1
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Peruzzotti-Jametti L, Willis CM, Krzak G, Hamel R, Pirvan L, Ionescu RB, Reisz JA, Prag HA, Garcia-Segura ME, Wu V, Xiang Y, Barlas B, Casey AM, van den Bosch AMR, Nicaise AM, Roth L, Bates GR, Huang H, Prasad P, Vincent AE, Frezza C, Viscomi C, Balmus G, Takats Z, Marioni JC, D'Alessandro A, Murphy MP, Mohorianu I, Pluchino S. Mitochondrial complex I activity in microglia sustains neuroinflammation. Nature 2024; 628:195-203. [PMID: 38480879 PMCID: PMC10990929 DOI: 10.1038/s41586-024-07167-9] [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: 10/03/2022] [Accepted: 02/06/2024] [Indexed: 03/17/2024]
Abstract
Sustained smouldering, or low-grade activation, of myeloid cells is a common hallmark of several chronic neurological diseases, including multiple sclerosis1. Distinct metabolic and mitochondrial features guide the activation and the diverse functional states of myeloid cells2. However, how these metabolic features act to perpetuate inflammation of the central nervous system is unclear. Here, using a multiomics approach, we identify a molecular signature that sustains the activation of microglia through mitochondrial complex I activity driving reverse electron transport and the production of reactive oxygen species. Mechanistically, blocking complex I in pro-inflammatory microglia protects the central nervous system against neurotoxic damage and improves functional outcomes in an animal disease model in vivo. Complex I activity in microglia is a potential therapeutic target to foster neuroprotection in chronic inflammatory disorders of the central nervous system3.
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Affiliation(s)
- L Peruzzotti-Jametti
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - C M Willis
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - G Krzak
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - R Hamel
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - L Pirvan
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - R-B Ionescu
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - J A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - H A Prag
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - M E Garcia-Segura
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - V Wu
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Y Xiang
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - B Barlas
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - A M Casey
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - A M R van den Bosch
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - A M Nicaise
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - L Roth
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - G R Bates
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - H Huang
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - P Prasad
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - A E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - C Frezza
- University Hospital Cologne, Cologne, Germany
| | | | - G Balmus
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
- Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, Cluj-Napoca, Romania
| | - Z Takats
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - J C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - A D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - M P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - I Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - S Pluchino
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK.
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2
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Colzani M, Bargehr J, Mescia F, Williams EC, Knight-Schrijver V, Lee J, Summers C, Mohorianu I, Smith KGC, Lyons PA, Sinha S. Proinflammatory cytokines driving cardiotoxicity in COVID-19. Cardiovasc Res 2024; 120:174-187. [PMID: 38041432 PMCID: PMC10936751 DOI: 10.1093/cvr/cvad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 12/03/2023] Open
Abstract
AIMS Cardiac involvement is common in patients hospitalized with COVID-19 and correlates with an adverse disease trajectory. While cardiac injury has been attributed to direct viral cytotoxicity, serum-induced cardiotoxicity secondary to serological hyperinflammation constitutes a potentially amenable mechanism that remains largely unexplored. METHODS AND RESULTS To investigate serological drivers of cardiotoxicity in COVID-19 we have established a robust bioassay that assessed the effects of serum from COVID-19 confirmed patients on human embryonic stem cell (hESC)-derived cardiomyocytes. We demonstrate that serum from COVID-19 positive patients significantly reduced cardiomyocyte viability independent of viral transduction, an effect that was also seen in non-COVID-19 acute respiratory distress syndrome (ARDS). Serum from patients with greater disease severity led to worse cardiomyocyte viability and this significantly correlated with levels of key inflammatory cytokines, including IL-6, TNF-α, IL1-β, IL-10, CRP, and neutrophil to lymphocyte ratio with a specific reduction of CD4+ and CD8+ cells. Combinatorial blockade of IL-6 and TNF-α partly rescued the phenotype and preserved cardiomyocyte viability and function. Bulk RNA sequencing of serum-treated cardiomyocytes elucidated specific pathways involved in the COVID-19 response impacting cardiomyocyte viability, structure, and function. The observed effects of serum-induced cytotoxicity were cell-type selective as serum exposure did not adversely affect microvascular endothelial cell viability but resulted in endothelial activation and a procoagulant state. CONCLUSION These results provide direct evidence that inflammatory cytokines are at least in part responsible for the cardiovascular damage seen in COVID-19 and characterise the downstream activated pathways in human cardiomyocytes. The serum signature of patients with severe disease indicates possible targets for therapeutic intervention.
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Affiliation(s)
- Maria Colzani
- Wellcome – MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, CB2 0AW Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Addenbrooke's Hospital, Hills Rd, CB2 0SP Cambridge, UK
| | - Johannes Bargehr
- Wellcome – MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, CB2 0AW Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Addenbrooke's Hospital, Hills Rd, CB2 0SP Cambridge, UK
| | - Federica Mescia
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Addenbrooke's Hospital, Hills Rd, CB2 0SP Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, CB2 0AW Cambridge, UK
| | - Eleanor C Williams
- Wellcome – MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, CB2 0AW Cambridge, UK
| | - Vincent Knight-Schrijver
- Wellcome – MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, CB2 0AW Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Addenbrooke's Hospital, Hills Rd, CB2 0SP Cambridge, UK
| | - Jonathan Lee
- Wellcome – MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, CB2 0AW Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Addenbrooke's Hospital, Hills Rd, CB2 0SP Cambridge, UK
| | - Charlotte Summers
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Addenbrooke's Hospital, Hills Rd, CB2 0SP Cambridge, UK
- Wolfson Lung Injury Unit, Heart and Lung Research Institute, Cambridge Biomedical Campus, Papworth Road, CB2 0BB Cambridge, UK
| | - Irina Mohorianu
- Wellcome – MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, CB2 0AW Cambridge, UK
| | - Kenneth G C Smith
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Addenbrooke's Hospital, Hills Rd, CB2 0SP Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, CB2 0AW Cambridge, UK
| | - Paul A Lyons
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Addenbrooke's Hospital, Hills Rd, CB2 0SP Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, CB2 0AW Cambridge, UK
| | - Sanjay Sinha
- Wellcome – MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, CB2 0AW Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Addenbrooke's Hospital, Hills Rd, CB2 0SP Cambridge, UK
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3
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Chen H, King FJ, Zhou B, Wang Y, Canedy CJ, Hayashi J, Zhong Y, Chang MW, Pache L, Wong JL, Jia Y, Joslin J, Jiang T, Benner C, Chanda SK, Zhou Y. Drug target prediction through deep learning functional representation of gene signatures. Nat Commun 2024; 15:1853. [PMID: 38424040 PMCID: PMC10904399 DOI: 10.1038/s41467-024-46089-y] [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: 09/20/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
Many machine learning applications in bioinformatics currently rely on matching gene identities when analyzing input gene signatures and fail to take advantage of preexisting knowledge about gene functions. To further enable comparative analysis of OMICS datasets, including target deconvolution and mechanism of action studies, we develop an approach that represents gene signatures projected onto their biological functions, instead of their identities, similar to how the word2vec technique works in natural language processing. We develop the Functional Representation of Gene Signatures (FRoGS) approach by training a deep learning model and demonstrate that its application to the Broad Institute's L1000 datasets results in more effective compound-target predictions than models based on gene identities alone. By integrating additional pharmacological activity data sources, FRoGS significantly increases the number of high-quality compound-target predictions relative to existing approaches, many of which are supported by in silico and/or experimental evidence. These results underscore the general utility of FRoGS in machine learning-based bioinformatics applications. Prediction networks pre-equipped with the knowledge of gene functions may help uncover new relationships among gene signatures acquired by large-scale OMICs studies on compounds, cell types, disease models, and patient cohorts.
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Affiliation(s)
- Hao Chen
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA.
- Department of Computer Science and Engineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
| | - Frederick J King
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Bin Zhou
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Yu Wang
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Carter J Canedy
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Joel Hayashi
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Yang Zhong
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Max W Chang
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Lars Pache
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Julian L Wong
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Yong Jia
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - John Joslin
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sumit K Chanda
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA
| | - Yingyao Zhou
- Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA.
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4
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Taylor HJ, Hung YH, Narisu N, Erdos MR, Kanke M, Yan T, Grenko CM, Swift AJ, Bonnycastle LL, Sethupathy P, Collins FS, Taylor DL. Human pancreatic islet microRNAs implicated in diabetes and related traits by large-scale genetic analysis. Proc Natl Acad Sci U S A 2023; 120:e2206797120. [PMID: 36757889 PMCID: PMC9963967 DOI: 10.1073/pnas.2206797120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
Genetic studies have identified ≥240 loci associated with the risk of type 2 diabetes (T2D), yet most of these loci lie in non-coding regions, masking the underlying molecular mechanisms. Recent studies investigating mRNA expression in human pancreatic islets have yielded important insights into the molecular drivers of normal islet function and T2D pathophysiology. However, similar studies investigating microRNA (miRNA) expression remain limited. Here, we present data from 63 individuals, the largest sequencing-based analysis of miRNA expression in human islets to date. We characterized the genetic regulation of miRNA expression by decomposing the expression of highly heritable miRNAs into cis- and trans-acting genetic components and mapping cis-acting loci associated with miRNA expression [miRNA-expression quantitative trait loci (eQTLs)]. We found i) 84 heritable miRNAs, primarily regulated by trans-acting genetic effects, and ii) 5 miRNA-eQTLs. We also used several different strategies to identify T2D-associated miRNAs. First, we colocalized miRNA-eQTLs with genetic loci associated with T2D and multiple glycemic traits, identifying one miRNA, miR-1908, that shares genetic signals for blood glucose and glycated hemoglobin (HbA1c). Next, we intersected miRNA seed regions and predicted target sites with credible set SNPs associated with T2D and glycemic traits and found 32 miRNAs that may have altered binding and function due to disrupted seed regions. Finally, we performed differential expression analysis and identified 14 miRNAs associated with T2D status-including miR-187-3p, miR-21-5p, miR-668, and miR-199b-5p-and 4 miRNAs associated with a polygenic score for HbA1c levels-miR-216a, miR-25, miR-30a-3p, and miR-30a-5p.
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Affiliation(s)
- Henry J. Taylor
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, CambridgeCB2 0BB, UK
- Heart and Lung Research Institute, University of Cambridge, CambridgeCB2 0BB, UK
| | - Yu-Han Hung
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY14853
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Michael R. Erdos
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Matthew Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY14853
| | - Tingfen Yan
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Caleb M. Grenko
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Amy J. Swift
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Lori L. Bonnycastle
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY14853
| | - Francis S. Collins
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - D. Leland Taylor
- Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD20892
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5
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Moutsopoulos I, Williams EC, Mohorianu II. bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data. Brief Bioinform 2023; 24:6965538. [PMID: 36583521 PMCID: PMC9851288 DOI: 10.1093/bib/bbac591] [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: 08/11/2022] [Revised: 10/12/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
Bulk sequencing experiments (single- and multi-omics) are essential for exploring wide-ranging biological questions. To facilitate interactive, exploratory tasks, coupled with the sharing of easily accessible information, we present bulkAnalyseR, a package integrating state-of-the-art approaches using an expression matrix as the starting point (pre-processing functions are available as part of the package). Static summary images are replaced with interactive panels illustrating quality-checking, differential expression analysis (with noise detection) and biological interpretation (enrichment analyses, identification of expression patterns, followed by inference and comparison of regulatory interactions). bulkAnalyseR can handle different modalities, facilitating robust integration and comparison of cis-, trans- and customised regulatory networks.
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Affiliation(s)
- Ilias Moutsopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
| | - Eleanor C Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
| | - Irina I Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
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6
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Bulstrode H, Girdler GC, Gracia T, Aivazidis A, Moutsopoulos I, Young AMH, Hancock J, He X, Ridley K, Xu Z, Stockley JH, Finlay J, Hallou C, Fajardo T, Fountain DM, van Dongen S, Joannides A, Morris R, Mair R, Watts C, Santarius T, Price SJ, Hutchinson PJA, Hodson EJ, Pollard SM, Mohorianu I, Barker RA, Sweeney TR, Bayraktar O, Gergely F, Rowitch DH. Myeloid cell interferon secretion restricts Zika flavivirus infection of developing and malignant human neural progenitor cells. Neuron 2022; 110:3936-3951.e10. [PMID: 36174572 PMCID: PMC7615581 DOI: 10.1016/j.neuron.2022.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/10/2022] [Accepted: 09/01/2022] [Indexed: 02/02/2023]
Abstract
Zika virus (ZIKV) can infect human developing brain (HDB) progenitors resulting in epidemic microcephaly, whereas analogous cellular tropism offers treatment potential for the adult brain cancer, glioblastoma (GBM). We compared productive ZIKV infection in HDB and GBM primary tissue explants that both contain SOX2+ neural progenitors. Strikingly, although the HDB proved uniformly vulnerable to ZIKV infection, GBM was more refractory, and this correlated with an innate immune expression signature. Indeed, GBM-derived CD11b+ microglia/macrophages were necessary and sufficient to protect progenitors against ZIKV infection in a non-cell autonomous manner. Using SOX2+ GBM cell lines, we found that CD11b+-conditioned medium containing type 1 interferon beta (IFNβ) promoted progenitor resistance to ZIKV, whereas inhibition of JAK1/2 signaling restored productive infection. Additionally, CD11b+ conditioned medium, and IFNβ treatment rendered HDB progenitor lines and explants refractory to ZIKV. These findings provide insight into neuroprotection for HDB progenitors as well as enhanced GBM oncolytic therapies.
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Affiliation(s)
- Harry Bulstrode
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Gemma C Girdler
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Tannia Gracia
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Ilias Moutsopoulos
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Adam M H Young
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John Hancock
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Xiaoling He
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Katherine Ridley
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Zhaoyang Xu
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John H Stockley
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John Finlay
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Clement Hallou
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Teodoro Fajardo
- Department of Virology, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Virology, Royal London Hospital, Barts Health NHS Trust, London E1 2ES, UK
| | | | | | - Alexis Joannides
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Robert Morris
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Richard Mair
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Colin Watts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK
| | - Thomas Santarius
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Stephen J Price
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Peter J A Hutchinson
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Emma J Hodson
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Irina Mohorianu
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Roger A Barker
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Trevor R Sweeney
- Department of Virology, University of Cambridge, Cambridge CB2 0QQ, UK; The Pirbright Institute, Guildford, Surrey GU24 0NF, UK
| | | | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - David H Rowitch
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK.
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7
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Williams EC, Chazarra-Gil R, Shahsavari A, Mohorianu I. The Sum of Two Halves May Be Different from the Whole-Effects of Splitting Sequencing Samples Across Lanes. Genes (Basel) 2022; 13:genes13122265. [PMID: 36553532 PMCID: PMC9777937 DOI: 10.3390/genes13122265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
The advances in high-throughput sequencing (HTS) have enabled the characterisation of biological processes at an unprecedented level of detail; most hypotheses in molecular biology rely on analyses of HTS data. However, achieving increased robustness and reproducibility of results remains a main challenge. Although variability in results may be introduced at various stages, e.g., alignment, summarisation or detection of differential expression, one source of variability was systematically omitted: the sequencing design, which propagates through analyses and may introduce an additional layer of technical variation. We illustrate qualitative and quantitative differences arising from splitting samples across lanes on bulk and single-cell sequencing. For bulk mRNAseq data, we focus on differential expression and enrichment analyses; for bulk ChIPseq data, we investigate the effect on peak calling and the peaks' properties. At the single-cell level, we concentrate on identifying cell subpopulations. We rely on markers used for assigning cell identities; both smartSeq and 10× data are presented. The observed reduction in the number of unique sequenced fragments limits the level of detail on which the different prediction approaches depend. Furthermore, the sequencing stochasticity adds in a weighting bias corroborated with variable sequencing depths and (yet unexplained) sequencing bias. Subsequently, we observe an overall reduction in sequencing complexity and a distortion in the biological signal across technologies, experimental contexts, organisms and tissues.
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Affiliation(s)
- Eleanor C. Williams
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Ruben Chazarra-Gil
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Life Sciences-Transcriptomics and Functional Genomics Lab, Barcelona Supercomputing Center (BSC-CNS), 08034 Barcelona, Spain
| | - Arash Shahsavari
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Correspondence:
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Britto C, Mohorianu I, Yeung T, Cheung E, Novak T, Hall MW, Mourani PM, Weiss SL, Thomas NJ, Markovitz B, Randolph AG, Moffitt KL. Host respiratory transcriptome signature associated with poor outcome in children with influenza-Staphylococcus aureus pneumonia. J Infect Dis 2022; 226:1286-1294. [PMID: 35899844 DOI: 10.1093/infdis/jiac325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/25/2022] [Indexed: 11/14/2022] Open
Abstract
Respiratory coinfection of influenza with Staphylococcus aureus often causes severe disease; methicillin resistant S. aureus (MRSA) coinfection is frequently fatal. Understanding disease pathogenesis may inform therapies. We aimed to identify host and pathogen transcriptomic (mRNA) signatures from the respiratory compartment of patients with influenza-S. aureus coinfection (ISAC) critical illness that predict worse outcomes. mRNA extracted from endotracheal aspirates was evaluated for S. aureus and host transcriptomic biosignatures. Influenza-MRSA outcomes were worse, but of 190 S. aureus virulence-associated genes, 6 were differentially expressed between MRSA- versus methicillin-susceptible S. aureus coinfected patients and none discriminated outcome. Host gene expression in ISAC patients was compared to influenza infection alone. Patients with poor clinical outcomes (death or prolonged multi-organ dysfunction) had relatively reduced expression of interferons and down-regulation of interferon gamma-induced immune cell chemoattractants CXCL10 and CXCL11. In influenza-S. aureus respiratory coinfection, airway host but not pathogen gene expression profiles predicted worse clinical outcomes.
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Affiliation(s)
- Carl Britto
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK.,Division of Infectious Disease, St. John's Research Institute, Bengaluru, India
| | - Irina Mohorianu
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK.,Wellcome-MRC Cambridge, Stem Cell Institute, University of Cambridge, UK
| | - Tracy Yeung
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Elaine Cheung
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Tanya Novak
- Department of Anesthesia, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Anesthesia, Harvard Medical School, Boston, MA, USA
| | - Mark W Hall
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Peter M Mourani
- Department of Pediatrics, Section of Critical Care Medicine, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Scott L Weiss
- Division of Critical Care, Department of Anesthesiology and Critical Care, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Neal J Thomas
- Department of Pediatrics, Penn State Hershey Children's Hospital, Penn State University College of Medicine, Hershey, PA, USA
| | - Barry Markovitz
- Department of Anesthesiology Critical Care Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Adrienne G Randolph
- Department of Anesthesia, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Anesthesia, Harvard Medical School, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Kristin L Moffitt
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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