VISICORT meeting with Epimune Diagnostics


Epimune (www.epimune-dx.com) and the VISICORT Consortium are interested in entering into a collaboration in the field of diagnosis and monitoring of corneal transplant recipients using epigenetic immune cell quantification. The goal of the collaboration is the exploration of epigenetic immune cell quantification to monitor patients after corneal transplantation and to detect (and potentially predict) adverse events earlier than with currently available methods.

The face to face meeting on Tuesday 10th October 2019 with Dr Christoph Sachsenmeier from Epimune Diagnostics was an opportunity to discuss the collaboration further and to explore new collaborations within the diabetic kidney and ophthalmology research areas.

Pictured L to R: Matt Griffin, Conor Murphy, Joan Ní Gabhann, Christoph Sachsenmeier and Diana Malata at the RCSI, Dublin

Attendees included VISICORT Coordinator Prof. Matt Griffin and Dr Siobhán Gaughan from NUI Galway, VISICORT team members from the Royal College of Surgeons in Ireland PI Prof. Conor Murphy, Dr Joan Ní Gabhann and Diana Malata of the RCSI, the Royal College of Surgeons in Ireland and Dr Christoph Sachsenmeier, the VP Business Development at Epimune.

Epimune’s goal is to revolutionize diagnosis and monitoring of patients with disorders of the immune system.  Epimune develops in vitro diagnostic (IVD) tests using proprietary epigenetic immune cell quantification technology (Baron et al., 2018). This approach allows for broad immune cell profiling from minute sample amounts (e.g. blood – fresh/frozen/dried; other bodily fluids; tissue). Epimune uses proprietary real-time PCR-based assays for quantification of more than 20 different immune cell types.

VISICORT clinical trial listed on Charité’s BeCAT website

“An outstanding project within the VISICORT consortium is a Phase 1B clinical trial testing the safety and feasibility of intravenously administered allogeneic mesenchymal stromal cells (allo-MSC) as an immunotherapy for patients at high risk of keratoplasty. Following recent regulatory and ethical approval for the first clinical study on the risk therapy for cell therapy in risk keratoplasty, the inclusion of the first patients is imminent.”

VISICORT’s clinical trial is listed on the BeCAT web page. BeCAT, the Berlin Center for Advanced Therapy is Charité’s an amalgamation of cross-disciplinary project teams that develop and manufacture Advanced Therapy Medicinal Products (ATMP) for somatic cell therapeutics, gene therapeutics, and tissue engineering biotechnological tissue. Read about BeCAT and VISICORT (in German and English) here.

VISICORT PI Ritter, NUI Galway joins Therapeutics Delivery COST Action

Prof. Thomas Ritter of NUI Galway has joined “DARTER”- a COST Action CA 17103- Delivery of Antisense RNA Therapeutics. Here, Thomas aims to broaden his research network and to forge new partnerships to explore novel, RNA-based therapies for the treatment of ocular defects and the modulation of corneal transplant rejection.

DARTER has three research objectives- delivery strategies, model systems, safety and toxicology. In addition, there is a capacity-building group for stakeholder communications with the objective to achieve consensus on protocols and assessment of ASO delivery and toxicology and training new researchers within a cooperative research framework. The DARTER COST network includes academics, industrial partners, patient representatives and clinicians and it is open to other interested stakeholders.

COST Actions create spaces where scientists are in the driving seat (bottom-up) and ideas can grow through a flexible and open approach. By enabling researchers from academia, industry and the public and private sector to work together in open networks that transcend borders, COST helps to advance science, stimulates knowledge sharing and pools resources.

Interview 2: Proteomics Specialist Lisa Imrie, U of Edinburgh offers a research career snapshot

In the 5 years since its launch, VISICORT has gathered a unique collection of biological samples from corneal transplant recipients across 5 European countries. We are especially motivated to ensure that the generosity of these patients has a legacy of new research that continues to grow beyond the life-time of the project itself. Lisa’s exciting PhD project is a perfect example of this potential. I am particularly proud that we have been able to attract a talented scientist at the University of Edinburgh into the field of corneal transplant biology and that her research has the potential to directly benefit patients with corneal disease in the future.

VISICORT Coordinator, Professor Matthew Griffin
Lisa Imrie, University of Edinburgh, EdinOmics

Lisa Imrie is a Proteomics Specialist at the University of Edinburgh and a graduate of Edinburgh Napier University with a degree in microbiology and biotechnology. She has recently started her PhD studies taking a unique perspective in the analysis of biosamples from the VISICORT Foundation Biobank.

In this interview (2 of 2), Danielle Nicholson, Pintail Limited poses questions to Lisa about her work in proteomics, what a career in laboratory science really looks like and her PhD research.

What is proteomics and how did this become an interest for you?

Proteomics is the large-scale study of proteomes (a set of proteins produced by an organism/system).  It can be used to investigate when/where proteins are expressed, protein production rates, protein modifications (e.g. PTMs), protein-protein interactions, and how proteins are involved in metabolic pathways, amongst other things. 

I first became interested in proteomics between the third and fourth year of my undergraduate degree.  I worked for the summer in a local research institute in what was then their “Functional Genomics Unit” which had one mass spectrometer which I used to identify proteins that were present in researcher’s samples by peptide mass fingerprinting.  I was then invited back to complete my honours project within the same unit and that’s when I was hooked.  As luck would have it, on the completion of my honours project a position came up within the expanding unit that I successfully applied for and thus began my career in mass spectrometry and proteomics.

What are your main goals as a PhD researcher?

One main goal of this project is to identify clinically useful biomarkers in eye disease patients.  To this end, I will use mass spectrometry instrumentation to identify proteomic, metabolomic and lipidomic markers in different eye tissues across both keratoconus and FECD.  This will be the first time in ophthalmic research that this combination of omics data sets will be integrated to provide a better understanding of the disease mechanisms of these corneal diseases.

Another goal is to build as wide a knowledge base as possible around my chosen topic.  Every day I’m learning more and more and each new fact will undoubtedly lead to more research down a different avenue.  Compiling all this information to give me the best chance of successfully completing this project will be an ongoing effort.

“I love immersing myself in the literature related to this topic, applying it to my own work and theories and seeing what direction my research will take me in on a daily basis!”

Lisa Imrie, PhD candidate at the University of Edinburgh

Give us a snapshot of your work environment and day.

I work in the Kings Buildings campus of the University of Edinburgh.  There are many campuses across the city and we’re based on the south side.  All of Science and Engineering (including the School of Biological Sciences where I work) are based on this campus.  The facility I work in is called EdinOmics and there are currently four staff members who work here:  an academic leader, a metabolomics specialist, a proteomics specialist (me) and a lab manager.  Our mass spectrometry lab is situated on the ground floor and we all have offices dotted about the building.  I have an office just opposite the lab which is great for popping in and checking on the status of all the instruments and generally keeping an eye on things.  For all sample preparation, we have a wet lab on the first floor which has all the general lab equipment you’d expect to see in any biological lab.  Within our building, there are six different research groups and we all share the same wet lab, however, our mass spectrometry lab is just dedicated to the EdinOmics group and the instruments. 

Describe your typical day. What do you do? What skills do you need?

A normal day for me would start with arriving at work at around 8.30 and heading straight to the mass spectrometry lab.  The first thing I like to do before anything else is to check that the instruments are working as expected and there are no blinky red lights on anything – not good news!  If there have been samples run the previous day or through the night I’ll start the data analysis for them which will involve the files being converted into a database searchable format which can take a little time.  Whilst this is ticking over I’ll head to the office and switch on my PC before making myself a cup of coffee.  My day will then consist of any combination of:

·      Data analysis from samples run the previous day/overnight

·      Reporting of results to clients either by email or in person

·      Meeting with potential clients who are interested in using the facility to answer their research questions

·      Any general lab maintenance requiring attention

Throughout all this, whenever I have time, I will focus on my own PhD project.  At the moment this will include the ongoing literature search to broaden my knowledge of the topic and keep up to date with what’s been achieved in the field so far as well as planning any pilot experiments to work up the methods I plan to use throughout my project.  All this juggling requires a lot of time management skill and it is definitely one of the most difficult parts of my job.  Finding time for both running the facility and my PhD project can be challenging!

What are your main interests outside science?

I have a young family (11yr old daughter and 7yr old son) so my interests outside of work revolve mainly around them!  They definitely have better social lives than I do and between my husband and myself, we spend most of our time taxiing them around to various clubs/sports.  It’s great to see them grow into confident young people so I wouldn’t have it any other way.  If I manage to get a minute to myself I like to socialise with family and friends and put the world to rights over dinner & drinks.

What advice would you give to a young person wanting to pursue a career in science?

Keep an open mind and don’t try to “specialise” too early.  I went from an interest in marine biology to microbiology to biotechnology and ended up working with mass spectrometers in the omics fields.  Similarly, don’t be scared to branch out even when you have decided on your field of interest.  If someone had told me a couple of years ago that I’d be doing a PhD related to ophthalmology I would have laughed at them.  It’s amazing where a career in science can take you!

Sum up what you find most interesting about your work now in just one sentence.

I love immersing myself in the literature related to this topic, applying it to my own work and theories and seeing what direction my research will take me in on a daily basis!

International Clinical Trials Day 2019, Galway

The HRB Clinical Research Facility Galway in Ireland hosted a public event to celebrate International Clinical Trials Day on May 20th 2019. Exhibition stands were on display and informational meetings were held throughout the day to inform the public of all areas of clinical research being undertaken at the facility.

A particular stand was dedicated to the CRF Galway’s stem cell work to inform the public of the cell therapy projects being undertaken with partners within the National University of Ireland Galway and with European partners.  VISICORT was showcased here, as were the related projects NEPHSTROM and ADIPOA-2.

Great interest was expressed in this evolving therapeutic area with approximately 100 members of the public stopping by to hear about what cell therapy involves and to learn about the projects from the clinical researchers on the day.

Dr Veronica McInerney, CRF Galway
Dr Veronica McInerney, NUI Galway

Interview: Lisa Imrie, U of Edinburgh uses the VISICORT Biobank

Lisa Imrie, PhD candidate, University of Edinburgh uses VISICORT Foundation Biobank

Lisa Imrie is a Proteomics Specialist at the University of Edinburgh and a graduate of Edinburgh Napier University with a degree in microbiology and biotechnology. She has recently started her PhD studies taking a unique perspective in the analysis of biosamples from the VISICORT Foundation Biobank.

Danielle Nicholson, Pintail Limited caught up with Lisa Imrie after the latest plenary meeting in Galway to pose a few questions about her PhD research. In this interview (1 of 2), Lisa discusses her PhD project, how new techniques in the lab and with the data set analyses will carry the results of VISICORT forward and contribute to the field of proteomics.

What is the main focus of your PhD project?

To characterise different eye tissues and identify clinically relevant biomarkers in both keratoconus and Fuch’s Endothelial Corneal Dystrophy (FECD) using a multi-omics approach.

Why have you focussed on that in particular? What is it that interests you about it?

Until recently my career has been very technically orientated as I currently provide a proteomics service for a mass spectrometry core facility within the University of Edinburgh.  This has allowed me a brief snapshot of other researcher’s work however I’ve never had any biological research of my own to focus on.  In 2015 I was charged with helping the groups postdoc, Khadar Dudekula, with her proteomics profiling of eye tissue samples from the VISICORT project.  This area of research piqued my interest and from becoming more involved in the sample analysis and also attending the plenary meetings it became apparent that there was massive scope to carry this research forward in any number of directions.  Within my facility, I have a number of high-end mass spectrometers that can carry out various “omics” analyses so this PhD project seemed like a golden opportunity to utilise them to analyse the large number of samples available to me within Biostor Ireland.  There are thousands of samples within this biobank so it was sensible to narrow down my thesis question and focus on looking at a couple of conditions to start with (keratoconus and FECD).

“It is really gratifying to see how the VISICORT project has led to the development of a new and exciting approach for analysing the invaluable collection of our biological samples. We can look forward to being able to identify important new and medically important Biomarkers from Lisa’s VISICORT-inspired PhD.”

Professor Malcolm Walkinshaw, University of Edinburgh

What big questions do you want to answer?

I want to characterise keratoconus and FECD using a multi-omic approach combining proteomic, metabolomic and lipidomic analyses.  This will include developing a method for the efficient extraction of lipids, metabolites and proteins from a single sample, enabling the targeted and untargeted analyses of each eye tissue.  Extracting multiple “omes” in one step will ensure like for like comparisons and give a genuine snapshot of the biological status of the system. This will result in much better correlations between differences in metabolites/proteins and we can obtain greater insights into the metabolic pathways comparing healthy and disease states through interrogation and integration of the different omics datasets.  This method will be unique in eye tissue omics studies to date.

What are the biggest obstacles to answering these questions?

My biggest challenges in this project will be all the sample prep method development.  I’ve seen a similar one-step extraction method used before on plant material but never on the eye tissues that I’ll be working with.  All the different tissues, e.g. tears, aqueous humor, cornea, all have very different compositions so it’ll be interesting to see if the one method works with all sample types. 

Another challenge I’ll face is the data integration and interpretation.  To date, I have only ever run single omics experiments which require just one software analysis approach.  I’ll now have to find a way to integrate all the data generated from the proteomics, metabolomics and lipidomics analyses.  Fortunately, there’s a symposium towards the end of the year which deals with Multiomics data integration that I’ll be attending so hopefully this will give me some idea of the best way to deal with these large datasets.

How has VISICORT contributed to your project concept and research?

VISICORT Foundation Biobank brochure

Without VISICORT it may never have occurred to me to embark on my own PhD project.  Because the subject matter interested me so much and due to the large number of samples available in the Biostór it was an easy jump to design a project to expand on the profiling data already generated by mass spectrometry.  The challenge was distilling it down to look at a couple of biological questions as there were a large number of avenues we could have pursued.  The two plenary meetings I have presented at, the first in Berlin to pitch the idea of the PhD project and the second in Galway to present a more definite structure, have been invaluable to me.  Getting advice and suggestions from experts in the field has definitely shaped my work going forward.

New VISICORT publication from NUI Galway team

“TNF-α/IL-1β-licensed mesenchymal stromal cells promote corneal allograft survival via myeloid cell-mediated induction of Foxp3+ regulatory T cells in the lung” was published online in the FASEB Journal on May 20, 2019. The authors of the study from NUI Galway are Nick Murphy, Oliver Treacy, Kevin Lynch, Maurice Morcos, Paul Lohan, Linda Howard, Gerry Fahy, Matthew D. Griffin, Aideen E. Ryan, and Thomas Ritter.

Congratulations to the team!

FASEB J. 2019 May 20:fj201900047R. DOI: 10.1096/fj.201900047R. [Epub ahead of print]

PI Conor Murphy presents VISICORT at Royal Victoria Eye and Ear Hospital

VISICORT PI Prof and Consultant Ophthalmologist Conor C. Murphy of the RCSI (Royal College of Surgeons in Ireland) presented “What’s new (and old) in corneal transplantation” on the 5th of April 2019. The audience included a group of 40 surgical theatre nurses at the Royal Victoria Eye and Ear Hospital in Dublin. The VISICORT project concept and clinical trial were presented in slides 45-49.

Conor’s presentation can be viewed here.

VISICORT presentation in Berlin aims to recruit potential patients to the clinical trial

VISICORT PI Uwe Pleyer at Charité Universitätsmedizin Berlin organized a seminar entitled “Autologe Stammzelltherapie zur Prophylaxe der Immunreaktion bei Risikokeratoplastik”. The Anterior Segment Symposium on April 27th, 2019 in Berlin included a presentation on the VISICORT project with the aim to recruit potential patients for the Phase 1 trial.


Pictured above Prof. Dr Rieck and Prof. Dr Uwe Pleyer

VISICORT PI Nico Degauque, INSERM presents at Swedish Registry for Corneal Transplant

VISICORT PI Nicolas Degauque from INSERM in Nantes was an invited speaker at the annual meeting for participants in the Swedish Registry for Corneal Transplant which for many years have served as the registry for all Swedish and Danish patients undergoing corneal transplantation. The meeting took place at Riksgränsen at the very north of Sweden on April 11, 2019. Through Nico’s talk entitled “Innate-like functions of human TEMRA CD8 and their involvement in kidney allograft outcome”, he presented the recent advances in identifying biomarkers for transplant survival learned from kidney transplantations. It is the hope that the extension of these studies can provide biomarkers for corneal transplant survival.

The meeting was attended by VISICORT partners John Armitage from the University of Bristol and Jesper Hjortdal, Aarhus University Hospital.