Department of Urology

Medical Center-University of Freiburg, DKTK partner site, Germany

E-mail: jatin.bedi@uniklinik-freiburg.de





Project title: Investigating the consequences and therapeutic vulnerabilities of KDM6A and KDM6C mutations in Urothelial carcinoma

KDM6A and KDM6C, tumor suppressor genes on the X and Y chromosomes, are frequently inactivated in male bladder cancer. This project investigates their roles in bladder carcinogenesis. KDM6A often undergoes inactivating mutations, while KDM6C is inactivated through Y chromosome loss. These genes will be knocked in bladder cancer cells, followed by phenotypic assessment including proliferation, migration, invasion, as well as changes in chromatin modifications and protein interactions. Finally, utilizing chemical screening, we will identify synthetic lethalities with 
gene loss, in hope of elucidation their role for potential therapies.

Division of Radiopharmaceutical Development

German Cancer Consortium (DKTK), Partner Site Freiburg
Department of Nuclear Medicine
University Medical Center, Freiburg
Head of Biotechnological Development and Preclinical Imaging

Project title: Development and translation of novel theranostic hybrid molecules for pre-, intra-, and postoperative diagnosis and therapy of cancer

Our research is focusing on identifying new biomarkers for the classification of tumors, assessing metastasizing potential and monitoring therapy. In particular my group is working on the development of small molecule peptides with a strong focus on hybrid molecules suitable for preoperative imaging, intraoperative navigation as well as for targeted endoradiotherapy of different cancer types. Therefore, we are using innovative biological, biotechnological and chemical approaches to identify novel peptides to a variety of clinically relevant target structures. Our development pipeline comprises the identification of potential binders, their detailed preclinical characterization including imaging studies finally leading to clinical translation.

Institute for Surgical Pathology

University Medical Center Freiburg

E-Mail: matthias.fahrner@uniklinik-freiburg.de





 

Project title: In-depth proteogenomics of solid tumors to expand and complement routine molecular diagnostics and support personalized therapeutical strategies

Proteogenomics describes the integration of proteomics to multi-omics studies that integrate DNARNA-, and protein-level omics-data. In my research I apply in-depth proteogenomics on solid tumors to address two different aspects:

a) Corroboration of determined sequence variants (DNA or RNA-level) on the proteome level; an approach which may also yield information on the proteomic penetrance of said variants. Results may aid in prioritization of potential treatment schemes if there is co-occurrence of multiple variants with clinical implications.

b) Determine the impact of genomic aberrations on oncogenic signaling pathways; many genomic aberrations are linked to oncogenic signaling and proteomic approaches enable corroborative, direct probing of this impact.

Institute of Surgical Pathology

University Medical Center Freiburg

E-Mail: melanie.foell@uniklinik-freiburg.de

Group Website

Project title: Spatially resolved metabolomics and proteomics of solid tumors

My junior research group “MALDI imaging” investigates tumor tissue cohorts and organotypic tissue slice cultures by MALDI mass spectrometry imaging and complementary omics and imaging modalities. MALDI imaging derives hundreds of molecular distribution maps directly from thin tissue slices. We apply MALDI imaging of metabolites and peptides to investigate spatially resolved tumor biology and to derive spatio-molecular signatures with diagnostic and prognostic potential. Furthermore, we establish open-source analysis tools and workflows in the Galaxy platform and work towards standardization and reproducibility of MALDI imaging, which lays the foundation for future clinical applications.
 

Department of Thoracic Surgery – Division of Cancer Research, University

Medical Center Freiburg
German Cancer Consortium (DKTK), Partner Site Freiburg

Breisacher Str. 115, 79106 Freiburg i.Br.

E-Mail: avantika.ghosh@dkfz-heidelberg.de


Project title: Systematic analysis of nonstop extension mutations in high throughput

Research in our group has shown that nonstop mutations are associated with cancer and are known to have a functional impact on protein expression and function. Our group has created the database NonStopDB, a comprehensive set of nonstop mutations in human cancer. In this project we aim to systematically analyse the functional impact of all non-stop extension mutations found somatically in human cancer in a pooled format using reporters and next generation sequencing. 

Department of Urology

Medical Center-University of Freiburg, DKTK partner site, Germany

E-Mail: ezgi.oezyerli.goeknar@uniklinik-freiburg.de





Project title: Deciphering Menin-MLL inhibitors to better target MLL/KMT2A-rearranged leukemia via combinatorial genetic and epigenetic targeting approaches.

Targeting protein-protein interactions (PPIs) with small-molecule inhibitors has become a hotbed of modern drug development. In this project, we investigate effect of PPI inhibitors that block Menin from binding to MLL proteins. Menin acts as an essential cofactor for MLL/KMT2A-rearranged leukemia. Menin-MLL inhibitors have recently entered phase I/II clinical trials for treating MLL/KMT2A translocated or NPM1 mutant leukemia. Understanding the complete mechanism of action of Menin-MLL inhibitors as well as developing novel epigenetic/ genetic combinatorial treatment strategies to better eradicate MLL-rearranged leukemia are main objectives of the project. 
 

Department of Hematology, Oncology, and Stem Cell Transplantation

University Medical Center Freiburg

Project title: Impact of CD30-mediated immune response in T-cell-lymphomas

The aim of this project is to get a better understanding of CD30-axis in disease progression in ALK-induced T-cell lymphomas with focus on immune response, immune escape mechanisms like immunoediting, involved pathways and other immune evasion mechanisms.

Experimental Immunology

University Zürich

Switzerland





 

Project title: The immune environment of acute myeloid leukemia

Acute myeloid leukemia (AML) is the most common hematologic malignancy in adults. It is characterized by poor outcome with an overall 5-year-survival of only 50% in young patients and 20% in elderly patients. As the curative potential of allogeneic hematopoietic stem cell transplantation is dependent on immunotherapeutic effects (graft-versus-leukemia effects), immune evasion seems to play a pivotal role in the pathogenesis of AML. A comprehensive research program using highdimensional single cell cytometry combined with bioinformatic analyses represents a powerful tool to gain deep and unbiased insights into the immune signatures of AML patients. Immune patterns that predict response may be integrated into the stratification of AML, particularly in the absence of predictive genetic markers. To verify the impact of the identified signatures, detailed functional analyses of patient mononuclear cells will be performed in vitro to investigate the effect of cell-intrinsic and -extrinsic alterations on anti-AML immunity. The ultimate goal is to identify novel stratifying biomarkers and/or therapeutic targets to overcome immune evasion of AML cells and achieve improved patient outcome.

Department of Thoracic Surgery – Division of Cancer Research, University Medical Center Freiburg

German Cancer Consortium (DKTK), Partner Site Freiburg

Breisacherstr. 115, 79106 Freiburg i.Br.

E-Mail: carla.schmidt@dkfz-heidelberg.de



 

Project title: Discovering non-canonical driver mutations in cancer in high-throughput using endogenous models

Most point mutations found in cancer are functionally uncharacterized and hence cannot be exploited for patient stratification and therapy decisions. Current approaches to study mutations endogenously are time-consuming and lack the possibility for high-throughput. In this project, we focus on the introduction of comprehensive libraries of targeted mutations endogenously into the cell genome using innovative CRISPR-derived tools to assess their functional impact and their impact on therapy response and resistance.

AG Börries, Institute of Medical Bioinformatics and Systems Medicine, University Hospital Freiburg









Project title: Characterization and Molecular Targeting of Patient-derived Organoids

This project aims at achieving a comprehensive understanding of pancreatic ductal adenocarcinoma (PDAC) at both the single-cell level and through patient-derived organoids. To deconvolute the heterogeneity of the tumor and its microenvironment, single-cell RNA sequencing will be performed on biopsy samples from primary PDAC patients. In parallel, these biopsies will be used to establish patient-derived organoids (PDOs), which can be used as a model system to predict patient response to chemotherapeutic agents and targeted therapies. The rapid development of chemoresistance poses a substantial challenge in the treatment of PDAC patients. To address this, we plan to continuously expose PDOs to sub-lethal doses of chemotherapeutic drugs over an extended period to induce chemoresistance in vitro. Through a multi-omics approach, including whole genome sequencing (WGS), RNA sequencing, and metabolomics, we aim to identify the molecular mechanisms driving chemoresistance, providing potential targets for overcoming resistance.

Institut für Medizinische Bioinformatik und Systemmedizin

Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg

Arbeitsgruppe Boerries für Systembiologie und Systemmedizin am DKFZ Partnerstandort Freiburg - DKTK

Institut für Molekulare Medizin und Zellforschung, Albert-Ludwigs-Universität Freiburg

 

1. Project title: Genotypic and phenotypic characterization of patient-derived melanoma cell lines

Based on a transcriptome analysis, the aim of this project is to characterize the phenotypic properties of the four individual malignant melanoma cell lines, such as cell survival, proliferation, migration, and invasion. Furthermore, we are studying the underlying mechanisms, which effectuate the phenotype of the melanoma cell lines. Therein, we mainly focus on the MAPK/ERK or PI3K pathways, components of which are frequently mutated and thus are often constitutively active in cancer cells, driving their development and enhanced survival.

2. Project title: Identification of early detection markers in pancreatic ductal adenocarcinoma (PDAC)

The aim of this project is to establish an early genetic classifier of PDAC based on a meta-analysis of independent studies. In combination with system biology and bioinformatics approaches, it is our aim to identify early markers of PDAC in patient-derived samples (eg. liquid biopsies). This may allow the differentiation of PDAC from early pancreatic intraepithelial neoplasia (PanIN), pancreatitis, and healthy tissues. In a parallel approach, we seek to inactivate the classifier genes in established PDAC cell lines and to assess the effects of the inactivation on the functionality of these cells.

Klinik für Innere Medizin II
TEXIMMED2-FR (Translational Experimental Immunology lab)
AG Prof. Dr. Dr. Bengsch
Universitätsklinikum Freiburg

E-Mail: solene.besson@uniklinik-freiburg.de


Project title:
Developing a Standardized Immune Profiling Pipeline for Classifying Hepatocellular Carcinoma Patients to Guide Personalized Treatment Strategies

Our research aims to improve immunotherapies in Hepatocellular Carcinoma (HCC). We recently defined spatial immunotypes of HCC patients using Imaging Mass Cytometry (IMC) on diagnostic biopsies that correlates with therapy outcome. Although our immune profiling analysis pipeline is highly advanced, it needs to be simplified and standardized for clinical use so that it can be routinely applied to diagnostic biopsies from HCC patients. Moreover, we seek to understand how different immunotherapies impact therapeutic outcome, how they are connected to the tumor microenvironnement and the peripheral immune response.

Klinik für Neurochirurgie

DKTK Standort Freiburg

Universitätsklinikum Freiburg

E-Mail: georg.kastner@uniklinik-freiburg.de 

Project title: HematoTrac - Environmental impact of spatiotemporal trajectories from intratumoral hematopoietic stem-cell differentiation

Glioblastoma is the most aggressive and also the most common form of malignant primary brain tumor. The tumor microenvironment (TME) of glioblastoma comprises a complex network of both tumor and non-tumor cells that tends to be immunosuppressive and unresponsive to immunotherapies. Tumor-associated hematopoietic stem and progenitor cells (HSPCs) have been found to be positively linked to glioblastoma progression. As a young mathematician in the HematoTrac project, I aim to trace transcriptional and epigenetic trajectories of HSPCs in the glioblastoma TME using multi-omic analysis at single-cell and spatial resolution. 

MILO Lab

Department of Neurosurgery

University Hospital Freiburg

E-Mail: elena.grabis@uniklinik-freiburg.de

 

Project Title: Decoding the Spatial Architecture of Integrated Electrophysiological and Transcriptomic Diversity in Malignant Brain Tumors

Glioma cells integrate into neural circuits by forming neuron-glioma synapses, which shape a distinct tumor-associated microenvironment and drive tumor progression and therapy resistance. Using high-density electrophysiology, spatial transcriptomics, and functional imaging on human glioma tissue, we map these interactions and the molecular landscape of highly connected brain regions. By integrating electrophysiological, molecular, and transcriptomic data, we gain multiperspective insights into glioma–neuronal crosstalk and aim to identify therapeutic strategies to disrupt these tumor-supportive networks and ultimately improve patient outcomes.
 

Department of Thoracic Surgery – Division of Cancer Research, University Medical Center Freiburg

German Cancer Consortium (DKTK), Partner Site Freiburg

Breisacherstr.115, 79106 Freiburg i.Br.

E-Mail: annika.metzner@dkfz-heidelberg.de

Project title: Impact of FGFR2 mutation on targeted therapy response and downstream signaling

Fibroblast Growth Factor Receptors (FGFRs) regulate cell proliferation, migration, survival, and 
downstream signaling, with genetic alterations driving tumorigenesis and influencing treatment 
response. This project investigates FGFR2 mutations, including both activating and resistance-conferring variants, to determine their impact on sensitivity to FGFR inhibitors such as Lenvatinib and Erdafitinib, downstream pathway activation, and co-occurring alterations. Through saturation mutagenesis and high-throughput functional screening, we aim to comprehensively map mutation-specific signaling dynamics and drug responses, advancing precision therapies for FGFR-driven cancers.

Institute of Neuropathology (Prof. Dr. Marco Prinz)

University Medical Center Freiburg

E-Mail: lauritz.miarka@uniklinik-freiburg.de







 

Project title: Mapping the spatial organization and multicellular interactions of myeloid cell states in human central nervous system lymphoma

Central nervous system B cell lymphomas are highly aggressive yet often untreatable: high-dose chemotherapy cures some, but toxicity excludes many patients and relapse is usually fatal. Immunotherapies work well for B cell lymphomas outside the brain but translating them to the CNS is complicated by the brains opaque immune microenvironment. I will create a high dimensional spatial map of CNS lymphomas, focusing on the functionally diverse myeloid cell compartment that may drive immunotherapy response, resistance and neurotoxicity, to guide safer, precise immunotherapies.