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Aney KJ, Jeong WJ, Vallejo AF, Burdziak C, Chen E, Wang A, Koak P, Wise K, Jensen K, Pe'er D, Dougan SK, Martelotto L, Nissim S. Novel Approach for Pancreas Transcriptomics Reveals the Cellular Landscape in Homeostasis and Acute Pancreatitis. Gastroenterology 2024; 166:1100-1113. [PMID: 38325760 PMCID: PMC11102849 DOI: 10.1053/j.gastro.2024.01.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND & AIMS Acinar cells produce digestive enzymes that impede transcriptomic characterization of the exocrine pancreas. Thus, single-cell RNA-sequencing studies of the pancreas underrepresent acinar cells relative to histological expectations, and a robust approach to capture pancreatic cell responses in disease states is needed. We sought to innovate a method that overcomes these challenges to accelerate study of the pancreas in health and disease. METHODS We leverage FixNCut, a single-cell RNA-sequencing approach in which tissue is reversibly fixed with dithiobis(succinimidyl propionate) before dissociation and single-cell preparation. We apply FixNCut to an established mouse model of acute pancreatitis, validate findings using GeoMx whole transcriptome atlas profiling, and integrate our data with prior studies to compare our method in both mouse and human pancreas datasets. RESULTS FixNCut achieves unprecedented definition of challenging pancreatic cells, including acinar and immune populations in homeostasis and acute pancreatitis, and identifies changes in all major cell types during injury and recovery. We define the acinar transcriptome during homeostasis and acinar-to-ductal metaplasia and establish a unique gene set to measure deviation from normal acinar identity. We characterize pancreatic immune cells, and analysis of T-cell subsets reveals a polarization of the homeostatic pancreas toward type-2 immunity. We report immune responses during acute pancreatitis and recovery, including early neutrophil infiltration, expansion of dendritic cell subsets, and a substantial shift in the transcriptome of macrophages due to both resident macrophage activation and monocyte infiltration. CONCLUSIONS FixNCut preserves pancreatic transcriptomes to uncover novel cell states during homeostasis and following pancreatitis, establishing a broadly applicable approach and reference atlas for study of pancreas biology and disease.
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Affiliation(s)
- Katherine J Aney
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts; Health Sciences & Technology Program, Harvard-MIT, Boston, Massachusetts; Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Woo-Jeong Jeong
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Cassandra Burdziak
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ethan Chen
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Austin Wang
- Harvard University, Cambridge, Massachusetts
| | - Pal Koak
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kellie Wise
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, South Australia, Australia; South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, South Australia, Australia
| | - Kirk Jensen
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, South Australia, Australia; South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, South Australia, Australia; Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York; Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Stephanie K Dougan
- Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Luciano Martelotto
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, South Australia, Australia; South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, South Australia, Australia.
| | - Sahar Nissim
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts; Health Sciences & Technology Program, Harvard-MIT, Boston, Massachusetts; Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Boston, Massachusetts; Gastroenterology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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2
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Schiff HF, Walker NF, Ugarte-Gil C, Tebruegge M, Manousopoulou A, Garbis SD, Mansour S, Wong PHM, Rockett G, Piazza P, Niranjan M, Vallejo AF, Woelk CH, Wilkinson RJ, Tezera LB, Garay-Baquero D, Elkington P. Integrated plasma proteomics identifies tuberculosis-specific diagnostic biomarkers. JCI Insight 2024; 9:e173273. [PMID: 38512356 DOI: 10.1172/jci.insight.173273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUNDNovel biomarkers to identify infectious patients transmitting Mycobacterium tuberculosis are urgently needed to control the global tuberculosis (TB) pandemic. We hypothesized that proteins released into the plasma in active pulmonary TB are clinically useful biomarkers to distinguish TB cases from healthy individuals and patients with other respiratory infections.METHODSWe applied a highly sensitive non-depletion tandem mass spectrometry discovery approach to investigate plasma protein expression in pulmonary TB cases compared to healthy controls in South African and Peruvian cohorts. Bioinformatic analysis using linear modeling and network correlation analyses identified 118 differentially expressed proteins, significant through 3 complementary analytical pipelines. Candidate biomarkers were subsequently analyzed in 2 validation cohorts of differing ethnicity using antibody-based proximity extension assays.RESULTSTB-specific host biomarkers were confirmed. A 6-protein diagnostic panel, comprising FETUB, FCGR3B, LRG1, SELL, CD14, and ADA2, differentiated patients with pulmonary TB from healthy controls and patients with other respiratory infections with high sensitivity and specificity in both cohorts.CONCLUSIONThis biomarker panel exceeds the World Health Organization Target Product Profile specificity criteria for a triage test for TB. The new biomarkers have potential for further development as near-patient TB screening assays, thereby helping to close the case-detection gap that fuels the global pandemic.FUNDINGMedical Research Council (MRC) (MR/R001065/1, MR/S024220/1, MR/P023754/1, and MR/W025728/1); the MRC and the UK Foreign Commonwealth and Development Office; the UK National Institute for Health Research (NIHR); the Wellcome Trust (094000, 203135, and CC2112); Starter Grant for Clinical Lecturers (Academy of Medical Sciences UK); the British Infection Association; the Program for Advanced Research Capacities for AIDS in Peru at Universidad Peruana Cayetano Heredia (D43TW00976301) from the Fogarty International Center at the US NIH; the UK Technology Strategy Board/Innovate UK (101556); the Francis Crick Institute, which receives funding from UKRI-MRC (CC2112); Cancer Research UK (CC2112); and the NIHR Biomedical Research Centre of Imperial College NHS.
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Affiliation(s)
- Hannah F Schiff
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, Southampton, United Kingdom
| | - Naomi F Walker
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Cesar Ugarte-Gil
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Epidemiology, School of Public and Population Health, University of Texas Medical Branch, Galveston, Texas, USA
| | - Marc Tebruegge
- Department of Infection, Immunity & Inflammation, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Department of Paediatrics, Klinik Ottakring, Wiener Gesundheitsverbund, Vienna, Austria
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Antigoni Manousopoulou
- Proteas Bioanalytics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Spiros D Garbis
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Proteas Bioanalytics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Salah Mansour
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, Southampton, United Kingdom
| | | | - Gabrielle Rockett
- Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paolo Piazza
- Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mahesan Niranjan
- Institute for Life Sciences, Southampton, United Kingdom
- Electronics and Computer Sciences, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom
| | - Andres F Vallejo
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Robert J Wilkinson
- Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, and
- Department of Medicine, University of Cape Town, Observatory, Republic of South Africa
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Liku B Tezera
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, Southampton, United Kingdom
| | - Diana Garay-Baquero
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, Southampton, United Kingdom
| | - Paul Elkington
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, Southampton, United Kingdom
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3
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Sirvent S, Vallejo AF, Corden E, Teo Y, Davies J, Clayton K, Seaby EG, Lai C, Ennis S, Alyami R, Douilhet G, Dean LSN, Loxham M, Horswill S, Healy E, Roberts G, Hall NJ, Friedmann PS, Singh H, Bennett CL, Ardern-Jones MR, Polak ME. Impaired expression of metallothioneins contributes to allergen-induced inflammation in patients with atopic dermatitis. Nat Commun 2023; 14:2880. [PMID: 37208336 DOI: 10.1038/s41467-023-38588-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/29/2023] [Indexed: 05/21/2023] Open
Abstract
Regulation of cutaneous immunity is severely compromised in inflammatory skin disease. To investigate the molecular crosstalk underpinning tolerance versus inflammation in atopic dermatitis, we utilise a human in vivo allergen challenge study, exposing atopic dermatitis patients to house dust mite. Here we analyse transcriptional programmes at the population and single cell levels in parallel with immunophenotyping of cutaneous immunocytes revealed a distinct dichotomy in atopic dermatitis patient responsiveness to house dust mite challenge. Our study shows that reactivity to house dust mite was associated with high basal levels of TNF-expressing cutaneous Th17 T cells, and documents the presence of hub structures where Langerhans cells and T cells co-localised. Mechanistically, we identify expression of metallothioneins and transcriptional programmes encoding antioxidant defences across all skin cell types, that appear to protect against allergen-induced inflammation. Furthermore, single nucleotide polymorphisms in the MTIX gene are associated with patients who did not react to house dust mite, opening up possibilities for therapeutic interventions modulating metallothionein expression in atopic dermatitis.
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Affiliation(s)
- Sofia Sirvent
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Emma Corden
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Ying Teo
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - James Davies
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Haematology, University College London (UCL) Cancer Institute, London, WC1E 6DD, UK
| | - Kalum Clayton
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Eleanor G Seaby
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Chester Lai
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Sarah Ennis
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rfeef Alyami
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gemma Douilhet
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Lareb S N Dean
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Matthew Loxham
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarah Horswill
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Eugene Healy
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Graham Roberts
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nigel J Hall
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- University Surgery Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Peter S Friedmann
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Harinder Singh
- Departments of Immunology and Computational and Systems Biology, The University of Pittsburgh, Pittsburgh, USA
| | - Clare L Bennett
- Department of Haematology, University College London (UCL) Cancer Institute, London, WC1E 6DD, UK
| | - Michael R Ardern-Jones
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Marta E Polak
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
- Institute for Life Sciences, University of Southampton, Southampton, UK.
- Janssen R&D, 1400 McKean Road, Spring House, PA, 19477, USA.
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4
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Penrice-Randal R, Dong X, Shapanis AG, Gardner A, Harding N, Legebeke J, Lord J, Vallejo AF, Poole S, Brendish NJ, Hartley C, Williams AP, Wheway G, Polak ME, Strazzeri F, Schofield JPR, Skipp PJ, Hiscox JA, Clark TW, Baralle D. Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19. Front Immunol 2022; 13:988685. [PMID: 36203591 PMCID: PMC9530807 DOI: 10.3389/fimmu.2022.988685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe COVID-19 pandemic has created pressure on healthcare systems worldwide. Tools that can stratify individuals according to prognosis could allow for more efficient allocation of healthcare resources and thus improved patient outcomes. It is currently unclear if blood gene expression signatures derived from patients at the point of admission to hospital could provide useful prognostic information.MethodsGene expression of whole blood obtained at the point of admission from a cohort of 78 patients hospitalised with COVID-19 during the first wave was measured by high resolution RNA sequencing. Gene signatures predictive of admission to Intensive Care Unit were identified and tested using machine learning and topological data analysis, TopMD.ResultsThe best gene expression signature predictive of ICU admission was defined using topological data analysis with an accuracy: 0.72 and ROC AUC: 0.76. The gene signature was primarily based on differentially activated pathways controlling epidermal growth factor receptor (EGFR) presentation, Peroxisome proliferator-activated receptor alpha (PPAR-α) signalling and Transforming growth factor beta (TGF-β) signalling.ConclusionsGene expression signatures from blood taken at the point of admission to hospital predicted ICU admission of treatment naïve patients with COVID-19.
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Affiliation(s)
- Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
- *Correspondence: Rebekah Penrice-Randal,
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andrew George Shapanis
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Aaron Gardner
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
| | | | - Jelmer Legebeke
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F. Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stephen Poole
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nathan J. Brendish
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Anthony P. Williams
- Cancer Sciences Division, Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gabrielle Wheway
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Marta E. Polak
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Paul J. Skipp
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
- Centre for Proteomic Research, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- ASTAR Infectious Diseases Laboratories (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR) Singapore, Singapore, Singapore
| | - Tristan W. Clark
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
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5
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Davies J, Sirvent S, Vallejo AF, Clayton K, Douilhet G, Keeler PS, West J, Ardern-Jones M, MacArthur BD, Singh H, Polak ME. Transcriptional programming of immunoregulatory responses in human Langerhans cells. Front Immunol 2022; 13:892254. [PMID: 36203560 PMCID: PMC9530347 DOI: 10.3389/fimmu.2022.892254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/25/2022] [Indexed: 11/27/2022] Open
Abstract
Human epidermal Langerhans cells (LCs) maintain immune homeostasis in the skin. To examine transcriptional programming of human primary LCs during homeostasis, we performed scRNA-seq analysis of LCs before and after migration from the epidermis, coupled with functional assessment of their regulatory T cell priming capabilities. The analysis revealed that steady-state LCs exist in a continuum of maturation states and upregulate antigen presentation genes along with an immunoregulatory module including the genes IDO1, LGALS1, LAMTOR1, IL4I, upon their migration. The migration-induced transition in genomic state is accompanied by the ability of LCs to more efficiently prime regulatory T cell responses in co-culture assays. Computational analyses of the scRNAseq datasets using SCENIC and Partial Information Decomposition in Context identified a set of migration-induced transcription factors including IRF4, KLF6 and RelB as key nodes within a immunoregulatory gene regulatory network. These findings support a model in which efficient priming of immunoregulatory responses by LCs is dependent on coordinated upregulation of a migration-coupled maturation program with a immunoregulation-promoting genomic module.
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Affiliation(s)
- James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sofia Sirvent
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F. Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kalum Clayton
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gemma Douilhet
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Patrick S. Keeler
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jonathan West
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Michael Ardern-Jones
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ben D. MacArthur
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Harinder Singh
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, The University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Marta E. Polak, ; Harinder Singh,
| | - Marta E. Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- *Correspondence: Marta E. Polak, ; Harinder Singh,
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6
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Legebeke J, Lord J, Penrice-Randal R, Vallejo AF, Poole S, Brendish NJ, Dong X, Hartley C, Holloway JW, Lucas JS, Williams AP, Wheway G, Strazzeri F, Gardner A, Schofield JPR, Skipp PJ, Hiscox JA, Polak ME, Clark TW, Baralle D. Evaluating the Immune Response in Treatment-Naive Hospitalised Patients With Influenza and COVID-19. Front Immunol 2022; 13:853265. [PMID: 35663963 PMCID: PMC9160963 DOI: 10.3389/fimmu.2022.853265] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022] Open
Abstract
The worldwide COVID-19 pandemic has claimed millions of lives and has had a profound effect on global life. Understanding the body’s immune response to SARS-CoV-2 infection is crucial in improving patient management and prognosis. In this study we compared influenza and SARS-CoV-2 infected patient cohorts to identify distinct blood transcript abundances and cellular composition to better understand the natural immune response associated with COVID-19, compared to another viral infection being influenza, and identify a prognostic signature of COVID-19 patient outcome. Clinical characteristics and peripheral blood were acquired upon hospital admission from two well characterised cohorts, a cohort of 88 patients infected with influenza and a cohort of 80 patients infected with SARS-CoV-2 during the first wave of the pandemic and prior to availability of COVID-19 treatments and vaccines. Gene transcript abundances, enriched pathways and cellular composition were compared between cohorts using RNA-seq. A genetic signature between COVID-19 survivors and non-survivors was assessed as a prognostic predictor of COVID-19 outcome. Contrasting immune responses were detected with an innate response elevated in influenza and an adaptive response elevated in COVID-19. Additionally ribosomal, mitochondrial oxidative stress and interferon signalling pathways differentiated the cohorts. An adaptive immune response was associated with COVID-19 survival, while an inflammatory response predicted death. A prognostic transcript signature, associated with circulating immunoglobulins, nucleosome assembly, cytokine production and T cell activation, was able to stratify COVID-19 patients likely to survive or die. This study provides a unique insight into the immune responses of treatment naïve patients with influenza or COVID-19. The comparison of immune response between COVID-19 survivors and non-survivors enables prognostication of COVID-19 patients and may suggest potential therapeutic strategies to improve survival.
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Affiliation(s)
- Jelmer Legebeke
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andres F Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stephen Poole
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom.,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nathan J Brendish
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom.,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - John W Holloway
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom
| | - Jane S Lucas
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom.,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Anthony P Williams
- Cancer Sciences Division, Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gabrielle Wheway
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Aaron Gardner
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
| | | | - Paul J Skipp
- TopMD Precision Medicine Ltd, Southampton, United Kingdom.,Centre for Proteomic Research, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,ASTAR Infectious Diseases Laboratories (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR) Singapore, Singapore, Singapore
| | - Marta E Polak
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Tristan W Clark
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom.,School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, United Kingdom
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7
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West HC, Davies J, Henderson S, Adegun OK, Ward S, Ferrer IR, Tye CA, Vallejo AF, Jardine L, Collin M, Polak ME, Bennett CL. Loss of T cell tolerance in the skin following immunopathology is linked to failed restoration of the dermal niche by recruited macrophages. Cell Rep 2022; 39:110819. [PMID: 35584681 DOI: 10.1016/j.celrep.2022.110819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 03/17/2022] [Accepted: 04/22/2022] [Indexed: 11/03/2022] Open
Abstract
T cell pathology in the skin leads to monocyte influx, but we have little understanding of the fate of recruited cells within the diseased niche, or the long-term impact on cutaneous immune homeostasis. By combining a murine model of acute graft-versus-host disease (aGVHD) with analysis of patient samples, we demonstrate that pathology initiates dermis-specific macrophage differentiation and show that aGVHD-primed macrophages continue to dominate the dermal compartment at the relative expense of quiescent MHCIIint cells. Exposure of the altered dermal niche to topical haptens after disease resolution results in hyper-activation of regulatory T cells (Treg), but local breakdown in tolerance. Disease-imprinted macrophages express increased IL-1β and are predicted to elicit altered TNF superfamily interactions with cutaneous Treg, and we demonstrate the direct loss of T cell regulation within the resolved skin. Thus, T cell pathology leaves an immunological scar in the skin marked by failure to re-set immune homeostasis.
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Affiliation(s)
- Heather C West
- Department of Haematology, University College London (UCL) Cancer Institute, London WC1E 6DD, UK; Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - James Davies
- Department of Haematology, University College London (UCL) Cancer Institute, London WC1E 6DD, UK; Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Stephen Henderson
- Bill Lyons Informatics Centre, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Oluyori K Adegun
- Department of Cellular Pathology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Sophie Ward
- Department of Haematology, University College London (UCL) Cancer Institute, London WC1E 6DD, UK; Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Ivana R Ferrer
- Department of Haematology, University College London (UCL) Cancer Institute, London WC1E 6DD, UK; Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Chanidapa A Tye
- Department of Haematology, University College London (UCL) Cancer Institute, London WC1E 6DD, UK; Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Andres F Vallejo
- Clinical and Experimental Sciences (Sir Henry Wellcome Laboratories, Faculty of Medicine) and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Matthew Collin
- Newcastle University Translational and Clinical Research Institute and NIHR Newcastle Biomedical Research Centre, Newcastle University, Newcastle Upon Tyne, UK
| | - Marta E Polak
- Clinical and Experimental Sciences (Sir Henry Wellcome Laboratories, Faculty of Medicine) and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Clare L Bennett
- Department of Haematology, University College London (UCL) Cancer Institute, London WC1E 6DD, UK; Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK.
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8
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Harrington J, Esteban LB, Butement J, Vallejo AF, Lane SIR, Sheth B, Jongen MSA, Parker R, Stumpf PS, Smith RCG, MacArthur BD, Rose-Zerilli MJJ, Polak ME, Underwood T, West J. Dual dean entrainment with volume ratio modulation for efficient droplet co-encapsulation: extreme single-cell indexing. Lab Chip 2021; 21:3378-3386. [PMID: 34240097 PMCID: PMC8383763 DOI: 10.1039/d1lc00292a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/21/2021] [Indexed: 06/01/2023]
Abstract
The future of single cell diversity screens involves ever-larger sample sizes, dictating the need for higher throughput methods with low analytical noise to accurately describe the nature of the cellular system. Current approaches are limited by the Poisson statistic, requiring dilute cell suspensions and associated losses in throughput. In this contribution, we apply Dean entrainment to both cell and bead inputs, defining different volume packets to effect efficient co-encapsulation. Volume ratio scaling was explored to identify optimal conditions. This enabled the co-encapsulation of single cells with reporter beads at rates of ∼1 million cells per hour, while increasing assay signal-to-noise with cell multiplet rates of ∼2.5% and capturing ∼70% of cells. The method, called Pirouette coupling, extends our capacity to investigate biological systems.
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Affiliation(s)
- Jack Harrington
- Cancer Sciences, Faculty of Medicine, University of Southampton, UK.
| | - Luis Blay Esteban
- Faculty of Engineering and Physical Sciences, University of Southampton, UK
| | - Jonathan Butement
- Cancer Sciences, Faculty of Medicine, University of Southampton, UK.
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, UK
| | - Simon I R Lane
- Faculty of Engineering and Physical Sciences, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Bhavwanti Sheth
- School for Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, UK
| | - Maaike S A Jongen
- Cancer Sciences, Faculty of Medicine, University of Southampton, UK.
| | - Rachel Parker
- Cancer Sciences, Faculty of Medicine, University of Southampton, UK.
| | - Patrick S Stumpf
- Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, UK
| | - Rosanna C G Smith
- Cancer Sciences, Faculty of Medicine, University of Southampton, UK.
| | - Ben D MacArthur
- Institute for Life Sciences, University of Southampton, UK
- Mathematical Sciences, University of Southampton, UK
| | - Matthew J J Rose-Zerilli
- Cancer Sciences, Faculty of Medicine, University of Southampton, UK.
- Institute for Life Sciences, University of Southampton, UK
| | - Marta E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Tim Underwood
- Cancer Sciences, Faculty of Medicine, University of Southampton, UK.
- Institute for Life Sciences, University of Southampton, UK
| | - Jonathan West
- Cancer Sciences, Faculty of Medicine, University of Southampton, UK.
- Institute for Life Sciences, University of Southampton, UK
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9
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Miow QH, Vallejo AF, Wang Y, Hong JM, Bai C, Teo FS, Wang AD, Loh HR, Tan TZ, Ding Y, She HW, Gan SH, Paton NI, Lum J, Tay A, Chee CB, Tambyah PA, Polak ME, Wang YT, Singhal A, Elkington PT, Friedland JS, Ong CW. Doxycycline host-directed therapy in human pulmonary tuberculosis. J Clin Invest 2021; 131:e141895. [PMID: 34128838 DOI: 10.1172/jci141895] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 06/11/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUNDMatrix metalloproteinases (MMPs) are key regulators of tissue destruction in tuberculosis (TB) and may be targets for host-directed therapy. We conducted a phase II double-blind, randomized, controlled trial investigating doxycycline, a licensed broad-spectrum MMP inhibitor, in patients with pulmonary TB.METHODSThirty patients with pulmonary TB were enrolled within 7 days of initiating anti-TB treatment and randomly assigned to receive either 100 mg doxycycline or placebo twice a day for 14 days, in addition to standard care.RESULTSWhole blood RNA-sequencing demonstrated that doxycycline accelerated restoration of dysregulated gene expression in TB towards normality, rapidly down-regulating type I and II interferon and innate immune response genes, and up-regulating B-cell modules relative to placebo. The effects persisted for 6 weeks after doxycycline discontinuation, concurrent with suppressed plasma MMP-1. Doxycycline significantly reduced sputum MMP-1, -8, -9, -12 and -13, suppressed type I collagen and elastin destruction, reduced pulmonary cavity volume without altering sputum mycobacterial loads, and was safe.CONCLUSIONAdjunctive doxycycline with standard anti-TB treatment suppressed pathological MMPs in PTB patients. Larger studies on adjunctive doxycycline to limit TB immunopathology are merited.TRIAL REGISTRATIONClinicalTrials.gov NCT02774993.FUNDINGSingapore National Medical Research Council (NMRC/CNIG/1120/2014, NMRC/Seedfunding/0010/2014, NMRC/CISSP/2015/009a); the Singapore Infectious Diseases Initiative (SIDI/2013/013); National University Health System (PFFR-28 January 14, NUHSRO/2014/039/BSL3-SeedFunding/Jul/01); the Singapore Immunology Network Immunomonitoring platform (BMRC/IAF/311006, H16/99/b0/011, NRF2017_SISFP09); an ExxonMobil Research Fellowship, NUHS Clinician Scientist Program (NMRC/TA/0042/2015, CSAINV17nov014); the UK Medical Research Council (MR/P023754/1, MR/N006631/1); a NUS Postdoctoral Fellowship (NUHSRO/2017/073/PDF/03); The Royal Society Challenge Grant (CHG\R1\170084); the Sir Henry Dale Fellowship, Wellcome Trust (109377/Z/15/Z); and A*STAR.
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Affiliation(s)
- Qing Hao Miow
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Yu Wang
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jia Mei Hong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chen Bai
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Felicia Sw Teo
- Division of Respiratory and Critical Care Medicine, University Medicine Cluster, National University Hospital, National University Health System, Singapore
| | - Alvin Dy Wang
- Department of Medicine, Ng Teng Fong General Hospital, Singapore
| | - Hong Rong Loh
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ying Ding
- National Centre for Infectious Diseases, Singapore
| | - Hoi Wah She
- Tuberculosis Control Unit, Tan Tock Seng Hospital, Singapore
| | - Suay Hong Gan
- Tuberculosis Control Unit, Tan Tock Seng Hospital, Singapore
| | - Nicholas I Paton
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Alicia Tay
- Singapore Immunology Network, A*STAR, Singapore
| | - Cynthia Be Chee
- Tuberculosis Control Unit, Tan Tock Seng Hospital, Singapore
| | - Paul A Tambyah
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Marta E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Yee Tang Wang
- Tuberculosis Control Unit, Tan Tock Seng Hospital, Singapore
| | | | - Paul T Elkington
- NIHR Respiratory Biomedical Research Centre, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Catherine Wm Ong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Institute for Health Innovation and Technology, National University of Singapore, Singapore
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10
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Reichmann MT, Tezera LB, Vallejo AF, Vukmirovic M, Xiao R, Reynolds J, Jogai S, Wilson S, Marshall B, Jones MG, Leslie A, D’Armiento JM, Kaminski N, Polak ME, Elkington P. Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets. J Clin Invest 2021; 131:148136. [PMID: 34128839 PMCID: PMC8321576 DOI: 10.1172/jci148136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB) is a persistent global pandemic, and standard treatment for it has not changed for 30 years. Mycobacterium tuberculosis (Mtb) has undergone prolonged coevolution with humans, and patients can control Mtb even after extensive infection, demonstrating the fine balance between protective and pathological host responses within infected granulomas. We hypothesized that whole transcriptome analysis of human TB granulomas isolated by laser capture microdissection could identify therapeutic targets, and that comparison with a noninfectious granulomatous disease, sarcoidosis, would identify disease-specific pathological mechanisms. Bioinformatic analysis of RNAseq data identified numerous shared pathways between TB and sarcoidosis lymph nodes, and also specific clusters demonstrating TB results from a dysregulated inflammatory immune response. To translate these insights, we compared 3 primary human cell culture models at the whole transcriptome level and demonstrated that the 3D collagen granuloma model most closely reflected human TB disease. We investigated shared signaling pathways with human disease and identified 12 intracellular enzymes as potential therapeutic targets. Sphingosine kinase 1 inhibition controlled Mtb growth, concurrently reducing intracellular pH in infected monocytes and suppressing inflammatory mediator secretion. Immunohistochemical staining confirmed that sphingosine kinase 1 is expressed in human lung TB granulomas, and therefore represents a host therapeutic target to improve TB outcomes.
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Affiliation(s)
- Michaela T. Reichmann
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Liku B. Tezera
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Department of Infection and Immunity, University College London, London, United Kingdom
| | - Andres F. Vallejo
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Milica Vukmirovic
- Firestone Institute for Respiratory Health-Division of Respirology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Rui Xiao
- Columbia University Medical Center, New York, New York, USA
| | | | - Sanjay Jogai
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Susan Wilson
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ben Marshall
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Mark G. Jones
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Alasdair Leslie
- Department of Infection and Immunity, University College London, London, United Kingdom
- Africa Health Research Institute, KwaZulu Natal, South Africa
| | | | - Naftali Kaminski
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Marta E. Polak
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Paul Elkington
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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11
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Davies J, Vallejo AF, Sirvent S, Porter G, Clayton K, Qumbelo Y, Stumpf P, West J, Gray CM, Chigorimbo-Murefu NTL, MacArthur B, Polak ME. An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells. Front Immunol 2021; 12:665312. [PMID: 34211464 PMCID: PMC8239435 DOI: 10.3389/fimmu.2021.665312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/25/2021] [Indexed: 12/27/2022] Open
Abstract
Langerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels, coordinating both immunogenic and tolerogenic immune responses. To determine molecular switches directing induction of LC immune activation, we performed mathematical modelling of gene regulatory networks identified by single cell RNA sequencing of LCs exposed to TNF-alpha, a key pro-inflammatory signal produced by the skin. Our approach delineated three programmes of LC phenotypic activation (immunogenic, tolerogenic or ambivalent), and confirmed that TNF-alpha enhanced LC immunogenic programming. Through regulon analysis followed by mutual information modelling, we identified IRF1 as the key transcription factor for the regulation of immunogenicity in LCs. Application of a mathematical toggle switch model, coupling IRF1 with tolerance-inducing transcription factors, determined the key set of transcription factors regulating the switch between tolerance and immunogenicity, and correctly predicted LC behaviour in LCs derived from different body sites. Our findings provide a mechanistic explanation of how combinatorial interactions between different transcription factors can coordinate specific transcriptional programmes in human LCs, interpreting the microenvironmental context of the local tissue microenvironments.
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Affiliation(s)
- James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sofia Sirvent
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gemma Porter
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kalum Clayton
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Yamkela Qumbelo
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Patrick Stumpf
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Jonathan West
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Clive M Gray
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nyaradzo T L Chigorimbo-Murefu
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ben MacArthur
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Marta E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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12
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Rettman P, Blunt MD, Fulton RJ, Vallejo AF, Bastidas-Legarda LY, España-Serrano L, Polak ME, Al-Shamkhani A, Retiere C, Khakoo SI. Peptide: MHC-based DNA vaccination strategy to activate natural killer cells by targeting killer cell immunoglobulin-like receptors. J Immunother Cancer 2021; 9:e001912. [PMID: 34016721 PMCID: PMC8141441 DOI: 10.1136/jitc-2020-001912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Natural killer (NK) cells are increasingly being recognized as agents for cancer immunotherapy. The killer cell immunoglobulin-like receptors (KIRs) are expressed by NK cells and are immunogenetic determinants of the outcome of cancer. In particular, KIR2DS2 is associated with protective responses to several cancers and also direct recognition of cancer targets in vitro. Due to the high homology between activating and inhibitory KIR genes to date, it has been challenging to target individual KIR for therapeutic benefit. METHODS A novel KIR2DS2-targeting therapeutic peptide:MHC DNA vaccine was designed and used to immunize mice transgenic for KIR genes (KIR-Tg). NK cells were isolated from the livers and spleens of vaccinated mice and then analyzed for activation by flow cytometry, RNA profiling and cytotoxicity assays. In vivo assays of NK cell function using a syngeneic cancer model (B16 melanoma) and an adoptive transfer model for human hepatocellular carcinoma (Huh7) were performed. RESULTS Injecting KIR-Tg mice with the vaccine construct activated NK cells in both liver and spleens of mice, with preferential activation of KIR2DS2-positive NK cells. KIR-specific activation was most marked on the CD11b+CD27+ mature subset of NK cells. RNA profiling indicated that the DNA vaccine upregulated genes associated with cellular metabolism and downregulated genes related to histone H3 methylation, which are associated with immune cell maturation and NK cell function. Vaccination led to canonical and cross-reactive peptide:MHC-specific NK cell responses. In vivo, DNA vaccination led to enhanced antitumor responses against B16F10 melanoma cells and also enhanced responses against a tumor model expressing the KIR2DS2 ligand HLA-C*0102. CONCLUSION We show the feasibility of a peptide-based KIR-targeting vaccine strategy to activate NK cells and hence generate functional antitumor responses. This approach does not require detailed knowledge of the tumor peptidomes nor HLA matching with the patient. It therefore offers a novel opportunity for targeting NK cells for cancer immunotherapy.
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MESH Headings
- Animals
- Cancer Vaccines/administration & dosage
- Cancer Vaccines/genetics
- Cancer Vaccines/immunology
- Cell Line, Tumor
- Cytotoxicity, Immunologic/drug effects
- HLA-C Antigens/administration & dosage
- HLA-C Antigens/genetics
- HLA-C Antigens/immunology
- Haplotypes
- Humans
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lectins, C-Type/genetics
- Lectins, C-Type/immunology
- Lectins, C-Type/metabolism
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/immunology
- Liver Neoplasms/metabolism
- Lymphocyte Activation/drug effects
- Lymphocytes, Tumor-Infiltrating/drug effects
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Melanoma, Experimental/drug therapy
- Melanoma, Experimental/genetics
- Melanoma, Experimental/immunology
- Melanoma, Experimental/metabolism
- Mice, Inbred C57BL
- Mice, Transgenic
- Peptides/administration & dosage
- Peptides/genetics
- Peptides/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Receptors, Immunologic/metabolism
- Receptors, KIR/genetics
- Receptors, KIR/immunology
- Receptors, KIR/metabolism
- Skin Neoplasms/drug therapy
- Skin Neoplasms/genetics
- Skin Neoplasms/immunology
- Skin Neoplasms/metabolism
- Vaccination
- Vaccines, DNA/administration & dosage
- Vaccines, DNA/genetics
- Vaccines, DNA/immunology
- Mice
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Affiliation(s)
- Pauline Rettman
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Matthew D Blunt
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rebecca J Fulton
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andres F Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Leidy Y Bastidas-Legarda
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Laura España-Serrano
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Marta E Polak
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Aymen Al-Shamkhani
- Antibody and Vaccine Group, Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Salim I Khakoo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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13
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Vallejo AF, Davies J, Grover A, Tsai CH, Jepras R, Polak ME, West J. Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering. iScience 2021; 24:102147. [PMID: 33665566 PMCID: PMC7900351 DOI: 10.1016/j.isci.2021.102147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/09/2020] [Accepted: 01/31/2021] [Indexed: 12/24/2022] Open
Abstract
Single-cell transcriptomics suffer from sensitivity limits that restrict low abundance transcript identification, affects clustering and can hamper downstream analyses. Here, we describe Constellation sequencing (Constellation-Seq), a molecular transcriptome filter that delivers two orders of magnitude sensitivity gains by maximizing read utility while reducing the data sparsity and sequencing costs. The technique reliably measures changes in gene expression and was demonstrated by resolving rare dendritic cell populations from a peripheral blood mononuclear cell sample sample and exploring their biology with extreme resolution. The simple and powerful method is fully compatible with standard scRNA-Seq library preparation protocols and can be used for hypothesis testing, marker validation or investigating pathways.
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Affiliation(s)
- Andres F. Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
| | - James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
| | - Amit Grover
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Ching-Hsuan Tsai
- GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Robert Jepras
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Marta E. Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Jonathan West
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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14
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Ashton JJ, Boukas K, Davies J, Stafford IS, Vallejo AF, Haggarty R, Coelho TAF, Batra A, Afzal NA, Vadgama B, Williams AP, Beattie RM, Polak ME, Ennis S. Ileal Transcriptomic Analysis in Paediatric Crohn's Disease Reveals IL17- and NOD-signalling Expression Signatures in Treatment-naïve Patients and Identifies Epithelial Cells Driving Differentially Expressed Genes. J Crohns Colitis 2020; 15:774-786. [PMID: 33232439 PMCID: PMC8095388 DOI: 10.1093/ecco-jcc/jjaa236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] arises through host-environment interaction. Abnormal gene expression results from disturbed pathway activation or response to bacteria. We aimed to determine activated pathways and driving cell types in paediatric CD. METHODS We employed contemporary targeted autoimmune RNA sequencing, in parallel to single-cell sequencing, to ileal tissue derived from paediatric CD and controls. Weighted gene co-expression network analysis [WGCNA] was performed and differentially expressed genes [DEGs] were determined. We integrated clinical data to determine co-expression modules associated with outcomes. RESULTS In all, 27 treatment-naive CD [TN-CD], 26 established CD patients and 17 controls were included. WGCNA revealed a 31-gene signature characterising TN-CD patients, but not established CD, nor controls. The CSF3R gene is a hub within this module and is key in neutrophil expansion and differentiation. Antimicrobial genes, including S100A12 and the calprotectin subunit S100A9, were significantly upregulated in TN CD compared with controls [p = 2.61 x 10-15 and p = 9.13 x 10-14, respectively] and established CD [both p = 0.0055]. Gene-enrichment analysis confirmed upregulation of the IL17-, NOD- and Oncostatin-M-signalling pathways in TN-CD patients, identified in both WGCNA and DEG analyses. An upregulated gene signature was enriched for transcripts promoting Th17-cell differentiation and correlated with prolonged time to relapse [correlation-coefficient-0.36, p = 0.07]. Single-cell sequencing of TN-CD patients identified specialised epithelial cells driving differential expression of S100A9. Cell groups, determined by single-cell gene expression, demonstrated enrichment of IL17-signalling in monocytes and epithelial cells. CONCLUSIONS Ileal tissue from treatment-naïve paediatric patients is significantly upregulated for genes driving IL17-, NOD- and Oncostatin-M-signalling. This signal is driven by a distinct subset of epithelial cells expressing antimicrobial gene transcripts.
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Affiliation(s)
- James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK,Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Konstantinos Boukas
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
| | - James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Imogen S Stafford
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rachel Haggarty
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Tracy A F Coelho
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Akshay Batra
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Nadeem A Afzal
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Bhumita Vadgama
- Department of Paediatric Histopathology, Southampton Children’s Hospital, Southampton, UK
| | - Anthony P Williams
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - R Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Marta E Polak
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK,Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK,Corresponding author: Professor Sarah Ennis, PhD, Human Genetics and Genomic Medicine, University of Southampton, Duthie Building [Mailpoint 808], Southampton General Hospital, Southampton SO16 6YD, UK. Tel.: +44 [0]23 8079 8614;
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15
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Garay-Baquero DJ, White CH, Walker NF, Tebruegge M, Schiff HF, Ugarte-Gil C, Morris-Jones S, Marshall BG, Manousopoulou A, Adamson J, Vallejo AF, Bielecka MK, Wilkinson RJ, Tezera LB, Woelk CH, Garbis SD, Elkington P. Comprehensive plasma proteomic profiling reveals biomarkers for active tuberculosis. JCI Insight 2020; 5:137427. [PMID: 32780727 PMCID: PMC7526553 DOI: 10.1172/jci.insight.137427] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUNDTuberculosis (TB) kills more people than any other infection, and new diagnostic tests to identify active cases are required. We aimed to discover and verify novel markers for TB in nondepleted plasma.METHODSWe applied an optimized quantitative proteomics discovery methodology based on multidimensional and orthogonal liquid chromatographic separation combined with high-resolution mass spectrometry to study nondepleted plasma of 11 patients with active TB compared with 10 healthy controls. Prioritized candidates were verified in independent UK (n = 118) and South African cohorts (n = 203).RESULTSWe generated the most comprehensive TB plasma proteome to date, profiling 5022 proteins spanning 11 orders-of-magnitude concentration range with diverse biochemical and molecular properties. We analyzed the predominantly low-molecular weight subproteome, identifying 46 proteins with significantly increased and 90 with decreased abundance (peptide FDR ≤ 1%, q ≤ 0.05). Verification was performed for novel candidate biomarkers (CFHR5, ILF2) in 2 independent cohorts. Receiver operating characteristics analyses using a 5-protein panel (CFHR5, LRG1, CRP, LBP, and SAA1) exhibited discriminatory power in distinguishing TB from other respiratory diseases (AUC = 0.81).CONCLUSIONWe report the most comprehensive TB plasma proteome to date, identifying novel markers with verification in 2 independent cohorts, leading to a 5-protein biosignature with potential to improve TB diagnosis. With further development, these biomarkers have potential as a diagnostic triage test.FUNDINGColciencias, Medical Research Council, Innovate UK, NIHR, Academy of Medical Sciences, Program for Advanced Research Capacities for AIDS, Wellcome Centre for Infectious Diseases Research.
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Affiliation(s)
- Diana J Garay-Baquero
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California, USA
| | - Cory H White
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | - Naomi F Walker
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Department of Medicine, University of Cape Town, Observatory 7925, South Africa.,TB Centre and Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marc Tebruegge
- Department of Paediatric Infectious Diseases & Immunology, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom.,Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Hannah F Schiff
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | - Cesar Ugarte-Gil
- TB Centre and Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom.,Instituto de Medicina Tropical Alexander von Humboldt, School of Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Stephen Morris-Jones
- Department of Microbiology, University College London Hospitals NHS Trust, London, United Kingdom.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Ben G Marshall
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,National Institute for Health Research (NIHR) Biomedical Research Centre, University Hospital NHS Foundation Trust, Southampton, Southampton, United Kingdom
| | | | - John Adamson
- Pharmacology Core, Africa Health Research Institute (AHRI), Durban, South Africa
| | - Andres F Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, and
| | | | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Department of Medicine, University of Cape Town, Observatory 7925, South Africa.,The Francis Crick Institute, London, United Kingdom.,Department of Infectious Diseases, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Liku B Tezera
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Spiros D Garbis
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California, USA.,Cancer Sciences Division, Faculty of Medicine, University of Southampton, United Kingdom
| | - Paul Elkington
- School of Clinical and Experimental Sciences, Faculty of Medicine, and.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.,National Institute for Health Research (NIHR) Biomedical Research Centre, University Hospital NHS Foundation Trust, Southampton, Southampton, United Kingdom
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16
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Sirvent S, Vallejo AF, Davies J, Clayton K, Wu Z, Woo J, Riddell J, Chaudhri VK, Stumpf P, Nazlamova LA, Wheway G, Rose-Zerilli M, West J, Pujato M, Chen X, Woelk CH, MacArthur B, Ardern-Jones M, Friedmann PS, Weirauch MT, Singh H, Polak ME. Genomic programming of IRF4-expressing human Langerhans cells. Nat Commun 2020; 11:313. [PMID: 31949143 PMCID: PMC6965086 DOI: 10.1038/s41467-019-14125-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 12/19/2019] [Indexed: 02/07/2023] Open
Abstract
Langerhans cells (LC) can prime tolerogenic as well as immunogenic responses in skin, but the genomic states and transcription factors (TF) regulating these context-specific responses are unclear. Bulk and single-cell transcriptional profiling demonstrates that human migratory LCs are robustly programmed for MHC-I and MHC-II antigen presentation. Chromatin analysis reveals enrichment of ETS-IRF and AP1-IRF composite regulatory elements in antigen-presentation genes, coinciding with expression of the TFs, PU.1, IRF4 and BATF3 but not IRF8. Migration of LCs from the epidermis is accompanied by upregulation of IRF4, antigen processing components and co-stimulatory molecules. TNF stimulation augments LC cross-presentation while attenuating IRF4 expression. CRISPR-mediated editing reveals IRF4 to positively regulate the LC activation programme, but repress NF2EL2 and NF-kB pathway genes that promote responsiveness to oxidative stress and inflammatory cytokines. Thus, IRF4-dependent genomic programming of human migratory LCs appears to enable LC maturation while attenuating excessive inflammatory and immunogenic responses in the epidermis. Langerhans cells (LC) can prime tolerogenic as well as immunogenic responses in the skin. Here the authors show, by transcriptomic, epigenetic and CRISPR editing analyses, that during LC migration and maturation the transcription factor IRF4 regulates expression of antigen presentation and co-stimulatory gene modules while attenuating inflammatory response genes.
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Affiliation(s)
- Sofia Sirvent
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Kalum Clayton
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Zhiguo Wu
- Division of Immunobiology & Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jeongmin Woo
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Jeremy Riddell
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Virendra K Chaudhri
- Division of Immunobiology & Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, The University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Patrick Stumpf
- Human Development and Health, Faculty of Medicine, University of Southampton, SO17 1BJ, Southampton, UK
| | - Liliya Angelova Nazlamova
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, SO17 1BJ, Southampton, UK
| | - Matthew Rose-Zerilli
- Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Jonathan West
- Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK.,Institute for Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Mario Pujato
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | | | - Ben MacArthur
- Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK.,Institute for Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Michael Ardern-Jones
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Peter S Friedmann
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
| | - Harinder Singh
- Division of Immunobiology & Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA. .,Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, The University of Pittsburgh, Pittsburgh, PA, 15213, USA.
| | - Marta E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK. .,Institute for Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK.
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17
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Hydes TJ, Blunt MD, Naftel J, Vallejo AF, Seumois G, Wang A, Vijayanand P, Polak ME, Khakoo SI. Constitutive Activation of Natural Killer Cells in Primary Biliary Cholangitis. Front Immunol 2019; 10:2633. [PMID: 31803181 PMCID: PMC6874097 DOI: 10.3389/fimmu.2019.02633] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
Natural killer (NK) cells are innate immune cells that interface with the adaptive immune system to generate a pro-inflammatory immune environment. Primary Biliary Cholangitis (PBC) is a hepatic autoimmune disorder with extrahepatic associations including systemic sclerosis, Sjogren's syndrome and thyroiditis. Immunogenetic studies have identified polymorphisms of the IL-12/STAT4 pathway as being associated with PBC. As this pathway is important for NK cell function we investigated NK cells in PBC. Circulating NK cells from individuals with PBC were constitutively activated, with higher levels of CD49a and the liver-homing marker, CXCR6, compared to participants with non-autoimmune chronic liver disease and healthy controls. Stimulation with minimal amounts of IL-12 (0.005 ng/ml) led to significant upregulation of CXCR6 (p < 0.005), and enhanced IFNγ production (p < 0.02) on NK cells from PBC patients compared to individuals with non-autoimmune chronic liver disease, indicating dysregulation of the IL-12/STAT4 axis. In RNAseq studies, resting NK cells from PBC patients had a constitutively activated transcriptional profile and upregulation of genes associated with IL-12/STAT4 signaling and metabolic reprogramming. Consistent with these findings, resting NK cells from PBC patients expressed higher levels of pSTAT4 compared to control groups (p < 0.001 vs. healthy controls and p < 0.05 vs. liver disease controls). In conclusion NK cells in PBC are sensitive to minute quantities of IL-12 and have a “primed” phenotype. We therefore propose that peripheral priming of NK cells to express tissue-homing markers may contribute to the pathophysiology of PBC.
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Affiliation(s)
- Theresa J Hydes
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Matthew D Blunt
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jennifer Naftel
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Grégory Seumois
- Department of Medicine, La Jolla Institute for Allergy and Immunology, University of California, San Diego, San Diego, CA, United States
| | - Alice Wang
- Department of Medicine, La Jolla Institute for Allergy and Immunology, University of California, San Diego, San Diego, CA, United States
| | - Pandurangan Vijayanand
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Department of Medicine, La Jolla Institute for Allergy and Immunology, University of California, San Diego, San Diego, CA, United States
| | - Marta E Polak
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Salim I Khakoo
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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18
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Vallejo AF, Read RC, Arevalo-Herrera M, Herrera S, Elliott T, Polak ME. Malaria systems immunology: Plasmodium vivax induces tolerance during primary infection through dysregulation of neutrophils and dendritic cells. J Infect 2018; 77:440-447. [PMID: 30248353 PMCID: PMC6203889 DOI: 10.1016/j.jinf.2018.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/14/2018] [Accepted: 09/15/2018] [Indexed: 12/19/2022]
Abstract
OBJECTIVES To dissect the transcriptional networks underpinning immune cells responses during primary Plasmodium vivax infection of healthy human adults. METHODS We conducted network co-expression analysis of next-generation RNA sequencing data from whole blood from P. vivax and P. falciparum controlled human malaria infection (CHMI) of healthy naïve and malaria-exposed volunteers. Single cell transcription signatures were used to deconvolute the bulk RNA-Seq data into cell-specific signals. RESULTS Initial exposure to P. vivax induced activation of innate immunity, including efficient antigen presentation and complement activation. However, this effect was accompanied by strong immunosuppression mediated by dendritic cells via the induction of Indoleamine 2,3-Dioxygenase 1(IDO1) and Lymphocyte Activation Gene 3 (LAG3). Additionally, P. vivax induced depletion of neutrophil populations associated with down regulation of 3G-protein coupled receptors, CRXCR1, CXCR2 and CSF3R. Accordingly, in malaria-exposed volunteers the inflammatory response was attenuated, with a decreased class II antigen presentation in dendritic cells. While the immunosuppressive signalling was maintained between plasmodium species, response to P. falciparum was significantly more immunogenic. CONCLUSIONS In silico analyses suggest that primary infection with P. vivax induces potent immunosuppression mediated by dendritic cells, conditioning subsequent anti-malarial immune responses. Targeting immune evasion mechanisms could be an effective alternative for improving vaccine efficacy.
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Affiliation(s)
- Andres F Vallejo
- Clinical and Experimental Sciences and NIHR Southampton Biomedical Research Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, LE59, MP813, SO16 6YD, Southampton, UK
| | - Robert C Read
- Clinical and Experimental Sciences and NIHR Southampton Biomedical Research Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, LE59, MP813, SO16 6YD, Southampton, UK
| | - Myriam Arevalo-Herrera
- Caucaseco Scientific Research Center, Cali, 760043, Colombia; School of Health, Universidad del Valle, Cali, 76001, Colombia
| | | | - Tim Elliott
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK; Institute for Life Sciences, University of Southampton, SO17 1BJ, UK
| | - Marta E Polak
- Clinical and Experimental Sciences and NIHR Southampton Biomedical Research Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, LE59, MP813, SO16 6YD, Southampton, UK; Institute for Life Sciences, University of Southampton, SO17 1BJ, UK.
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19
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Abstract
Langerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels. These cells determine the appropriate adaptive immune response (inflammation or tolerance) by interpreting the microenvironmental context in which they encounter foreign substances. In a normal physiological, "non-dangerous" situation, LCs coordinate a continuous state of immune tolerance, preventing unnecessary and harmful immune activation. Conversely, when they sense a danger signal, for example during infection or when the physical integrity of skin has been compromised as a result of a trauma, they instruct T lymphocytes of the adaptive immune system to mount efficient effector responses. Recent advances investigating the molecular mechanisms underpinning the cross talk between LCs and the epidermal microenvironment reveal its importance for programming LC biology. This review summarizes the novel findings describing LC origin and function through the analysis of the transcriptomic programs and gene regulatory networks (GRNs). Review and meta-analysis of publicly available datasets clearly delineates LCs as distinct from both conventional dendritic cells (DCs) and macrophages, suggesting a primary role for the epidermal microenvironment in programming LC biology. This concept is further supported by the analysis of the effect of epidermal pro-inflammatory signals, regulating key GRNs in human and murine LCs. Applying whole transcriptome analyses and in silico analysis has advanced our understanding of how LCs receive, integrate, and process signals from the steady-state and diseased epidermis. Interestingly, in homeostasis and under immunological stress, the molecular network in LCs remains relatively stable, reflecting a key evolutionary need related to tissue localization. Importantly, to fulfill their key role in orchestrating antiviral adaptive immune responses, LC share specific transcriptomic modules with other DC types able to cross-present antigens to cytotoxic CD8+ T cells, pointing to a possible evolutionary convergence mechanism. With the development of more advanced technologies allowing delineation of the molecular networks at the level of chromatin organization, histone modifications, protein translation, and phosphorylation, future "omics" investigations will bring in-depth understanding of the complex molecular mechanisms underpinning human LC biology.
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Affiliation(s)
- Kalum Clayton
- Systems Immmunology Group, Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F Vallejo
- Systems Immmunology Group, Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - James Davies
- Systems Immmunology Group, Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sofia Sirvent
- Systems Immmunology Group, Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Marta E Polak
- Systems Immmunology Group, Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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20
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Lennon SE, Miranda A, Henao J, Vallejo AF, Perez J, Alvarez A, Arévalo-Herrera M, Herrera S. Malaria elimination challenges in Mesoamerica: evidence of submicroscopic malaria reservoirs in Guatemala. Malar J 2016; 15:441. [PMID: 27577992 PMCID: PMC5006524 DOI: 10.1186/s12936-016-1500-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/20/2016] [Indexed: 11/23/2022] Open
Abstract
Background Even though malaria incidence has decreased substantially in Guatemala since 2000, Guatemala remains one of the countries with the highest malaria transmission in Mesoamerica. Guatemala is committed to eliminating malaria as part of the initiative ‘Elimination of Malaria in Mesoamerica and the Island of Hispaniola’ (EMMIE); however, it is still in the control phase. During the past decade, the government strengthened malaria control activities including mass distribution of long-lasting insecticide-impregnated bed nets, early diagnosis and prompt treatment. This study aimed to determine the prevalence of malaria, including gametocytes, in three areas of Guatemala using active case detection (ACD) and quantitative polymerase chain reaction (qPCR). Methods Cross-sectional surveys were conducted in three departments with varying transmission intensities: Escuintla, Alta Verapaz and Zacapa. Blood samples from 706 volunteers were screened for malaria using microscopy and qPCR which was also used to determine the prevalence of gametocytes among infected individuals. Results were collected and analysed using REDCap and R Project, respectively. Results Malaria was diagnosed by microscopy in only 2.8 % (4/141) of the volunteers from Escuintla. By contrast, qPCR detected a prevalence of 7.1 % (10/141) in the same volunteers, 8.4 % (36/429) in Alta Verapaz, and 5.9 % (8/136) in Zacapa. Overall, 7.6 % (54/706) of the screened individuals were positive, with an average parasitaemia level of 40.2 parasites/μL (range 1–1133 parasites/μL) and 27.8 % carried mature gametocytes. Fifty-seven percent (31/54) of qPCR positive volunteers were asymptomatic and out of the 42.6 % of symptomatic individuals, only one had a positive microscopy result. Conclusions This study found a considerable number of asymptomatic P. vivax infections that were mostly submicroscopic, of which, approximately one-quarter harboured mature gametocytes. This pattern is likely to contribute to maintaining transmission across the region. Robust surveillance systems, molecular diagnostic tests and tailored malaria detection activities for each endemic site may prove to be imperative in accelerating malaria elimination in Guatemala and possibly across all of Mesoamerica. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1500-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Adolfo Miranda
- Centro Nacional de Epidemiología (CNE), Guatemala City, Guatemala
| | - Juliana Henao
- Malaria Vaccine and Drug Development Center (MVDC), Cali, Colombia
| | - Andres F Vallejo
- Malaria Vaccine and Drug Development Center (MVDC), Cali, Colombia
| | - Julianh Perez
- Malaria Vaccine and Drug Development Center (MVDC), Cali, Colombia
| | - Alvaro Alvarez
- Malaria Vaccine and Drug Development Center (MVDC), Cali, Colombia
| | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center (CSRC)/Centro Latino Americano de Investigación en Malaria (CLAIM), Cali, Colombia.,Facultad de Salud, Universidad del Valle, Cali, Colombia
| | - Sócrates Herrera
- Malaria Vaccine and Drug Development Center (MVDC), Cali, Colombia. .,Caucaseco Scientific Research Center (CSRC)/Centro Latino Americano de Investigación en Malaria (CLAIM), Cali, Colombia.
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21
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Vallejo AF, Martinez NL, Tobon A, Alger J, Lacerda MV, Kajava AV, Arévalo-Herrera M, Herrera S. Global genetic diversity of the Plasmodium vivax transmission-blocking vaccine candidate Pvs48/45. Malar J 2016; 15:202. [PMID: 27067024 PMCID: PMC4828788 DOI: 10.1186/s12936-016-1263-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/31/2016] [Indexed: 12/17/2022] Open
Abstract
Background Plasmodium vivax 48/45 protein is expressed on the surface of gametocytes/gametes and plays a key role in gamete fusion during fertilization. This protein was recently expressed in Escherichia coli host as a recombinant product that was highly immunogenic in mice and monkeys and induced antibodies with high transmission-blocking activity, suggesting its potential as a P. vivax transmission-blocking vaccine candidate. To determine sequence polymorphism of natural parasite isolates and its potential influence on the protein structure, all pvs48/45 sequences reported in databases from around the world as well as those from low-transmission settings of Latin America were compared. Methods Plasmodium vivax parasite isolates from malaria-endemic regions of Colombia, Brazil and Honduras (n = 60) were used to sequence the Pvs48/45 gene, and compared to those previously reported to GenBank and PlasmoDB (n = 222). Pvs48/45 gene haplotypes were analysed to determine the functional significance of genetic variation in protein structure and vaccine potential. Results Nine non-synonymous substitutions (E35K, Y196H, H211N, K250N, D335Y, E353Q, A376T, K390T, K418R) and three synonymous substitutions (I73, T149, C156) that define seven different haplotypes were found among the 282 isolates from nine countries when compared with the Sal I reference sequence. Nucleotide diversity (π) was 0.00173 for worldwide samples (range 0.00033–0.00216), resulting in relatively high diversity in Myanmar and Colombia, and low diversity in Mexico, Peru and South Korea. The two most frequent substitutions (E353Q: 41.9 %, K250N: 39.5 %) were predicted to be located in antigenic regions without affecting putative B cell epitopes or the tertiary protein structure. Conclusions There is limited sequence polymorphism in pvs48/45 with noted geographical clustering among Asian and American isolates. The low genetic diversity of the protein does not influence the predicted antigenicity or protein structure and, therefore, supports its further development as transmission-blocking vaccine candidate.
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Affiliation(s)
| | | | | | - Jackeline Alger
- Facultad de Ciencias Médicas, Hospital Escuela Universitario, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Marcus V Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Andrey V Kajava
- Centre de Recherches Biochimie Macromoléculaire (CRBM), Institut de Biologie Computationnelle (IBC), CNRS, University of Montpellier, Montpellier, France.,Institute of Bioengineering, University ITMO, Saint Petersburg, Russia
| | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia.,School of Health, Universidad del Valle, Cali, Colombia
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Winter DJ, Pacheco MA, Vallejo AF, Schwartz RS, Arevalo-Herrera M, Herrera S, Cartwright RA, Escalante AA. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia. PLoS Negl Trop Dis 2015; 9:e0004252. [PMID: 26709695 PMCID: PMC4692395 DOI: 10.1371/journal.pntd.0004252] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/30/2015] [Indexed: 11/24/2022] Open
Abstract
Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. Although P. vivax is not as deadly as the more widely studied P. falciparum, it remains a pressing global health problem. Here we report the results of a whole-genome study of P. vivax from Cordóba, Colombia, in South America. This parasite is the most prevalent in this region. We show that the parasite population is genetically diverse, which is contrary to expectations from earlier studies from the Americas. We also find molecular evidence that resistance to an anti-malarial drug has arisen recently in this region. This selective sweep indicates that the parasite has been exposed to a drug that is not used as first-line treatment for this malaria parasite. In addition to extensive single nucleotide and microsatellite polymorphism, we report 18 new genetic loci that might be helpful for fine-scale studies of this species in the Americas.
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Affiliation(s)
- David J. Winter
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- * E-mail: (DJW); (AAE)
| | - M. Andreína Pacheco
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
| | | | - Rachel S. Schwartz
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Myriam Arevalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia
- Faculty of Health, Universidad del Valle, Cali, Colombia
| | | | - Reed A. Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- The School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Ananias A. Escalante
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (DJW); (AAE)
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Escalante AA, Ferreira MU, Vinetz JM, Volkman SK, Cui L, Gamboa D, Krogstad DJ, Barry AE, Carlton JM, van Eijk AM, Pradhan K, Mueller I, Greenhouse B, Andreina Pacheco M, Vallejo AF, Herrera S, Felger I. Malaria Molecular Epidemiology: Lessons from the International Centers of Excellence for Malaria Research Network. Am J Trop Med Hyg 2015; 93:79-86. [PMID: 26259945 PMCID: PMC4574277 DOI: 10.4269/ajtmh.15-0005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 05/15/2015] [Indexed: 01/31/2023] Open
Abstract
Molecular epidemiology leverages genetic information to study the risk factors that affect the frequency and distribution of malaria cases. This article describes molecular epidemiologic investigations currently being carried out by the International Centers of Excellence for Malaria Research (ICEMR) network in a variety of malaria-endemic settings. First, we discuss various novel approaches to understand malaria incidence and gametocytemia, focusing on Plasmodium falciparum and Plasmodium vivax. Second, we describe and compare different parasite genotyping methods commonly used in malaria epidemiology and population genetics. Finally, we discuss potential applications of molecular epidemiological tools and methods toward malaria control and elimination efforts.
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Affiliation(s)
- Ananias A. Escalante
- *Address correspondence to Ananias A. Escalante, Institute for Genomics and Evolutionary Medicine, Temple University, SERC Building, 1925 N. 12th Street Philadelphia, PA 19122-1801, E-mail: or Marcelo U. Ferreira, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 1374 - Edifício Biomédicas II, São Paulo, Brazil CEP CEP 05508-900, E-mail: or Ingrid Felger, Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland, E-mail:
| | - Marcelo U. Ferreira
- *Address correspondence to Ananias A. Escalante, Institute for Genomics and Evolutionary Medicine, Temple University, SERC Building, 1925 N. 12th Street Philadelphia, PA 19122-1801, E-mail: or Marcelo U. Ferreira, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 1374 - Edifício Biomédicas II, São Paulo, Brazil CEP CEP 05508-900, E-mail: or Ingrid Felger, Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland, E-mail:
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ingrid Felger
- *Address correspondence to Ananias A. Escalante, Institute for Genomics and Evolutionary Medicine, Temple University, SERC Building, 1925 N. 12th Street Philadelphia, PA 19122-1801, E-mail: or Marcelo U. Ferreira, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 1374 - Edifício Biomédicas II, São Paulo, Brazil CEP CEP 05508-900, E-mail: or Ingrid Felger, Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland, E-mail:
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Vallejo AF, Chaparro PE, Benavides Y, Álvarez Á, Quintero JP, Padilla J, Arévalo-Herrera M, Herrera S. High prevalence of sub-microscopic infections in Colombia. Malar J 2015; 14:201. [PMID: 25971594 PMCID: PMC4438632 DOI: 10.1186/s12936-015-0711-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/23/2015] [Indexed: 11/18/2022] Open
Abstract
Background Malaria transmission in Latin America is typically characterized as hypo-endemic and unstable with ~170 million inhabitants at risk of malaria infection. Although Colombia has witnessed an important decrease in malaria transmission, the disease remains a public health problem with an estimated ~10 million people currently living in areas with malaria risk and ~61,000 cases reported in 2012. This study aimed to establish the malaria prevalence in three endemic regions of Colombia to aid in designing new interventions for malaria elimination. Methods A cross-sectional survey was conducted in three regions of Colombia with different malaria epidemiological profiles: Tierralta (Ta), Tumaco (Tu) and Buenaventura (Bv). The Annual Parasite Index (API) was 10.7, 6.9 and 3.1, respectively. Participants were asked to respond to a sociodemographic questionnaire and then were bled to determine the Duffy genotype and the prevalence of malaria infection by microscopy and quantitative real-time PCR (qPCR). Results The study was conducted between October 2011 and January 2012. Eight sentinel sites with 1,169 subjects from 267 households were included. The overall prevalence of sub-microscopic infections measured by thick blood smear (TBS) was 0.3% (n = 4) whereas by qPCR it was 9.7% (n = 113), with a greater proportion (13%) in 40-50 years old individuals. Furthermore, different regions displayed different prevalence of sub-microscopic infections: Bv 12%, Ta 15%, and Tu 4%. From these 113 samples (qPCR), 74% were positive for P. vivax and 22% for P. falciparum, and 4% were mixed infections, which correlates to the overall parasite prevalence in Colombia. This study showed that in the southern Pacific coast of Colombia (Bv and Tu), around 56% of the population have a Duffy-negative genotype, compared to the northern region (Ta) where the percentage of Duffy-negative genotype is around 3%. Conclusions Sub-microscopic infections are prevalent across different regions in Colombia, particularly in areas with relatively low transmission intensity. The poor microscopy results suggest the need for more sensitive diagnostic tools for detection of sub-microscopic infections. This study underscores the importance of conducting active case surveillance to more accurately determine malaria incidence, and highlights the need for updating the malaria guidelines to track and treat sub-microscopic malaria infections.
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Affiliation(s)
| | | | | | | | | | - Julio Padilla
- Ministry of Health and Social Protection of Colombia, Bogotá, Colombia.
| | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia. .,Latin American Center for Malaria Research, Cali, Colombia. .,School of Health, Universidad del Valle, Cali, Colombia.
| | - Sócrates Herrera
- Caucaseco Scientific Research Center, Cali, Colombia. .,Latin American Center for Malaria Research, Cali, Colombia.
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25
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Forero DA, Chaparro PE, Vallejo AF, Benavides Y, Gutiérrez JB, Arévalo-Herrera M, Herrera S. Knowledge, attitudes and practices of malaria in Colombia. Malar J 2014; 13:165. [PMID: 24885909 PMCID: PMC4113137 DOI: 10.1186/1475-2875-13-165] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/22/2014] [Indexed: 12/24/2022] Open
Abstract
Background Although Colombia has witnessed an important decrease in malaria transmission, the disease remains a public health problem with an estimated ~10 million people currently living in areas with malaria risk and ~61,000 cases reported in 2012. This study aimed to determine and compare the level of knowledge, attitudes and practices (KAP) about malaria in three endemic communities of Colombia to provide the knowledge framework for development of new intervention strategies for malaria elimination. Methods A cross-sectional KAP survey was conducted in the municipalities of Tierralta, Buenaventura and Tumaco, categorized according to high risk (HR) and moderate risk (MR) based on the annual parasite index (API). Surveys were managed using REDCap and analysed using MATLAB and GraphPad Prism. Results A total of 267 residents, mostly women (74%) were surveyed. Although no differences were observed on the knowledge of classical malaria symptoms between HR and MR regions, significant differences were found in knowledge and attitudes about transmission mechanisms, anti-malarial use and malaria diagnosis. Most responders in both regions (93.5% in MR, and 94.3% in HR areas) indicated use of insecticide-treated nets (ITNs) to protect themselves from malaria, and 75.5% of responders in HR indicated they did nothing to prevent malaria transmission outdoors. Despite a high level of knowledge in the study regions, significant gaps persisted relating to practices. Self-medication and poor adherence to treatment, as well as lack of both indoor and outdoor vector control measures, were significantly associated with higher malaria risk. Conclusions Although significant efforts are currently being made by the Ministry of Health to use community education as one of the main components of the control strategy, these generic education programmes may not be applicable to all endemic regions of Colombia given the substantial geographic, ethnic and cultural diversity.
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Comba González N, Vallejo AF, Sánchez-Gómez M, Montoya D. Protein identification in two phases of 1,3-propanediol production by proteomic analysis. J Proteomics 2013; 89:255-64. [PMID: 23811541 DOI: 10.1016/j.jprot.2013.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 05/04/2013] [Accepted: 06/13/2013] [Indexed: 10/26/2022]
Abstract
UNLABELLED Proteomic analysis by two-dimensional electrophoresis (2D)-mass spectrometry was used to identify differentially expressed proteins in the Clostridium sp. native strain (IBUN 158B) in two phases of the 1,3-propanediol (1,3-PD) production (lag phase and exponential growth phase). Intracellular protein fraction extraction conditions were standardised, as well as the 2D electrophoresis. Differences were found between both of the growth phases evaluated here. Thirty-two of the differentially expressed proteins were chosen to be identified by tandem mass spectrometry (MALDI TOF/TOF). The presence of four enzymes implicated in the 1,3-PD metabolic pathway was recorded: one from the reductive route (1,3-propanediol dehydrogenase) and three from the oxidative route (3-hydroxybutyryl-CoA dehydrogenase, NADPH-dependent butanol dehydrogenase and phosphate butyryl transferase). The following enzymes which have not been previously reported for Clostridium sp., were also identified: phosphoglycerate kinase, glucose 6-phosphate isomerase, deoxyribose phosphate aldolase, transketolase, cysteine synthetase, O-acetylhomoserine sulphhydrylase, glycyl-tRNA ligase, aspartate-β-semialdehyde dehydrogenase, inosine-5-monophosphate dehydrogenase, aconitate hydratase and the PrsA protein. The foregoing provides a novel contribution towards knowledge of the native strain for the purpose of designing genetic manipulation strategies to obtain strains with high production of 1,3-PD. BIOLOGICAL SIGNIFICANCE The article "Protein identification in two phases of 1,3-propanediol production by proteomic analysis" provides a novel contribution towards knowledge regarding the Colombian Clostridium sp. native strain (IBUN 158B) because this is a new approximation in comparative proteomics in two phases of the bacterial growth and 1,3-propanediol (1,3-PD) production conditions. The proteomic studies are very important to identify the enzymes that are expressed at different stages of production and therefore genes of interest in the genetic manipulation strategies; the results can be taken into account in future studies in metabolic engineering when optimising 1,3-PD production, in a cost-effective process having direct industrial applications.
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Affiliation(s)
- Natalia Comba González
- Bioprocesses and Bioprospecting Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
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