein, we share our experience regarding main challenges and critical success factors faced when industrializing the platform and broadening its applications to neurological diseases. We emphasize the importance of integrating such platforms in an end-to-end drug discovery process and engaging human experts early on to ensure a transforming impact.
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5
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Ranjbar M, Cusack RP, Whetstone CE, Nawaz S, Khoury C, Wattie J, Wiltshire L, Le Roux J, Cheng E, Srinathan T, Ho T, Sehmi R, Duong M, Gauvreau GM. Gene Polymorphisms of Epithelial Cell-Derived Alarmins and Their Effects on Protein Levels and Disease Severity in Patients with COVID-19. Genes (Basel) 2023; 14:1721. [PMID: 37761861 PMCID: PMC10530834 DOI: 10.3390/genes14091721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The immune response in COVID-19 is characterized by the release of alarmin cytokines, which play crucial roles in immune activation and inflammation. The interplay between these cytokines and genetic variations may influence disease severity and outcomes, while sex differences might further contribute to variations in the immune response. METHODS We measured the levels of alarmin cytokines in a cohort of COVID-19 and non-COVID-19 patients using a sensitive Meso Scale Discovery system. Additionally, we conducted an SNP analysis to identify genetic variations within the IL-33 and TSLP genes. The association between these genetic variations, cytokine production, and COVID-19 severity was examined. RESULTS Our findings revealed elevated levels of IL-33 and IL-25 in COVID-19-positive patients compared to COVID-19-negative patients (p < 0.05), indicating their potential as therapeutic targets for disease modulation. Moreover, a minor allele within the IL-33 gene (rs3939286) was found to be associated with a protective effect against severe COVID-19 (p < 0.05), and minor alleles of the TSLP gene (rs2289276 and rs13806933) were found to significantly reduce TSLP protein levels in serum (p < 0.05). Sex-specific effects of TSLP and IL-33 SNPs were observed, suggesting a potential influence of sex hormones and genetic variations on the regulation of cytokine production. CONCLUSION The present study highlights the importance of alarmin cytokines and genetic variations in COVID-19 severity, providing valuable insights into personalized treatment approaches. Our results suggest that targeting alarmin cytokines may offer potential therapeutic benefits in managing COVID-19. Furthermore, the sex-specific effects of genetic variations emphasize the need to consider individual genetic profiles and sex differences when designing targeted interventions.
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Affiliation(s)
- Maral Ranjbar
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
| | - Ruth P. Cusack
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
| | - Christiane E. Whetstone
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
| | - Shiraz Nawaz
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
| | - Christopher Khoury
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
| | - Jennifer Wattie
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
| | - Lesley Wiltshire
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
| | | | - Eric Cheng
- St. Joseph’s Healthcare Hamilton, Hamilton, ON L8N 4A6, Canada; (E.C.)
| | - Thivya Srinathan
- St. Joseph’s Healthcare Hamilton, Hamilton, ON L8N 4A6, Canada; (E.C.)
| | - Terence Ho
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
- St. Joseph’s Healthcare Hamilton, Hamilton, ON L8N 4A6, Canada; (E.C.)
- The Research Institute of St. Joe’s Hamilton, Firestone Institute for Respiratory Health, St. Joseph’s Healthcare Hamilton, Hamilton, ON L8N 4A6, Canada
| | - Roma Sehmi
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
- St. Joseph’s Healthcare Hamilton, Hamilton, ON L8N 4A6, Canada; (E.C.)
- The Research Institute of St. Joe’s Hamilton, Firestone Institute for Respiratory Health, St. Joseph’s Healthcare Hamilton, Hamilton, ON L8N 4A6, Canada
| | - MyLinh Duong
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
- St. Joseph’s Healthcare Hamilton, Hamilton, ON L8N 4A6, Canada; (E.C.)
- The Research Institute of St. Joe’s Hamilton, Firestone Institute for Respiratory Health, St. Joseph’s Healthcare Hamilton, Hamilton, ON L8N 4A6, Canada
- Population Health Research Institute, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Gail M. Gauvreau
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON L8N 3Z5, Canada; (M.R.); (R.P.C.); (C.E.W.); (S.N.); (C.K.); (J.W.); (L.W.); (T.H.); (R.S.); (M.D.)
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6
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Van Damme KFA, Hoste L, Declercq J, De Leeuw E, Maes B, Martens L, Colman R, Browaeys R, Bosteels C, Verwaerde S, Vermeulen N, Lameire S, Debeuf N, Deckers J, Stordeur P, Depuydt P, Van Braeckel E, Vandekerckhove L, Guilliams M, Schetters STT, Haerynck F, Tavernier SJ, Lambrecht BN. A complement atlas identifies interleukin-6-dependent alternative pathway dysregulation as a key druggable feature of COVID-19. Sci Transl Med 2023; 15:eadi0252. [PMID: 37611083 DOI: 10.1126/scitranslmed.adi0252] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]
Abstract
Improvements in COVID-19 treatments, especially for the critically ill, require deeper understanding of the mechanisms driving disease pathology. The complement system is not only a crucial component of innate host defense but can also contribute to tissue injury. Although all complement pathways have been implicated in COVID-19 pathogenesis, the upstream drivers and downstream effects on tissue injury remain poorly defined. We demonstrate that complement activation is primarily mediated by the alternative pathway, and we provide a comprehensive atlas of the complement alterations around the time of respiratory deterioration. Proteomic and single-cell sequencing mapping across cell types and tissues reveals a division of labor between lung epithelial, stromal, and myeloid cells in complement production, in addition to liver-derived factors. We identify IL-6 and STAT1/3 signaling as an upstream driver of complement responses, linking complement dysregulation to approved COVID-19 therapies. Furthermore, an exploratory proteomic study indicates that inhibition of complement C5 decreases epithelial damage and markers of disease severity. Collectively, these results support complement dysregulation as a key druggable feature of COVID-19.
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Affiliation(s)
- Karel F A Van Damme
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Levi Hoste
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University, Ghent, Belgium
| | - Jozefien Declercq
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Elisabeth De Leeuw
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Bastiaan Maes
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Liesbet Martens
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Belgium
| | - Roos Colman
- Biostatistics Unit, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Robin Browaeys
- Bioinformatics Expertise Unit, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Cédric Bosteels
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Respiratory Infection and Defense Lab, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Stijn Verwaerde
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Nicky Vermeulen
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University, Ghent, Belgium
| | - Sahine Lameire
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Nincy Debeuf
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Julie Deckers
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Patrick Stordeur
- Belgian National Reference Center for the Complement System, Laboratory of Immunology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Pieter Depuydt
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Intensive Care Unit, Ghent University Hospital, Ghent, Belgium
| | - Eva Van Braeckel
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Respiratory Infection and Defense Lab, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Belgium
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
| | - Martin Guilliams
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Belgium
| | - Sjoerd T T Schetters
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University, Ghent, Belgium
| | - Simon J Tavernier
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Primary Immune Deficiency Research Laboratory, Department of Internal Diseases and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University, Ghent, Belgium
| | - Bart N Lambrecht
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, Netherlands
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7
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Guo TJF, Singhera GK, Leung JM, Dorscheid DR. Airway Epithelial-Derived Immune Mediators in COVID-19. Viruses 2023; 15:1655. [PMID: 37631998 PMCID: PMC10458661 DOI: 10.3390/v15081655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
The airway epithelium, which lines the conducting airways, is central to the defense of the lungs against inhaled particulate matter and pathogens such as SARS-CoV-2, the virus that causes COVID-19. Recognition of pathogens results in the activation of an innate and intermediate immune response which involves the release of cytokines and chemokines by the airway epithelium. This response can inhibit further viral invasion and influence adaptive immunity. However, severe COVID-19 is characterized by a hyper-inflammatory response which can give rise to clinical presentations including lung injury and lead to acute respiratory distress syndrome, viral pneumonia, coagulopathy, and multi-system organ failure. In response to SARS-CoV-2 infection, the airway epithelium can mount a maladaptive immune response which can delay viral clearance, perpetuate excessive inflammation, and contribute to the pathogenesis of severe COVID-19. In this article, we will review the barrier and immune functions of the airway epithelium, how SARS-CoV-2 can interact with the epithelium, and epithelial-derived cytokines and chemokines and their roles in COVID-19 and as biomarkers. Finally, we will discuss these immune mediators and their potential as therapeutic targets in COVID-19.
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Affiliation(s)
- Tony J. F. Guo
- Centre for Heart Lung Innovation, Providence Healthcare Research Institute, St. Paul’s Hospital, University of British Columbia, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
| | - Gurpreet K. Singhera
- Centre for Heart Lung Innovation, Providence Healthcare Research Institute, St. Paul’s Hospital, University of British Columbia, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Medicine, University of British Columbia, 2775 Laurel St., Vancouver, BC V5Z 1M9, Canada
| | - Janice M. Leung
- Centre for Heart Lung Innovation, Providence Healthcare Research Institute, St. Paul’s Hospital, University of British Columbia, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Medicine, University of British Columbia, 2775 Laurel St., Vancouver, BC V5Z 1M9, Canada
| | - Delbert R. Dorscheid
- Centre for Heart Lung Innovation, Providence Healthcare Research Institute, St. Paul’s Hospital, University of British Columbia, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Medicine, University of British Columbia, 2775 Laurel St., Vancouver, BC V5Z 1M9, Canada
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8
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Moingeon P. Artificial intelligence-driven drug development against autoimmune diseases. Trends Pharmacol Sci 2023; 44:411-424. [PMID: 37268540 DOI: 10.1016/j.tips.2023.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 06/04/2023]
Abstract
Artificial intelligence (AI)-based predictive models are being used to foster a precision medicine approach to treat complex chronic diseases such as autoimmune and autoinflammatory disorders (AIIDs). In the past few years the first models of systemic lupus erythematosus (SLE), primary Sjögren syndrome (pSS), and rheumatoid arthritis (RA) have been produced by molecular profiling of patients using omic technologies and integrating the data with AI. These advances have confirmed a complex pathophysiology involving multiple proinflammatory pathways and also provide evidence for shared molecular dysregulation across different AIIDs. I discuss how models are used to stratify patients, assess causality in pathophysiology, design drug candidates in silico, and predict drug efficacy in virtual patients. By relating individual patient characteristics to the predicted properties of millions of drug candidates, these models can improve the management of AIIDs through more personalized treatments.
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Affiliation(s)
- Philippe Moingeon
- Research and Development, Servier Laboratories, 50 Rue Carnot, 92150 Suresnes, France; French Academy of Pharmacy, 4 Avenue de l'Observatoire, 75006 Paris, France.
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Moingeon P, Chenel M, Rousseau C, Voisin E, Guedj M. Virtual patients, digital twins and causal disease models: paving the ground for in silico clinical trials. Drug Discov Today 2023; 28:103605. [PMID: 37146963 DOI: 10.1016/j.drudis.2023.103605] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/22/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
Computational models are being explored to simulate in silico the efficacy and safety of drug candidates and medical devices. Disease models that are based on patients' profiling data are being produced to represent interactomes of genes or proteins and to infer causality in the pathophysiology {AuQ: Edit OK?}, which makes it possible to mimic the impact of drugs on relevant targets. Virtual patients designed from medical records as well as digital twins were generated to simulate specific organs and to predict treatment efficacy at the individual patient level {AuQ: Edit OK?}. As the acceptance of digital evidence by regulators grows, predictive artificial intelligence (AI)-based models will support the design of confirmatory trials in humans and will accelerate the development of efficient drugs and medical devices.
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10
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Gerla L, Moitra S, Pink D, Govindasamy N, Duchesne M, Reklow E, Hillaby A, May A, Lewis JD, Melenka L, Hobman TC, Mayers I, Lacy P. SARS-CoV-2-Induced TSLP Is Associated with Duration of Hospital Stay in COVID-19 Patients. Viruses 2023; 15:v15020556. [PMID: 36851770 PMCID: PMC9959394 DOI: 10.3390/v15020556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Thymic stromal lymphopoietin (TSLP) is an epithelium-derived pro-inflammatory cytokine involved in lung inflammatory responses. Previous studies show conflicting observations in blood TSLP in COVID-19, while none report SARS-CoV-2 inducing TSLP expression in bronchial epithelial cells. Our objective in this study was to determine whether TSLP levels increase in COVID-19 patients and if SARS-CoV-2 induces TSLP expression in bronchial epithelial cells. Plasma cytokine levels were measured in patients hospitalized with confirmed COVID-19 and age- and sex-matched healthy controls. Demographic and clinical information from COVID-19 patients was collected. We determined associations between plasma TSLP and clinical parameters using Poisson regression. Cultured human nasal (HNEpC) and bronchial epithelial cells (NHBEs), Caco-2 cells, and patient-derived bronchial epithelial cells (HBECs) obtained from elective bronchoscopy were infected in vitro with SARS-CoV-2, and secretion as well as intracellular expression of TSLP was detected by immunofluorescence. Increased TSLP levels were detected in the plasma of hospitalized COVID-19 patients (603.4 ± 75.4 vs 997.6 ± 241.4 fg/mL, mean ± SEM), the levels of which correlated with duration of stay in hospital (β: 0.11; 95% confidence interval (CI): 0.01-0.21). In cultured NHBE and HBECs but not HNEpCs or Caco-2 cells, TSLP levels were significantly elevated after 24 h post-infection with SARS-CoV-2 (p < 0.001) in a dose-dependent manner. Plasma TSLP in COVID-19 patients significantly correlated with duration of hospitalization, while SARS-CoV-2 induced TSLP secretion from bronchial epithelial cells in vitro. Based on our findings, TSLP may be considered an important therapeutic target for COVID-19 treatment.
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Affiliation(s)
- Luke Gerla
- Alberta Respiratory Centre (ARC) Research, Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Subhabrata Moitra
- Alberta Respiratory Centre (ARC) Research, Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Desmond Pink
- Nanostics Inc., Edmonton, AB T6G 2E9, Canada
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2H6, Canada
| | - Natasha Govindasamy
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2H6, Canada
- Entos Pharmaceuticals, Edmonton, AB T6G 3Q5, Canada
| | - Marc Duchesne
- Alberta Respiratory Centre (ARC) Research, Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Eileen Reklow
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H6, Canada
| | - Angela Hillaby
- Alberta Respiratory Centre (ARC) Research, Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Amy May
- Alberta Respiratory Centre (ARC) Research, Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - John D. Lewis
- Nanostics Inc., Edmonton, AB T6G 2E9, Canada
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2H6, Canada
| | - Lyle Melenka
- Alberta Respiratory Centre (ARC) Research, Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Synergy Respiratory Care, Sherwood Park, AB T6G 2E9, Canada
| | - Tom C. Hobman
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H6, Canada
| | - Irvin Mayers
- Alberta Respiratory Centre (ARC) Research, Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Paige Lacy
- Alberta Respiratory Centre (ARC) Research, Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Correspondence: ; Tel.: +1-780-492-6085
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11
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Guedj M, Swindle J, Hamon A, Hubert S, Desvaux E, Laplume J, Xuereb L, Lefebvre C, Haudry Y, Gabarroca C, Aussy A, Laigle L, Dupin-Roger I, Moingeon P. Industrializing AI-powered drug discovery: lessons learned from the Patrimony computing platform. Expert Opin Drug Discov 2022; 17:815-824. [PMID: 35786124 DOI: 10.1080/17460441.2022.2095368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION As a mid-size international pharmaceutical company, we initiated four years ago the launch of a dedicated high-throughput computing platform supporting drug discovery. The platform named "Patrimony" was built-up on the initial predicate to capitalize on our proprietary data while leveraging public data sources in order to foster a Computational Precision Medicine approach with the power of Artificial Intelligence. AREAS COVERED Specifically, Patrimony is designed to identify novel therapeutic target candidates. With several successful use cases in Immuno-inflammatory diseases, and current ongoing extension to applications to Oncology and Neurology, we document how this industrial computational platform has had a transformational impact on our R&D, making it more competitive, as well time and cost effective through a model-based educated selection of therapeutic targets and drug candidates. EXPERT OPINION We report our achievements, but also our challenges in implementing data access and governance processes, building-up hardware and user interfaces, and acculturing scientists to use predictive models to inform decisions.
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Affiliation(s)
- Mickaël Guedj
- Servier, Research & Development, Suresnes Cedex, France
| | - Jack Swindle
- Lincoln, Research & Development, Boulogne-Billancourt Cedex, France
| | - Antoine Hamon
- Lincoln, Research & Development, Boulogne-Billancourt Cedex, France
| | - Sandra Hubert
- Servier, Research & Development, Suresnes Cedex, France
| | - Emiko Desvaux
- Servier, Research & Development, Suresnes Cedex, France
| | | | - Laura Xuereb
- Servier, Research & Development, Suresnes Cedex, France
| | | | | | | | - Audrey Aussy
- Servier, Research & Development, Suresnes Cedex, France
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12
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A comprehensive review of Artificial Intelligence and Network based approaches to drug repurposing in Covid-19. Biomed Pharmacother 2022; 153:113350. [PMID: 35777222 PMCID: PMC9236981 DOI: 10.1016/j.biopha.2022.113350] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022] Open
Abstract
Conventional drug discovery and development is tedious and time-taking process; because of which it has failed to keep the required pace to mitigate threats and cater demands of viral and re-occurring diseases, such as Covid-19. The main reasons of this delay in traditional drug development are: high attrition rates, extensive time requirements, and huge financial investment with significant risk. The effective solution to de novo drug discovery is drug repurposing. Previous studies have shown that the network-based approaches and analysis are versatile platform for repurposing as the network biology is used to model the interactions between variety of biological concepts. Herein, we provide a comprehensive background of machine learning and deep learning in drug repurposing while specifically focusing on the applications of network-based approach to drug repurposing in Covid-19, data sources, and tools used. Furthermore, use of network proximity, network diffusion, and AI on network-based drug repurposing for Covid-19 is well-explained. Finally, limitations of network-based approaches in general and specific to network are stated along with future recommendations for better network-based models.
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Han NR, Moon PD, Nam SY, Ko SG, Park HJ, Kim HM, Jeong HJ. TSLP up-regulates inflammatory responses through induction of autophagy in T cells. FASEB J 2022; 36:e22148. [PMID: 34997949 DOI: 10.1096/fj.202101447r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 12/19/2022]
Abstract
Thymic stromal lymphopoietin (TSLP), a type I cytokine belonging to the IL-2 cytokine family, promotes Th2-mediated inflammatory responses. The aim of this study is to investigate whether TSLP increases inflammatory responses via induction of autophagy using a murine T cell lymphoma cell line, EL4 cells, and lipopolysaccharide (LPS)-injected mice. TSLP increased expression levels of autophagy-related factors, such as Beclin-1, LC3-II, p62, Atg5, and lysosome associated membrane protein 1/2, whereas these factors increased by TSLP disappeared by neutralization of TSLP in EL4 cells. TSLP activated JAK1/JAK2/STAT5/JNK/PI3K, while the blockade of JAK1/JAK2/STAT5/JNK/PI3K signaling pathways reduced the expression levels of Beclin-1, LC3-II, and p62 in TSLP-stimulated EL4 cells. In addition, TSLP simultaneously increased levels of inflammatory cytokines via induction of autophagy by activation of JAK1/JAK2/STAT5/JNK/PI3K signaling pathways. In an LPS-induced acute liver injury (ALI) mouse model, exogenous TSLP increased expression levels of Beclin-1 and LC3-II, whereas functional deficiency of TSLP by TSLP siRNA resulted in lower expression of Beclin-1, LC3-II, and inflammatory cytokines, impairing their ability to form autophagosomes in ALI mice. Thus, our findings show a new role of TSLP between autophagy and inflammatory responses. In conclusion, regulating TSLP-induced autophagy may be a potential therapeutic strategy for inflammatory responses.
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Affiliation(s)
- Na-Ra Han
- College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea.,Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Phil-Dong Moon
- Center for Converging Humanities, Kyung Hee University, Seoul, Republic of Korea
| | - Sun-Young Nam
- Department of Pharmacology, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Seong-Gyu Ko
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea.,Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hi-Joon Park
- Department of Anatomy & Information Sciences, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hyung-Min Kim
- Department of Pharmacology, College of Korean Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hyun-Ja Jeong
- Department of Food Science & Technology, Hoseo University, Asan, Republic of Korea
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Tiyo BT, Schmitz GJH, Ortega MM, da Silva LT, de Almeida A, Oshiro TM, Duarte AJDS. What Happens to the Immune System after Vaccination or Recovery from COVID-19? Life (Basel) 2021; 11:1152. [PMID: 34833028 PMCID: PMC8619084 DOI: 10.3390/life11111152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/17/2022] Open
Abstract
Due to its leading role in fighting infections, the human immune system has been the focus of many studies in the context of Coronavirus disease 2019 (COVID-19). In a worldwide effort, the scientific community has transitioned from reporting about the effects of the novel coronavirus on the human body in the early days of the pandemic to exploring the body's many immunopathological and immunoprotecting properties that have improved disease treatment and enabled the development of vaccines. The aim of this review is to explain what happens to the immune system after recovery from COVID-19 and/or vaccination against SARS-CoV-2, the virus that causes the disease. We detail the way in which the immune system responds to a SARS-CoV-2 infection, including innate and adaptive measures. Then, we describe the role of vaccination, the main types of COVID-19 vaccines and how they protect us. Further, we explain the reason why immunity after COVID-19 infection plus a vaccination appears to induce a stronger response compared with virus exposure alone. Additionally, this review reports some correlates of protection from SARS-CoV-2 infection. In conclusion, we reinforce that vaccination is safe and important in achieving herd immunity.
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