Research

QUOD & Evotec: An academia-industry partnership built on complementary strengths

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Tobias Bohnenpoll, Evotec SE

Evotec SE and the University of Oxford have recently renewed their collaboration agreement, reflecting a robust and sustainable partnership to profile tissue biopsies collected, processed and stored by the QUOD programme. Through this partnership, Evotec has already generated genome-wide bulk transcriptomic data from about 2,000 donor biopsies (895 kidney and 910 liver), complementing the rich clinical records and technical metadata collected by NHSBT and QUOD. Evotec is currently extending the analysis to heart biopsies and high-resolution single cell and spatial transcriptomics, which will allow in-depth molecular characterisation of tissue microenvironments. Together, we aim to generate mechanistic insights to improve the quality of organ donation and transplantation, and to identify targetable mechanism of injury and repair that will open new avenues for therapeutic intervention and patient stratification in metabolic, cardiac and renal diseases.

The multimodal characterisation of organ biopsies using state-of-the-art, high-throughput analysis is an important cornerstone of Evotec’s Molecular Patient Databases (E.MPD), an industry-leading, proprietary collection of curated human datasets for translational research and patient-centric target and biomarker discovery. However, the integration of complex clinical and molecular data into curated multidimensional datasets poses great challenges to scientific teams and requires interdisciplinary approaches. Evotec and QUOD researchers have assembled an expert team that efficiently combines domain knowledge in medicine and biology with high-throughput molecular analysis and modern data science. Together, we are exploring the complex relationships between biopsy molecular profiles, donor and recipient clinical phenotypes, and graft outcomes in all major organ recovery and transplant conditions. This exploratory analysis of biopsy transcriptomes involves unsupervised clustering, dimensionality reduction and embedding of clinical data and molecular signatures to enable a data-driven hypothesis generation.

Importantly, the multidimensional characterisation of QUOD biopsy transcriptomes has enormous potential beyond research in organ donation and transplantation, with direct applications in modern drug discovery. First, samples from healthy organ donors that are obtained from the Oxford Transplant Biobank (OTB) can serve as reference for the molecular analysis of other disease-focused prospective cohort studies, which often lack appropriate controls. Second, organ donors often present with early, subclinical disease phenotypes that potentially provide unique insights into the onset and early progression of metabolic and other common diseases. For example, Evotec has integrated a data-driven selection of QUOD and NURTuRE (National Unified Renal Translational Research Enterprise) kidney biopsy transcriptomes ranging from healthy to end-stage chronic kidney disease to model disease initiation and progression at the molecular level. We are also combining transcriptomic analysis with AI-assisted digital pathology to characterise liver biopsies for steatosis, inflammation and fibrosis and determine their position along the spectrum of fatty liver disease.

Ultimately, these systems biology approaches aim to positively impact the lives of patients with organ transplantation, cardiometabolic diseases and related complications by leveraging advanced molecular analysis and interdisciplinary expertise. This transformative work is only possible through close collaboration between academia and industry, combining their strengths and resources to achieve meaningful advances in knowledge that will help improve patient care and therapeutic intervention.

British Transplantation Society Conference 2022 debrief – by Azita Mellati

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After a year of virtual meetings and conferences, this year the British Transplantation Society (BTS) congress was again held in person at the ICC Belfast. The conference provided a great opportunity for clinicians and researchers to meet up and share the latest about their research and developments on their projects. Over the 3 days of the conference including 31 sessions, more than 100 talks were presented.

Our team from the Nuffield Department of Surgical Sciences (NDS) actively participated in the conference with a total 3 presentations and 1 poster. Dr Mohamed Elzawahry and Dr Letizia Lo Faro presented their research work on “Safety and feasibility of oxygenated hypothermic machine perfusion in the preservation of donor organs for pancreas transplantation” and “Normothermic machine perfusion of the liver supports protein translation and mitochondrial function while reducing protein degradation and metabolic imbalance: a proteomics study” in the “Dragon’s Den” and “Medawar medal presentations” sessions, respectively. The poster titled “Evaluation of kidney injury after treatment with CC-4066 during cold storage and assessment during normothermic reperfusion in a porcine ischemia reperfusion injury model” by Ms. Pommelien Meertens (as part of her Research Internship at NDS) was presented during the conference as well. I also had the opportunity to present my own research on “Investigation into the effect of Alpha-1 antitrypsin delivered via different preservation methods on ischemia-reperfusion injury in pig kidneys” as part of the “Science oral presentations” session. I received very interesting feedback on my project and had the great fortune to discuss details and plans with the audience and other attendees.

In addition to the scientific part of the conference, we also had the opportunity to enjoy and come together to celebrate the 50th Anniversary of the BTS. Over the course of the Gala Dinner themed “the 70s”, members shared good laughter and created wonderful memories. The conference also provided the opportunity to acknowledge and celebrate the lifetime of research work of several members of the BTS, including Professor Peter Friend from within our own department. Overall, this year’s BTS congress was a major success and a great sign that in person, scientific gatherings are back again for the better.

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

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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 Knight, Mr 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’

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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.

COVID BioArchive Update

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Since March 2020 the QUOD team has been supporting the national effort in the fight against COVID-19. QUOD’s extensive biobanking expertise, infrastructure and personnel have served to set up the NHSBT Oxford COVID BioArchive (COBA).  Over 68,000 blood samples from convalescent plasma donors who have recovered from COVID-19 have been collected and processed as part of the NHSBT Convalescent Plasma programme. In addition, since September COBA has received over 18,000 samples collected from recipients of convalescent plasma and monoclonal antibody treatment in the international RECOVERY trial.

These samples were used by a number of research groups, NHSBT and Public Health England in a variety of projects, including assessment of novel COVID-19 tests, characterisation of COVID-19 antibody function, and analysis of the efficacy of convalescent plasma treatment. With this COVID BioArchive, we have been able to establish a robust and sustainable resource for future validation and research helping us to gain better insight into COVID-19 and anticipate targeted intervention.

You may have heard that on 15th January randomisations of patients into convalescent plasma was paused following disappointing interim results that showed no evidence that convalescent plasma has an overall benefit on patient outcomes in moderately ill people.  Work to search for evidence of benefit in subgroups before organ damage and hospitalisation occurs is now under consideration.

Given the quantity of samples now available, it has been decided that collection of further plasma samples will not be resumed.  The news may seem discouraging, however an important scientific question has been answered.  In terms of the scale and volume of the operation this was a considerable undertaking that has proved that the QUOD infrastructure in close collaboration with the NHSBT’s Blood Service has the capacity and versatility to help and meet such an important demand.

Over 250,000 samples are currently stored in the COVID BioArchive to be used for dedicated research questions and validation of novel tests. Applications are welcome from national and international research groups or health care authorities.

BTS & NHSBT Congress 2021 Roundup

QUOD Research

by Rebecca Vaughan

This year, as has become our new norm, the BTS Congress 2021 was hosted using an online platform, allowing delegates to experience interactive plenary sessions and parallel sessions similar to when attending the conference.  However unique to the online experience was the opportunity to access content ‘on-demand’, including the additional option to listen to pre-recorded abstract talks, at a time that suits you.  Although, many were saddened by the lost opportunity to meet with colleagues and friends, the commitment from BTS to provide an opportunity for clinicians and researchers to gather and share their research from the last 12-months was an absolute success and credit to the organisers. 

For this conference, I submitted an abstract titled ‘Brain death specific glomerular matrix degradation profiles are associated with long-term graft dysfunction in kidney transplant’ on behalf of our teams at NHSBT and the Oxford Transplant research lab in University of Oxford.  This abstract was selected for presentation as part of the ‘Medawar Award Session’, where my abstract and presentation was considered for the award along with three other researchers who also submitted abstracts for basic science in transplantation. I feel incredibly fortunate to have had our abstract considered for the Medawar award, and was excited to highlight how we have utilised invaluable samples from the QUOD biobank.  Our research utilised 60 kidney biopsies from the QUOD biobank from both DBD and DCD donors.  Our work described a DBD specific degradation profile for cytoskeletal proteins in donor kidneys that linked to suboptimal 12month posttransplant function.  Our research was considered novel in that it indicates that protein degradation may affect donor kidneys and post-transplant function. Preparing for my live presentation was also a memorable experience, involving many rehearsals with my supervisors Dr Kaisar and Prof Ploeg and colleagues, many adjustments and changes before the final live talk.

Our group also had a second opportunity to present our research work involving the analysis of  QUOD samples. A second abstract titled ‘Protein profiles in deceased donor kidneys associated with 12-Month post-transplant kidney function’ was accepted as a pre-recorded talk, presented by our colleague Priyanka Joshi.  This study utilised 185 kidney biopsies from the QUOD biobank for proteomic analysis, comparing DBD and DCD donors with differing functional outcomes 12mth posttransplantation.  This study showed that protein markers in donor kidneys associate to posttransplant outcomes and indicate which biological pathways may play a role in determining the donor kidney quality.

Our research work has highlighted the value of the QUOD samples; based on the collection protocols, these samples provide us with confidence regarding sample quality and collection continuity.  Importantly, our sample selection and analysis is linked with the clinical and demographic metadata that we receive from the National Transplant Registry from NHSBT. The combination of the selection of QUOD samples and donor and recipient metadata makes a unique research resource.  

The overarching focus of the BTS congress was the impact of COVID-19 on transplantation, with NHSBT statistics team highlighting changes in trends of donation and transplantation due to the pandemic.  An invited keynote speaker focused on ‘resilience’  encouraging people to reflect on their own resilience and how they have adjusted to the inevitable changes that have come along with a global pandemic, whilst looking to the future with reasonable caution but also excitement.  Several talks also touched on emerging perfusion technologies and the improvements they may have on outcomes in the future, and evaluating single centre experiences.

Overall the BTS Congress 2021 was a great success despite the mammoth task of moving the conference to an online platform.  The opportunity to bring together scientists and clinicians to discuss research, trends and experiences in transplantation is essential to moving the field forward.  The conference provided an excellent opportunity to showcase research work, however the opportunity to interact with each other; ask questions, discuss and debate ideas was lacking and greatly missed.  The representation of QUOD, NHSBT and the University of Oxford was strong, and hopefully more researchers were inspired to consider QUOD samples for their ongoing work.

Congratulations to Charlotte Brown (Wales Kidney Research Unit) and Maria Ibrahim (NHSBT Bristol) who were awarded the 2021 Medawar Medals at the congress. Click here to read about their research.

Increasing the Number of Organs Available for Research (INOAR)

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Until recently, only organs removed for transplant, but subsequently not transplanted were available to researchers.  Thanks to a collaboration between QUOD and Newcastle University, in partnership with NHS Blood and Transplant, new arrangements have been implemented that will allow hearts, lungs and pancreases which are unsuitable for transplantation to be retrieved for research purposes. This will greatly facilitate ongoing research into developing ways more donated organs can be converted into successful life-saving transplants.

Clare Denison, Lead Specialist – Innovation and Research ODT at NHS Blood and Transplant, said: “This is a significant moment for our organisation and researchers across the country. INOAR will change the face of transplantation and ultimately improve patient outcomes and quality of life in the future.”

This development is particularly exciting for diabetes researchers. Almost 4 million people in the UK are living with diabetes. The condition occurs when the pancreas doesn’t produce enough insulin, or when it can’t produce any at all, which leads to blood glucose levels being too high. Until now, the pancreas has not been removed, or even sampled following the death of people with diabetes during organ donation for transplantation.  Research into the mechanisms preventing normal pancreatic insulin production in diabetes has therefore been limited to the small number of post-mortem samples currently stored in the UK.

Dr Elizabeth Robertson, Director of Research at Diabetes UK, said: “This is an exciting step forward that we hope will rapidly advance our understanding of the causes and progression of diabetes … world-class scientists will now have vital access to pancreatic tissue, propelling our knowledge of diabetes forward and bringing us a step closer to a world where diabetes can do no harm.”

QUOD Partners with Blood Donor Service to Support National Research to Combat COVID-19

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QUOD is very pleased to collaborate with the Blood Donor Service to support two major research projects related to COVID-19.

First, QUOD is providing support for the Convalescent Plasma Trials, REMAP-CAP and RECOVERY. The trials will collect plasma samples from patients who have recovered from COVID-19 to administer to patients suffering from serious symptoms in the hope that this will boost their production of antibodies. QUOD personnel are assisting with the preparation and distribution of plasma from recovered patients, as well as the acceptance, storage, and distribution of plasma from trial participants.

In addition, assistance from QUOD was essential in the effort to rapidly scale up validation of COVID-19 antibody tests. COVID negative plasma samples from the QUOD biobank were used to provide a ‘healthy patient’ control group to test for false positives. QUOD personnel have also been hard at work preparing additional plasma samples provided by the Blood Donor Service for testing. Initial results of this antibody testing are described in this pre-print.

The swift and efficient deployment of QUOD resources and personnel to support these efforts is a strong testimony to the strategic value of the research platform we have built together. We are glad to have a meaningful role in enabling the national response to the crisis.