Research projects

Group Lugli Our group works on extracting information from colorectal tissue biopsies to aid prognosis of disease evolution and prediction of therapy success in patients with inflammatory bowel disease (IBD). In Bern, we are working on implementing the IBD-DCA score in clinical practice. In parallel, we are establishing its prognostic value and develop an AI algorithm to automatize the scoring. In collaboration with gastroenterologists in Europe (Switzerland, Netherlands), we hope to identify tissue-based markers that allow a personalized treatment strategy in asymptomatic patients diagnosed with IBD during colorectal cancer screening.

Schematic overview of how information extracted from colorectal biopsies may be used to guide treatment strategy in asymptomatic patients diagnosed with inflammatory bowel disease during colon cancer screening.

Group Krebs The mechanisms leading to severe inflammatory lung disease in some COVID-19 patients are unknown. In this project, we will analyze the cells in the lung lavage of these patients and compare these findings with results from collaborators working on a mouse model of COVID-19. We hope so to reveal targets for COVID-19 therapy.

Graphical abstract 

Group Freigang Natural killer T (NKT) cells are innate-like T cells with powerful immunoregulatory functions that recognize self and microbial glycolipids presented by CD1d molecules. While the efficacy of NKT cell agonists is currently explored in the immunotherapy of infectious diseases and cancer, the mechanisms that control CD1d antigen presentation and NKT cell activation in vivo still remain incompletely understood. This project characterizes pathways linking CD1d antigen presentation to lipid metabolism, and aims to define critical effector functions of NKT cells in microbial infections. 

Group Freigang Atherosclerosis-related diseases remain the leading cause of mortality worldwide; and chronic inflammation represents a major driver of disease progression. First clinical trials demonstrated the beneficial effects of anti-inflammatory therapies in CVD patients, a better understanding of the molecular mechanisms of vascular inflammation is required to develop more effective treatment strategies. In this project we investigate how dyslipidemia and the resulting lipid metabolism perturbation in immune cells affects physiological immune responses and contribute to vascular immunopathology in atherosclerosis.

En face preparations of the mouse aorta. The atherosclerotic lesions induced by feeding a high fat diet were revealed by staining with Oil Red O

Group Freigang Invasive fungal infections have high mortality rates with limited therapeutic options. We recently identified macrophage-secreted IL-1 receptor antagonist (IL- 1Ra) as an innate immune checkpoint that facilitates fungal dissemination and candidiasis pathology. We showed that therapeutic IL-1Ra neutralization protects against lethal Candida sepsis, whereas interferon-driven amplification of IL-1Ra during viral infections exacerbates fungal disease. This project explores IL-1/IFN I crosstalk mechanisms, particularly IL-1Ra, as potential biomarkers and therapeutic targets in microbial infection.

Immunofluorescence staining of an infected mouse kidney. The tissue dissemination of the fungus Candida albicans was visualized by staining of the fungal cell wall.

Group Krebs Inflammation is a driver of cancer. We have shown that IL-33 signaling is important for the development of myeloproliferative neoplasms (MPN), a type of blood cancer, and for promoting colorectal cancer (CRC) (Mager, J Clin Invest, 2015; Mertz, OncoImmunology, 2015; Pastille, Mucosal Immunol, 2019; Yeoh & Vu, Cytokine, 2022). We currently investigate the contribution of IL-33 to MPN progression and to the cellular and molecular mechanisms underlying IL-33-dependent CRC. For these studies, we use patient-derived samples and mouse models.

Increased levels of IL-33 protein in bone marrow of MPN patients. IL-33: brown; CD34 (endothelial cells): red

Group Krebs The intestinal barrier is often disrupted during intestinal diseases, causing gut leakiness. We have recently shown that the protein ESRP1, a regulator of mRNA splicing in epithelial cells, has a critical function to maintain the integrity of the intestinal barrier (Mager et al., eLife, 2017). In this project, we further investigate how loss or reduction of ESRP1 leads to intestinal homeostasis and pathogenesis, including inflammatory bowel disease and colorectal cancer.

Bacteria (white arrows) penetrate the leaky intestinal barrier of Esrp1 mutant mice. Scale bars: 100 μm (from Mager et al., eLife, 2017)

Group Krebs The vertebrate immune system comprises the innate immune system, providing the first line of defense, and the adaptive immune system, which is triggered at a later stage and is responsible for memory. 
In this project, we use different murine models to better understand the role of specific genes in the regulation of these immune cell subsets and how disbalance in this process may lead to immunopathology in different disease contexts, including pathogen infection (Cardoso Alves, EMBO Reports, 2020).

Changes in immune infiltrate composition and transcriptomic landscape in the lungs of diseased mice with a defect in immunoregulation. A. Immune cells were isolated from lung tissues of healthy and diseased mice and analyzed by flow cytometry to distinguish between immune cell subtypes, which are displayed in a tSNE representation. B. Alternatively, lung innate immune lymphocytes were analyzed using single-cell RNA sequencing.

Group Lugli Immune checkpoint inhibitors are increasingly used in the adjuvant therapy of locally advanced, neoadjuvantly treated adenocarcinomas of the esophagus. Reliable predictive biomarkers are essential to identify the patient population that shows a significant response to immune checkpoint inhibitors. We are studying the transcriptome, methylome and immunohistochemical expression profile of immunomodulatory molecules in human tumor samples.  The aim is to identify key molecules that may influence the response to therapy.  In addition, the impact of neoadjuvant therapy on these immunomodulatory molecules will be investigated.

Identification of differentially expressed genes in esophageal adenocarcinomas depending on PD-L1 status

Group Vassella Medulloblastomas are the most common aggressive pediatric brain tumors, molecularly defined by different groups and subgroups. Although medulloblastoma is a rare disease, it has been also described in postpubertal and adult patients. The lack of studies exclusively on adult medulloblastomas means that the therapeutic approach in these patients is mainly based on existing data from studies on pediatric medulloblastomas. For these reasons, and given that adult patients do not have a satisfactory clinical outcome after therapy, we would like to study a large cohort of adult medulloblastomas and medulloblastoma relapses on a clinical, pathological and molecular level in order to further characterize the biology of these tumors for developing a targeted therapy adapted to their molecular profile.

Classic histomorphology of an adult medulloblastoma

Group Perren Acquired drug resistance (ADR) is a major clinical challenge to all current and future cancer treatments, including chemo, radiation, targeted, and immune therapies and accounts for 90% of cancer mortality. Due to the stochastic, nature of mutation-driven  ADR, multiple different resistance mechanisms can co-evolve within in the same tumour or across metastatic lesions in the same patient, requiring individualized therapeutic approaches. This project seeks to identify and test novel strategies to target drug- tolerant persister cells (DTPs), which comprise an early, reversible bottleneck phase of ADR. RNAseq and high content imaging-guided molecular and phenotypic analysis will delineate the early dynamic changes during DTP development in 2D and 3D ADR models of PanNET.

(A) DTPs precede acquired drug resistance (ADR). (B) Time laps fluorescence microscopy of PanNET shows therapy-induced loss of sensitive cells and emergence of DTPs. Single-cell phenotypic and molecular analysis to identify drugs for repurposing against (DTPs. 

Group Schenk The tumor immune microenvironment in pancreatic ductal adenocarcinoma (PDAC) is diverse, comprising various cell types that may either enhance or attenuate tumor immunity and disease progression, as well as response to therapies. It is therefore essential to dissect the immunological landscape in human PDAC tissues and to assess the correlation of various cell subsets and tumor-derived immunosuppressive factors to patient survival and other clinical parameters. Utilizing a novel approach to perform spatially resolved multiplex immunohistochemistry, we intend to delineate the phenotypes of tumor-infiltrating immune subpopulations in exquisite detail. Integrating these findings with transcriptomic data and tumor genotype signatures will allow us to unravel the mechanistic and prognostic relevance of certain immune markers in PDAC.

25-plex imaging mass cytometry (IMC) image of a human PDAC tissue section shown in four images with 6 markers each. Overview (top), zoom (bottom)

Group Lugli The main aim of the GI Tissue Medicine research group concerning tumor budding in CRC is the following: to identify potential target molecules in tumor buds and develop an anti-budding therapy. The focus lies on four clinical scenarios: pT1 CRC, stage II CRC, rectal cancer (preoperative) and colorectal liver metastases. Additionally, our group is also a member of the International Budding Consortium (IBC).  

pT1 colorectal cancer with high grade budding (H&E staining)

Group Perren We focus on understanding epigenetic changes occurring in PanNET and their impact on progression and metastasis formation. Based on DNA methylation we identified subgroups of PanNETs with: specific cell of origin, genetic background and clinical outcome. Integrating epigenetic and transcriptomic profiles we found that cell dedifferentiation and metabolic changes characterize progression from small PanNET to more advanced ones. We are currently investigating spatial and temporal heterogeneity of PanNET using multi-omic approaches.

Graphical representation of PanNET progression

Group Perren Up to date, no therapy prediction based on specific molecular profile is possible for PanNET patients. We recently established patient-derived tumoroid cultures from PanNEN patients which resemble features of original tumor tissue and which can be used for in vitro drug screenings. We demonstrated the utility of PanNEN tumoroids to predict patient therapy response and we identified novel epigenetic treatment options. Recently we established xenograft of PanNEN on Zebrafish embryos to further exploit in precision medicine.

Precision medicine for PanNEN patient. PanNEN tumoroids in culture, H&E staining and synaptophysin staining of embedded tumoroids (middle). Zebrafish xenotransplant, red: tumor cells, green: endothelial cells.

Group Perren Critical metabolic changes are early hallmarks of cancer cells. Emerging epigenetic, transcriptional and translational data suggest that PanNET cells undergo substantial metabolic reprogramming and develop distinct metabolic subtypes. However, the identity, functional consequences and therapeutic potential of metabolic changes in PanNET remain up until now largely unknown and untested. Our multimodal, integrated analysis of PanNET cell culture and tissue samples of various stages by modern mass spectrometry, fluorescence microscopy and RNAseq data will delineate these metabolic changes and test novel therapeutic strategies.      

(A) Tissue mass spectrometry identified five metabolic subtypes. (B) Immunohistochemistry and (C) Fluorescence microscopy show metabolic heterogeneity. 

Group Tschan Metastasis formation accounts for the majority of deaths from breast cancer, making it imperative to better understand the mechanisms driving the metastatic cascade in order to develop therapeutic interventions to target it. We earlier discovered an oncogenic splice variant of a transcription factor and named it DMTF1β. We now show that DMTF1β promotes invasion and tumor-initiating capacity of breast cancer cells by activating autophagy. It has also been shown that inhibition of autophagy can have undesirable effects in some cancer types and induce epithelial to mesenchymal transition (EMT), one of the early steps of metastasis. Our aim is to identify cellular conditions in which autophagy inhibition will decrease migration, and those in which the inhibition of autophagy will promote invasiveness.

Cancer-associated fibroblast from breast cancer patient

Group Tschan The transcription factor PU.1 (SPI1) plays a key role in myeloid differentiation as well as in myeloid cell survival. Aberrant low PU.1 expression contributes to an immature myeloid phenotype, e.g., acute myeloid leukemia (AML). Interestingly, two studies indicate that high PU.1 protein levels were associated with alternative splicing promoted by either direct binding to splice factors or by mRNA binding. Our data indicate that PU.1 controls splicing of the anti-apoptotic CFLAR (cFLIP) gene, and thereby regulates cell death during myeloid differentiation.

Schematic representation of how PU.1 might regulate splicing of the anti-apoptotic gene CFLAR

Group Tschan Apart from glycolysis and OXPHOS, lipid metabolism is frequently reprogrammed in leukemic cells to support cellular growth. Particularly, the protein important for de novo lipid synthesis, fatty acid synthase (FASN), is frequently upregulated in tumor cells. We found that high FASN expression in acute myeloid leukemia (AML) cells is associated with an immature hematopoietic phenotype. Decreasing FASN levels by RNAi or epigallocatechin-3-gallate (EGCG) treatment, but no blocking its enzymatic function, resulted in improved response of AML cells to differentiation therapy.

FASN localizes at the lysosome (LAMP1) to increase mTOR activity. NB4 APL cells were differentiated towards neutrophils with all-trans retinoid acid (ATRA)

Group Schenk Only specific subsets of DC are able to present tumor antigens to CD8+ T cells in a process called cross-presentation. We aim to elucidate the mechanism(s) of cross-presentation and how this process can be manipulated in melanoma. Therefore, we are establishing models to test human monocyte derived DC as well as mouse bone marrow derived DC (BM-DC) for their ability to cross-present antigen. The knowledge of how cross-presentation is regulated in vitro may allow us to manipulate this process in vivo. Treated BM-derived DC will be tested in adoptive transfer experiments as prophylactic and therapeutic treatment for established melanoma. Together, these data should identify ways to promote frequency and enhance function of cross-presenting DC and to contribute to anti-tumor response.

Cross-presentation by Dendritic Cells: Different pathways of antigen processing and transport leading to presentation of exogenous antigen on MHC class I to CD8+ T cells

Group Schenk The activation of an effective adaptive anti-tumor response relies mainly on presentation of tumor antigens and stimulation by DC. Despite extensive research, the phenotypes and functions of tumor-infiltrating DC (TIDC) remain largely elusive and cross-presentation of tumor antigen is not well understood. We are elucidating the phenotypes and functions of TIDC and how to manipulate them both in vitro and in vivo to induce a tumor- specific CTL response in melanoma. Thereby, we aim to identify ways to reprogram TIDC to present tumor antigens and activate an adaptive immune response against melanoma.

Group Vassella Glioblastoma (GBM) is the most heterogeneous and aggressive primary brain tumors, and represents a particular challenge of therapeutic intervention. In a single-center retrospective study of 43 matched initial and post-therapeutic GBM cases with exceptionally long recurrence period, we performed whole exome sequencing in combination with mRNA and microRNA expression profiling with the aim to identify processes altered in recurrent GBM. Seven mRNAs coding for proteins implicated in Epithelial to Mesenchymal Transition (EMT) and 13 miRNAs implicated in Tumor Necrosis Factor (TNF) and Wnt signaling pathways were significantly dysregulated. To the best of our knowledge, this is the largest cohort of recurrent GBM with long-term resection intervals, that has been analyzed by multi-omics approaches In future, this approach may help for the development of new personalized medicine. This project is currently supported by the Swiss National Science Foundation.

Heat map analysis of recurrent glioblastoma

Group Vassella We followed an unbiased approach for the identification of microRNAs that are most efficient at conferring resistance to the alkylating agent temozolomide in glioblastoma cells, which are the most common and most aggressive primary malignant brain tumour.  To this end, glioblastoma cell lines were screened with a lentiviral microRNA library and selected for temozolomide resistance. miRNAs identified by this screen showed downregulation of serine-threonine phosphatases, which in turn caused enhanced phosphorylaton of ERK and AKT, modulated the activity of DNA repair enzymes, and thereby confer resistance to TMZ response. 

Screening for microRNAs conferring temozolomide resistance in glioblastoma cell lines

Group Zlobec, Williams The cancer ecosystem comprises tumour, stroma (cellular component) and extracellular matrix (ECM), together the stroma and ECM make the tumour microenvironment (TME). The Williams group utilises spatially resolved technologies including Nanostring GeoMx Digital Spatial Profiler (DSP), CosMx Spatial Molecular Imager (SMI) and MACSima platforms to examine how the composition and architecture of the cancer ecosystem defines disease phenotypes. Current projects include: Examination of TME heterogeneity and its association with epithelial identity and plasticity in colorectal cancer. Deep characterisation of the biochemical and structural properties of the ECM for predictive and prognostic biomarker identification.

Spatially resolved transcriptomic profiling of the cancer ecosystem in colorectal cancer. Primary antibodies for tissue visualisation - Green: PanCK (epithelium), Blue: DNA (nuclei). Region of interest selection – Red: tumour, Yellow: tumour microenvironment

Group Zlobec, Williams In addition to exploratory tissue analysis, our team builds, tests and validates in-house, open-source and commercially available algorithms for potential diagnostic use and workflow integration. We are generating a pan-lymph node metastasis algorithm using state-of-the-art deep learning methods. We then streamline processes from the lab to data analysis, and on to visualisation of results and interaction of our algorithms with pathologists scores and feedback. Together with our expert pathologist colleagues, we collaborate on a variety of algorithms including PD-L1 (Tereza Losmanova), H. pylori (Bastian Dislich), IBD scoring (Aart Mookhoek), tumor budding- CD8 scores (Heather Dawson), breast biomarkers (Wiebke Solass) and pancreas pathology (Martin Wartenberg).

Computational Analysis of Colorectal Cancer Metastases in Lymph Nodes

Group Zlobec, Williams Our Sinergia project uses AI to gain new insights into the biology of colorectal cancers. We investigate morphomolecular relationships, including the molecular subtypes and intratumoral heterogeneity in order to learn new interpretable & clinically important features from histopathology images. We use various computational methods, including graphs and deep learning) to evaluate the structural and spatial patterns at the tumor invasion front in neoadjuvantly treated patients. We’ve extended our scope to understanding transcriptional subtypes using spatial transcriptomic and spatial protein expression analysis. The tumor microenvironment, with its complex stromal patterns and immune contexture are important focus points. Collaborators on this project include M. Rodriguez (IBM Research), M. Anisimova (ZHAW), B. Snijder (ETH Zürich), A. Fischer (HES-SO & UniFribourg) and V. Koelzer (UniZürich).

Epithelial cell and lymphocyte graphs in colorectal cancer