What is your role in the 3TR team at IKMB? As of now, I am responsible for the overview of IBD samples collection, selection and transfer to sequencing and/or biobank storage. I also contribute to the bioinformatic group decisions, in particular, when it includes single RNA-seq analysis, which is my area of expertise. What are you currently working on? What’s your major research interest? I mainly work in longitudinal changes of cellular and molecular features associated with treatments of IBD. By collecting RNA-seq data throughout the course of treatment, I aim to understand target engagement patterns, as well as identify early signatures of therapy response. In general, I hope to contribute to better understanding of therapies mechanism of actions, which can ultimately be used to identify patients that will respond better to a particular treatment and improve general response rates in IBD. What motivates you, personally? What made you go into science? It has always been important for me to question why? For this reason, I follow a career in Biology, where I started studying the development of the immune system. I witnessed first-hand the power of OMICs data, so going forward, I thought I should use my knowledge in an applied field. This is when I joined the systems immunology group. I think it is crucial to study how new therapies engage and treat inflammatory diseases. I hope my expertise in data analysis can create new insights in how a good response to treatment should look like and be used in precision medicine. Why do you think, the 3TR research is important? I think the 3TR project is extremely important because it creates a space for researchers who study chronic inflammatory diseases to work together. Sometimes it is difficult to see the bigger picture when talking about inflammatory diseases. By putting together experts of different areas, we not only share our latest technological advances but we are also able to compare patterns which might otherwise be elusive when studying a disease on its own.

What is your role in the 3TR team at CNAG-CRG? I am a PhD student under the supervision of Dr. Gut, affiliated with the University of Barcelona and the Center for Genomic Regulation. I am a full-stack developer working mainly in Python, R, and JavaScript (React) and also take care of tasks related to project management. I closely follow all developments and new products in the field of biological data management to make sure that we are using the state-of-the-art technologies within the data warehouse we are setting up for 3TR. What are you currently working on? What’s your major research interest? I am finalizing the data submission portal for 3TR’s data warehouse where all members of the 3TR consortium are able to easily upload and share their datasets. I also look into which third party data visualisation and analysis tools are ideal to be integrated with the data warehouse because we are envisioning to provide not only a simple data storage but a low code “one-stop-shop” multi-omics analyses. All the work I have done so far for 3TR aligns perfectly with my PhD thesis topic What motivates you, personally? What made you go into science? Doing now what researchers need next. Admittedly this sentence is originally not mine but an adapted version of Roche’s mission: Doing now what patients need next. But it perfectly describes my personal motivation since for me the most important part in any job is that it contributes to a greater good. I deeply believe that the biological data management needs to improve as quickly as possible. That’s why I did not hesitate a second when Dr. Gut offered me the PhD position to work on this development for 3TR. Why do you think, the 3TR research is important? Autoimmune and inflammatory diseases, although being quite common, are still difficult to diagnose and treat. Here we have the opportunity to positively impact the lives of millions around the globe. Be it by better understanding of the disease progression, discovering novel drug targets, identifying new biomarkers for relapse and flare, or just better elucidating the molecular bases of these diseases. On top, we have the rare opportunity to investigate not one disease on its own but integrate findings across them.

What is your role in the 3TR team at Queen Mary University London? I am analyzing differentially expressed genes between responders and non-responders to biologic treatment using RNA-Seq data from synovial biopsies of rheumatoid arthritis patients. With modular analysis I summarize the function of those genes. My outputs then feed into our teams’ pathway analysis and machine learning approaches. What are you currently working on? What’s your major research interest? I am working on arthritis with a focus on the joint microenvironment. This specifically includes bulk-RNAseq analysis and BCR receptor sequencing from biopsies obtained from inflamed joints. My major research interest is to contribute to the understanding what drives inflammation and destruction in autoimmunity and autoinflammatory conditions to improve patient treatment. What motivates you, personally? What made you go into science? Even though I am not a clinician, I had the opportunity to meet and talk to patients, both children and adults, with autoimmune diseases and arthritis and the thought I may improve lives of people with such conditions is a major motivation. This also made me go into science, but I always loved analyzing things, looking into details and solving jigsaw puzzles. All this I found in science as well and it gives me a lot of joy. Why do you think, the 3TR research is important? 3TR merges diseases but also expertise from many countries and from private as well as the academic sector. This strengthens the research enormously. Looking together across many diseases for response and non-response can help repurpose existing drugs for different diseases, identify targets for new drugs with future trials spanning across diseases. Furthermore, it can greatly improve our knowledge about disease mechanisms and change patient management towards a stratified medicine approach.

What is your role in the 3TR team team at University of Southampton, UK? I am Senior Research Assistant at the University of Southampton, United Kingdom. What are you currently working on? What’s your major research interest? I am working on the development of a Core Outcome Set (COS) for children and adults with severe asthma which will allow to harmonize the way outcome measures are reported in clinical studies investigating biological therapies. The COS will form the development of patient-centered definitions of response to biological therapy for these patients. These definitions will help clinicians and patients in deciding whether patients have responded to a biological and assist regulators in determining whether a new therapy is effective. What motivates you, personally? What made you go into science? As a clinician and researcher, I am passionate about always learning and developing novel ideas on how to overcome different challenges to find the most efficient path to improve the health of patients and achieve the best outcomes. I feel highly motivated knowing that the results of my published research could contribute to making a difference in quality of the lives of patients and their families. Why do you think, the 3TR research is important? The aim of the 3TR research is to better understand the mechanisms of non-response and response to treatment while working as part of an expert team of clinicians, researches, patients, pharmaceutical representatives, and health regulators from across Europe. Working together is essential to succeed in the development of novel approaches to patient-centered treatment selection and management of patients with different autoimmune, inflammatory, and allergic diseases.

What is your role in the 3TR team at Amsterdam UMC? I am a member of the 3TR Air BioCohort (ABC) Study, a multicenter observational prospective cohort study in patients with severe asthma, where I am supervised by Prof. Dr. Maitland van der Zee. The study focuses on deepening our knowledge of asthma symptoms and treatments. I have been leading the creation and development of the protocol and I am organizing its submission to the Medical Ethics Board. Upon its approval, I will be involved in the recruitment of patients and data collection. I am also part of the 3TR COPD working group and I have contributed to the survey regarding the 3TR Core Outcome Set for adults with severe asthma. What are you currently working on? What’s your major research interest? I am a Respiratory Physician, enrolled as a PhD student, at the Academic Medical Center of the University of Amsterdam. I am involved in several research projects primarily focusing on precision medicine and exhaled breath biomarkers in chronic airway diseases. My major research interest is to understand the mechanisms of (severe) asthma and to discover new biomarkers that will guide physicians to optimize asthma treatment, i.e. through the identification of specific and possible new phenotypes and endotypes, which will improve the classification of patients and will support patient-centered care aimed at treating specific components of the disorder. What motivates you, personally? What made you go into science? My passion for science started during my school years and it has been growing since. My medical school thesis was my first research experience and I was thrilled to be involved in cross-functional studies and collaborative research projects. I believe that pursuing a scientific career will give me the opportunity to investigate the mechanisms underlying chronic airway diseases, which is one of my passions and which will make me a better doctor by helping me to provide the best care to my patients. Why do you think, the 3TR research is important? The 3TR Consortium is a unique opportunity to investigate a large and international real-life cohort of patients, to deepen the knowledge of precision medicine, learn novel screening techniques, and to refine personalized therapies for patients with respiratory and other chronic diseases. With 3TR research, there is the possibility of discovering potential new targets for asthma treatment as well as find new predictors of response to current therapies. 3TR will harmonize methodologies and create a research biobank that will guide future research on autoimmune, inflammatory, and allergic diseases.

What is your role in the 3TR team at QMUL? I am a PhD Student at QMUL co-supervised by Dr. Myles Lewis and Prof. Michael Barnes. I work collaboratively with the Centre for Experimental Medicine & Rheumatology (EMR) and the Centre for Translational Bioinformatics (C4TB). As part of the 3TR project, I focus primarily on analysing data from the PEAC and STRAP rheumatoid arthritis trials (work package 6). What are you currently working on? What’s your major research interest? I work on integrating multi-omic data in autoimmune diseases using bioinformatic pipelines. I combine data from multiple biological sources including the genome, transcriptome, and clinical records to study disease in a concerted way. The ultimate goal of this research is to predict specific phenotypes and drivers of disease in order to move towards personalised medicine and improve patient response to treatment. What motivates you, personally? What made you go into science? I have always enjoyed puzzles and problem-solving so it was clear to me from an early age that I wanted to study the quantitative sciences. While I loved my undergraduate degree in Astrophysics, the work was not very tangible, and I wanted to move into a field where I could address some of the big issues people face as part of their daily lives. Bioinformatics provides a platform to tackle these real-world problems, whilst also satisfying my enthusiasm for analytical and computational research. Why do you think, the 3TR research is important? Unfortunately, autoimmune diseases seem to run in my family so I can understand some of the difficulties that come from living with such conditions. This is why I find the work of 3TR so important - it allows us to identify novel biomarkers of disease and better understand the molecular pathways involved. This in turn leads to improved prediction of disease progression and response as well as steering us towards personalised therapy, whereby patients are prescribed therapies best suited to them.

What is your role in the 3TR team at EMR? I am part of the bioinformatic team headed by Dr. Myles Lewis. I work in close contact with the other members of the team to support clinician’s research questions with deep transcriptomic analyses on clinical trials. What are you currently working on? What’s your major research interest? My major research interest lies on the development and validation of transcriptomic-based models for classifying and predicting treatment response in rheumatoid arthritis. I am currently working on a novel network-based tool able to detect differential, functionally relevant gene-gene interactions between subgroups of patients. I make use of robust linear modelling incorporating interaction terms to statistically evaluate the predictability of those gene-gene ratios that are significantly associated with response to csDMARD.

What motivates you, personally? What made you go into science? I am genuinely interested in making my data science and statistical skills being useful for the real needs of healthcare. I started traveling down the scientific path powered by my learning experiences and curiosity about the underpinning biological mechanisms of life. Later, I realised I wated to go beyond curiosity and put all my efforts into the medical research to improve patient’s lives. Why do you think, the 3TR research is important? The 3TR project is a unique opportunity to cross-check and validate research hypotheses on diseases whose etiology and/or development is still unclear. For the first time we have access to a vast amount of data from 50 clinical trials. Knowledge transfer and collaboration between companies and academic institutions across Europe have never been so empowered.

What is your role in the 3TR team at UBO LBAI? My role in the 3TR team would be to analyze the 3TR data when they will be available (as my PhD project involves the segmentation and analysis of regions of interest in biopsy slides following acquisition of images using the Hyperion mass cytometer imager). What are you currently working on? What’s your major research interest? My PhD project is based on the segmentation and analysis of images acquired by a mass cytometer from biopsy slides. Thanks to the mass cytometer, we can analyze simultaneously up to 40 markers on a single biopsy slide, whereas conventional techniques allow the analysis of only 6 to 7 markers at the same time. With the additional development of parametric analysis tools, the outcome of this project would be to develop a user-friendly interface to provide a diagnostic software for clinicians. What motivates you, personally? What made you go into science? I have always been interested in the hard sciences in general, especially mathematics and medicine/biology. I chose to study mathematics because I know this field is applicable in all other sciences. That is why I am really very happy to do a PhD in bioinformatics. Why do you think, the 3TR research is important? I consider the 3TR research to be important because first of all, it targets well-known diseases, which do not necessarily have miracle treatments. In addition, this European project aims to collect a large sample of patient data. As a mathematician, I am convinced that if we manage all this data from sick patients the right way, it could pave the way for new therapies.