About our Department
Our research
The research of our Department has been organised in four research clusters which have extensive thematic interconnections, and together span the full breadth of tissue-based research, from the initial conception and investigation of molecular alterations to in vitro testing of such concepts, and resulting diagnostic advances and treatments as well as their eventual clinical applicability Clinical Pathology, all supported by a state of-the-art laboratory facility and imaging service PARTS/OIC and integrated computational support Computational Pathology.
The Clinical Pathology (ClinPath) research cluster brings together clinicians, biologists, immunologists, and specialists in pharmaceutical sciences and nanotechnology. The incentive of clinical pathology research is to directly improve health care by focusing on diagnosis, prediction of therapeutic outcome, understanding disease pathophysiology and implementing nanotechnology. We focus on improving diagnostic classification and risk stratification, support clinical decision-making and prediction of therapeutic response, investigate the impact of (tumour) pathophysiology on disease progression, and study how nanosystems behave in certain pathologies to improve treatment outcome. By doing so we interact directly with the MolPath and ComPath lines, and with OIC and PARTS. Clinical Pathology is embedded in the Cancer and Transplantation Institutes of the Erasmus MC (with manifold collaborations with clinical departments), and in national and international clinical and scientific networks (e.g. NWO consortia and roadmaps, NIH), aligning with current trends towards health care centralisation and higher-level organisation. The Molecular Pathology (MolPath) research cluster encompasses a broad spectrum of diseases (cancer and non-cancer related) and of research lines focussing on different aspects of the underlying cellular and molecular mechanisms. The overall aim, in close interaction with, and support of, clinical pathologists and the innovative technology platforms, is to translate basic knowledge into preventive, diagnostic, and prognostic l applications. Currently, two main long-term research lines are on (a) phenotypic plasticity as a key hallmark of cancer initiation (cell-of-origin), metastatic spread, and therapy resistance, and on (b) viral infection, persistence, and pathogenesis in patient-derived models. The research within this cluster is both fundamental in identifying targetable molecular players and unravelling pathophysiological and molecular mechanisms for key events in tumorigenesis, progression, and viral infection, as well as translational to identify novel biomarkers for disease progression and therapeutic response. The MolPath cluster is strongly linked to and supported by the innovation platforms (i.e. OIC, PARTS) and services from ComPath, and has access to highly specialized imaging platforms (super-resolution and light-sheet microscopy), single-cell and tissue-based-omics tools (e.g. spatial transcriptomics), and AI/ML-based image analysis of histopathologic sections. The Computational Pathology (ComPath) cluster includes research lines of computational scientist PIs who are (a) focusing on tissue-slide based computational image analysis and AI to objectify and quantify microscopic features related to disease outcome in close collaboration with clinical pathologists. In addition, (b) this cluster is establishing robust bioinformatic pipelines for a variety of high-throughput molecular data sets together with molecular biologists of our department and Erasmus MC partners. Our PHANTOM (PatHology Artificial iNTelligence platfOrM) platform is closely collaborating with TU Delft amongst others within the Convergence “CanMicrobes” project, the “Organ Transplantation: making unsuitable donor organs suitable“ and “AI for Diagnostics” Flagships. Importantly, these bioinformatic pipelines are not limited only to the research lines within pathology, but are also leveraged extensively in collaborations on cardiac, infectious and immunological research lines with other departments, while for hardware support, we collaborate, notably with the Dept. of Radiology and nuclear medicine and the BIGR computational cluster in house. The fourth part of our research strategy is called the PARTS/OIC facility. The PARTS (Pathology Research and Trial Service) bundles our collective infrastructure to support ClinPath and MolPath. In addition, the PARTS facility also provides this service to other researchers within Erasmus MC. PARTS also includes the tissue bank, and both PARTS and tissue bank are ISO-15189 certified. PARTS’s unique selling point is an array of techniques applicable on our formalin-fixed paraffin-embedded (FFPE) and frozen archive-biobank. PARTS serves our own researchers to do experiments, as frugally as possible, on FFPE tissues. The PARTS also supports researchers all over the Erasmus MC (particularly internal medicine, pulmonary medicine and dermatology) and currently has more than 200 tissue-based research projects. PARTS is our strategic infrastructure for both reducing costs of research personnel for the department as well as enabling acquisition of dedicated technological platforms for research. The OIC (Optical Imaging Centre) facility is formally not part of Pathology and Clinical Bioinformatics and separate from PARTS, it provides high-end microscopy techniques which reside under the Core Facility OIC (Optical Imaging Centre) and is under governance outside the department, but for its research, the OIC scientists are hosted by the department to ensure continued scientific integration between OIC and Pathology. Altogether, PARTS/OIC underpin our research.
Our research team
Head of the Department
Prof.dr. F.J. (Folkert) van Kemenade
Deputy Head of Department
Full Professors:
Professor of Experimental Pathology
Prof.dr. A.B. (Adriaan) Houtsmuller
Professor of Functional Cell Anatomy
Prof.dr. G.J.L.H. (Arno) van Leenders
Professor of Urological Pathology
Prof.dr. P.J. (Peter) van der Spek
Professor of Clinical Bioinformatics
Prof.dr. T. (Tokameh) Mahmoudi
Professor of Molecular Mechanisms in Disease
Prof.dr. E.J.M. (Ernst Jan) Speel
Head of Molecular Diagnostics
Prof.dr. M.H. (Manfred) Kayser
Professor of Forensic Molecular Biology
Professor of Neuropathology
Associate Professors:
Dr. C.H.M. (Carolien) van Deurzen
Assistant Professors:
Dr. M.P.A. (Martijn) Starmans (shared Radiology)
Dr. A.F. (Arwin) Ralf
Researchers:
Dr. R.J.T.S. (Robert Jan) Palstra
Dr. T.P.P (Thierry) van den Bosch
Pathologist Researchers:
Dr. M.C. (Marian) Clahsen-van Groningen
KMBP researchers:
Research Coordinator:
Research lines
Clinical Pathology (ClinPath) focuses on improving diagnoses and prediction of therapeutic outcome by researching novel methods of diagnostic classification and risk stratification, to support clinical decision-making. We study (tumour) pathophysiology with respect to disease progression and how nanosystems behave in certain pathologies to improve treatment outcome. This line aims to improve clinical risk classification of breast, lung, prostate and rare cancers. The department’s long-term clinical research in these tumour types is renowned for its impact on patient management. In line with both the “Integraal Zorg Akkoord” (IZA) and Erasmus MC Koers28, we typically execute research 1) in collaboration with our clinical and regional scientific network partners e.g. the Anser Prostate Network and Amphia hospital (providing access to large well-characterised patient cohorts) and 2) are continuing and expanding our tertiary profile by also focusing research activities on rare cancers and solid organ transplantation.
Specific research lines and aims include: 1. In breast cancer patients, optimising HER2-low detection and (in triple negative tumours) identification of targetable events; 3. Multicentre trials to assess the clinical utility of our established tissue-based AI algorithms to determine outcome and therapy-response in lung, thymic, melanoma and breast cancer patients; 4. Optimizing biopsy grading and risk stratification to personalize therapy in prostate cancer patients; 5. Determining the prognostic value of clinicopathological and molecular alterations in rare cancers such as conjunctival melanoma, penile and thymic tumours and male breast cancer; 6. Better classification of solid organ transplant pathology by deciphering pathologic mechanisms of rejection; 7. Local high dose therapy of advanced and recurrent breast cancer with thermosensitive liposomes and hyperthermia. (NWO); 8. Combination immunotherapy of solid cancers through nanobiotechnology. Understanding interaction of nano-based immune therapeutics (LNP-RNAs, liposomal therapeutics) with the tumour microenvironment;
Molecular Pathology (MolPath) is a long-term research line focussed on the elucidation of mechanisms underlying cancer initiation and malignant progression in specific neoplasms is central to our cluster. A distinct, non-oncology related research line focuses on organ transplant rejection, viral infection, latency, and pathogenesis. Common to the above lines is the identification of novel therapeutically targetable molecular effectors as well as biomarkers for early disease detection, and of response and resistance to therapy. The integration of MolPath with the OIC and PARTS tech-platforms allows us to investigate biological processes in disease models and in patient-derived samples by coupling -omics with highly specialised imaging platforms. Finally, the integration of Computational Pathology further extends our research tools with AI/ML-driven computational biology
Specific research lines and aims include:
1. The non-stem origin of cancer and its progression in the context of inflammation driven by Western lifestyles;
2. The elucidation of the epigenetic mechanisms underlying phenotypic plasticity during local and distant metastasis, and the development of therapy-resistance;
3. The analysis of the in situ invasive progression of breast and prostate cancer;
4. The identification of tissue-related factors responsible for the development of (chronic) renal transplant damage;
5. The molecular mechanisms of persistence and pathogenesis by HIV-1 and HBV in primary and patient-derived (organoid) ex vivo platforms;
6. Identification of prognostic molecular markers and therapeutic vulnerabilities in (lung) neuroendocrine tumours;
7. Molecular mechanisms underlying carcinogenesis and progression of HPV-positive and -negative head and neck tumours.
The Computational Pathology (ComPath) theme focuses on tissue-based image analysis, computational pathology, and AI for objective quantification, improved risk stratification, and therapeutic response prediction. In addition, we are continuing our long-term research activities on development of robust bioinformatic workflows for RNA- and DNA-sequencing, thereby a) enabling comprehensive understanding of the genetic basis of traits, diseases and biological processes, and b) contributing to discovery of novel biomarkers. Once novel image-based algorithms and bioinformatic workflows are established, practical clinical utility is assessed by the ClinPath theme and pipelines are integrated as end-to-end PARTS services for the department and its Erasmus MC partners. The PHANTOM (PatHology Artificial iNTelligence platfOrM) group in ComPath have embarked on creating a world class AI partnership with Radiology (BIGR), TU Delft and international research partners.
Specific research lines and aims include to:
1. Develop integrated tissue-based AI models for classification and prediction of clinical behaviour of breast, lung, neuroendocrine, pancreas, skin, eye and thymus tumours (collaboration with ClinPath);
2. Deliver pan-cancer AI models, specifically deep learning, to integrate radiology and pathology tumour features (RadioPathomics);
3. Develop bioinformatic workflows analysing newly generated single cell- and spatial transcriptomics data (collaboration with PARTS);
4. Develop multi-omic bioinformatic workflows and AI models for biomarker discovery, to predict therapeutic response in oncology and transplant pathologies, and to determine antimicrobial resistance (collaboration with MolPath).
The Pathology Research and Trial Service (PARTS) specialises in long-honoured pathology techniques such as immunohistochemistry, in situ hybridization, molecular assays (including WGS and liquid biopsies) on FFPE and liquid biopsies, scanning of slides, multiplex scanning, tissue microarray production, spatial transcriptomics Within its mission, the PARTS invests in operational excellence (delivering services within reasonable times and without ISO norms). The PARTS continues to invest in platforms to facilitate new research. In 2024, PARTS acquired two highly innovative, end-to-end platforms: 10x Genomics spatial transcriptomics and DeepCell AI-driven morphotyping of single cells in cytological specimens, blood and urine. These platforms will enhance individualised risk prediction, early disease detection, and monitoring of treatment efficacy through integration of multimodal data. Since PARTS is a facility for research, it will adjust its strategic lines with the requirements of the other three lines of the department. The Erasmus Optical Imaging Centre (OIC) is a microscopy expert centre and officially installed Core Facility, led by Prof. Dr A. B. Houtsmuller. The OIC offers access to more than twenty advanced and diverse microscope systems, supporting the application of cutting-edge microscopy in research at Erasmus MC and beyond. In addition, OIC develops novel methodology aimed at specific biomedical applications.
