AAIR Charity awards applications (2016) – Funded projects
Stephan Holgate PhD Studentship: The role of ADAM33 in pre- and perinatal airway remodeling and the early life development of asthma.
Awarded to: Hans Michael Haitchi and Christopher Woelk, awarded to Joanne Kelly
Amount: £58,100 (additional University of Southampton, Faculty of Medicine funding £48,100) (October 2014 – October 2018)
Lay summary: In October 2015 Joanne spent 3 weeks (supported by AAIR travel grant) in the pulmonary biology and bioinformatics group in Cincinnati Children’s Hospital in the USA. Here she learned how to analyse large data sets from “next generation gene sequencing” (NGS) from our lung samples from our ADAM33 asthma model compared with “normal” lung samples. Back in Southampton she further studied the list of genes that were different in the ADAM33 asthma model in our existing lung samples.
Furthermore, Joanne successfully established an epithelial cell culture model by growing the cells that line the major airways from our ADAM33 asthma model. She studied the function and leakiness of these cells in the presence of the ADAM33 protein and will also study the list of genes she discovered by NGS in our ADAM33 asthma model in these cells.
From the NGS data Jo has discovered a potential interaction between ADAM33 induced airway remodelling and airway inflammation, which she is studying in fibroblasts, structural airway cells that do or do not express ADAM33 protein.
During this PhD fellowship Joanne has also made contributions to and is a co-author in a recent publication in the Journal of Clinical Investigation (JCI) Insight about how ADAM33 initiates airway remodelling to promote asthma in early life.
E.R. Davies, J.F.C. Kelly, P.H. Howarth, D.I Wilson, S.T. Holgate, D.E. Davies, J.A. Whitsett, H.M. Haitchi. Soluble ADAM33 initiates airway remodeling to promote susceptibility for allergic asthma in early life. JCI Insight. 2016 Jul 21;1(11). pii: e87632.
The press release from the University of Southampton related to our research publication had been widely covered by most major national newspapers as well as national radio and many other international media.
PhD Studentship: Information provision preferences of food allergic and intolerant consumers when eating
Awarded to: Jane Lucas
Amount: £11,800 (March 2014 – March 2017)
Lay summary: During the initial stages of the PhD studentship, an exploratory study was conducted to capture online discussions surrounding the implementation of new EU-labelling law. These regulations require consumers to have access to information about allergen ingredients when buying foods. Discussions via Twitter revolved around several key themes: mobilisation around the legislation the impact of legislation, continuing frustration when eating out, and the preparedness of businesses. This study was presented as a poster at the University of Bath’s Faculty Research Showcase.
A further study focussed on discussions around a news article in which chefs had voiced concerns about the introduction of the new legislation. Sources of data soon after the original news article included subsequent news articles, online comments on the original article, Twitter posts and discussions. Frames identified from a qualitative analysis emphasised medical concerns, responsibility, fairness of access, the political nature of the debate, and financial implications. This project was presented at the Psychology Conference, and Changing Lives, Changing Worlds Conference (both at the University of Bath). It was also presented in poster form at the Faculty Research Showcase, where it won the gold award, and at the International Conference of Social Media and Society at Goldsmiths University. The accompanying research paper is currently under review following journal submission.
The studentship continues to investigate how and why food allergic/intolerant individuals use social media (e.g., for support reasons, or gaining information), and investigate how credibility is inferred for the sources of information encountered.
Funding from AAIR has allowed research collaboration and communication through attendance at advisory meetings/workshops (e.g. with the FSA and associated researchers), meetings with allergy charities (e.g., Allergy UK, Anaphylaxis Campaign, and Coeliac UK), conference presentations, and associated training.
Hamshaw, R. J. T. (2015, June). Perceptions of new food allergen legislation on Twitter. Poster presented at the Humanities & Social Sciences Faculty Research Showcase, University of Bath, England. Abstract available from http://www.bath.ac.uk/hss/pdf/postgraduate-research-showcase/richard-hamshaw.pdf
Hamshaw, R. J. T. (2016, May) A frame analysis utilising media and social media sources: The 100 chefs incident. Poster presented at the Humanities & Social Sciences Faculty Research Showcase, University of Bath, England. Available from http://www.bath.ac.uk/hss/news/documents/richard-hamshaw.pdf
This research poster was awarded 1st Prize in the Post-Confirmation category
Hamshaw, R. J. T. (2016, June) A frame analysis utilising media and social media sources: The 100 chefs incident. Research presented at the 3rd Annual Postgraduate Psychology Conference, University of Bath, England.
Hamshaw, R. J. T. (2016, July) A frame analysis utilising media and social media sources: The 100 chefs incident. Research presented at the 3rd Annual Faculty of Humanities & Social Sciences Postgraduate Conference, University of Bath, England.
Hamshaw, R. J. T. & Barnet, J. (2016, July) A frame analysis utilising media and social media sources: The 100 chefs incident. Poster presented at the International Conference of Social Media & Society, Goldsmiths University, England. Information available from https://socialmediaandsociety.org/past-conferences/2016-2/2016-schedule/
Hamshaw, R. J. T., Barnett, J., & Lucas, J. S. (2016). Framing Events and Taking Positions in an Online Food Allergen Debate: The 100 Chefs Incident. Manuscript submitted for publication.
Research award: Development and validation of age specific health related quality of life measures for patients with primary ciliary dyskinesia
Awarded to: Laura Behan and J. Lucas
Lay summary: Support from the AAIR Charity, co-funded by FP7 BESTCILIA, has led to age-specific quality of life measures for patients with primary ciliary dyskinesia (QOL-PCD). This work has provided the first disease-specific outcome measures to monitor PCD patients clinically, document the progression of their illness and assess the effectiveness of therapeutic interventions in clinical trials. Researchers from University of Southampton led the development and validation of QOL-PCD, involving patients from across Europe and North America. Our findings have shown QOL-PCD to be robust, reliable, responsive and valid.
In rare disease such as PCD, international collaborations are vital. It is important that QoL measures used in clinical trials are translated and tested comprehensively in each language. AAIR funding has enabled the QOL-PCD measures to be comprehensively translated in a number of languages for widespread use in international clinical trials across Europe, North America and the Middle East. The English, Danish, Dutch and German languages versions of the measures are already being used as outcome measures for a randomised clinical trial of azithromycin.
Finally, AAIR funding has enabled the PhD student working on this study to analyse the data, prepare a number of manuscripts, and submit her final thesis. It has also allowed for findings of the study to be presented to an international forum at the European Respiratory Society Congress, American Thoracic Society and at the COST Action BEAT-PCD Training School in Paris http://www.beatpcd.org/
- Behan, Laura. Leigh, Margaret W. Dell, Sharon D. Dunn Galvin, Audrey. Quittner, Alexandra L. Lucas, Jane S. Validation of a health-related quality of life instrument for primary ciliary dyskinesia: QOL-PCD (Submitted to Thorax).
- Dell SD, Leigh MW, Lucas JS, Ferkol TW, Knowles MR, Alpern A, et al. Primary Ciliary Dyskinesia: First Health-related Quality of Life Measures for Pediatric Patients. Annals of the American Thoracic Society. 2016. (in press)
- Laura Behan: Health related quality of life measures for PCD. Cost Action BEAT PCD Inaugural Conference 2016
- Jane Lucas: American Thoracic Society, San Francisco May 2016. Scientific symposium: The link between ciliary assembly defects, neonatal respiratory distress and bronchiectasis in adulthood: a primer on primary ciliary dyskinesia
- Jane Lucas: European Respiratory Society Congress, London September 2016. Scientific Symposium: Diagnosing primary ciliary dyskinesia (PCD) in a molecular age
- Laura Behan, Alexandra L. Quittner, Anika Lofruthe, Anu Kalayamthanam, Aristoula Toliop Audrey DunnGalvin, Bridget Contreras, Christine Edelbusch, Claudia E. Kuehni, Claudius Werner, Elizabeth Maurer, Eric G. Haarman, Helene Elgaard Kobbernagel, Irma Bon, Konstantinos Giannakou, Lea Heisch, Maria Philipsen, Niels Rutjes, Panagiotis Kouis, Tamara Paff, Jane S Lucas. Translation of QOL-PCD: a cross-cultural patient-reported outcome measure for patients with primary ciliary dyskinesia. European Respiratory Society Congress 2016.
- Claire O’Neill, Guillaume Thouvenin, Laura Behan, Delphine Habouria, Harriet Corvol, Annick Clément, Jane S Lucas, Aline Tamalet. French translation and linguistic validation of the QOL-PCD, a quality of life questionnaire for patients with Primary Ciliary Dyskinesia. European Respiratory Society Congress 2016.
- Behan, Laura. Dunn Galvin, Audrey. Alpern, A. Morris, AM. Carroll, MP. Knowles, MR. Leigh, MW. Quittner, AL. Lucas, JS. Development, Translation and Validation of Health-Related Quality of Life Measures for Primary Ciliary Dyskinesia. Cost Action BEAT-PCD Training School 2016.
- Behan L, Dunn Galvin A, Alpern A, Morris AM, Carroll MP, Knowles MR, Leigh MW, Quittner AL, Lucas JS. Development and validation of QOL-PCD – collaboration, participation and recruitment. Cost Action BEAT-PCD Training School 2016.
Travel Grant: Travel Fellowship for training in RNA-Seq Analysis of Lungs from Transgenic Mice Expressing Human ADAM33 pro and metalloprotease domains – A model for Asthmatic Airway Remodelling
Awarded to: Joanne Kelly and H. M. Haitchi
Lay summary: In October 2015 the AAIR Charity funded a travel grant so that I could visit our collaborators at Cincinnati Children’s Hospital in Ohio in the USA. The purpose of this trip was to learn, first-hand, how to process and interoperate complex data sets generated by state-of-the-art technology called next generation gene sequencing.
Using this technology the bioinformatics team at the Children’s Hospital were able to analyse lung samples from our ADAM33 asthma susceptibility model and compare them with “normal” lung samples. This method generates extensive lists of genes, identifying those that are different between the two types of lung sample. This method can provide data for the expression of all 30,000+ possible genes present in the lung and therefore it requires considerable expertise to analyse them.
After 3 weeks shadowing the expert team in Cincinnati I am now able to analyse the data generated from our lung samples here in Southampton, which should shed light on the processes by which ADAM33 initiates asthma at the origin of the disease. This time in Cincinnati was an invaluable experience, which will also help me to analyse results from our future research using this novel technology, as well as aiding others in data analysis of this sort.
Research equipment: Meso QuickplexSQ120
Awarded to: Laure Lau, P. Howarth, H. Arshad, A. Walls and H. M. Haitchi
Lay Summary: The multi user MSD Quickplex SQ120 was purchased through AAIR Charity after receiving matching funding from the Head of CES and the Faculty of Medicine Research Management Committee. This has been up and running since March 2016. Several projects in CES have already been benefited from this equipment. By taking advantage of the high sensitivity of MSD ELISA plate assays:
- Dr Emily Swindle’s PhD student was able to detect IFN-beta release from human mast cells infected with cold virus.
- Professor Christodouldas’ group has used the MSD ELISA plates to measure the IL-18 and IL-1beta release in human primary corneal fibroblasts in different conditions of Pseudomonas aeruginosa infection.
- Dr Richard Felwick has been studying human colonic explant cultures for his PhD project. The MSD assay has provided him a high sensitivity platform in which to measure pro-inflammatory cytokine release from these samples. The multiplex format and small sample volumes needed were critical for these precious samples.
- Dr Deiphine Boche‘s group were able to explore the inflammatory responses in precious post-mortem brain tissue from patients who had suffered from dementia and Alzheimer’s disease. She has measured pro-inflammatory cytokines.
Drs Walls and Lau have been seeking to establish an association between pro-inflammatory cytokines and mast cell proteases in the serum of patients with anaphylaxis in order to identify those susceptible to severe reaction.
Research equipment: Centrifuge Heraeus Megafuge 40R
Awarded to: R-M. Mackay, A. Walls, A. Postle, J. Madsen, H. Clark, P. Howarth
Lay summary: Since purchasing our centrifuge, it has contributed to several lines of work. For example PhD and postdoctoral work investigating lung disease, infection and immunity. As well as industrial collaborations with Chiesi and GlaxoSmithKline. In addition, lipidomics, biochemists, immunologists and cellular biologists within the laboratory use the equipment, the results from these experiments, if successful will provide the basis of several research publications for several different fields of enquiry.
Yaroslav Shkanov, Rose-Marie A Mackay, Rhys George, Laurie CK Lau, Rana
Abadalkareem, John Pedersen, Andrew F Walls. Dipeptidyl peptidase I (DPPI) cleaves surfactant protein D (SP-D): A mechanism for immune compromise in the lung. The Europeon respiratory society, London 2016.
Yaroslav Shkanov, Rose-Marie Mackay and Andrew Walls. Characterisation of the interaction between mast cell proteases and surfactant protein. British Society for Allergy & Clinical Immunology (BSACI), London 2016.
Research Award: Investigating whether a species-dependent rhinovirus response in infected cells might be linked to respiratory disease outcome
Awarded to: Christopher McCormick and D. E. Davies
Lay Summary: Rhinoviruses cause the common cold. While rhinovirus infection is a minor inconvenience for most people, in individuals with asthma infection can be life threatening. Rhinovirus produces two types of enzymes called proteases. It is known that the activity of one of the two proteases varies between different strains of rhinovirus, and it is also known that some strains are more pathogenic (ie. cause more illness) than others. We suspect that variation in pathogenicity may be linked to variation in protease activity. If correct, understanding how variation in protease activity alters an infected cell response could give us important insight into what is happening in the lungs of individuals with rhinovirus-induced severe asthma exacerbation.
Using AAIR funding we have developed two novel systems to look at the role of the viral proteases in airway disease. We have already found that there are big differences in the extent to which the proteases stop cells being able to produce their own proteins, and allow the virus to produce its own proteins. This has important consequences for the ability of the infected cell to fight off the invading virus and signal to the immune system for help. On-going work is trying to gain a better understanding of the molecular events underlying these observations.
AAIR funding covered the entire cost of lab reagents used and helped pay for someone to be in the lab doing the work. Data generated has allowed us to put in applications for studentship funding from Asthma UK, Wessex Trust and Kerkut Trust. A paper detailing our findings will soon be submitted for publication. We intend to submit a full grant application to continue this work next year.
Research Award: Do fibrous mineral dust particles elicit a pro-fibrotic response in a conditioned medium model of the distal airways?
Awarded to: R. Latouche, D. Smart and M. Loxham
Lay Summary: Airborne dusts in the Afghan desert have been seen to cause lung disease in soldiers returning from the area, but we know little about their make-up and effect. I previously found that this dust contains significant amounts of a mineral called palygorskite, which is of a fibrous shape similar to asbestos. Palygorskite is not, however, found only is desert dust, but is used in a range of cosmetics and animal products, meaning that there is the potential for widespread exposure among the general population. As such, we need to better understand its potential effects on the airways after inhalation. The AAIR award allowed me to examine the effects of this dust in a model of the airways, constructed using cells from the airway surface, called epithelial cells, and cells called macrophages which patrol the surface of the airways and “eat” particles which we inhale. The aim was to better understand how the presence of dust alters the way in which these two cell types communicate with each other – a process which is important in maintaining healthy airways. I found that the two cell types do not react in the same way, with the macrophages being more susceptible than the epithelial cells to the toxic effects of the dust, but also potentially protected by the presence of the epithelial cells. I also found that these effects were greater using pure palygorskite compared to the whole dust samples, suggesting that the palygorskite is a particular toxic component of desert dust. Finally, I saw that desert dust caused increases in the levels of various molecules released by the two cell types, but that these responses were different when the cells were exposed together, compared to when only one cell type was studied. As a result, we now better understand how desert dust might cause lung disease, and also have developed knowledge and experience of interactions between different lung cells when exposed to such dust.
The research which has been performed as a result of this award will be written up into two papers – one focusing on the mineralogy and chemistry of the desert dust samples used, and another examining the effects of cellular exposure to the minerals. Both will include reference to the AAIR charity award in the Acknowledgements/Funders section. In addition, it will form a key part of my doctoral thesis, which will be submitted to the Faculty in December 2016.
Research Award: Evaluation of alternatively spliced Th2–related genes in alveolar macrophages and bronchial epithelial cells by Frac-seq, to investigate their influence on the modulation of proteomic output and relationship to disease severity in asthma.
Awarded to: R. T. Martinez-Nunez
Lay Summary: Asthma has a strong genetic component, but we do not fully understand its molecular mechanisms. This hinders development of more efficient drugs targeting specific molecules in the lungs of people with asthma. Genes (mRNA) contain information to produce proteins, the main functional units in the cell. Traditional scientific approaches investigate levels of genes translating them into levels of protein production. We now know this is not accurate, as genes exist in different forms (isoforms), of which only a fraction generate proteins affected by regulators called microRNAs.
I developed Frac-seq, a technique measuring isoforms bound to the cellular machinery converting mRNA into proteins (ribosomes). Those mRNAs in ribosomes are missed with conventional scientific techniques. I analysed the role of microRNAs, key regulators of protein production, applying this method and comparing airway cells from volunteers with severe asthma against healthy volunteers. This revealed new asthma-specific microRNAs influencing nearly half of the changes we detected in asthma-related isoforms. These findings would be missed without applying Frac-seq. These microRNAs are potential novel candidates for drug development. Thanks to the AAIR Charity grant I have been able to fund part of this research hoping to publish my findings soon. The AAIR Charity funds also allowed me to investigate alveolar macrophages, key guardians of our lung immune response, uncontrolled in asthma. I am investigating novel isoforms related to inflammation not responding to current treatment options.
- Martinez-Nunez R. T. , Wallace A., Coyne D., Bailey J., Jansson L., Ennajdaoui H., Rush M., Deinhardt K., Sanchez-Elsner T., Sanford J.R§. Rapamycin modulates nonsense mediated decay. doi: http://dx.doi.org/10.1101/028332. Manuscript accepter in Nucleic Acids Research. I conceived, conducted and analysed experiments, as well as writing of the manuscript. I am also the corresponding author. This paper benefited from overleft reagents purchased thanks to this grant, allowing me to explore RNA decay by mTOR signalling, of potential application in asthma in future projects.
- Martinez-Nunez R. T., Rupani H., Niranjan M., Howarth P.H., Sanchez-Elsner T. MicroRNAs underlie genome wide transcriptome and translatome dysregulation in severe asthma airway epithelium. Manuscript in submission (November 2016). I conceived, conducted and analysed experiments, as well as writing of the manuscript. I am also the corresponding author. This is the main paper arising from the AAIR Charity grant.
- Studying post-transcriptional gene regulation with Frac-seq: rapamycin modulates nonsense mediated decay and microRNAs predominantly regulate genome-wide translation in asthma. Invited Talk in London RNA Club, November 2016.
- Coordination of alternative splicing, translation and mRNA stability – all you ever wanted to know about polyribosomal mRNA sequencing – in human primary cells. DC/Macrophage Forum University of Southampton, September 2016.
- Bronchial epithelium in severe asthma shows a mismatch between transcription and translation, as revealed by RibomiR-seq. Invited Talk in University College London, hosted by Prof Rachel Chambers. May 2016.
Conference Oral Presentations:
- RibomiR-seq reveals that global microRNA binding fine-tunes the transcriptome but profoundly alters the translatome in severe asthma. SouthWest RNA Club, May 2016.
- Global microRNA binding fine-tunes the transcriptome but profoundly alters the translatome: the application of RibomiR-seq to the understanding of epithelial cell activation in severe asthma. 31st Symposium Collegium Internationale Allergologicum, Charleston, South Carolina, April 2016.
- RibomiR-seq reveals microRNAs fine-tune the transcriptome but profoundly alter translation in severe asthma. 14th Lung Science Conference, European Respiratory Society. Estoril, March 2016.
- CES Club, Faculty of Medicine, University of Southampton. “microRNAs and translation two sides of the same coin”. March 2015.
- Bioinformatics Journal Club, University of Southampton. “Frac-seq in asthma: RNA-seq of polyribosomes gives a new picture of disease”. January 2015.
Conference Poster Presentations:
- T. Martinez-Nunez, H. Rupani, T. Sanchez-Elsner, P.H.Howarth. Polyribosome profiling and RNA-sequencing of human primary bronchial epithelial cells reveals novel and unique signatures of severe asthma. Lung Science Conference, European Respiratory Society. Estoril, March 2015. Poster Presentation and Travel Award.
PhD Studentship: The contribution of mast cells to rhinovirus infections in asthma
Awarded to: E. Swindle and D.E. Davies
Amount: £27,000 (October 2013 – September 2016)
Lay Summary: Asthma is a disease of the airways (the tubes that carry air into the lungs) which narrow from time-to-time (exacerbation) by triggers in the air making it difficult to breathe. Mast cells are a rare type of white blood cell that contribute to the symptoms of asthma triggered by allergens (e.g. pollen and dust). However, the common cold virus is a major trigger of asthma exacerbations and we do not know exactly how this occurs. We also do not know if or how mast cells respond to the common cold virus but we do know that these cells form part of an early warning system following infection with bugs (e.g. bacteria and viruses). Therefore this PhD studentship has been investigating how mast cells respond to infection with the common cold virus to help us understand their potential contribution to viral-induced asthma exacerbations. Charlene Akoto, who is in the final year of her PhD studentship, has shown that mast cells become infected with the common cold virus and are protected from infection following exposure to antiviral chemicals. She has presented her work at 2 international conferences (European Mast Cell and Basophil Research Network (EMBRN; Oct 2015) and European Academy of Allergy and Clinical Immunology (EAACI; June 2016)) and the Faculty of Medicine Research Conference (June 2016). At the EAACI Congress she received a travel scholarship to attend the meeting and also won ‘best oral abstract in session’. Charlene continues to make excellent progress in her PhD studies which are to be completed in Sept 2017.
- Oral presentation entitled ‘Mast cells support the replication of major and minor group rhinoviruses’ at the 7th European Mast Cell and Basophil Research Network (EMBRN) International Mast Cell and Basophil Meeting, Marseille, France (Oct 2015)
- Oral presentation entitled ‘Human mast cells support rhinovirus replication but are protected from infection by IFN-β’ at the European Academy of Allergy and Clinical Immunology (EAACI) Congress, Vienna, Austria (June 2016)
- Oral presentation entitled ‘Rhinovirus infection of human mast cells results in viral shedding which is inhibited by interferon’ at the Faculty of Medicine Research Conference, University of Southampton, Southampton, UK (June 2016).
Charlene has also prepared a manuscript of her current work entitled ‘Mast cells are permissive for rhinovirus replication: implications for asthma exacerbations’ which is currently under review in Clinical and Experimental Allergy (submitted Sept 2016). She also has received a Primerdesign silver studentship which gives her a discount on PCR reagents for gene expression analysis.