PMI Young Scientist Retreat
March 16-17, 2021 | Online-Symposium
|09:00 – 09:25||Welcome address|
|09:25 – 11:00||Session 1: Application of multi-omics data in the context of precision medicine | Chairs: Celia Escudero Hernández, Elisa Rosati|
|09:25 – 09:55||Hot data for cold cases - how multi-omics approaches find new disease evidence |
|09:55 – 10:15||Multi-omics analysis of chronic inflammatory diseases to identify core disease signatures|
|10:15 – 10:35||Population structure and transmission dynamics of multidrug-resistant Mycobacterium tuberculosis strains in Sierra Leone and India|
Harriet Blankson, Viola Dreyer
|10:35 – 10:55||Single and cross-tissue conditional transcriptome-wide analyses reveal independent and shared susceptibility genes for psychiatric traits and inflammatory bowel diseases|
|10:55 – 11:30||Coffee Break and Networking|
|11:30 – 13:00||Session 2: Impact of host-microbiome interactions on diseases and therapies | Chairs: Anja Kerstein-Stähle, Jan Henrik Schirmer|
|11:30 – 12:00||Development of new sustainable antibiotic therapy using evolutionary principles|
|12:00 – 12:20||Microbiome-directed therapeutic interventions in CIBD|
|12:20 – 12:40||Gut microbiome: a computational metabolic modelling approach|
Georgios Marinos, Lady Johanna Forero Rodríguez
|12:40 – 13:00||Escherichia coli populations undergo changes in metabolic repertoire during evolution under chronic inflammation|
|13:00 – 13:05||Group Photo|
|13:05 – 14:00||Coffee Break and Networking|
|14:00 – 16:00|
Workshops – Parallel sessions
Workshop 2: Clinical studies
|16:00 – 17:00||Meet the PI|
Gabriela Riemekasten, Stefan Schreiber, Stefan Niemann, Hauke Busch, Matthias Laudes, Thomas Bahmer, Diamant Thaci, Klaus Rabe
|09:00 – 10:30||Session 3: Immunophenotyping and immunotherapies |
Chairs: Lena Best, Florian Tran
|09:00 – 09:30||Immunophenotyping|
|09:30 – 09:50||Atopic dermatitis displays stable and dynamic skin transcriptome signatures as well as an elevated NK-cell transcriptomic signature|
|09:50 – 10:00||Complement-T cell interaction in ANCA-associated Vasculitis|
|10:00 – 10:10||IL-13 as marker for vascular complications in systemic sclerosis|
|10:10 – 10:20||The atopic dermatitis microbiota affect the expression of skin differentiation markers in a 3D skin equivalent|
|10:20 – 10:30||Deep immunophenotyping as a strategy to identify new therapeutic targets in experimental models of mucous membrane pemphigoid and epidermolysis bullosa acquisita|
Maike M. Holtsche
|10:30 – 11:00||Coffee Break and Networking|
11:00 – 12.30
|Session 4: Laboratory models for inflammation|
Chairs: Handan Yasak, Simon Lohse
|11:00 – 11.30||A mouse model to study molecular mechanisms of interstitial lung diseases|
|11:30 – 11:50||The MERMAID Project - PET imaging of zebrafish|
Milan Zvolsky, Steven Seeger
|11:50 – 12:10||Advanced imaging techniques for pre-symptomatic detection and monitoring of inflammatory skin diseases|
Madita Göb, Hubertus Hakert, Caren Jacobi, Linh Ha
|12:10 – 12:20||Patients’ and professionals’ views related to ethical issues in precision medicine: A narrative review|
|12:20 – 12:30||Precision Medicine in Chronic Inflammation – a Review of Methodological Challenges and Existing Economic Evaluation Studies|
|12:30 – 12:45||Closing Remarks |
Nadine Höft, Florian Bleibaum, Daniela Esser, Ulf Geisen, Inken Wohlers
|12:45 – 13:30||Coffee Break and Networking|
|13:30 – 15:30|
Workshops – Parallel sessions
Workshop 4: Study design of pre-clinicial studies: Integrating antigen-specificity in preclinical models and the analysis of human samples
Workshop 1: Data management I
Prof. Dr. Josef Ingenerf, University of Luebeck, Institute of Medical Informatics / IT Center for Clinical Research, University of Luebeck
Dr. Ann-Kristin Kock-Schoppenhauer, ITCR L/IT Center for Clinical Research, University of Lübeck
In Workshop 1, relevant knowledge on data management to support translational research in medicine will be conveyed. In particular, essential requirements will be addressed for the reuse of patient data from health care, e.g. with regard to broad consent, use/access procedures, anonymisation/pseudonymisation procedures as well as basic requirements for data quality and interoperability through the use of standardised data formats. Relevant national projects and institutions involved in these topics are presented on a site-specific basis. The mentioned aspects will be demonstrated using the example of the Molecular Tumour Board (MTB).
In the workshop, a large period of time will be allocated for interaction in order to be able to take up and discuss further topics of interest.
Workshop 2: Clinical studies
Workshop Clinical Studies
Clinical studies provide the ultimate translational step to test the feasibility of a therapeutic concept in patient care. Background knowledge on the regulatory affairs, the appropriate study design and the interaction with responsible authorities are necessary to facilitate clinical trials.
In Workshop 2 we will provide a general overview about the design of clinical studies and the necessary interaction with regulatory authorities. We will specifically focus on investigator initiated trials (IIT) and show current pitfalls and in the transition from a clinical research idea into a therapeutic compound tested in a clinical trial.
Clinical studies are yearlong endeavors, but everything starts with a sound research idea!
We therefore ask everybody to share his/her research idea in a 1-2 slide power point presentation and the vision on how this could be tested in a clinical trial.
Workshop 3: Data management II
In Workshop 2 basic concepts for OMICs data management will be provided. In addition an overview of international and national initiatives and resources will be provided and end-user solutions for OMICs data management will be introduced.
In detail, addressed topics/questions will be the following:
- What are OMICs data and why do we need to manage them?
- NGS, GEO, raw data, result data … size considerations
- Different levels of DM (data lifecycle, metadata levels, etc.)
- What do funding agencies expect?
- What do you get out of good DM?
- The FAIR Principles
- International and national initiatives and resources for OMICs-DM
- EGA, SRA, GEO
- How structured bioinformatics pipelines can help with DM
- nextflow, nf-core standardized pipelines
- Amazon Cloud AWS – Compute + Data services in the cloud
- Legal perspective
- Are OMICs data sensitive data?
- data encryption: crypt4ga, boxcryptor
- data protection offices: UKSH, CAU, UzL
- Overview DM tools for end-user:
- Data Warehouse: Cohort selector; Analysis GUI; Quality Check
- Middle Ware: Unify complex storage landscape; Meta Data; Automate processes (replication, hot cold storage)
- “Cloud storage”DM Plan helper: Online tools, Templates
- Introduction and Demo:
- YODA data management solution
- RedCap for clinical data management
Workshop 4: Study design of preclinicial studies
Precision medicine requires preclinical models, allowing to precisely address and dissect the pathomechanism of interest. These comprise animal models as well as precise analysis tools to study human samples as the basis to define patient-variability and the prerequisite for personalized medicine. In most chronic inflammatory diseases (CIDs) studied in PMI, adaptive immunity is a driving force. This is organized by rare antigen-specific T and B lymphocytes, which most likely initiate the disease and contribute to the characteristic chronicity and treatment resistance of CID via the formation of long-lived memory cells. However only in rare cases these antigen-specific immune cells are characterized and targeted specifically by immune therapies. This knowledge gap is a major hurdle for precision medicine and novel treatment strategies targeting the cause rather than the symptoms of a disease. Vice versa treatments based on the knowledge of the target antigens and antigen-specific cells are the basis of some of the most spectacular and long-lasting successes in medicine: Vaccination, immunotherapy of cancer and specific immunotherapy (SIT) in allergic diseases.
In this tutorial we will touch:
- Challenges to identify disease-relevant antigen-specific T/B cells (and their target antigens)
- Methods allowing to identify antigen-specific T and B cells and integrating them into multi-omics analysis approaches
- Animal models in comparison with analysis of human cells/tissues: basic considerations, chances and limitations in the translation of approaches
- SIT is currently the only antigen-specific therapy to achieve a long-term improvement in CID: principles and challenges to determine the mechanism of action and to improve efficacy.
We would encourage active contributions by the participants. Since it will not be possible to cover all aspects of specific diseases, the participants are invited to send in their prime interests, regarding antigen-specificity in a particular disease or experimental model or contribute a 1-2 slides with a challenging problem or example, which we can discuss together.
Please send in suggestions/ contributions until Friday March 12 to: Alexander.firstname.lastname@example.org