The Power of Dual Training

A crucial missing link in the current research environment is the lack of qualified individuals who possess the immunology skills to recognise and define important scientific questions amenable to -omics approaches and also the bioinformatic expertise to interrogate and interpret the resulting big data appropriately. As a consequence, large datasets can be acquired on particular TRM cell populations, but not utilised optimally because of insufficient expertise in bioinformatics. Although the need to train young immunologists to formulate intelligent hypotheses based on big data resources has been recognised, most immunologists are still not empowered to interrogate big data in the way that is needed to move the field forward. Equally, the expertise of bioinformaticians is frequently not harnessed to design better experiments – they merely become the end point for data processing.

The aim of ENLIGHT TEN+ is to train a cohort of early-stage researchers (ESRs) to be comfortable in both arenas: to have an in-depth understanding of T cell immunology and also expertise in bioinformatic processing of large datasets. By exposing young researchers to both angles during their early training, ENLIGHT-TEN+ will generate a cohort of individuals who can craft innovative questions in the area of TRM cells, gather large-scale data making use of rapidly developing technologies, translate the data into biological knowledge using cutting-edge bioinformatic tools and artificial intelligence, and utilise this knowledge to identify novel biomarkers for precision diagnostics and therapeutic targets. Thereto, ENLIGHT-TEN+ has developed a cross-disciplinary training programme to provide all its PhD students with specialist high-level research training, a broad scientific skill set and experience in both academic and industrial working environments. In addition to excellent research skills, future scientific leaders and innovators require additional personal development with respect to team-leading abilities, communication, project management and entrepreneurship. ENLIGHT-TEN+ offers its ESRs flexible opportunities to acquire transferrable and communication skills, including working in multi-disciplinary teams, project management, business-related aspects of research, research ethics and scientific integrity, as well as scientific and grant writing. With careful attention being paid to their personal development, ESRs will graduate from ENLIGHT-TEN+ with an excellent and exclusive research qualification, placing them extremely well to successfully compete for academic or industrial life science-related positions.

ENLIGHT-TEN+ has developed the following eight specific training modules:

Module 1 - Personal Career Development Plan

The PCDP will be the key tool to provide each ESR with tailored training and to support their long-term career ambitions. It will contain a description of the research project, including the work plan, information on secondments and interdisciplinary activities, the publications status as well as an overview of research-related and complementary skills trainings, offered by the universities to which the ESRs will be affiliated. It will be regularly updated and reviewed to ensure effective monitoring of the progress. The PCDP will ensure that all ESRs are empowered to take responsibility at an for the scope, direction and progress of the project and that they receive all the training and mentoring support required for the successful completion of their PhD and further career development.

Module 2 - Research project-based training

All ESRs will work on cutting-edge research projects at the interface of T cell biology and big data analysis. The projects are carefully designed to be innovative, but at the same time set-up in a way that will ensure successful completion of the PhD. In addition to the primary supervisor, each ESR will be assigned to an experienced researcher at the host institution that will provide support and guidance e.g. in experimental design, implementation of good scientific practice and introduction to new techniques and analyses. Regular reporting on the progress of the research project at lab meetings, institutional seminars and international conferences will not only train complementary skills, such as presentation and data communication skills, but at the same time deepen the ESR’s understanding of the research field.

Methods and techniques skill levels at the end of research project-based training

Method/technique - ESR#123456789101112131415
Isolation and characterisation of human/murine TRM cells232333332311111
Multi-parameter flow cytometry of animal/patient samples233333332311111
Single-cell RNAseq213211231211312
Bisulfite amplicon sequencing and methylation arrays311121123111132
TCR repertoire analysis113211133112221
Analysis of (mitochondrial) proteomics datasets111321111122211
Metabolic analysis of TRM cells111231111112111
Immunotoxicological risk prediction111112311122111
Basic bioinformatics analysis333333333333333
Integration of multi-omics data222221222233333
Bioinformatics analysis of gene regulatory networks212222131233323
Computational models for predicting immune response111113211233213
In silico modelling of ectopic GCs111111111212111
Machine- and deep-learning approaches211112111133213

1 : has a theoretical knowledge; 2 : is able to independently apply the technique & analyse the data; 3 : is able to refine the technique and/or troubleshoot and/or train others

Module 3 - Host institution-based training

All ESRs of ENLIGHT-TEN+ will be enrolled in university-based PhD programmes and will attend courses, lectures and seminars as required for the successful completion of the respective programmes. For ESRs that are based at a company (BAYER, IBM, QIAGEN) or a non-university research institute (BI, HZI, IMM, INSERM, SANGER), agreements with universities are in place to ensure that all ESRs will be granted a doctorate upon successful compilation of their PhD thesis and defence. The host institution-based training will provide the opportunity to further improve the ESRs’ transferable skills and interdisciplinary knowledge. In addition, courses will ensure compliance with national or local rules and regulations regarding good scientific practice, informed consent and animal welfare. Interacting with other PhD students in these programmes will be an important opportunity for interdisciplinary exchange and networking with fellow students.

Module 4 - Secondments

Secondments are an integral part of all research projects as they maximise the use of complementarity resources and expertise within the consortium, ensure cross-sectoral exposure and offer to experience different ways of lab organisation and culture. Secondments have been designed to provide the ESRs with the opportunity to execute a well-defined research project component in a different research environment. Typically, two secondments have been scheduled for each ESR.

Module 5 - E-learning

ENLIGHT TEN+ will use preparatory e-learning to maximise the learning outcome of face-to-face courses and as an important source to complement local programmes where necessary. ENLIGHT TEN+ also plans to be a provider of e-learning, be it in form of webinars or YouTube tutorials in areas of demand such as How to generate and analyse scRNAseq data or How to use and interpret computational models.

Module 6 - Summer Schools

The four Summer Schools are the core of the network-wide training and are planned as 5-day training sessions. Each Summer School will expand scientific, transferrable and intersectoral skills. Training sessions within the Summer Schools will be designed to simultaneously address several aspects. To consolidate the learning, newly acquired skills will be put into practice, e.g. by giving oral presentations or working on a case study.

School 1: Understand and communicate key concepts and innovative methods in immunology
  • Basic concepts and experimental methods in immunology
  • Tissue-resident T cells
  • Human immunology
  • Immune cell memory and vaccination approaches
  • The ageing immune system
  • Understanding cellular heterogeneity: single-cell genomics
  • Interactive workshop: How to create science videos and optimise their distribution
  • Interactive workshop: Experiences with Open Science in Vienna and how ENLIGHT-TEN+ can make it a reality
  • Interactive workshop: Challenging perceptions: Is use of war-like terminology in immunology narrowing our minds?
  • Interactive workshop: Tools to understand your role in a team and team building exercise
School 2: Data resources and machine-learning tools for T cell immunologists
  • Immunology resources: 3i, IMPC and beyond
  • scRNAseq bioinformatics
  • Tools for pathway analysis
  • Molecular interaction databases
  • Basic concepts of machine- and deep-learning
  • Integration of -omics data for human health: lessons from the EU project COSMIC
  • Genetics of molecular and immune phenotypes
  • Open Data and entrepreneurship – a contradiction?
  • High-throughput sequencing: material sharing, dissemination and reusability
School 3: Translational research and medicine development
  • Why patients want to get involved in research
  • Cooperative board game on drug development
  • R&D strategies in big pharma and public private collaborations
  • Therapeutic approaches using CRISPR/Cas9
  • From biomarker discovery to clinical validation and development into clinical test
  • Interactive workshop: Regulatory issues: The FDA decision on Eteplirsen
  • Interactive workshop: Presentation skills
School 4: What to do with a PhD – a hands-on workshop for job hunters
  • From basic research to business: My unexpected career as a managing director of a start-up
  • Careers in industry, academia, regulatory agencies, NGOs and governments
  • Workshop: Proposal writing, job interview training, how to improve your CV document
Module 7 - Annual network meetings

The annual network meetings will be used for presentations by the ESRs on their research projects and secondments. During these presentations, as part of the scientific training, the ESRs will not only receive feedback on their research projects but also on their presentation skills, ability to lead scientific discussions as well as time management skills. In addition, workshop will address a mix of current scientific developments and training in key aspects, including gender/sex in immunology and big data analyses, the 3R principle in animal experimentation, research ethics, good scientific practive and measures to increase reproducibility of scientific results, interaction with patient organisations and policy makers, Open Access and FAIR data management, as well as intellectual property rights and entrepreneurship.

Module 8 - International Symposium

In the final year of the project, the ESRs will take the lead to organise a 2-day International Symposium "How -omics and artificial intelligence can advance T cell immunology".