Research projects
Project 1: DC 1
- Beneficiary: Mosaiques Diagnostics GmbH (MOS)
- Project Title: -omics based stratification markers for discriminating significant PCa
- Tasks:
1) Definition of clinically relevant endpoints;
2) Training in evaluating pathology and follow up data
3) Delivery of urinary- based machine learning models based on integrative urinary -omics to guide intervention for PCa;
4) Strategic steps to reach implementation; on the basis of the urinary integrative models
- Supervisor: Dr. Frantzi; Academic Supervisor: Prof. Merseburger; PhD program supervisor: Prof. Jankowski
- PhD awarding entity: RWTH Aachen University
- Planned secondments: UKSH: Education on clinical parameters and evaluating pathology and follow up data; BRFAA: Verification of markers via targeted MS
Project 2: DC 2
- Beneficiary: Biomedical Research Foundation Academy Of Athens (BRFAA)
- Project Title: -omics data integration to map PCa progression
- Tasks:
1) -omics data retrieval via a systematic search
2) Data alignment and downstream integration
3) Functional annotation to define PCa-related pathways.
- Supervisor: Prof. Vlahou; Non-Academic Supervisor: Prof. Mischak; PhD program supervisors: Prof. Vlahou, Prof. Roubelakis
- PhD awarding entity: National and Kapodistrian University of Athens
- Planned secondments: KRESK: Training in programming for big data integration; MOS: Systems and bioinformatics analysis; D4: Retrieve data on existing drugs for the pathways of interest
Project 3: DC 3
- Beneficiary: Mosaiques Diagnostics GmbH (MOS)
- Project Title: -omics data integration for drug re-purposing in advanced PCa
- Tasks:
1) Drug re-purposing strategies for previously defined agents based on single -omics
2) Preclinical testing of previously identified drug candidates in cell line and animal models
3) Computational drug screening to identify compounds for pre-clinical testing, including different strategies for computational drug screening to be aligned and compared to define selected drugs based on multi-omics integration
4) Application of machine learning and advanced statistics to ascertain correlations among predicted drugs to order them by importance
- Supervisor: Prof. Mischak, Dr. Frantzi; Academic Supervisor: Prof. Vlahou; PhD program supervisor: Prof. Jankowski
- PhD awarding entity: RWTH Aachen University
- Planned secondments: MUI: Testing of compounds; FC.ID: training in application machine learning and advanced statistics to ascertain correlations among predicted drugs
Project 4: DC 4
- Beneficiary: Medical University of Innsbruck (MUI)
- Project Title: Cell line characterisation and pre-clinical testing of predicted agents in PCa models
- Tasks:
1) Cell line characterisation at the proteomics level
2) Preclinical testing of -omics based predicted agents in cell line and animal models
3) Proteomics profiling of drug effects to investigate downstream activators
4) Testing of drug combinations to assess synthetic lethal interactions
- Supervisor: Prof. Culig, Prof. Heidegger; Non- Academic Supervisor: Dr. Perco; PhD program supervisor: Prof. Culig
- PhD awarding entity: The Medical University of Innsbruck - Medical University of Innsbruck (i-med.ac.at)
- Planned secondments: MOS: Analyse proteomics profiles from PCa cell lines models; FC.ID: training in advanced statistics to define key features in cell line data; D4: assessing synthetic lethality
Project 5: DC 5
- Beneficiary: FCiências.ID – Associação para a Investigação e Desenvolvimento de Ciências (FC.ID)
- Project Title: Development of pathomics model for PCa stratification
- Tasks:
1) Develop pipeline for pathomics feature extraction from deep learning models
2) Develop and validate DL based pathomics models for PCa stratification and prediction of progression & recurrence
3) Statistical study of associations between imaging -omics features and proteomics features
- Supervisor: Prof. Cruz Da Conceição; Non-academic Supervisor: Dr. Finn; PhD program supervisor: Prof. Cruz Da Conceição
- PhD awarding entity: FCiências.ID – Associação para a Investigação e Desenvolvimento de Ciências (FC.ID)
- Planned secondments: BRFAA: evaluating pathomics model in tissue images; KRESK: Statistical associations between imaging (MRI and pathology) with proteomics.
Project 6: DC 6
- Beneficiary: Kresk - Healthcare Solutions
- Project Title: AI-derived radiomics and multi-omics models to improve non-invasive stratification of prostate cancer risk
- Tasks:
1) Standardise magnetic resonance imaging parameters, stability analysis of extracted features
2) Extract radiomics features from deep learning models
3) Develop and validate combined deep learning and radiomics models for pre-biopsy stratification;
4) Develop and validate combined -omics models with a focus on accurately ruling out unnecessary biopsies.
- Supervisor: Dr. Finn; Academic Supervisor: Prof. Cruz Da Conceição, Dr. Roesch; PhD program supervisor: Prof. Cruz Da Conceição
- PhD awarding entity: Faculdade de Ciências da Universidade de Lisboa
- Planned secondments: FC.ID: integration of omics and imaging (MRI and pathology) models; MOS: validation of integrative models
Project 7: DC 7
- Beneficiary: Universitäts-klinikum Schleswig-Holstein (UKSH)
- Project Title: Definition of clinically relevant endpoints and verification of key pathway components at human PCa tissue
- Tasks:
1) Establishment of a data management platform
2) Definition of clinically relevant endpoints focusing on primary diagnosis setting
3) Definition of clinically relevant endpoints focusing on metastatic setting
4) Verification of key pathway components at human tissue specimen
5) validation of protein biomarkers at human PCa tissue via immunohistochemistry
- Supervisor: Prof. Merseburger, Dr. Roesch; Non- academic Supervisor: Dr. Frantzi; PhD program supervisor: Prof. Merseburger, Dr. Roesch
- PhD awarding entity: Universität zu Lübeck
- Planned secondments: KRESK: Clinical data extraction related to radiology images; MOS: Data management platform development
Project 8: DC 8
- Beneficiary: Medical University of Innsbruck (MUI)
- Project Title: Computational drug screening and synthetic lethality drug repurposing
- Tasks:
1) Consolidation of omics data in the context of prostate cancer
2) Generation of a network-based molecular prostate cancer model
3) Alignment of drug repurposing methods
4) Computational drug screening to identify compounds for pre-clinical testing
5) Identification of drug combinations addressing synthetic lethal interactions
- Supervisor: Dr. Perco; Academic Supervisor: Prof. Heidegger; PhD program supervisor: Prof. Culig
- PhD awarding entity: Medical University of Innsbruck
- Planned secondments: MOS: align drug repurposing methods; MUI: testing of drug combinations derived from the analysis of synthetic lethal interactions
The PROMOTE project has received funding from the European Union’s Horizon Europe Marie Skłodowska-Curie Actions Doctoral Networks - Industrial Doctorates Programme (HORIZON-MSCA-2023-DN-01) under grant agreement No 101169245.
Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union. Neither the European Union nor the granting authority can be held responsible for them.
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