Spotlight on a QUOD Colleague – Lewis Simmonds, Data Analyst QUOD

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This week I ‘met up’ with QUOD colleague Lewis Simmonds, of NHS Blood & Transplant.  Lewis is a statistician and provides QUOD with the data required for researchers.

Lewis joined the QUOD family in July last year after graduating from Bristol University with a First-Class degree in Maths and was given the task of streamlining the way QUOD’s data is gathered and extracted.

When a research scientist requests clinical data (for example donor, retrieval and recipient follow up data) to go alongside samples from QUOD, they must first select the data variables appropriate to their research question, which are listed on the QUOD website. This process then generates a spreadsheet that is communicated to our QUOD Data Coordinator here in Oxford, who then completes the data access request and sends it over to Lewis so that he can extract the requested data from the NHSBT database. 

When Lewis first joined us in the summer this process was rather lengthy and variables were colour coded into categories according to the lead times to receive the data, these were anything from under a month to more than three months.  This system has worked well until now, but as QUOD has become more well known, its activity has increased and the requests for samples have multiplied.  Lewis has turned this around by building a new database that produces the information easily at the click of a button, that will eventually be able to be run by any member of trained NHSBT staff within a much shorter timescale. It has taken quite some work to harmonise the data into a uniformly functioning format with fine tuning of the interactions between bodies of data but he says this work is almost complete. In just 6 months Lewis has transformed the process and QUOD is ready for action!  He will continue to work with QUOD to make changes to the website and before long researchers will be able to reap the benefit.

I asked him if he had learned his skills during his university studies.  He told me that he had learned Python, R, SQL and SAS, all of which are high level programming languages, at university but it is his fascination with how programmes interact with data structures and tables that led him to play around with programming in his spare time, testing his theories in developing games amongst other things.  His latest interest has expanded to website design and how the information that a website user taps into an interface is routed behind the scenes to create datasets, purchases, bookings or information collection.  He told me he has always been interested by how different systems can work together and loves exploring the possibilities to render systems compatible to a desired purpose. 

Lewis is based in Bristol and like a lot of us is still working from home though he enjoys going into the office one day a week.  The thing he likes best about his role is the creative freedom he has to seek out ways to improve systems and increase efficiency.  When he first took on the role, the biggest challenge was to familiarise himself with the many databases and their different properties in terms of function, formatting and location.

The most unusual thing Lewis has done in a job was when he was still at school.  As a fresh-faced sixth former he helped a friend run a mail/internet order business selling glowsticks, glow ears, flashing dog collars, baseball caps and light up bouncy balls!

In his spare time, other than tinkering with programming he is very keen on music with a particular penchant for Drum & Bass which has led him to DJing in and around Bristol on the weekends.  In lockdown he developed a taste for Hip Hop and Rap and he also enjoys cycling and a round of golf!

QUOD named UK Biobank of the Year 2022!

The UKCRC Tissue Directory and Coordination Centre awarded QUOD first place in the UK Biobank of the Year.

The UK Biobanking Showcase is the UK’s leading event for those who work in biobanking and human tissue research and took place online over three days with interesting talks and presentations from biobanks all over the UK.

Please see below some extracts from the Judging Panel’s comments: 

‘… the Biobank provides a highly specialist resource which is of immense value to the organ donation field.  Despite being so specialised, … QUOD nevertheless responded flexibly during the pandemic to participate in the RECOVERY trial and in the development of the NHSBT Oxford COVID BioArchive (COBA).  …  The panel particularly commended the quality and range of the Biobank’s outreach and engagement activities which unusually included providing work experience to college students during the pandemic.’

Professor Ploeg, Director of QUOD (Quality in Organ Donation) and Dr Sarah Cross National Operational Coordinator of QUOD are delighted with this wonderful achievement: ‘This award is an important milestone in our pursuit to increase research in donation and transplantation, increasing organ utilisation and providing more and better organs for our patients’. They congratulate the whole QUOD team including the Specialist Nurses in Organ Donation and NORS teams based in the 61 NHS partner trusts across the UK, as well as the core team in Oxford, the Directors of NHS Blood and Transplant, the Medical Research Council and our academic collaborators without whom none of this would have been possible.

Dr Maria Kaisar – Developing new ways to assess kidneys so transplants last for longer.

With funding from Kidney Research UK, a team of researchers from the University of Oxford, the University of Nottingham and University College London will develop ways to assess donor kidneys and predict how well they will work after transplant.

Having a kidney transplant is the best treatment for kidney failure, but the demand for donated kidneys is high.

To save more lives, doctors are now accepting kidneys from older or higher risk donors. These kidneys may also work less well after transplantation. This can have devastating effects, causing patients once recovering from transplantation to also go back on to dialysis, and wait for another transplant.

Right now, doctors cannot accurately assess donor kidneys. This makes it difficult to predict how well a transplant will work and how long a kidney will last after it has been transplanted.

Thanks to Kidney Research UK’s grant award of £237,626, (in partnership with the Stoneygate Trust), the ADMIRE study ‘Assessing Donor kidneys and Monitoring Transplant Recipients’ aims to address this clinical challenge.

Dr Maria Kaisar

Dr Maria Kaisar from Oxford University’s Nuffield Department of Surgical Sciences (NDS) is the Principal Investigator on the study and leads a team of co-investigators from NDS (Professor Rutger Ploeg, Dr Edward Sharples, Mr Simon KnightMr James Hunter and Dr Sadr Shaheed), the Oxford Big Data Institute (Dr Alberto Santos Delgado and Dr Philip Charles) and the Radcliffe Department of Medicine (Dr Elizabeth Tunnicliffe)

Dr Maria Kaisar and her team will utilise the Oxford Transplant Biobank (OTB) and the Quality in Organ Donation (QUOD) biobank to look for marker proteins in the donors’ blood samples. They use these samples to develop a mathematical model to predict how well donor kidneys will work after transplantation. The successful model would allow doctors to accurately assess kidneys and only transplant those that will function well. It could also identify suitable kidneys previously deemed too high risk to transplant.

With Professors Sue Francis and David Long from the University of Nottingham and University College London, the NDS team will use the QUOD X platform to also develop a monitoring strategy. MRI scanning methods will be performed on both the donor organ before it is transplanted, and later on after transplantation. This will allow us to monitor how well the transplanted organ is functioning.

“I am absolutely delighted that our study received this funding award by Kidney Research UK in partnership with The Stoneygate Trust,” said Maria. “This funding will enable us to bring scientific and clinical expertise together in collaboration, to develop novel non-invasive methods to better assess donor kidneys and, predict how well a transplant will work in the recipient. We also envisage that our planned scientific work will offer many opportunities to our early career scientists, to further develop their skills and research expertise in studying kidney disease. “

Letizia Lo Faro – Use of QUOD samples in research ‘Case Study’

My name is Letizia Lo Faro and I am a Post-Doctoral research scientist in the Oxford Transplant research group. I have so far used QUOD samples in 4 or 5 separate research studies. In one of these, conducted together with Ms Flavia Neri (University of Padova), we were interested in studying the molecular features of donor kidneys with acute kidney injury (AKI) having different functional outcomes after transplant.

Letizia Lo Faro

Once we fully characterised our research question, we moved onto donor sample selection. We decided to compare 4 different groups of donors: with or without AKI and each with good (≥45 mL/min) or poor (<45 mL/min) function (eGFR) 12 months post-transplant, for a total of 40 donors. We maximised the difference between outcomes as much as possible and to allow for fair comparisons we decided to match the groups for several other variables (donor age and gender, BMI, cold ischaemia time, recipient age, recipient gender…just to name a few). I believe appropriate sample selection is a key step in such retrospective studies and we engaged with the QUOD Data Manager earlier on in the process. This provided us with a great overview of all the variables available and also made sure our groups were nicely balanced.

Once we were happy with the donor selection, we proceeded with requesting the samples from the biobank. In this case they were full RNAlater frozen kidney biopsies and formalin-fixed paraffin-embedded (FFPE) kidney tissue slides. In this study we were interested in studying protein expression, so first of all we processed the tissue biopsies to mechanically homogenise them and extract the proteins. Later on the proteins were quantified and the expression of 17 proteins of interest was analysed by Western Blotting (a technique where a mixture of proteins is separated on a gel, based on the molecular weight, and, following transfer on a membrane, proteins of interest are identified by binding to specific antibodies). Results were then analysed with statistical tools.

A set of FFPE slides was then utilised for histological assessment, by standard staining with haematoxylin and eosin (H&E), to quantify chronic and acute tissue damage. One additional set of slides was utilised for confirmation of the western blotting results by immunohistochemistry, another method which allows to check for the presence of certain proteins/products in a tissue, by binding with labelled antibodies.

Results from this study were presented at the British Transplantation Society meeting last year and we are currently finalising a manuscript for publication.

Our results suggested that specific molecular patterns are recognizable in acutely inured kidneys that proceed towards worse function after transplantation. In particular, Peroxisome proliferator-activated receptor gamma (PPAR gamma) specifically increased after acute injury that progressed to worse function, underlining a potential role of metabolic dysfunction in the development of kidney disease (Figure 1).

Figure 1. The protein PPARg, quantified by western blotting analysis, is significantly increased in AKI kidneys with poor outcomes 12months post-transplant.

Our findings have helped identify potential molecular mechanisms involved in the progression of acute kidney injury to chronic kidney disease and post-transplant dysfunction and may constitute a therapeutic target of further interventions aimed at improving the quality of donated kidneys with an acute injury.

Working with QUOD samples has allowed us to really dive deep into the study of molecular mechanisms of kidney injury and the availability of different sample types also allowed us to apply various techniques and methods to validate our findings.

5th National QUOD Symposium – 18 November 2019

We would like to invite you to the 2019 Autumn QUOD Symposium to be held in Manchester.

If you are interested in the pursuit of improvement of outcomes after transplantation through translational science, please register and join us for:

  • Consortium Research Presentations
  • Operational Highlights
  • Upcoming Developments
  • Partner Announcements

Time

  • 12pm Arrival and registration
  • 12.15pm Networking and buffet lunch
  • 1pm Symposium starts

Full programme to follow.

Register Here!

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