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Attig J, Pape J, Doglio L, Kazachenka A, Ottina E, Young GR, Enfield KS, Aramburu IV, Ng KW, Faulkner N, Bolland W, Papayannopoulos V, Swanton C, Kassiotis G. Human endogenous retrovirus onco-exaptation counters cancer cell senescence through calbindin. J Clin Invest 2023; 133:e164397. [PMID: 37192000 PMCID: PMC10348765 DOI: 10.1172/jci164397] [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] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/11/2023] [Indexed: 05/17/2023] Open
Abstract
Increased levels and diversity of human endogenous retrovirus (HERV) transcription characterize most cancer types and are linked with disease outcomes. However, the underlying processes are incompletely understood. Here, we show that elevated transcription of HERVH proviruses predicted survival of lung squamous cell carcinoma (LUSC) and identified an isoform of CALB1, encoding calbindin, ectopically driven by an upstream HERVH provirus under the control of KLF5, as the mediator of this effect. HERVH-CALB1 expression was initiated in preinvasive lesions and associated with their progression. Calbindin loss in LUSC cell lines impaired in vitro and in vivo growth and triggered senescence, consistent with a protumor effect. However, calbindin also directly controlled the senescence-associated secretory phenotype (SASP), marked by secretion of CXCL8 and other neutrophil chemoattractants. In established carcinomas, CALB1-negative cancer cells became the dominant source of CXCL8, correlating with neutrophil infiltration and worse prognosis. Thus, HERVH-CALB1 expression in LUSC may display antagonistic pleiotropy, whereby the benefits of escaping senescence early during cancer initiation and clonal competition were offset by the prevention of SASP and protumor inflammation at later stages.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - George Kassiotis
- Retroviral Immunology
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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2
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Ng KW, Boumelha J, Enfield KSS, Almagro J, Cha H, Pich O, Karasaki T, Moore DA, Salgado R, Sivakumar M, Young G, Molina-Arcas M, de Carné Trécesson S, Anastasiou P, Fendler A, Au L, Shepherd STC, Martínez-Ruiz C, Puttick C, Black JRM, Watkins TBK, Kim H, Shim S, Faulkner N, Attig J, Veeriah S, Magno N, Ward S, Frankell AM, Al Bakir M, Lim EL, Hill MS, Wilson GA, Cook DE, Birkbak NJ, Behrens A, Yousaf N, Popat S, Hackshaw A, Hiley CT, Litchfield K, McGranahan N, Jamal-Hanjani M, Larkin J, Lee SH, Turajlic S, Swanton C, Downward J, Kassiotis G. Antibodies against endogenous retroviruses promote lung cancer immunotherapy. Nature 2023; 616:563-573. [PMID: 37046094 PMCID: PMC10115647 DOI: 10.1038/s41586-023-05771-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 01/30/2023] [Indexed: 04/14/2023]
Abstract
B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS)1,2. Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive1,2. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma3. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Jesse Boumelha
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Katey S S Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Jorge Almagro
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Hongui Cha
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Takahiro Karasaki
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Queensland, Australia
| | - Monica Sivakumar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - George Young
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, UK
| | | | | | | | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Hyemin Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seohee Shim
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Nikhil Faulkner
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jan Attig
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Neil Magno
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
- CRUK Convergence Science Centre, Imperial College, London, UK
| | - Nadia Yousaf
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Lung Unit, The Royal Marsden Hospital, London, UK
| | - Sanjay Popat
- Lung Unit, The Royal Marsden Hospital, London, UK
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, London, UK
| | - Crispin T Hiley
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK.
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.
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3
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Ng KW, Hobbs A, Wichmann C, Victora GD, Donaldson GP. B cell responses to the gut microbiota. Adv Immunol 2022; 155:95-131. [PMID: 36357013 DOI: 10.1016/bs.ai.2022.08.003] [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] [Indexed: 11/07/2022]
Abstract
Most antibody produced by humans originates from mucosal B cell responses. The rules, mechanisms, and outcomes of this process are distinct from B cell responses to infection. Within the context of the intestine, we discuss the induction of follicular B cell responses by microbiota, the development and maintenance of mucosal antibody-secreting cells, and the unusual impacts of mucosal antibody on commensal bacteria. Much remains to be learned about the interplay between B cells and the microbiota, but past and present work hints at a complex, nuanced relationship that may be critical to the way the mammalian gut fosters a beneficial microbial ecosystem.
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Affiliation(s)
- Kevin W Ng
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States
| | - Alvaro Hobbs
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States
| | - Christopher Wichmann
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States; Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, United States; Immune Regulation Group, Department of Pediatrics, University Medical Center Rostock, Rostock, Germany
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States.
| | - Gregory P Donaldson
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, United States.
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4
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Ng KW, Faulkner N, Finsterbusch K, Wu M, Harvey R, Hussain S, Greco M, Liu Y, Kjaer S, Swanton C, Gandhi S, Beale R, Gamblin SJ, Cherepanov P, McCauley J, Daniels R, Howell M, Arase H, Wack A, Bauer DLV, Kassiotis G. SARS-CoV-2 S2-targeted vaccination elicits broadly neutralizing antibodies. Sci Transl Med 2022; 14:eabn3715. [PMID: 35895836 DOI: 10.1126/scitranslmed.abn3715] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Several variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged during the current coronavirus disease 2019 (COVID-19) pandemic. Although antibody cross-reactivity with the spike glycoproteins (S) of diverse coronaviruses, including endemic common cold coronaviruses (HCoVs), has been documented, it remains unclear whether such antibody responses, typically targeting the conserved S2 subunit, contribute to protection when induced by infection or through vaccination. Using a mouse model, we found that prior HCoV-OC43 S-targeted immunity primes neutralizing antibody responses to otherwise subimmunogenic SARS-CoV-2 S exposure and promotes S2-targeting antibody responses. Moreover, vaccination with SARS-CoV-2 S2 elicited antibodies in mice that neutralized diverse animal and human alphacoronaviruses and betacoronaviruses in vitro and provided a degree of protection against SARS-CoV-2 challenge in vivo. Last, in mice with a history of SARS-CoV-2 Wuhan-based S vaccination, further S2 vaccination induced broader neutralizing antibody response than booster Wuhan S vaccination, suggesting that it may prevent repertoire focusing caused by repeated homologous vaccination. These data establish the protective value of an S2-targeting vaccine and support the notion that S2 vaccination may better prepare the immune system to respond to the changing nature of the S1 subunit in SARS-CoV-2 variants of concern, as well as to future coronavirus zoonoses.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Katja Finsterbusch
- Immunoregulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mary Wu
- High Throughput Screening STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Maria Greco
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yafei Liu
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Sonia Gandhi
- Neurodegradation Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Cherepanov
- Chromatin structure and mobile DNA Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rodney Daniels
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Infectious Disease, St Mary's Hospital, Imperial College London, London W2 1PG, UK
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5
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Xu F, Vasilescu DM, Kinose D, Tanabe N, Ng KW, Coxson HO, Cooper JD, Hackett TL, Verleden SE, Vanaudenaerde BM, Stevenson CS, Lenburg ME, Spira A, Tan WC, Sin DD, Ng RT, Hogg JC. The molecular and cellular mechanisms associated with the destruction of terminal bronchioles in COPD. Eur Respir J 2022; 59:2101411. [PMID: 34675046 DOI: 10.1183/13993003.01411-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 09/27/2021] [Indexed: 11/05/2022]
Abstract
RATIONALE Peripheral airway obstruction is a key feature of chronic obstructive pulmonary disease (COPD), but the mechanisms of airway loss are unknown. This study aims to identify the molecular and cellular mechanisms associated with peripheral airway obstruction in COPD. METHODS Ten explanted lung specimens donated by patients with very severe COPD treated by lung transplantation and five unused donor control lungs were sampled using systematic uniform random sampling (SURS), resulting in 240 samples. These samples were further examined by micro-computed tomography (CT), quantitative histology and gene expression profiling. RESULTS Micro-CT analysis showed that the loss of terminal bronchioles in COPD occurs in regions of microscopic emphysematous destruction with an average airspace size of ≥500 and <1000 µm, which we have termed a "hot spot". Based on microarray gene expression profiling, the hot spot was associated with an 11-gene signature, with upregulation of pro-inflammatory genes and downregulation of inhibitory immune checkpoint genes, indicating immune response activation. Results from both quantitative histology and the bioinformatics computational tool CIBERSORT, which predicts the percentage of immune cells in tissues from transcriptomic data, showed that the hot spot regions were associated with increased infiltration of CD4 and CD8 T-cell and B-cell lymphocytes. INTERPRETATION The reduction in terminal bronchioles observed in lungs from patients with COPD occurs in a hot spot of microscopic emphysema, where there is upregulation of IFNG signalling, co-stimulatory immune checkpoint genes and genes related to the inflammasome pathway, and increased infiltration of immune cells. These could be potential targets for therapeutic interventions in COPD.
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Affiliation(s)
- Feng Xu
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
| | - Dragoş M Vasilescu
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
| | - Daisuke Kinose
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
- Division of Respiratory Medicine, Department of Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Naoya Tanabe
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
- Dept of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Harvey O Coxson
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
| | - Joel D Cooper
- Division of Thoracic Surgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Tillie-Louise Hackett
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
| | - Stijn E Verleden
- Laboratory of Respiratory Diseases, BREATHE, Dept of CHROMETA, KU Leuven, Leuven, Belgium
| | | | | | - Marc E Lenburg
- Division of Computational Biomedicine, Dept of Medicine, Boston University, Boston, MA, USA
| | - Avrum Spira
- Division of Computational Biomedicine, Dept of Medicine, Boston University, Boston, MA, USA
| | - Wan C Tan
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
| | - Don D Sin
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
| | - Raymond T Ng
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
- Dept of Computer Science, The University of British Columbia, Vancouver, BC, Canada
| | - James C Hogg
- The Centre for Heart Lung Innovation, The University of British Columbia, located at St Paul's Hospital, Vancouver, BC, Canada
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6
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Fendler A, Au L, Shepherd STC, Byrne F, Cerrone M, Boos LA, Rzeniewicz K, Gordon W, Shum B, Gerard CL, Ward B, Xie W, Schmitt AM, Joharatnam-Hogan N, Cornish GH, Pule M, Mekkaoui L, Ng KW, Carlyle E, Edmonds K, Rosario LD, Sarker S, Lingard K, Mangwende M, Holt L, Ahmod H, Stone R, Gomes C, Flynn HR, Agua-Doce A, Hobson P, Caidan S, Howell M, Wu M, Goldstone R, Crawford M, Cubitt L, Patel H, Gavrielides M, Nye E, Snijders AP, MacRae JI, Nicod J, Gronthoud F, Shea RL, Messiou C, Cunningham D, Chau I, Starling N, Turner N, Welsh L, van As N, Jones RL, Droney J, Banerjee S, Tatham KC, Jhanji S, O'Brien M, Curtis O, Harrington K, Bhide S, Bazin J, Robinson A, Stephenson C, Slattery T, Khan Y, Tippu Z, Leslie I, Gennatas S, Okines A, Reid A, Young K, Furness AJS, Pickering L, Gandhi S, Gamblin S, Swanton C, Nicholson E, Kumar S, Yousaf N, Wilkinson KA, Swerdlow A, Harvey R, Kassiotis G, Larkin J, Wilkinson RJ, Turajlic S. Functional antibody and T cell immunity following SARS-CoV-2 infection, including by variants of concern, in patients with cancer: the CAPTURE study. Nat Cancer 2021; 2:1321-1337. [PMID: 35121900 DOI: 10.1038/s43018-021-00275-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022]
Abstract
Patients with cancer have higher COVID-19 morbidity and mortality. Here we present the prospective CAPTURE study, integrating longitudinal immune profiling with clinical annotation. Of 357 patients with cancer, 118 were SARS-CoV-2 positive, 94 were symptomatic and 2 died of COVID-19. In this cohort, 83% patients had S1-reactive antibodies and 82% had neutralizing antibodies against wild type SARS-CoV-2, whereas neutralizing antibody titers against the Alpha, Beta and Delta variants were substantially reduced. S1-reactive antibody levels decreased in 13% of patients, whereas neutralizing antibody titers remained stable for up to 329 days. Patients also had detectable SARS-CoV-2-specific T cells and CD4+ responses correlating with S1-reactive antibody levels, although patients with hematological malignancies had impaired immune responses that were disease and treatment specific, but presented compensatory cellular responses, further supported by clinical recovery in all but one patient. Overall, these findings advance the understanding of the nature and duration of the immune response to SARS-CoV-2 in patients with cancer.
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Affiliation(s)
- Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Maddalena Cerrone
- Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laura Amanda Boos
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | | | - William Gordon
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Benjamin Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Camille L Gerard
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Barry Ward
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Wenyi Xie
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Andreas M Schmitt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | | | - Georgina H Cornish
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Martin Pule
- Department of Haematology, University College London Cancer Institute, London, UK
- Autolus Ltd., London, UK
| | | | - Kevin W Ng
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Eleanor Carlyle
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lyra Del Rosario
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Sarah Sarker
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Karla Lingard
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Mary Mangwende
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lucy Holt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Hamid Ahmod
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Richard Stone
- Experimental Histopathology Laboratory, The Francis Crick Institute, London, UK
| | - Camila Gomes
- Experimental Histopathology Laboratory, The Francis Crick Institute, London, UK
| | - Helen R Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Ana Agua-Doce
- Flow Cytometry Scientific Technology Platform, The Francis Crick Institute, London, UK
| | - Philip Hobson
- Flow Cytometry Scientific Technology Platform, The Francis Crick Institute, London, UK
| | - Simon Caidan
- Safety, Health and Sustainability, The Francis Crick Institute, London, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, London, UK
| | - Mary Wu
- High Throughput Screening Laboratory, The Francis Crick Institute, London, UK
| | - Robert Goldstone
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Margaret Crawford
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Laura Cubitt
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Mike Gavrielides
- Scientific Computing Scientific Technology Platform, The Francis Crick Institute, London, UK
| | - Emma Nye
- Experimental Histopathology Laboratory, The Francis Crick Institute, London, UK
| | - Ambrosius P Snijders
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - James I MacRae
- Metabolomics Scientific Technology Platform, The Francis Crick Institute, London, UK
| | - Jerome Nicod
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Firza Gronthoud
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Robyn L Shea
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London, UK
- Translational Cancer Biochemistry Laboratory, The Institute of Cancer Research, London, UK
| | - Christina Messiou
- Department of Radiology, The Royal Marsden NHS Foundation Trust, London, UK
| | - David Cunningham
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey, London, UK
| | - Ian Chau
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey, London, UK
| | - Naureen Starling
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey, London, UK
| | - Nicholas Turner
- Breast Unit, The Royal Marsden NHS Foundation Trust, London, UK
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Liam Welsh
- Neuro-oncology Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Nicholas van As
- Clinical Oncology Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Robin L Jones
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, UK
| | - Joanne Droney
- Palliative Medicine, The Royal Marsden NHS Foundation Trust, London, UK
| | - Susana Banerjee
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kate C Tatham
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Shaman Jhanji
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London, UK
| | - Mary O'Brien
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Olivia Curtis
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kevin Harrington
- Head and Neck Unit, The Royal Marsden NHS Foundation Trust, London, UK
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | - Shreerang Bhide
- Head and Neck Unit, The Royal Marsden NHS Foundation Trust, London, UK
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | - Jessica Bazin
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Anna Robinson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | | | - Tim Slattery
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Yasir Khan
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Zayd Tippu
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Isla Leslie
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Spyridon Gennatas
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, UK
- Department of Medical Oncology, Guy's Hospital, London, UK
| | - Alicia Okines
- Breast Unit, The Royal Marsden NHS Foundation Trust, London, UK
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, UK
| | - Alison Reid
- Uro-oncology Unit, The Royal Marsden NHS Foundation Trust, Surrey, UK
| | - Kate Young
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew J S Furness
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lisa Pickering
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London, UK
- UCL Queen Square Institute of Neurology, London, UK
| | - Steve Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- University College London Cancer Institute, London, UK
| | - Emma Nicholson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Sacheen Kumar
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey, London, UK
| | - Nadia Yousaf
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, UK
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, UK
| | - Katalin A Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- Wellcome Center for Infectious Disease Research in Africa, University Cape Town, Cape Town, Republic of South Africa
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology and Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - James Larkin
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Robert J Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
- Wellcome Center for Infectious Disease Research in Africa, University Cape Town, Cape Town, Republic of South Africa
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK.
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK.
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7
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Fendler A, Au L, Shepherd ST, Byrne F, Cerrone M, Boos LA, Rzeniewicz K, Gordon W, Shum B, Gerard CL, Ward B, Xie W, Schmitt AM, Joharatnam-Hogan N, Cornish GH, Pule M, Mekkaoui L, Ng KW, Carlyle E, Edmonds K, Del Rosario L, Sarker S, Lingard K, Mangwende M, Holt L, Ahmod H, Stone R, Gomes C, Flynn HR, Agua-Doce A, Hobson P, Caidan S, Howell M, Wu M, Goldstone R, Crawford M, Cubitt L, Patel H, Gavrielides M, Nye E, Snijders AP, MacRae JI, Nicod J, Gronthoud F, Shea RL, Messiou C, Cunningham D, Chau I, Starling N, Turner N, Welsh L, van As N, Jones RL, Droney J, Banerjee S, Tatham KC, Jhanji S, O’Brien M, Curtis O, Harrington K, Bhide S, Bazin J, Robinson A, Stephenson C, Slattery T, Khan Y, Tippu Z, Leslie I, Gennatas S, Okines A, Reid A, Young K, Furness AJ, Pickering L, Gandhi S, Gamblin S, Swanton C, Nicholson E, Kumar S, Yousaf N, Wilkinson KA, Swerdlow A, Harvey R, Kassiotis G, Larkin J, Wilkinson RJ, Turajlic S. Functional antibody and T-cell immunity following SARS-CoV-2 infection, including by variants of concern, in patients with cancer: the CAPTURE study. Res Sq 2021:rs.3.rs-916427. [PMID: 34580668 PMCID: PMC8475970 DOI: 10.21203/rs.3.rs-916427/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Patients with cancer have higher COVID-19 morbidity and mortality. Here we present the prospective CAPTURE study (NCT03226886) integrating longitudinal immune profiling with clinical annotation. Of 357 patients with cancer, 118 were SARS-CoV-2-positive, 94 were symptomatic and 2 patients died of COVID-19. In this cohort, 83% patients had S1-reactive antibodies, 82% had neutralizing antibodies against WT, whereas neutralizing antibody titers (NAbT) against the Alpha, Beta, and Delta variants were substantially reduced. Whereas S1-reactive antibody levels decreased in 13% of patients, NAbT remained stable up to 329 days. Patients also had detectable SARS-CoV-2-specific T cells and CD4+ responses correlating with S1-reactive antibody levels, although patients with hematological malignancies had impaired immune responses that were disease and treatment-specific, but presented compensatory cellular responses, further supported by clinical. Overall, these findings advance the understanding of the nature and duration of immune response to SARS-CoV-2 in patients with cancer.
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Affiliation(s)
- Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Equal contribution
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Equal contribution
| | - Scott T.C. Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Equal contribution
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Maddalena Cerrone
- Tuberculosis Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Infectious Disease, Imperial College London, W12 0NN, UK
| | - Laura Amanda Boos
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Karolina Rzeniewicz
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - William Gordon
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ben Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Camille L. Gerard
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Barry Ward
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Wenyi Xie
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Andreas M. Schmitt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | | | - Georgina H. Cornish
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Martin Pule
- Research Department of Haematology at University College London Cancer Institute, WC1E 6DD, London, UK
- Autolus Limited, The MediaWorks, 191 Wood Lane, London, W12 7F
| | - Leila Mekkaoui
- Autolus Limited, The MediaWorks, 191 Wood Lane, London, W12 7F
| | - Kevin W. Ng
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Eleanor Carlyle
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Lyra Del Rosario
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Sarah Sarker
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Karla Lingard
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Mary Mangwende
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Lucy Holt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Hamid Ahmod
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Richard Stone
- Autolus Limited, The MediaWorks, 191 Wood Lane, London, W12 7F
| | - Camila Gomes
- Autolus Limited, The MediaWorks, 191 Wood Lane, London, W12 7F
| | - Helen R. Flynn
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry Scientific Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry Scientific Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Simon Caidan
- Safety, Health & Sustainability, The Francis Crick Institute, London, NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Mary Wu
- High Throughput Screening Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Robert Goldstone
- Advanced Sequencing Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Margaret Crawford
- Advanced Sequencing Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Laura Cubitt
- Advanced Sequencing Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Harshil Patel
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Mike Gavrielides
- Scientific Computing Scientific Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Emma Nye
- Experimental Histopathology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ambrosius P Snijders
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - James I MacRae
- Metabolomics Scientific Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Jerome Nicod
- Advanced Sequencing Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Firza Gronthoud
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London, NW1 1AT, UK
| | - Robyn L. Shea
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London, NW1 1AT, UK
- Translational Cancer Biochemistry Laboratory, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Christina Messiou
- Department of Radiology, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - David Cunningham
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey SM2 5PT
| | - Ian Chau
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey SM2 5PT
| | - Naureen Starling
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey SM2 5PT
| | - Nicholas Turner
- Breast Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Liam Welsh
- Neuro-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Nicholas van As
- Clinical Oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Robin L. Jones
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, SW3 6JJ, UK
| | - Joanne Droney
- Palliative Medicine, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Susana Banerjee
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Kate C. Tatham
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Shaman Jhanji
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Mary O’Brien
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Olivia Curtis
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Kevin Harrington
- Head and Neck, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Targeted Therapy Team, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Shreerang Bhide
- Head and Neck, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Jessica Bazin
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Anna Robinson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Clemency Stephenson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Tim Slattery
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Yasir Khan
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Zayd Tippu
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Isla Leslie
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Spyridon Gennatas
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Department of Medical Oncology, 14th Floor, Great Maze Pond Road, Tower Wing, Guy’s Hospital, London SE1 9RY, UK
| | - Alicia Okines
- Breast Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Alison Reid
- Uro-oncology unit, The Royal Marsden NHS Foundation Trust, Surrey, SM2 5PT
| | - Kate Young
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Andrew J.S. Furness
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Lisa Pickering
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG
| | - Steve Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- University College London Cancer Institute, London WC1E 6DD, UK
| | - Emma Nicholson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Sacheen Kumar
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey SM2 5PT
| | - Nadia Yousaf
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Katalin A. Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Wellcome Center for Infectious Disease Research in Africa, University Cape Town, Observatory 7925, Republic of South Africa
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology and Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London, NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - James Larkin
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Robert J. Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Infectious Disease, Imperial College London, W12 0NN, UK
- Wellcome Center for Infectious Disease Research in Africa, University Cape Town, Observatory 7925, Republic of South Africa
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
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8
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Deakin CT, Cornish GH, Ng KW, Faulkner N, Bolland W, Hope J, Rosa A, Harvey R, Hussain S, Earl C, Jebson BR, Wilkinson MGLL, Marshall LR, O'Brien K, Rosser EC, Radziszewska A, Peckham H, Patel H, Heaney J, Rickman H, Paraskevopoulou S, Houlihan CF, Spyer MJ, Gamblin SJ, McCauley J, Nastouli E, Levin M, Cherepanov P, Ciurtin C, Wedderburn LR, Kassiotis G. Favorable antibody responses to human coronaviruses in children and adolescents with autoimmune rheumatic diseases. Med 2021; 2:1093-1109.e6. [PMID: 34414384 PMCID: PMC8363467 DOI: 10.1016/j.medj.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/25/2021] [Revised: 07/06/2021] [Accepted: 08/06/2021] [Indexed: 01/07/2023]
Abstract
BACKGROUND Differences in humoral immunity to coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), between children and adults remain unexplained, and the effect of underlying immune dysfunction or suppression is unknown. Here, we sought to examine the antibody immune competence of children and adolescents with prevalent inflammatory rheumatic diseases, juvenile idiopathic arthritis (JIA), juvenile dermatomyositis (JDM), and juvenile systemic lupus erythematosus (JSLE) against the seasonal human coronavirus (HCoV)-OC43 that frequently infects this age group. METHODS Sera were collected from JIA (n = 118), JDM (n = 49), and JSLE (n = 30) patients and from healthy control (n = 54) children and adolescents prior to the coronavirus disease 19 (COVID-19) pandemic. We used sensitive flow-cytometry-based assays to determine titers of antibodies that reacted with the spike and nucleoprotein of HCoV-OC43 and cross-reacted with the spike and nucleoprotein of SARS-CoV-2, and we compared them with respective titers in sera from patients with multisystem inflammatory syndrome in children and adolescents (MIS-C). FINDINGS Despite immune dysfunction and immunosuppressive treatment, JIA, JDM, and JSLE patients maintained comparable or stronger humoral responses than healthier peers, which was dominated by immunoglobulin G (IgG) antibodies to HCoV-OC43 spike, and harbored IgG antibodies that cross-reacted with SARS-CoV-2 spike. In contrast, responses to HCoV-OC43 and SARS-CoV-2 nucleoproteins exhibited delayed age-dependent class-switching and were not elevated in JIA, JDM, and JSLE patients, which argues against increased exposure. CONCLUSIONS Consequently, autoimmune rheumatic diseases and their treatment were associated with a favorable ratio of spike to nucleoprotein antibodies. FUNDING This work was supported by a Centre of Excellence Centre for Adolescent Rheumatology Versus Arthritis grant, 21593, UKRI funding reference MR/R013926/1, the Great Ormond Street Children's Charity, Cure JM Foundation, Myositis UK, Lupus UK, and the NIHR Biomedical Research Centres at GOSH and UCLH. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust.
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Affiliation(s)
- Claire T Deakin
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre at GOSH, London, UK
- OPAL Rheumatology Ltd, Sydney, NSW, Australia
| | - Georgina H Cornish
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Joshua Hope
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christopher Earl
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Bethany R Jebson
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre at GOSH, London, UK
| | - Meredyth G L L Wilkinson
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre at GOSH, London, UK
| | - Lucy R Marshall
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre at GOSH, London, UK
| | - Kathryn O'Brien
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre at GOSH, London, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Harsita Patel
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | | | | | | | - Catherine F Houlihan
- UCLH NHS Trust, London NW1 2BU, UK
- Division of Infection and Immunity, UCL, London WC1E 6BT, UK
| | - Moira J Spyer
- UCLH NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street ICH, UCL, London WC1N 1EH, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eleni Nastouli
- UCLH NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street ICH, UCL, London WC1N 1EH, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, UK
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Infectious Disease, St Mary's Hospital, Imperial College London, London W2 1NY, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospitals (UCLH), Great Ormond Street Hospital (GOSH), London, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre at GOSH, London, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Infectious Disease, St Mary's Hospital, Imperial College London, London W2 1NY, UK
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9
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Lee WT, Ng KW, Liao J, Luk ACS, Suen HC, Chan THT, Cheung MY, Chu D, Zhao M, Chan YL, Li TC, Lee TL. P–547 Single-cell RNA sequencing identifies molecular regulations associated with poor maturation performance on rescue in vitro matured oocytes. Hum Reprod 2021. [DOI: 10.1093/humrep/deab130.546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Study question
What is the transcriptome signature associated with rescuein vitro matured (rIVM) oocytes?
Summary answer
GATA–1/CREB1/WNT signaling axis was repressed in rIVM oocytes of poor quality.
What is known already
rIVM aims to produce mature oocytes (MII) for in vitro fertilization (IVF) through IVM of immature oocytes collected from stimulated ovaries. It is less popular due to limited success rate in infertility treatment. Genetic aberrations, cellular stress, and the absence of cumulus cell support in oocytes could account for the failure of rIVM.
Study design, size, duration
We applied single-cell RNA sequencing (scRNA-seq) to capture the transcriptomes of human in vivo (IVO) oocytes (n = 10) from 7 donors and rIVM oocytes (n = 10) from 10 donors, followed by studying the maternal age effect and ovarian responses on rIVM oocyte transcriptomes.
Participants/materials, setting, methods
Human oocytes were collected from donors aged 28–41 years with a body mass index of < 30. RNA extraction, cDNA generation, library construction and sequencing were performed in one preparation. scRNA-seq data were then processed and analyzed. Selected genes in therIVM vs. IVO comparison were validated by quantitative real-time PCR.
Main results and the role of chance
The transcriptome profiles of rIVM/IVO showed distinctive differences. A total of 1559 differentially expressed genes (DEGs, genes with at least two-fold change and adjusted p < 0.05) were found to be enriched in metabolic processes, biosynthesis, and oxidative phosphorylation. Among these DEGs, we identified a repression of WNT/β-catenin signaling in rIVM when compared with IVO oocytes. We found that estradiol level exhibited a significant age-independent correlation with the IVO mature oocyte ratio (MII ratio). rIVM oocytes with higher MII ratio showed over-represented cellular processes such as anti-apoptosis. To further identify targets that contribute to the poor outcomes of rIVM, we compared oocytes collected from young donors with high MII ratio versus donors of advanced maternal age and revealed CREB1was an important regulator in rIVM. Our study identified GATA–1/CREB1/WNT signaling was repressed in both rIVM condition and rIVM oocytes of low-quality.
Limitations, reasons for caution
In the rIVM oocytes of high- and low-quality comparison, the number of samples was limited after data filtering with stringent selection criteria. For the oocyte stage identification, we were unable to predict the presence of oocyte spindle so polar body extrusion was the only indicator.
Wider implications of the findings: This study showed that GATA–1/CREB1/WNT signaling and antioxidant actions were repressed in rIVM condition and was further downregulated in rIVM oocytes of low-quality, providing us the foundation of subsequent follow-up research on human subjects.
Trial registration number
Not applicable
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Affiliation(s)
- W T Lee
- The Chinese University of Hong Kong, School of Biomedical Sciences, Hong Kong, Hong Kong
| | - K W Ng
- The Chinese University of Hong Kong, School of Biomedical Sciences, Hong Kong, Hong Kong
| | - J Liao
- The Chinese University of Hong Kong, School of Biomedical Sciences, Hong Kong, Hong Kong
| | - A C S Luk
- The Chinese University of Hong Kong, School of Biomedical Sciences, Hong Kong, Hong Kong
| | - H C Suen
- The Chinese University of Hong Kong, School of Biomedical Sciences, Hong Kong, Hong Kong
| | - T H T Chan
- The Chinese University of Hong Kong, School of Biomedical Sciences, Hong Kong, Hong Kong
| | - M Y Cheung
- The Chinese University of Hong Kong, School of Biomedical Sciences, Hong Kong, Hong Kong
| | - D Chu
- The Chinese University of Hong Kong, School of Biomedical Sciences, Hong Kong, Hong Kong
| | - M Zhao
- The Chinese University of Hong Kong, Department of Obstetrics and Gynaecology, Hong Kong, Hong Kong
| | - Y L Chan
- The Chinese University of Hong Kong, Department of Obstetrics and Gynaecology, Hong Kong, Hong Kong
| | - T C Li
- The Chinese University of Hong Kong, Department of Obstetrics and Gynaecology, Hong Kong, Hong Kong
| | - T L Lee
- The Chinese University of Hong Kong, School of Biomedical Sciences, Hong Kong, Hong Kong
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10
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Faulkner N, Ng KW, Wu MY, Harvey R, Margaritis M, Paraskevopoulou S, Houlihan C, Hussain S, Greco M, Bolland W, Warchal S, Heaney J, Rickman H, Spyer M, Frampton D, Byott M, de Oliveira T, Sigal A, Kjaer S, Swanton C, Gandhi S, Beale R, Gamblin SJ, McCauley JW, Daniels RS, Howell M, Bauer D, Nastouli E, Kassiotis G. Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains. eLife 2021; 10:e69317. [PMID: 34323691 PMCID: PMC8352583 DOI: 10.7554/elife.69317] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 04/11/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Background The degree of heterotypic immunity induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains is a major determinant of the spread of emerging variants and the success of vaccination campaigns, but remains incompletely understood. Methods We examined the immunogenicity of SARS-CoV-2 variant B.1.1.7 (Alpha) that arose in the United Kingdom and spread globally. We determined titres of spike glycoprotein-binding antibodies and authentic virus neutralising antibodies induced by B.1.1.7 infection to infer homotypic and heterotypic immunity. Results Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa variant B.1.351 (Beta) than of the infecting variant. The drop in cross-reactivity was significantly more pronounced following B.1.1.7 than parental strain infection. Conclusions The results indicate that heterotypic immunity induced by SARS-CoV-2 variants is asymmetric. Funding This work was supported by the Francis Crick Institute and the Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg.
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Affiliation(s)
- Nikhil Faulkner
- Retroviral ImmunologyLondonUnited Kingdom
- National Heart and Lung Institute, Imperial College LondonLondonUnited Kingdom
| | - Kevin W Ng
- Retroviral ImmunologyLondonUnited Kingdom
| | - Mary Y Wu
- High Throughput Screening STPLondonUnited Kingdom
| | - Ruth Harvey
- Worldwide Influenza CentreLondonUnited Kingdom
| | - Marios Margaritis
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
| | | | - Catherine Houlihan
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
- Division of Infection and ImmunityLondonUnited Kingdom
| | - Saira Hussain
- Worldwide Influenza CentreLondonUnited Kingdom
- RNA Virus Replication LaboratoryLondonUnited Kingdom
| | - Maria Greco
- RNA Virus Replication LaboratoryLondonUnited Kingdom
| | | | | | - Judith Heaney
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
| | - Hannah Rickman
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
| | - Moria Spyer
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
- Department of Population, Policy and PracticeLondonUnited Kingdom
| | | | - Matthew Byott
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
| | - Tulio de Oliveira
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- KwaZulu-Natal Research Innovation and Sequencing PlatformDurbanSouth Africa
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
- Department of Global Health, University of WashingtonSeattleUnited States
| | - Alex Sigal
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- Africa Health Research InstituteDurbanSouth Africa
- Max Planck Institute for Infection BiologyBerlinGermany
| | | | - Charles Swanton
- Cancer Evolution and Genome Instability LaboratoryLondonUnited Kingdom
| | - Sonia Gandhi
- Neurodegradation Biology LaboratoryLondonUnited Kingdom
| | - Rupert Beale
- Cell Biology of Infection LaboratoryLondonUnited Kingdom
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | | | | | | | - David Bauer
- RNA Virus Replication LaboratoryLondonUnited Kingdom
| | - Eleni Nastouli
- Retroviral ImmunologyLondonUnited Kingdom
- Advanced Pathogen Diagnostics Unit UCLH NHS TrustLondonUnited Kingdom
- Department of Population, Policy and PracticeLondonUnited Kingdom
| | - George Kassiotis
- Retroviral ImmunologyLondonUnited Kingdom
- Department of Infectious Disease, St Mary's Hospital, Imperial College LondonLondonUnited Kingdom
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11
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Ng KW, Faulkner N, Wrobel AG, Gamblin SJ, Kassiotis G. Heterologous humoral immunity to human and zoonotic coronaviruses: Aiming for the achilles heel. Semin Immunol 2021; 55:101507. [PMID: 34716096 PMCID: PMC8542444 DOI: 10.1016/j.smim.2021.101507] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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] [Received: 06/08/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 02/04/2023]
Abstract
Coronaviruses are evolutionarily successful RNA viruses, common to multiple avian, amphibian and mammalian hosts. Despite their ubiquity and potential impact, knowledge of host immunity to coronaviruses remains incomplete, partly owing to the lack of overt pathogenicity of endemic human coronaviruses (HCoVs), which typically cause common colds. However, the need for deeper understanding became pressing with the zoonotic introduction of three novel coronaviruses in the past two decades, causing severe acute respiratory syndromes in humans, and the unfolding pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This renewed interest not only triggered the discovery of two of the four HCoVs, but also uncovered substantial cellular and humoral cross-reactivity with shared or related coronaviral antigens. Here, we review the evidence for cross-reactive B cell memory elicited by HCoVs and its potential impact on the puzzlingly variable outcome of SARS-CoV-2 infection. The available data indicate targeting of highly conserved regions primarily in the S2 subunits of the spike glycoproteins of HCoVs and SARS-CoV-2 by cross-reactive B cells and antibodies. Rare monoclonal antibodies reactive with conserved S2 epitopes and with potent virus neutralising activity have been cloned, underscoring the potential functional relevance of cross-reactivity. We discuss B cell and antibody cross-reactivity in the broader context of heterologous humoral immunity to coronaviruses, as well as the limits of protective immune memory against homologous re-infection. Given the bidirectional nature of cross-reactivity, the unprecedented current vaccination campaign against SARS-CoV-2 is expected to impact HCoVs, as well as future zoonotic coronaviruses attempting to cross the species barrier. However, emerging SARS-CoV-2 variants with resistance to neutralisation by vaccine-induced antibodies highlight a need for targeting more constrained, less mutable parts of the spike. The delineation of such cross-reactive areas, which humoral immunity can be trained to attack, may offer the key to permanently shifting the balance of our interaction with current and future coronaviruses in our favour.
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Affiliation(s)
- Kevin W. Ng
- Retroviral Immunology Laboratory, London, NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology Laboratory, London, NW1 1AT, UK,National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Antoni G. Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Steve J. Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, London, NW1 1AT, UK,Department of Infectious Disease, St Mary's Hospital, Imperial College London, London W2 1PG, UK,Corresponding author at: Retroviral Immunology Laboratory, London, NW1 1AT, UK
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12
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Rosa A, Pye VE, Graham C, Muir L, Seow J, Ng KW, Cook NJ, Rees-Spear C, Parker E, Dos Santos MS, Rosadas C, Susana A, Rhys H, Nans A, Masino L, Roustan C, Christodoulou E, Ulferts R, Wrobel AG, Short CE, Fertleman M, Sanders RW, Heaney J, Spyer M, Kjær S, Riddell A, Malim MH, Beale R, MacRae JI, Taylor GP, Nastouli E, van Gils MJ, Rosenthal PB, Pizzato M, McClure MO, Tedder RS, Kassiotis G, McCoy LE, Doores KJ, Cherepanov P. SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity. Sci Adv 2021; 7:eabg7607. [PMID: 33888467 PMCID: PMC8163077 DOI: 10.1126/sciadv.abg7607] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/02/2021] [Indexed: 05/11/2023]
Abstract
The coronaviral spike is the dominant viral antigen and the target of neutralizing antibodies. We show that SARS-CoV-2 spike binds biliverdin and bilirubin, the tetrapyrrole products of heme metabolism, with nanomolar affinity. Using cryo-electron microscopy and x-ray crystallography, we mapped the tetrapyrrole interaction pocket to a deep cleft on the spike N-terminal domain (NTD). At physiological concentrations, biliverdin significantly dampened the reactivity of SARS-CoV-2 spike with immune sera and inhibited a subset of neutralizing antibodies. Access to the tetrapyrrole-sensitive epitope is gated by a flexible loop on the distal face of the NTD. Accompanied by profound conformational changes in the NTD, antibody binding requires relocation of the gating loop, which folds into the cleft vacated by the metabolite. Our results indicate that SARS-CoV-2 spike NTD harbors a dominant epitope, access to which can be controlled by an allosteric mechanism that is regulated through recruitment of a metabolite.
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Affiliation(s)
- Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Luke Muir
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Kevin W Ng
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Nicola J Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Chloe Rees-Spear
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Eleanor Parker
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | | | - Carolina Rosadas
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Alberto Susana
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Hefin Rhys
- Flow Cytometry Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Laura Masino
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Charlotte-Eve Short
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Michael Fertleman
- Cutrale Perioperative and Ageing Group, Imperial College London, London, UK
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Weill Medical College of Cornell University, New York, NY, USA
| | - Judith Heaney
- Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Crick COVID-19 Consortium, The Francis Crick Institute, London, UK
| | - Moira Spyer
- Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Crick COVID-19 Consortium, The Francis Crick Institute, London, UK
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Andy Riddell
- Flow Cytometry Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London, UK
| | - James I MacRae
- Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Graham P Taylor
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Eleni Nastouli
- Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Crick COVID-19 Consortium, The Francis Crick Institute, London, UK
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, UK
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Myra O McClure
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Richard S Tedder
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Laura E McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK.
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
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13
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Xu F, Tanabe N, Vasilescu DM, McDonough JE, Coxson HO, Ikezoe K, Kinose D, Ng KW, Verleden SE, Wuyts WA, Vanaudenaerde BM, Verschakelen J, Cooper JD, Lenburg ME, Morshead KB, Abbas AR, Arron JR, Spira A, Hackett TL, Colby TV, Ryerson CJ, Ng RT, Hogg JC. The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF). EBioMedicine 2021; 66:103325. [PMID: 33862585 PMCID: PMC8054143 DOI: 10.1016/j.ebiom.2021.103325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 01/16/2021] [Revised: 03/12/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The transition from normal lung anatomy to minimal and established fibrosis is an important feature of the pathology of idiopathic pulmonary fibrosis (IPF). The purpose of this report is to examine the molecular and cellular mechanisms associated with this transition. METHODS Pre-operative thoracic Multidetector Computed Tomography (MDCT) scans of patients with severe IPF (n = 9) were used to identify regions of minimal(n = 27) and established fibrosis(n = 27). MDCT, Micro-CT, quantitative histology, and next-generation sequencing were used to compare 24 samples from donor controls (n = 4) to minimal and established fibrosis samples. FINDINGS The present results extended earlier reports about the transition from normal lung anatomy to minimal and established fibrosis by showing that there are activations of TGFBI, T cell co-stimulatory genes, and the down-regulation of inhibitory immune-checkpoint genes compared to controls. The expression patterns of these genes indicated activation of a field immune response, which is further supported by the increased infiltration of inflammatory immune cells dominated by lymphocytes that are capable of forming lymphoid follicles. Moreover, fibrosis pathways, mucin secretion, surfactant, TLRs, and cytokine storm-related genes also participate in the transitions from normal lung anatomy to minimal and established fibrosis. INTERPRETATION The transition from normal lung anatomy to minimal and established fibrosis is associated with genes that are involved in the tissue repair processes, the activation of immune responses as well as the increased infiltration of CD4, CD8, B cell lymphocytes, and macrophages. These molecular and cellular events correlate with the development of structural abnormality of IPF and probably contribute to its pathogenesis.
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Affiliation(s)
- Feng Xu
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - Naoya Tanabe
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada; Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Dragos M Vasilescu
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - John E McDonough
- Leuven Lung Transplant Unit, KU Leuven and UZ Gasthuisberg, Leuven, Belgium
| | - Harvey O Coxson
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - Kohei Ikezoe
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - Daisuke Kinose
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada; Division of Respiratory Medicine, Department of Medicine, Shiga University of Medical Science, Shiga, Japan
| | | | - Stijn E Verleden
- Laboratory of Respiratory Diseases, BREATHE, Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Wim A Wuyts
- Leuven Lung Transplant Unit, KU Leuven and UZ Gasthuisberg, Leuven, Belgium
| | | | - Johny Verschakelen
- Leuven Lung Transplant Unit, KU Leuven and UZ Gasthuisberg, Leuven, Belgium
| | - Joel D Cooper
- Division of Thoracic Surgery, University of Pennsylvania, USA
| | | | | | | | | | - Avrum Spira
- Boston University Medical Center, Boston, MA, USA
| | - Tillie-Louise Hackett
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - Thomas V Colby
- Department of Pathology and Laboratory Medicine, Mayo Clinic Arizona, USA
| | - Christopher J Ryerson
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada; Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Raymond T Ng
- Department of Computer Science, The University of British Columbia, Vancouver, Canada
| | - James C Hogg
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
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14
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Rosa A, Pye VE, Graham C, Muir L, Seow J, Ng KW, Cook NJ, Rees-Spear C, Parker E, dos Santos MS, Rosadas C, Susana A, Rhys H, Nans A, Masino L, Roustan C, Christodoulou E, Ulferts R, Wrobel A, Short CE, Fertleman M, Sanders RW, Heaney J, Spyer M, Kjær S, Riddell A, Malim MH, Beale R, MacRae JI, Taylor GP, Nastouli E, van Gils MJ, Rosenthal PB, Pizzato M, McClure MO, Tedder RS, Kassiotis G, McCoy LE, Doores KJ, Cherepanov P. SARS-CoV-2 recruits a haem metabolite to evade antibody immunity. medRxiv 2021:2021.01.21.21249203. [PMID: 33532784 PMCID: PMC7852234 DOI: 10.1101/2021.01.21.21249203] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The coronaviral spike is the dominant viral antigen and the target of neutralizing antibodies. We show that SARS-CoV-2 spike binds biliverdin and bilirubin, the tetrapyrrole products of haem metabolism, with nanomolar affinity. Using cryo-electron microscopy and X-ray crystallography we mapped the tetrapyrrole interaction pocket to a deep cleft on the spike N-terminal domain (NTD). At physiological concentrations, biliverdin significantly dampened the reactivity of SARS-CoV-2 spike with immune sera and inhibited a subset of neutralizing antibodies. Access to the tetrapyrrole-sensitive epitope is gated by a flexible loop on the distal face of the NTD. Accompanied by profound conformational changes in the NTD, antibody binding requires relocation of the gating loop, which folds into the cleft vacated by the metabolite. Our results indicate that the virus co-opts the haem metabolite for the evasion of humoral immunity via allosteric shielding of a sensitive epitope and demonstrate the remarkable structural plasticity of the NTD.
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Affiliation(s)
- Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Valerie E. Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, UK
| | - Luke Muir
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, UK
| | - Kevin W. Ng
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Nicola J. Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Chloe Rees-Spear
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Eleanor Parker
- Department of Infectious Disease, St-Mary’s Campus, Imperial College London, UK
| | | | - Carolina Rosadas
- Department of Infectious Disease, St-Mary’s Campus, Imperial College London, UK
| | - Alberto Susana
- Department of Cellular, Computational and Integrative Biology, University of Trento, Italy
| | - Hefin Rhys
- Flow Cytometry Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Laura Masino
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London, UK
| | - Antoni Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Charlotte-Eve Short
- Department of Infectious Disease, St-Mary’s Campus, Imperial College London, UK
| | | | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Weill Medical College of Cornell University, New York, US
| | - Judith Heaney
- Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Crick COVID-19 Consortium, The Francis Crick Institute, London, UK
| | - Moira Spyer
- Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Crick COVID-19 Consortium, The Francis Crick Institute, London, UK
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Andy Riddell
- Flow Cytometry Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London, UK
| | - James I. MacRae
- Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Graham P. Taylor
- Department of Infectious Disease, St-Mary’s Campus, Imperial College London, UK
| | - Eleni Nastouli
- Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Crick COVID-19 Consortium, The Francis Crick Institute, London, UK
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, UK
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology, University of Trento, Italy
| | - Myra O. McClure
- Department of Infectious Disease, St-Mary’s Campus, Imperial College London, UK
| | - Richard S. Tedder
- Department of Infectious Disease, St-Mary’s Campus, Imperial College London, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, St-Mary’s Campus, Imperial College London, UK
| | - Laura E. McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Katie J. Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, UK
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, St-Mary’s Campus, Imperial College London, UK
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15
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Ng KW, Faulkner N, Cornish GH, Rosa A, Harvey R, Hussain S, Ulferts R, Earl C, Wrobel AG, Benton DJ, Roustan C, Bolland W, Thompson R, Agua-Doce A, Hobson P, Heaney J, Rickman H, Paraskevopoulou S, Houlihan CF, Thomson K, Sanchez E, Shin GY, Spyer MJ, Joshi D, O'Reilly N, Walker PA, Kjaer S, Riddell A, Moore C, Jebson BR, Wilkinson M, Marshall LR, Rosser EC, Radziszewska A, Peckham H, Ciurtin C, Wedderburn LR, Beale R, Swanton C, Gandhi S, Stockinger B, McCauley J, Gamblin SJ, McCoy LE, Cherepanov P, Nastouli E, Kassiotis G. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science 2020; 370:1339-1343. [PMID: 33159009 DOI: 10.1101/2020.05.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 05/20/2023]
Abstract
Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christopher Earl
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Chloe Roustan
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Judith Heaney
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Hannah Rickman
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | | | - Catherine F Houlihan
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Kirsty Thomson
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Emilie Sanchez
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Gee Yen Shin
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Moira J Spyer
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Dhira Joshi
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip A Walker
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Riddell
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Bethany R Jebson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Meredyth Wilkinson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Lucy R Marshall
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Eleni Nastouli
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK.
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
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16
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Ng KW, Faulkner N, Cornish GH, Rosa A, Harvey R, Hussain S, Ulferts R, Earl C, Wrobel AG, Benton DJ, Roustan C, Bolland W, Thompson R, Agua-Doce A, Hobson P, Heaney J, Rickman H, Paraskevopoulou S, Houlihan CF, Thomson K, Sanchez E, Shin GY, Spyer MJ, Joshi D, O'Reilly N, Walker PA, Kjaer S, Riddell A, Moore C, Jebson BR, Wilkinson M, Marshall LR, Rosser EC, Radziszewska A, Peckham H, Ciurtin C, Wedderburn LR, Beale R, Swanton C, Gandhi S, Stockinger B, McCauley J, Gamblin SJ, McCoy LE, Cherepanov P, Nastouli E, Kassiotis G. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science 2020; 370:1339-1343. [PMID: 33159009 PMCID: PMC7857411 DOI: 10.1126/science.abe1107] [Citation(s) in RCA: 574] [Impact Index Per Article: 143.5] [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: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christopher Earl
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Chloe Roustan
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Judith Heaney
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Hannah Rickman
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | | | - Catherine F Houlihan
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Kirsty Thomson
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Emilie Sanchez
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Gee Yen Shin
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Moira J Spyer
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Dhira Joshi
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip A Walker
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Riddell
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Bethany R Jebson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Meredyth Wilkinson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Lucy R Marshall
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Eleni Nastouli
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK.
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
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17
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Ng KW, Attig J, Bolland W, Young GR, Major J, Wrobel AG, Gamblin S, Wack A, Kassiotis G. Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option. Nat Genet 2020; 52:1294-1302. [PMID: 33077915 PMCID: PMC7610354 DOI: 10.1038/s41588-020-00732-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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: 07/24/2020] [Accepted: 09/29/2020] [Indexed: 01/07/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2) is an entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and a regulator of several physiological processes. ACE2 has recently been proposed to be interferon (IFN) inducible, suggesting that SARS-CoV-2 may exploit this phenomenon to enhance viral spread and questioning the efficacy of IFN treatment in coronavirus disease 2019. Using a recent de novo transcript assembly that captured previously unannotated transcripts, we describe a new isoform of ACE2, generated by co-option of intronic retroelements as promoter and alternative exon. The new transcript, termed MIRb-ACE2, exhibits specific expression patterns across the aerodigestive and gastrointestinal tracts and is highly responsive to IFN stimulation. In contrast, canonical ACE2 expression is unresponsive to IFN stimulation. Moreover, the MIRb-ACE2 translation product is a truncated, unstable ACE2 form, lacking domains required for SARS-CoV-2 binding and is therefore unlikely to contribute to or enhance viral infection.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - Jan Attig
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - George R Young
- Retrovirus-Host Interactions, The Francis Crick Institute, London, UK
| | - Jack Major
- Immunoregulation, The Francis Crick Institute, London, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes, The Francis Crick Institute, London, UK
| | - Steve Gamblin
- Structural Biology of Disease Processes, The Francis Crick Institute, London, UK
| | - Andreas Wack
- Immunoregulation, The Francis Crick Institute, London, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London, UK.
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18
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Sage AP, Ng KW, Marshall EA, Stewart GL, Minatel BC, Enfield KSS, Martin SD, Brown CJ, Abraham N, Lam WL. Assessment of long non-coding RNA expression reveals novel mediators of the lung tumour immune response. Sci Rep 2020; 10:16945. [PMID: 33037279 PMCID: PMC7547676 DOI: 10.1038/s41598-020-73787-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 06/22/2020] [Accepted: 09/21/2020] [Indexed: 12/31/2022] Open
Abstract
The tumour immune microenvironment is a crucial mediator of lung tumourigenesis, and characterizing the immune landscape of patient tumours may guide immunotherapy treatment regimens and uncover novel intervention points. We sought to identify the landscape of tumour-infiltrating immune cells in the context of long non-coding RNA (lncRNAs), known regulators of gene expression. We examined the lncRNA profiles of lung adenocarcinoma (LUAD) tumours by interrogating RNA sequencing data from microdissected and non-microdissected samples (BCCRC and TCGA). Subsequently, analysis of single-cell RNA sequencing data from lung tumours and flow-sorted healthy peripheral blood mononuclear cells identified lncRNAs in immune cells, highlighting their biological and prognostic relevance. We discovered lncRNA expression patterns indicative of regulatory relationships with immune-related protein-coding genes, including the relationship between AC008750.1 and NKG7 in NK cells. Activation of NK cells in vitro was sufficient to induce AC008750.1 expression. Finally, siRNA-mediated knockdown of AC008750.1 significantly impaired both the expression of NKG7 and the anti-tumour capacity of NK cells. We present an atlas of cancer-cell extrinsic immune cell-expressed lncRNAs, in vitro evidence for a functional role of lncRNAs in anti-tumour immune activity, which upon further exploration may reveal novel clinical utility as markers of immune infiltration.
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Affiliation(s)
- Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.
| | - Greg L Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Katey S S Enfield
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Spencer D Martin
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ninan Abraham
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
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19
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Martinez VD, Marshall EA, Anderson C, Ng KW, Minatel BC, Sage AP, Enfield KSS, Xu Z, Lam WL. Discovery of Previously Undetected MicroRNAs in Mesothelioma and Their Use as Tissue-of-Origin Markers. Am J Respir Cell Mol Biol 2020; 61:266-268. [PMID: 31368811 DOI: 10.1165/rcmb.2018-0204le] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
| | | | | | - Kevin W Ng
- 2BC Cancer AgencyVancouver, British Columbia, Canadaand
| | | | - Adam P Sage
- 2BC Cancer AgencyVancouver, British Columbia, Canadaand
| | | | - Zhaolin Xu
- 3Dalhousie UniversityHalifax, Nova Scotia, Canada
| | - Wan L Lam
- 2BC Cancer AgencyVancouver, British Columbia, Canadaand
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20
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Ng KW, Attig J, Young GR, Ottina E, Papamichos SI, Kotsianidis I, Kassiotis G. Soluble PD-L1 generated by endogenous retroelement exaptation is a receptor antagonist. eLife 2019; 8:e50256. [PMID: 31729316 PMCID: PMC6877088 DOI: 10.7554/elife.50256] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 07/16/2019] [Accepted: 11/13/2019] [Indexed: 12/27/2022] Open
Abstract
Immune regulation is a finely balanced process of positive and negative signals. PD-L1 and its receptor PD-1 are critical regulators of autoimmune, antiviral and antitumoural T cell responses. Although the function of its predominant membrane-bound form is well established, the source and biological activity of soluble PD-L1 (sPD-L1) remain incompletely understood. Here, we show that sPD-L1 in human healthy tissues and tumours is produced by exaptation of an intronic LINE-2A (L2A) endogenous retroelement in the CD274 gene, encoding PD-L1, which causes omission of the transmembrane domain and the regulatory sequence in the canonical 3' untranslated region. The alternatively spliced CD274-L2A transcript forms the major source of sPD-L1 and is highly conserved in hominids, but lost in mice and a few related species. Importantly, CD274-L2A-encoded sPD-L1 lacks measurable T cell inhibitory activity. Instead, it functions as a receptor antagonist, blocking the inhibitory activity of PD-L1 bound on cellular or exosomal membranes.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick InstituteLondonUnited Kingdom
| | - Jan Attig
- Retroviral Immunology, The Francis Crick InstituteLondonUnited Kingdom
| | - George R Young
- Retrovirus-Host Interactions, The Francis Crick InstituteLondonUnited Kingdom
| | - Eleonora Ottina
- Retroviral Immunology, The Francis Crick InstituteLondonUnited Kingdom
| | - Spyros I Papamichos
- Department of HaematologyDemocritus University of Thrace Medical SchoolAlexandroupolisGreece
| | - Ioannis Kotsianidis
- Department of HaematologyDemocritus University of Thrace Medical SchoolAlexandroupolisGreece
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick InstituteLondonUnited Kingdom
- Department of MedicineFaculty of Medicine, Imperial College LondonLondonUnited Kingdom
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Ng KW, Marshall EA, Enfield KS, Martin SD, Milne K, Pewarchuk ME, Abraham N, Lam WL. Somatic mutation-associated T follicular helper cell elevation in lung adenocarcinoma. Oncoimmunology 2018; 7:e1504728. [PMID: 30524903 PMCID: PMC6279324 DOI: 10.1080/2162402x.2018.1504728] [Citation(s) in RCA: 8] [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: 02/26/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022] Open
Abstract
T follicular helper cells (Tfh) play crucial roles in the development of humoral immunity. In the B cell-rich germinal center of lymphoid organs, they select for high-affinity B cells and aid in their maturation. While Tfh have known roles in B cell malignancies and have prognostic value in some epithelial cancers, their role in lung tumour initiation and development is unknown. Through immune cell deconvolution, we observed significantly increased Tfh in tumours from two independent cohorts of lung adenocarcinomas and found that this upregulation occurs early in tumour development. A subset of tumours were stained for T and B cells using multicolour immunohistochemistry, which revealed the presence of tumour-adjacent tertiary lymphoid organs in 17/20 cases each with an average of 16 Tfh observed in the germinal center. Importantly, Tfh levels were correlated with tumour mutational load and immunogenic cancer testis antigens, suggesting their involvement in mounting an active immune response against tumour neoantigens.
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Affiliation(s)
- Kevin W Ng
- British Columbia Cancer Research Centre, Integrative Oncology Department, Vancouver, Canada
| | - Erin A Marshall
- British Columbia Cancer Research Centre, Integrative Oncology Department, Vancouver, Canada.,Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Katey Ss Enfield
- British Columbia Cancer Research Centre, Integrative Oncology Department, Vancouver, Canada.,Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Spencer D Martin
- British Columbia Cancer Research Centre, Integrative Oncology Department, Vancouver, Canada.,Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Katy Milne
- Deeley Research Centre, Victoria, Canada
| | - Michelle E Pewarchuk
- British Columbia Cancer Research Centre, Integrative Oncology Department, Vancouver, Canada
| | - Ninan Abraham
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Wan L Lam
- British Columbia Cancer Research Centre, Integrative Oncology Department, Vancouver, Canada.,Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Marshall EA, Anderson C, Ng KW, Minatel BC, Enfield KS, Sage AP, Xu Z, Lam WL, Martinez VD. Abstract B36: Novel miRNAs as tissue-of-origin markers for distinguishing malignant pleural mesothelioma from lung adenocarcinoma. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-b36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The outcome of patients with malignant pleural mesothelioma (MPM) is poor, and diagnosis is complicated by a lack of biomarkers capable of distinguishing primary MPM from cancers that have metastasized to the pleura. Clinical diagnosis and tissue of origin is currently assessed through the use of a panel of positive and negative markers; however, there remains a subset of cases that are not identifiable by current clinical biomarkers.
Recent studies suggest that the human genome encodes more miRNAs than are currently annotated, and that the novel miRNAs may display enhanced tissue and lineage specificity. We conducted a de novo search for novel miRNAs by applying a prediction algorithm to the small RNA-sequence data in a cohort of MPM tumors (n=87) from The Cancer Genome Atlas (TCGA). This analysis yielded 424 predicted novel miRNA-like sequences, which were subsequently filtered by RNA structure, abundance, and genomic location to identify 154 previously unannotated miRNA sequences. This represents a significant increase to the repertoire of 1,597 annotated miRNAs in MPM. Protein-coding genes predicted to be targeted by these novel miRNAs, using the miRanda algorithm, include genes involved in MPM biology. One of the most highly expressed novel miRNAs identified targets the Ataxia Telangiectasia Mutated (ATM) gene. Another target gene, BRCA1 Associated Protein 1 (BAP1), is also in the DNA damage response pathway.
To investigate the ability of these 154 novel miRNAs to distinguish MPM from other thoracic cancers, we assessed their expression in 1,093 lung tumors from four independent cohorts from TCGA and the BC Cancer Agency (BCCA): two adenocarcinoma (LUAD) cohorts (TCGA n=497, BCCA n=94) and two squamous cell carcinoma (LUSC) cohorts (TCGA n=467, BCCA n=35). Principal component analyses revealed that novel miRNA expression was able to unambiguously distinguish MPM from LUAD and LUSC. Furthermore, we developed an miRNA-based classifier model using the weighted voting class prediction method. A 10 novel miRNAs classifier was deduced by comparing MPM and LUAD cases from TCGA and validated by comparing MPM against LUAD cases from the BCCA cohort. Remarkably, this classifier successfully identified 86 out of the 87 MPM cases (98.8%) and 100% of LUAD cases (true positive rate = 98.85%, false positive rate = 1.15%). The strikingly high sensitivity and specificity in distinguishing MPM from LUAD illustrates the potential of using novel miRNAs to supplement current clinical markers to define MPM.
Citation Format: Erin A. Marshall, Christine Anderson, Kevin W. Ng, Brenda C. Minatel, Katey S.S. Enfield, Adam P. Sage, Zhaolin Xu, Wan L. Lam, Victor D. Martinez. Novel miRNAs as tissue-of-origin markers for distinguishing malignant pleural mesothelioma from lung adenocarcinoma [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr B36.
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Affiliation(s)
- Erin A. Marshall
- 1British Columbia Cancer Research Centre, Vancouver, BC, Canada,
| | | | - Kevin W. Ng
- 1British Columbia Cancer Research Centre, Vancouver, BC, Canada,
| | | | | | - Adam P. Sage
- 1British Columbia Cancer Research Centre, Vancouver, BC, Canada,
| | - Zhaolin Xu
- 2Dalhousie University, Halifax, NS, Canada
| | - Wan L. Lam
- 1British Columbia Cancer Research Centre, Vancouver, BC, Canada,
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Enfield KS, Ng KW, Marshall EA, Martin SD, Lam WL. Abstract B15: Increased presence of T follicular helper cells in lung adenocarcinoma is associated with mutational load. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-b15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tertiary lymphoid organs are ectopic lymphoid formations found in inflamed tissues such as tumors, and their presence has been associated with improved patient outcome. T follicular helper cells (Tfh) reside in the germinal centre of tertiary lymphoid organs, and are required for the maturation of B cells and subsequent antibody response. Whereas the prognostic value of Tfh has been described in breast and colon tumors, they remain uncharacterized in lung tumors. We hypothesize that Tfh cells reside in lung adenocarcinomas and are associated with an increased immune response due to neoantigen exposure.
Gene expression profiles were obtained from 83 paired lung adenocarcinomas and nonmalignant lung tissues from the BC Cancer Agency, and 571 unpaired samples from The Cancer Genome Atlas. Relative proportions of 22 immune cell subsets were inferred from gene expression data using CIBERSORT, a deconvolution algorithm. Identification of tertiary lymphoid organs was achieved through multicolor immunohistochemistry (IHC) staining for T- and B-cell lineage markers (CD3 and CD79a) using whole tissue sections. Proportions of Tfh cells were correlated with tumor mutation load defined as non-silent mutations per megabase (Mann Whitney U test) and patient outcome (Cox proportional hazard model).
The proportion of Tfh cells was significantly increased in tumor tissue compared to nonmalignant lung in both cohorts. We also observed concomitant upregulation of Tfh markers PD1 and CXCR5. Multicolor IHC validated the presence of tertiary lymphoid organs in 19 out of 20 cases assessed. Intriguingly, the increase in the proportion of Tfh cells revealed by CIBERSORT was observed across all disease stages and was validated in an additional cohort of Stage I lung adenocarcinomas. The relative proportion of Tfh cells did, however, increase with increasing tumor mutation burden, suggesting their involvement in an active immune response against tumor neoantigens.
Tfh recruitment appears to be an early event in lung tumor progression and a function of neoantigen exposure, suggesting involvement in an active antitumor response rather than a passive result of chronic inflammation. Further investigation into Tfh in lung adenocarcinomas may lead to prognostic applications.
Citation Format: Katey S.S. Enfield, Kevin W. Ng, Erin A. Marshall, Spencer D. Martin, Wan L. Lam. Increased presence of T follicular helper cells in lung adenocarcinoma is associated with mutational load [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr B15.
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Affiliation(s)
| | - Kevin W. Ng
- British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | | | | | - Wan L. Lam
- British Columbia Cancer Research Centre, Vancouver, BC, Canada
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Enfield KS, Marshall EA, Anderson C, Ng KW, Rahmati S, Xu Z, MacAulay CE, Lam S, Lockwood WW, Chari R, Karsan A, Jurisica I, Lam WL. Abstract A26: Identification of a novel therapeutic target in lung adenocarcinoma. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-a26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The reactivation of biologic signaling events that occur throughout fetal development has been observed during malignant cell transformation and tumor progression. Transcription factors are typically at the hub of these signaling events, such as NKX2-1 and several ETS transcription factors. ELF3 is an uncharacterized ETS family member that is highly expressed during fetal lung development and could play a biologic role in lung cancer based on its location within the recurrently gained chromosome 1q. We hypothesize that ELF3 is a novel oncogenic transcription factor and a therapeutic target.
Multiple independent datasets encompassing 1,685 clinical samples of lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), small cell lung cancer, and nonmalignant lung tissues were analyzed to establish the frequency of ELF3 overexpression and underlying genetic mechanisms of selection. ELF3 overexpression was validated by immunohistochemistry. Associations with patient survival were tested using the log-rank method. Isogenic cell lines were established to assess oncogenic phenotypes including tumor growth in a xenograft model. Protein-protein interaction (PPI) networks were constructed around ELF3, and integrated pathway analysis was performed to decipher the signaling network disruptions resulting from ELF3 overexpression.
ELF3 overexpression was frequently observed in LUAD (>2-fold: BCCA 73% TCGA 40%), but was not observed in other lung cancer subtypes. Similarly, high ELF3 expression was significantly associated with poor overall survival of LUAD patients (p<0.0001), but not LUSC patients. These clinical associations prompted further examination of ELF3 in the LUAD subtype of lung cancer. ELF3 knockdown in LUAD cell lines resulted in significantly reduced proliferation, viability, and anchorage-independent growth, demonstrating that ELF3 regulates oncogenic phenotypes. Loss of ELF3 abolished the ability of LUAD cells to establish tumors in xenograft mouse models, demonstrating the requirement of ELF3 expression for tumor growth. ELF3 overexpression is associated with remodeling of 23 direct PPI networks, resulting in loss of interaction with proteins such as NFKB1 and MYC, while forming new interactions with NKX2-1, HOXA5 and ERBB3. Pathway analysis suggests a transcriptional reprogramming from inflammatory and MAPK signallng in nonmalignant and ELF3-low tissues, to adhesion and motility pathways in transformed tissues displaying high ELF3 expression. Core pathways included cell cycle, apoptosis, WNT, and NOTCH signaling, agreeing with our cell models. While mutations in ELF3 were rare, up to 80% of LUAD patients harbored focal amplification, DNA gain, and/or promoter hypomethylation at the ELF3 locus, which resulted in transcript overexpression.
We have deciphered the oncogenic role of ELF3 in LUAD. Its requirement for tumor growth in our model indicates that therapeutic targeting of ELF3 could benefit the 73% of patients who display ELF3 overexpression.
Citation Format: Katey S.S. Enfield, Erin A. Marshall, Christine Anderson, Kevin W. Ng, Sara Rahmati, Zhaolin Xu, Calum E. MacAulay, Stephen Lam, William W. Lockwood, Raj Chari, Aly Karsan, Igor Jurisica, Wan L. Lam. Identification of a novel therapeutic target in lung adenocarcinoma [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A26.
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Affiliation(s)
| | - Erin A. Marshall
- 1British Columbia Cancer Research Centre, Vancouver, BC, Canada,
| | | | - Kevin W. Ng
- 1British Columbia Cancer Research Centre, Vancouver, BC, Canada,
| | - Sara Rahmati
- 2Krembil Discovery Tower, Toronto Western Hospital, Toronto, ON, Canada,
| | - Zhaolin Xu
- 3Dalhousie University, Halifax, NS, Canada,
| | | | - Stephen Lam
- 1British Columbia Cancer Research Centre, Vancouver, BC, Canada,
| | | | - Raj Chari
- 4Frederick National Lab for Cancer Research, Frederick, MD
| | - Aly Karsan
- 1British Columbia Cancer Research Centre, Vancouver, BC, Canada,
| | - Igor Jurisica
- 2Krembil Discovery Tower, Toronto Western Hospital, Toronto, ON, Canada,
| | - Wan L. Lam
- 1British Columbia Cancer Research Centre, Vancouver, BC, Canada,
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Minatel BC, Martinez VD, Ng KW, Sage AP, Tokar T, Marshall EA, Anderson C, Enfield KSS, Stewart GL, Reis PP, Jurisica I, Lam WL. Large-scale discovery of previously undetected microRNAs specific to human liver. Hum Genomics 2018; 12:16. [PMID: 29587854 PMCID: PMC5870816 DOI: 10.1186/s40246-018-0148-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 01/17/2018] [Accepted: 03/19/2018] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) are crucial regulators of gene expression in normal development and cellular homeostasis. While miRNA repositories contain thousands of unique sequences, they primarily contain molecules that are conserved across several tissues, largely excluding lineage and tissue-specific miRNAs. By analyzing small non-coding RNA sequencing data for abundance and secondary RNA structure, we discovered 103 miRNA candidates previously undescribed in liver tissue. While expression of some of these unannotated sequences is restricted to non-malignant tissue, downregulation of most of the sequences was detected in liver tumors, indicating their importance in the maintenance of liver homeostasis. Furthermore, target prediction revealed the involvement of the unannotated miRNA candidates in fatty-acid metabolism and tissue regeneration, which are key pathways in liver biology. Here, we provide a comprehensive analysis of the undiscovered liver miRNA transcriptome, providing new resources for a deeper exploration of organ-specific biology and disease.
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Affiliation(s)
- Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Tomas Tokar
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Christine Anderson
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Katey S S Enfield
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Greg L Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Patricia P Reis
- Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
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Sage AP, Minatel BC, Ng KW, Stewart GL, Dummer TJB, Lam WL, Martinez VD. Oncogenomic disruptions in arsenic-induced carcinogenesis. Oncotarget 2018; 8:25736-25755. [PMID: 28179585 PMCID: PMC5421966 DOI: 10.18632/oncotarget.15106] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 11/30/2016] [Accepted: 01/24/2017] [Indexed: 12/13/2022] Open
Abstract
Chronic exposure to arsenic affects more than 200 million people worldwide, and has been associated with many adverse health effects, including cancer in several organs. There is accumulating evidence that arsenic biotransformation, a step in the elimination of arsenic from the human body, can induce changes at a genetic and epigenetic level, leading to carcinogenesis. At the genetic level, arsenic interferes with key cellular processes such as DNA damage-repair and chromosomal structure, leading to genomic instability. At the epigenetic level, arsenic places a high demand on the cellular methyl pool, leading to global hypomethylation and hypermethylation of specific gene promoters. These arsenic-associated DNA alterations result in the deregulation of both oncogenic and tumour-suppressive genes. Furthermore, recent reports have implicated aberrant expression of non-coding RNAs and the consequential disruption of signaling pathways in the context of arsenic-induced carcinogenesis. This article provides an overview of the oncogenomic anomalies associated with arsenic exposure and conveys the importance of non-coding RNAs in the arsenic-induced carcinogenic process.
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Affiliation(s)
- Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Greg L Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Trevor J B Dummer
- Centre of Excellence in Cancer Prevention, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
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Martinez VD, Firmino NS, Marshall EA, Ng KW, Wadsworth BJ, Anderson C, Lam WL, Bennewith KL. Non-coding RNAs predict recurrence-free survival of patients with hypoxic tumours. Sci Rep 2018; 8:152. [PMID: 29317756 PMCID: PMC5760628 DOI: 10.1038/s41598-017-18462-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 05/19/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022] Open
Abstract
Hypoxia promotes tumour aggressiveness and reduces patient survival. A spectrum of poor outcome among patients with hypoxic tumours suggests that additional factors modulate how tumours respond to hypoxia. PIWI-interacting RNAs (piRNAs) are small non-coding RNAs with a pivotal role in genomic stability and epigenetic regulation of gene expression. We reported that cancer type-specific piRNA signatures vary among patients. However, remarkably homogenous piRNA profiles are detected across patients with renal cell carcinoma, a cancer characterized by constitutive upregulation of hypoxia-related signaling induced by common mutation or loss of von Hippel-Lindau factor (VHL). By investigating >3000 piRNA transcriptomes in hypoxic and non-hypoxic tumors from seven organs, we discovered 40 hypoxia-regulated piRNAs and validated this in cells cultured under hypoxia. Moreover, a subset of these hypoxia-regulated piRNAs are regulated by VHL/HIF signaling in vitro. A hypoxia-regulated piRNA-based score (PiSco) was associated with poor RFS for hypoxic tumours, particularly Stage I lung adenocarcinomas, suggesting that hypoxia-regulated piRNA expression can predict tumour recurrence even in early-stage tumours and thus may be of clinical utility.
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Affiliation(s)
- Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada.
| | - Natalie S Firmino
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Brennan J Wadsworth
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Christine Anderson
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Kevin L Bennewith
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
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Marshall EA, Sage AP, Ng KW, Martinez VD, Firmino NS, Bennewith KL, Lam WL. Small non-coding RNA transcriptome of the NCI-60 cell line panel. Sci Data 2017; 4:170157. [PMID: 29064465 PMCID: PMC5654365 DOI: 10.1038/sdata.2017.157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 06/30/2017] [Accepted: 09/05/2017] [Indexed: 01/01/2023] Open
Abstract
Only 3% of the transcribed human genome is translated into protein, and small non-coding RNAs from these untranslated regions have demonstrated critical roles in transcriptional and translational regulation of proteins. Here, we provide a resource that will facilitate cell line selection for gene expression studies involving sncRNAs in cancer research. As the most accessible and tractable models of tumours, cancer cell lines are widely used to study cancer development and progression. The NCI-60 panel of 59 cancer cell lines was curated to provide common models for drug screening in 9 tissue types; however, its prominence has extended to use in gene regulation, xenograft models, and beyond. Here, we present the complete small non-coding RNA (sncRNA) transcriptomes of these 59 cancer cell lines. Additionally, we examine the abundance and unique sequences of annotated microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs), and reveal novel unannotated microRNA sequences.
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Affiliation(s)
- Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada V5Z 1L3
| | - Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada V5Z 1L3
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada V5Z 1L3
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada V5Z 1L3
| | - Natalie S Firmino
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada V5Z 1L3
| | - Kevin L Bennewith
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada V5Z 1L3
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada V5Z 1L3
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Ng KW, Marshall EA, Bell JC, Lam WL. cGAS-STING and Cancer: Dichotomous Roles in Tumor Immunity and Development. Trends Immunol 2017; 39:44-54. [PMID: 28830732 DOI: 10.1016/j.it.2017.07.013] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 02/07/2023]
Abstract
cGMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) sensing has emerged as a key regulator of innate immune responses to both exogenous and endogenous DNA. Recent studies reveal critical roles for this pathway in natural antitumor immunity across cancer types as well as in immune checkpoint blockade therapy. However, it is also clear that some tumors evade cGAS-STING-mediated immune responses, and immunomodulatory therapeutics are currently being explored to target this pathway. Finally, we also discuss recent observations that cGAS-STING-mediated inflammation may promote tumor initiation, growth, and metastasis in certain malignancies and how this may complicate the utility of this pathway in therapeutic development.
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Affiliation(s)
- Kevin W Ng
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada; These authors contributed equally to this work
| | - Erin A Marshall
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada; These authors contributed equally to this work
| | - John C Bell
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
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Enterina JR, Enfield KSS, Anderson C, Marshall EA, Ng KW, Lam WL. DLK1-DIO3 imprinted locus deregulation in development, respiratory disease, and cancer. Expert Rev Respir Med 2017; 11:749-761. [PMID: 28715922 DOI: 10.1080/17476348.2017.1355241] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
INTRODUCTION The imprinted DLK1-DIO3 locus at 14q32.1-32.31 holds biological significance in fetal development, whereby imprinting errors are causal to developmental disorders. Emerging evidence has implicated this locus in other diseases including cancer, highlighting the biological parallels between fetal organ and tumour development. Areas covered: Controlled regulation of gene expression from the imprinted DLK1-DIO3 locus at 14q32.1-32.31 is crucial for proper fetal development. Deregulation of locus gene expression due to imprinting errors has been mechanistically linked to the developmental disorders Kagami-Ogata Syndrome and Temple Syndrome. In adult tissues, deregulation of locus genes has been associated with multiple malignancies although the causal genetic mechanisms remain largely uncharacterised. Here, we summarize the genetic mechanisms underlying the developmental disorders that arise as a result of improper locus imprinting and the resulting developmental phenotypes, emphasizing both the coding and noncoding components of the locus. We further highlight biological parallels common to both fetal development and disease, with a specific focus on lung development, respiratory disease, and lung cancer. Expert commentary: Many commonalities between respiratory and developmental defects have emerged with respect to the 14q32 locus, emphasizing the importance of studying the effects of imprinting on gene regulation patterns at this locus in both biological settings.
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Affiliation(s)
- Jhon R Enterina
- a British Columbia Cancer Research Centre , Vancouver , BC , Canada
| | | | | | - Erin A Marshall
- a British Columbia Cancer Research Centre , Vancouver , BC , Canada
| | - Kevin W Ng
- a British Columbia Cancer Research Centre , Vancouver , BC , Canada
| | - Wan L Lam
- a British Columbia Cancer Research Centre , Vancouver , BC , Canada
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31
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Marshall EA, Ng KW, Kung SHY, Conway EM, Martinez VD, Halvorsen EC, Rowbotham DA, Vucic EA, Plumb AW, Becker-Santos DD, Enfield KSS, Kennett JY, Bennewith KL, Lockwood WW, Lam S, English JC, Abraham N, Lam WL. Emerging roles of T helper 17 and regulatory T cells in lung cancer progression and metastasis. Mol Cancer 2016; 15:67. [PMID: 27784305 PMCID: PMC5082389 DOI: 10.1186/s12943-016-0551-1] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/18/2016] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is a leading cause of cancer-related deaths worldwide. Lung cancer risk factors, including smoking and exposure to environmental carcinogens, have been linked to chronic inflammation. An integral feature of inflammation is the activation, expansion and infiltration of diverse immune cell types, including CD4+ T cells. Within this T cell subset are immunosuppressive regulatory T (Treg) cells and pro-inflammatory T helper 17 (Th17) cells that act in a fine balance to regulate appropriate adaptive immune responses.In the context of lung cancer, evidence suggests that Tregs promote metastasis and metastatic tumor foci development. Additionally, Th17 cells have been shown to be an integral component of the inflammatory milieu in the tumor microenvironment, and potentially involved in promoting distinct lung tumor phenotypes. Studies have shown that the composition of Tregs and Th17 cells are altered in the tumor microenvironment, and that these two CD4+ T cell subsets play active roles in promoting lung cancer progression and metastasis.We review current knowledge on the influence of Treg and Th17 cells on lung cancer tumorigenesis, progression, metastasis and prognosis. Furthermore, we discuss the potential biological and clinical implications of the balance among Treg/Th17 cells in the context of the lung tumor microenvironment and highlight the potential prognostic function and relationship to metastasis in lung cancer.
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Affiliation(s)
- Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Sonia H Y Kung
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada. .,British Columbia Cancer Research Centre Centre, Vancouver, Canada.
| | - Emma M Conway
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Elizabeth C Halvorsen
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - David A Rowbotham
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Emily A Vucic
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Adam W Plumb
- Departments of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
| | | | - Katey S S Enfield
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Jennifer Y Kennett
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Kevin L Bennewith
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - William W Lockwood
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - John C English
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Ninan Abraham
- Departments of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada. .,British Columbia Cancer Research Centre Centre, Vancouver, Canada.
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Abstract
In standard multivariate statistical analysis, common hypotheses of interest concern changes in mean vectors and subvectors. In compositional data analysis it is now well established that compositional change is most readily described in terms of the simplicial operation of perturbation and that subcompositions replace the marginal concept of subvectors. Against the background of two motivating experimental studies in the food industry, involving the compositions of cow’s milk and chicken carcasses, this paper emphasizes the importance of recognizing this fundamental operation of change in the associated simplex sample space. Well-defined hypotheses about the nature of any compositional effect can be expressed, for example, in terms of perturbation values and subcompositional stability and testing procedures developed. These procedures are applied to lattices of such hypotheses in the two practical situations. We identify the two problems as being the counterpart of the analysis of paired comparison or split plot experiments and of separate sample comparative experiments in the jargon of standard multivariate analysis.
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Affiliation(s)
- J Aitchison
- Department of Statistics, University of Glasgow, UK,
| | - K W Ng
- Department of Statistics and Actuarial Science, University of Hong Kong, China
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33
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Enfield KSS, Rowbotham DA, Holly A, Anderson C, Ng KW, Minatel BDC, Dellaire G, Pastrello C, Jurisica I, MacAulay C, Lam S, Lam WL. Abstract A21: MiR-106a and miR-106b affect growth and metastasis of lung adenocarcinoma. Cancer Res 2016. [DOI: 10.1158/1538-7445.nonrna15-a21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: MiR-106a and miR-106b are paralogs of the oncogenic miR-17~92, and have been associated with poor outcome and metastasis in several solid tumors. Their role in lung cancer is relatively unexplored. We characterized the expression of miR-106a and miR-106b in a clinical cohort of lung adenocarcinoma (AC) tumors and assessed their ability to regulate growth and metastasis in cell models.
Methods: MicroRNA (miRNA) expression was deduced from small RNA sequencing data derived from clinical lung AC specimens (60 localized, 27 with lymph node invasion) and paired non-malignant tissues. MiR-106a and miR-106b overexpression vectors and controls were stably transfected into immortalized non-malignant Human Bronchial Epithelial Cells (HBECs) and stage I AC cell lines with epithelial expression patterns by lentiviral delivery. Migration and invasion was assessed by Boyden chamber assay, while cell proliferation was assessed by BrdU incorporation assay. Expression of epithelial-to-mesenchymal transition (EMT) markers and other proteins of interest were assessed by Western Blot. Clinical associations in an external cohort were derived using publically available TCGA data.
Results: MiR-106a and miR-106b were significantly overexpressed in lung AC with lymph node invasion. Overexpression of miR-106a and miR-106b significantly increased proliferation of lung AC cell lines, and was associated with decreased levels of predicted target, p21. AC cell lines displayed a marked increase in metastatic phenotypes in vitro, and were associated with increased mesenchymal and decreased epithelial markers, characteristic of EMT. Importantly, tumors with high expression of both miR-106a and miR-106b and mesenchymal marker vimentin had significantly poorer outcome.
Conclusions: MiR-106a and miR-106b are overexpressed in metastatic lung AC. Lung AC cell models indicate these miRNAs are metastatic agonists, affecting the metastatic potential of cells at least in part via induction of EMT. A deeper characterization of this observation may reveal therapeutic intervention points, or, with the development of miRNA therapeutics, miR-106a/b may be promising targets to prevent or treat metastatic disease.
Citation Format: Katey SS Enfield, David A. Rowbotham, Alice Holly, Christine Anderson, Kevin W. Ng, Brenda de Carvalho Minatel, Graham Dellaire, Chiara Pastrello, Igor Jurisica, Calum MacAulay, Stephen Lam, Wan L. Lam. MiR-106a and miR-106b affect growth and metastasis of lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A21.
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Affiliation(s)
| | | | | | | | - Kevin W. Ng
- 1BC Cancer Research Centre, Vancouver, BC, Canada,
| | | | | | | | - Igor Jurisica
- 3Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | - Stephen Lam
- 1BC Cancer Research Centre, Vancouver, BC, Canada,
| | - Wan L. Lam
- 1BC Cancer Research Centre, Vancouver, BC, Canada,
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34
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Enfield KS, Anderson C, Marshall E, Ng KW, de Carvalho Minatel B, Rowbotham DA, Chari R, Fuller M, Milne K, Becker-Santos DD, MacAulay C, Karsan A, Lam S, Lam WL. ELF3 amplification at 1q32.1 promotes SMAD4-independent tumorigenesis. J Thorac Oncol 2016. [DOI: 10.1016/j.jtho.2015.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Ng KW, Anderson C, Marshall EA, Minatel BC, Enfield KSS, Saprunoff HL, Lam WL, Martinez VD. Piwi-interacting RNAs in cancer: emerging functions and clinical utility. Mol Cancer 2016; 15:5. [PMID: 26768585 PMCID: PMC4714483 DOI: 10.1186/s12943-016-0491-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [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: 08/20/2015] [Accepted: 01/05/2016] [Indexed: 12/29/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are emerging players in cancer genomics. Originally described in the germline, there are over 20,000 piRNA genes in the human genome. In contrast to microRNAs, piRNAs interact with PIWI proteins, another member of the Argonaute family, and function primarily in the nucleus. There, they are involved in the epigenetic silencing of transposable elements in addition to the transcriptional regulation of genes. It has recently been demonstrated that piRNAs are also expressed across a variety of human somatic tissue types in a tissue-specific manner. An increasing number of studies have shown that aberrant piRNA expression is a signature feature across multiple tumour types; however, their specific tumorigenic functions remain unclear. In this article, we discuss the emerging functional roles of piRNAs in a variety of cancers, and highlight their potential clinical utilities.
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Affiliation(s)
- Kevin W Ng
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Christine Anderson
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Erin A Marshall
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Brenda C Minatel
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Katey S S Enfield
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | | | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Victor D Martinez
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
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36
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Chu PY, Tsang JPK, Wong WY, Chan WCS, Ng KW, Yuen MK. Magnetic Resonance Imaging Features and Assessment of Local Extent of Localised Giant Cell Tumour of the Tendon Sheath in Fingers. Hong Kong J Radiol 2015. [DOI: 10.12809/hkjr1515296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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37
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Marshall EA, Ng KW, Anderson C, Hubaux R, Thu KL, Lam WL, Martinez VD. Gene expression analysis of microtubule affinity-regulating kinase 2 in non-small cell lung cancer. Genom Data 2015; 6:145-8. [PMID: 26697357 PMCID: PMC4664690 DOI: 10.1016/j.gdata.2015.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide, and has a five-year survival rate of 18% [1]. MARK2 is a serine/threonine-protein kinase, and is a key component in the phosphorylation of microtubule-associated proteins [2], [3]. A recent study published by Hubaux et al. found that microtubule affinity-regulating kinase 2 (MARK2) showed highly frequent DNA and RNA level disruption in lung cancer cell lines and independent non-small cell lung cancer (NSCLC) cohorts [4]. These alterations result in the acquisition of oncogenic properties in cell lines, such as increased viability and anchorage-independent growth. Furthermore, a microarray-based transcriptome analysis of three short hairpin RNA (shRNA)-mediated MARK2 knockdown lung adenocarcinoma cell lines (GEO#: GSE57966) revealed an association between MARK2 gene expression and cell cycle activation and DNA damage response. Here, we present a detailed description of transcriptome analysis to support the described role of MARK2 in promoting a malignant phenotype.
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Affiliation(s)
- Erin A Marshall
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada
| | | | - Roland Hubaux
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada
| | - Kelsie L Thu
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada
| | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada
| | - Victor D Martinez
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada
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38
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Setyawati MI, Tay CY, Chia SL, Goh SL, Fang W, Neo MJ, Chong HC, Tan SM, Loo SCJ, Ng KW, Xie JP, Ong CN, Tan NS, Leong DT. Titanium dioxide nanomaterials cause endothelial cell leakiness by disrupting the homophilic interaction of VE-cadherin. Nat Commun 2013; 4:1673. [PMID: 23575677 DOI: 10.1038/ncomms2655] [Citation(s) in RCA: 332] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 02/27/2013] [Indexed: 02/07/2023] Open
Abstract
The use of nanomaterials has raised safety concerns, as their small size facilitates accumulation in and interaction with biological tissues. Here we show that exposure of endothelial cells to TiO₂ nanomaterials causes endothelial cell leakiness. This effect is caused by the physical interaction between TiO₂ nanomaterials and endothelial cells' adherens junction protein VE-cadherin. As a result, VE-cadherin is phosphorylated at intracellular residues (Y658 and Y731), and the interaction between VE-cadherin and p120 as well as β-catenin is lost. The resulting signalling cascade promotes actin remodelling, as well as internalization and degradation of VE-cadherin. We show that injections of TiO₂ nanomaterials cause leakiness of subcutaneous blood vessels in mice and, in a melanoma-lung metastasis mouse model, increase the number of pulmonary metastases. Our findings uncover a novel non-receptor-mediated mechanism by which nanomaterials trigger intracellular signalling cascades via specific interaction with VE-cadherin, resulting in nanomaterial-induced endothelial cell leakiness.
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Affiliation(s)
- M I Setyawati
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576, Singapore
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39
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Low YKA, Zou X, Fang YM, Wang JL, Lin WS, Boey FYC, Ng KW. β-Phase poly(vinylidene fluoride) films encouraged more homogeneous cell distribution and more significant deposition of fibronectin towards the cell-material interface compared to α-phase poly(vinylidene fluoride) films. Mater Sci Eng C Mater Biol Appl 2013; 34:345-53. [PMID: 24268268 DOI: 10.1016/j.msec.2013.09.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/19/2013] [Accepted: 09/21/2013] [Indexed: 11/26/2022]
Abstract
The piezoelectric response from β-phase poly(vinylidene fluoride) (PVDF) can potentially be exploited for biomedical application. We hypothesized that α and β-phase PVDF exert direct but different influence on cellular behavior. α- and β-phase PVDF films were synthesized through solution casting and characterized with FT-IR, XRD, AFM and PFM to ensure successful fabrication of α and β-phase PVDF films. Cellular evaluation with L929 mouse fibroblasts over one-week was conducted with AlamarBlue® metabolic assay and PicoGreen® proliferation assay. Immunostaining of fibronectin investigated the extent and distribution of extracellular matrix deposition. Image saliency analysis quantified differences in cellular distribution on the PVDF films. Our results showed that β-phase PVDF films with the largest area expressing piezoelectric effect elicited highest cell metabolic activity at day 3 of culture. Increased fibronectin adsorption towards the cell-material interface was shown on β-phase PVDF films. Image saliency analysis showed that fibroblasts on β-phase PVDF films were more homogeneously distributed than on α-phase PVDF films. Taken collectively, the different molecular packing of α and β-phase PVDF resulted in differing physical properties of films, which in turn induced differences in cellular behaviors. Further analysis of how α and β-phase PVDF may evoke specific cellular behavior to suit particular application will be intriguing.
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Affiliation(s)
- Y K A Low
- School of Materials Science and Engineering, Nanyang Technological University, N4.1 50 Nanyang Avenue, Singapore 639798, Singapore
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40
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Wong WY, Chan WCS, Chu PY, Ng KW, Hui PK, Yuen MK. Cemented Femoral Stem Loosening of Hip Arthroplasty: Ten-year Radiographic Analysis. Hong Kong J Radiol 2013. [DOI: 10.12809/hkjr1312155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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41
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Abstract
Modern Computer Aided Design/Modeling (CAD/CAM) software allows complex surgical simulations, but it is often difficult to transfer and execute precisely the planned scenarios during actual operations. We describe a new method of integrating CAD/CAM surgical plans directly into a computer surgical navigation system, and demonstrate its use to guide three complex orthopaedic surgical procedures: a periacetabular osteotomy of a dysplastic hip, a corrective osteotomy of a post-traumatic tibial deformity, and a multi-planar resection of a distal femoral tumor followed by reconstruction with a CAD custom prosthesis.
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Affiliation(s)
- K C Wong
- Orthopaedic Oncology, Department of Orthopaedics and Traumatology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong.
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42
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Low YKA, Meenubharathi N, Niphadkar ND, Boey FYC, Ng KW. α- and β-poly(vinylidene fluoride) evoke different cellular behaviours. J Biomater Sci Polym Ed 2010; 22:1651-67. [PMID: 20699059 DOI: 10.1163/092050610x519471] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
α-Phase poly(vinylidene fluoride) (PVDF) has chains of zero dipole moments and is, therefore, nonpiezoelectric, while β-phase PVDF has the most significant piezoelectric properties among the polymorphs due to its polar chains. Although many reports describe PVDF as a suitable biomaterial due to its stability and biocompatibility, few considered the specific effects that the different polymorphs exert on cellular behaviour. We hypothesized that α- and β-phase PVDF will exert direct but different influences on cell attachment and metabolic activity. PVDF films were fabricated using N,N-dimethylformamide (DMF) and hexamethylphosphoramide (HMPA) by solvent casting. Samples were characterized by differential scanning calorimetry, Fourier transform infrared spectroscopy and X-ray diffraction. Films containing 83.5% α-phase PVDF (DMF-PVDFα) and 91.4% of β-phase PVDF (HMPA-PVDFβ within the crystalline regions were produced and used to evaluate in vitro attachment and metabolic activity of L929 cells. Cell metabolic activity on both PVDF conformations increased 3-fold over the 1-week culture period, with higher cell metabolic activity observed on DMF-PVDFα on day 5 of culture, compared to HMPA-PVDFβ. Cells grown on DMF-PVDFα were well-spread, flat and expressed spotted paxillin in focal adhesions that were mainly localized to perinuclear regions of the cells, while a high proportion of cells on HMPA-PVDFβ were bulging, round and expressed relatively fewer paxillin spots. Our results suggest that α-phase PVDF supports higher cell metabolic activity and better cell spreading compared to β-phase PVDF. Such variations can potentially be exploited for different biomedical applications.
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Affiliation(s)
- Y K A Low
- School of Materials Science and Engineering, Nanyang Technological University, Singapore
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43
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Abstract
Anti-resorptives that prevent osteoclasts from resorbing bone are the mainstay of treatment for osteoporosis, while parathyroid hormone is the only agent available that stimulates osteoblasts to form bone. Advances in knowledge about metabolic pathways in bone cell biology have identified specific points of intervention whereby formation and function of osteoclasts and osteoblasts can be inhibited or stimulated. The next generation of therapies for osteoporosis may include molecules that antagonize integrin or inhibit Src tyrosine kinase, vacuolar H+-ATPase, chloride channel or cathepsin K, thus preventing osteoclasts from attaching to bone, form a ruffled border, acidify resorption lacunae or digest organic bone matrix. At least some of these may form a novel class of anti-resorptives capable of inhibiting bone resorption without being coupled to inhibition of bone formation. Human and mouse genetics studies demonstrating the pivotal role of the Wnt signaling pathway in bone metabolism have led to the development of strategies to disrupt Wnt signaling in order to increase bone formation. Selective androgen receptor modulators that produce an anabolic effect on muscle and bone without undesirable androgenic side effects can potentially be used to treat osteoporosis, aged-related frailty, muscle wasting disorders and glucocorticoid-induced osteoporosis. Studies involving these molecules are still in either preclinical or early investigational stage, without fracture data. Nonetheless, preliminary results hold the promise that at least some of these new therapies may develop into effective means of treating and preventing osteoporosis. Any new therapy for osteoporosis must take into consideration its safety, efficacy, affordability and specificity of action.
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Affiliation(s)
- K W Ng
- Department of Endocrinology & Diabetes, The University of Melbourne, St Vincent's Hospital, Fitzroy, Victoria 3065, Australia.
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44
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To KF, Leung WK, Ng KW, Tong JHM, Lung RWM. Sequencing analysis of the 3' region of the cagA gene in Helicobacter pylori isolated from Hong Kong Chinese patients. Hong Kong Med J 2010; 16:8-12. [PMID: 20864739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Affiliation(s)
- K F To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, SAR, China.
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45
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Choi MPK, Kang YH, Peng XL, Ng KW, Wong MH. Stockholm Convention organochlorine pesticides and polycyclic aromatic hydrocarbons in Hong Kong air. Chemosphere 2009; 77:714-719. [PMID: 19775721 DOI: 10.1016/j.chemosphere.2009.08.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 08/19/2009] [Accepted: 08/22/2009] [Indexed: 05/28/2023]
Abstract
Organochlorine pesticides (OCPs) including eight of the original nine pesticides listed in the Stockholm Convention on Persistent Organic Pollutants, and polycyclic aromatic hydrocarbons (PAHs) were measured in 90 air samples collected from January 2004 to March 2005, and in 304 air samples collected from January 1998 to December 2005 in Hong Kong, respectively. The annual average OCP concentrations at Tap Mun, Yuen Long and Tsuen Wan were 135+/-140 (ND-482), 186+/-183 (ND-656), and 190+/-239 fg m(-3) (ND-966), respectively, while annual (January 1998 to December 2005) average concentrations of total PAHs at Tsuen Wan, and Central/Western were 578+/-261 (117-938) and 588+/-248ngm(-3) (103-874), respectively. No seasonal and spatial variations in OCP concentrations were observed due to trace levels, and estimation of carcinogenic risks of OC pesticides was low. Naphthalene (>70%) was the dominant PAH in terms of concentrations measured. The sum of three-ring PAHs, including acenaphthene, acenaphthylene, anthracene, fluorene and phenanthrene, contributed to around 20% of the total PAH concentration while the contribution of heavier PAHs (sum of four-, five- and six-rings) was less than 5%. t-Values of the paired samples T-test for the individual PAHs showed that the concentrations of benzo(a)pyrene, the relative high cancer risk PAH, and most of the PAHs detected at Tsuen Wan and Central/Western were significantly different (p<0.01), with higher concentrations detected at Tsuen Wan. Several PAHs exhibited strong seasonality with higher concentrations in winter. Sources of PAHs were determined by investigating PAH isomer ratios which suggested petrogenic sources as primary sources of PAHs in Hong Kong air.
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Affiliation(s)
- M P K Choi
- Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University, Hong Kong, PR China
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46
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Ng KW, Chow A, Win MK, Dimatatac F, Neo HY, Lye DC, Leo YS. Clinical features and epidemiology of chikungunya infection in Singapore. Singapore Med J 2009; 50:785-790. [PMID: 19710977] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Chikungunya is a re-emerging mosquito-borne viral infection that has spread from East Africa to Indian Ocean islands and re-emerged in India since 2004. In Malaysia, chikungunya re-emerged after a hiatus of seven years, causing a localised outbreak in a north-western coastal town in 2006 and subsequently widespread outbreaks in 2008. Since the first local outbreak of chikungunya in Singapore in January 2008, chikungunya infections have been increasingly reported in Singapore. In this case series, five patients aged 37-62 years, with chikungunya infection confirmed in August 2008, were reported. Three of the five were male, and only one had medical comorbidities. Two had a travel history to Johor, Malaysia, where local outbreaks of chikungunya had been reported. Fever, arthralgia and rash were the most common symptoms. Fever lasted four to five days while viraemia lasted four to 11 days, persisting two to three days after defervescence in three patients. A biphasic pattern of fever was observed in two patients. Leucopenia was noted in all patients, while mild thrombocytopenia and transaminitis occurred in three of five patients. Two patients had persistent polyarthralgia at two to three weeks after the onset of symptoms. Fever, arthralgia and rash should prompt consideration of acute chikungunya in Singapore. While taking the travel history, doctors should be mindful that indigenous chikungunya cases can occur.
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Affiliation(s)
- K W Ng
- Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore
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47
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Bian L, Lima EG, Angione SL, Ng KW, Williams DY, Xu D, Stoker AM, Cook JL, Ateshian GA, Hung CT. Mechanical and biochemical characterization of cartilage explants in serum-free culture. J Biomech 2008; 41:1153-9. [PMID: 18374344 DOI: 10.1016/j.jbiomech.2008.01.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 01/28/2008] [Accepted: 01/31/2008] [Indexed: 10/22/2022]
Abstract
Allografts of articular cartilage are both used clinically for tissue-transplantation procedures and experimentally as model systems to study the physiological behavior of chondrocytes in their native extracellular matrix. Long-term maintenance of allograft tissue is challenging. Chemical mediators in poorly defined culture media can stimulate cells to quickly degrade their surrounding extracellular matrix. This is particularly true of juvenile cartilage which is generally more responsive to chemical stimuli than mature tissue. By carefully modulating the culture media, however, it may be possible to preserve allograft tissue over the long-term while maintaining its original mechanical and biochemical properties. In this study juvenile bovine cartilage explants (both chondral and osteochondral) were cultured in both chemically defined medium and serum-supplemented medium for up to 6 weeks. The mechanical properties and biochemical content of explants cultured in chemically defined medium were enhanced after 2 weeks in culture and thereafter remained stable with no loss of cell viability. In contrast, the mechanical properties of explants in serum-supplemented medium were degraded by ( approximately 70%) along with a concurrent loss of biochemical content (30-40% GAG). These results suggest that long-term maintenance of allografts can be extended significantly by the use of a chemically defined medium.
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Affiliation(s)
- L Bian
- Cellular Engineering Laboratory, Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
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48
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Martin TJ, Sims NA, Ng KW. Regulatory pathways revealing new approaches to the development of anabolic drugs for osteoporosis. Osteoporos Int 2008; 19:1125-38. [PMID: 18338097 DOI: 10.1007/s00198-008-0575-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 01/15/2008] [Indexed: 12/17/2022]
Abstract
The understanding of cell interactions and genetic controls of bone cells has provided new approaches to drug development for osteoporosis. Current emphasis in the development of new anabolic therapies is directed at modifying the effects of Wnt signalling on osteoblast differentiation and bone formation. Local signalling that results in bone formation during remodelling takes place in several ways. Growth factors released from resorbed bone matrix can contribute to preosteoblast differentiation and bone formation. Osteoclasts in the bone multicellular units (BMUs) might also generate activity that contributes to bone formation. The preosteoblasts themselves, growing in the resorption space, can communicate through cell contact and paracrine signalling mechanisms to differentiate. Osteocytes can sense the need for bone repair by detecting damage and pressure changes, and signalling to surface cells to respond appropriately. These recent insights into cell communication, together with discoveries from human and mouse genetics, have opened new pathways to drug development for osteoporosis. With the anabolic effect of parathyroid hormone on the skeleton having been established, human genetics revealed the major role of Wnt signalling in bone formation, and this has become the target of activity. Current approaches include activation at any of several points in the Wnt pathway, and neutralization of sclerostin, the protein product of the SOST gene that is produced in osteocytes as a powerful inhibitor of bone formation.
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Affiliation(s)
- T J Martin
- St Vincent's Institute of Medical Research, Melbourne, Australia.
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49
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Lima EG, Bian L, Ng KW, Mauck RL, Byers BA, Tuan RS, Ateshian GA, Hung CT. The beneficial effect of delayed compressive loading on tissue-engineered cartilage constructs cultured with TGF-beta3. Osteoarthritis Cartilage 2007; 15:1025-33. [PMID: 17498976 PMCID: PMC2724596 DOI: 10.1016/j.joca.2007.03.008] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 03/11/2007] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To determine whether the functional properties of tissue-engineered constructs cultured in a chemically-defined medium supplemented briefly with TGF-beta3 can be enhanced with the application of dynamic deformational loading. METHODS Primary immature bovine cells (2-3 months old) were encapsulated in agarose hydrogel (2%, 30 x 10(6)cells/ml) and cultured in chemically-defined medium supplemented for the first 2 weeks with transforming growth factor beta 3 (TGF-beta3) (10 microg/ml). Physiologic deformational loading (1 Hz, 3 h/day, 10% unconfined deformation initially and tapering to 2% peak-to-peak deformation by day 42) was applied either concurrent with or after the period of TGF-beta3 supplementation. Mechanical and biochemical properties were evaluated up to day 56. RESULTS Dynamic deformational loading applied concurrently with TGF-beta3 supplementation yielded significantly lower (-90%) overall mechanical properties when compared to free-swelling controls. In contrast, the same loading protocol applied after the discontinuation of the growth factor resulted in significantly increased (+10%) overall mechanical properties relative to free-swelling controls. Equilibrium modulus values reach 1306+/-79 kPa and glycosaminoglycan levels reach 8.7+/-1.6% w.w. during this 8-week period and are similar to host cartilage properties (994+/-280 kPa, 6.3+/-0.9% w.w.). CONCLUSIONS An optimal strategy for the functional tissue engineering of articular cartilage, particularly to accelerate construct development, may incorporate sequential application of different growth factors and applied deformational loading.
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Affiliation(s)
- E G Lima
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Avenue, New York, NY 10027, USA
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50
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Ng KW, DeFrancis JG, Kugler LE, Kelly TAN, Ho MM, O'Conor CJ, Ateshian GA, Hung CT. Amino acids supply in culture media is not a limiting factor in the matrix synthesis of engineered cartilage tissue. Amino Acids 2007; 35:433-8. [PMID: 17713744 PMCID: PMC3769193 DOI: 10.1007/s00726-007-0583-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 07/02/2007] [Indexed: 10/22/2022]
Abstract
Increased amino acid supplementation (0.5 x, 1.0 x, and 5.0 x recommended concentrations or additional proline) was hypothesized to increase the collagen content in engineered cartilage. No significant differences were found between groups in matrix content or dynamic modulus. Control constructs possessed the highest compressive Young's modulus on day 42. On day 42, compared to controls, decreased type II collagen was found with 0.5 x, 1.0 x, and 5.0 x supplementation and significantly increased DNA content found in 1.0 x and 5.0 x. No effects were observed on these measures with added proline. These results lead us to reject our hypothesis and indicate that the low collagen synthesis in engineered cartilage is not due to a limited supply of amino acids in media but may require a further stimulatory signal. The results of this study also highlight the impact that culture environment can play on the development of engineered cartilage.
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Affiliation(s)
- K W Ng
- Cellular Engineering Laboratory, Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
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