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Dr Karl J Staples BSc (Hons), PhD, FHEA

Associate Professor

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Dr Karl Staples is an Associate Professor at the University of Southampton Faculty of Medicine. His research focuses on host-pathogen interactions in chronic inflammatory airways diseases, such as asthma and Chronic Obstructive Pulmonary Disease (COPD), and the contribution of these interactions to exacerbations of these respiratory conditions. To study these interactions he has developed novel ex vivo models of bacterial and viral (incl. influenza, COVID-19) infection using human lung cells and tissue.  He is also the NIHR Southampton Biomedical Research Centre Respiratory & Critical Care Theme Training Lead and the Clinical & Experimental Sciences Doctoral Programme Lead.

Macrophages are often thought of as the housekeepers of the lung, removing dust and debris that are inhaled, but these cells act as an important brake on the immune system, keeping inflammation to a minimum. This braking effect appears to be reduced in asthma, COPD and by viral infections. My research concentrates on trying to restore this brake and reduce the inflammation in these diseases.

He was introduced to the respiratory immunology field during his doctoral studies with Professor Peter Barnes, FRS, and Dr Robert Newton at the NHLI, Imperial College, London. Here he investigated the mechanisms by which the release of the cytokines interleukin (IL)-5 and GM-CSF from T cells are modulated by anti-inflammatory therapeutics, such as glucocorticoids and phosphodiesterase (PDE) inhibitors. After an interesting postdoctoral post at Cornell University in New York investigating the function of STAT proteins, the key cytokine signalling molecules, he joined Prof. Löms Ziegler-Heitbrock at the University of Leicester to study cytokine release from macrophages.

A key factor in his move to Southampton was that it allowed him to expand his research interest back into airways disease. This interest led to the award of an Asthma UK project grant in 2008 to study the phenotype and function of macrophages derived from the airway of asthmatics.  Since the award of this first grant, he has developed ex vivo models of infection of lung samples that have led to further funding (e.g. BMA, AZ) and multiple publications.  These models are being expanded to investigate multiple hypotheses by his growing research team of postdoctoral scientists and PhD students.

Degree Qualifications

Appointments held

Research interests

Dr Staples’ research focuses on host-pathogen interactions in the respiratory system and specifically the impact of these interactions in chronic inflammatory airways diseases, such as asthma and COPD.  His current research is broadly split along the following lines:

1. Host-virus interactions

Based upon his experience of culturing and infecting human lung samples with influenza (Staples et al 2015, Nicholas et al 2015, McKendry et al 2016, Cooper et al 2018, Watson et al 2020) Dr Staples’ group is expanding these models to study Respiratory Syncytial Virus (MRC-funded Integrated PhD studentship) and the coronavirus responsible for COVID-19. These models will allow testing of novel therapeutics to combat these viruses and their inflammation they cause.

2. Host-bacterial interactions

It is now increasingly apparent that even in health the lungs are not sterile, being host to a diverse population of bacteria, known as the “microbiome”.  In COPD, this microbiome appears to be dysregulated (Mayhew et al 2017), with a substantial proportion of patients being chronically colonised with the bacteria non-typeable Haemophilus influenzae (NTHi) (Wilkinson et al 2017). Dr Staples’ group have developed co-culture models to analyse the NTHi-induced activation of conventional T cells and unconventional mucosal-associated invariant T cells (MAIT) from human blood (Hinks, Wallington et al 2016), and human lung explants (Wallington et al 2017). In collaboration with AstraZeneca, the group are now integrating transcriptomic and microbiome data derived from healthy volunteers and COPD patients to understand the impact of microbial colonisation on host gene expression.

3. Interaction of viruses and bacteria in the airways

Influenza infection is known to predispose to secondary bacterial pneumonias, possibly by disrupting the ability of macrophages to phagocytose bacteria (Cooper et al 2016). However, based on data from the Southampton AERIS longitudinal COPD cohort, it is also apparent that chronic colonisation with NTHi may also predispose to viral infections (Wilkinson et al 2017). Dr Staples’ Asthma UK-funded Integrated PhD student is investigating how lung macrophage anti-viral activity is modulated by infection with bacteria using dual RNASeq to understand not only host gene expression in response to infection but also changes in bacterial gene expression.

PhD research/supervision

  • 2014 Expression and function of programmed cell death Protein-1 (PD-1) and ligand PD-L1 in Chronic Obstructive Pulmonary Disease (MRC)
  • 2015 Characterisation of the human lung fibroblasts ability to act as an antigen-presenting cell for T helper cells of the immune system (Gerald Kerkut Trust)
  • 2017 The responses of conventional T cells and mucosal-associated invariant T cells to nontypeable Haemophilus influenzae infection (GSK)
  • 2018 Biomarkers of inflammation and infections in chronic obstructive pulmonary disease: utility of disease stratification and management (GSK)
  • 2018 Natural killer cell responses to influenza A virus in the human lung (MRC)

Research group

Clinical and Experimental Sciences

Research project(s)

Chinese Herbal medicine to aid AnTibiotic use reduction in exacerbation of Chronic Obstructive Pulmonary Disease (CHAT COPD)

Postgraduate student supervision

  • MPhil/PhD students

Faculty of Medicine

  • Clinical & Experimental Sciences Doctoral Programme Lead
  • CES Member of Faculty Graduate School Committee
  • Member PGR Special Considerations Board
  • Deputy Academic Lead, Containment Level 3 Laboratory
  • NIHR BRC Respiratory & Critical Care Theme Training Lead
  • Internal PhD Examiner

University of Southampton

  • Southampton Academy of Research Strategy Committee

National Responsibilities

  • Meetings Secretary of the British Association for Lung Research Committee
  • Scientific Consultant, Allergy UK
  • External Examiner, MRes Biomedical Sciences, Imperial College, London
  • External PhD Examiner
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Book Chapters




BM Programmes Pharmacology teaching

BM & MSc Student Personal Tutor

BMedSc & MMedSc. Research project supervisor

MSc Allergy. Allergic Airways Disease co-module leader and lecturer

Integrated PhD programme. Lecturer on Infection and Immunity module and MRes Research Project supervisor

Dr Karl J Staples
Wessex Investigational Sciences Hub, MP850, LF114, Southampton General Hospital, Tremona Road, Southampton SO16 6YD

Room Number : SGH/LF114/MP810

Facsimile: (023) 8070 1771

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