Research projects

Group Lugli Our group is currently working on the implementation of the biopsy-based IBD-DCA score to support the prognosis of disease development and the prediction of treatment success in patients with chronic inflammatory bowel disease (IBD). In parallel, in collaboration with the Institute of Pathology at St Vincent's University Hospital in Dublin, we are developing an AI algorithm to automate the scoring.

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 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 previously 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  This project investigates the mechanisms driving temozolomide (TMZ) resistance in adult recurrent IDH-wildtype glioblastomas, with a focus on synergistic microRNA (miRNA) networks that contribute to tumor relapse. Using a single-center paired cohort of good TMZ responders (relapse interval >1 year), we identified 13 miRNAs with highly correlated expression in the relapsed tumors. These miRNA hubs are hypothesized to act synergistically, regulating key resistance pathways such as DNA damage repair, tumor plasticity, and cell survival. Additionally, our analysis highlights their role in modulating oncogenic pathways, including Wnt and TGF-β signaling, which drive stemness, EMT, and adaptive resistance. Importantly, this study represents the largest miRNA cohort profiled to date. We are currently investigating the extent and specific perturbations of miRNA regulatory hubs in cases with short relapse intervals and poor therapy responses, aiming to identify miRNAs with prognostic and predictive value. Our established patient-derived glioblastoma stem cell models will be utilized to investigate whether these dynamic miRNA networks influence short-term and long-term therapeutic responses. By targeting these networks, we aim to sensitize glioblastoma stem cells to TMZ in vitro and in vivo, paving the way for miRNA-based therapies to overcome resistance. This work is supported by Krebsliga Bern and Stiftung Für Klinisch-Experimentelle Tumorforschung SKET (to E. Kashani).

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 We identified non-glycolytic, pro-survival functions of hexokinase HK3 in AML cells. Elevated HK3 mRNA levels are associated with myeloid oncogenes such as MLL/KMT2A rearrangements, and correlate with poor survival. Notably, high HK3 levels are linked to reduced initial responsiveness and secondary resistance to the BCL2 antagonist venetoclax. We propose that HK3 supports AML survival and dampens therapy responses through non-metabolic functions involving BCL2 family interactions and subcellular localization.

Nuclear localization of HK3 in myeloid cells and expression in macrophages of the colon

Group Tschan Although acute promyelocytic leukemia (APL) is effectively treated with all-trans retinoic acid (ATRA) and chemotherapy, other AML subtypes do not benefit from this differentiation therapy. Our data highlight the critical role of non-canonical autophagy during ATRA-therapy. We found significantly reduced expression of the non-canonical autophagy gene ATG16L2, but not the canonical ATG16L1, in APL. In line, depleting ATG16L2 attenuated differentiation. We propose that ATRA-induced APL differentiation requires selective cargo degradation via an ATG16L1-independent mechanism.

Transmission electron microscopy of NB4 APL cells upon ATRA treatment

Group Tschan We found that knocking down the oncogenic DMTF1β isoform reduces migration and invasion of prostate and breast cancer cells. Interestingly, this was accompanied by the downregulation of autophagy-related pathways and autophagic flux. Mechanistically, we identified the autophagy protein ULK1 as a novel interaction partner of DMTF1β, whereby DMTF1β promoted ULK1 protein stability. Additionally, we discovered that DMTF1β is a short-lived protein that undergoes polyubiquitination in a β-domain-specific manner, leading to proteasomal degradation.

β-specific domain DTMF1β is associated with poly-ubiquitination

Group Schenk Our research group employs cutting-edge methods to uncover key cellular mechanisms and molecular markers in atopic dermatitis (AD), aiming to identify innovative therapeutic targets and biomarkers. We study both adult and pediatric AD cohorts, focusing on interactions between innate and adaptive immunity, trained immunity, and immunoregulatory pathways. Our proteomic analyses have identified molecules modulating inflammation, revealing potential therapeutic strategies. Using advanced technologies like CITE-seq, CyTOF, imaging mass cytometry (IMC), and spatial transcriptomics, we investigate immune cell subsets and marker expression in blood and skin lesions, providing comprehensive insights into systemic and localized immune dynamics. Potential therapeutic targets are validated in murine AD models. Additionally, we explore the skin microbiome's composition and its critical role in AD, understanding its significant impact on immune responses and disease outcomes.

28-plex IMC image showing structural features, immune phenotypes, and activation markers in healthy skin (top) atopic dermatitis (bottom)

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  We conducted CRISPR/CAS interference library screens and identified SMG1, implicated in an evolutionarily conserved RNA quality control pathway - the nonsense-mediated mRNA decay (NMD) pathway. NMD leads to the degradation of transcripts containing premature stop codons, often occurring after temozolomide treatment. NMD may influence the mechanisms employed by tumour cells to repair DNA damage caused by temozolomide treatment. Hence, we hypothesise that the enhanced temozolomide response is due to reduced DNA repair capacity in SMG1-attenuated glioblastoma cells. The aim of this work is to further investigate the mechanisms leading to an enhanced temozolomide response in glioblastoma cells with attenuated SMG1. Since NMD efficiently suppresses truncated proteins, which are highly immunogenic, we hypothesise that SMG1 inhibition in temozolomide-resistant, recurrent glioblastoma may elicit tumour inflammation. Hence, we expect that NMD improves the treatment response to immune checkpoint inhibitors. This work is currently supported by the Swiss Cancer League.

Heat map analysis of recurrent glioblastoma

Group Vassella Glioblastoma is the most common and most aggressive primary malignant brain tumour in adults. 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. We identified miR-19b and its direct target PPP2R5E, a regulatory subunit of the PP2A serine phosphatase, in temozolomide response in glioblastoma. The mechanism was attributed to the induction of DNA damage via increased nuclear ROS production, ultimately leading to elevated ROS-mediated senescence and ferroptosis in cells with attenuated miR-19b/PPP2R5E expression. This project has been supported by the Swiss National Science Foundation. 

Screening for microRNAs conferring temozolomide resistance in glioblastoma cell lines

Group Zlobec, Williams The extracellular matrix (ECM, matrisome) forms part of the triad of the tumour ecosystem but is understudies in terms of its contribution to tumour biology. The Williams group utilizes spatially resolved mulit-matrisomics in 2D and 3D to deeply characterize the structural and biochemical manifestations of the matrisome and the association of this to patient outcome. We work across a variety of solid tumour types including colorectal cancer and pancreatic ductal adenocarcinoma.

Multi-modal assessment of extracellular matrix in solid tumours. Top: maximum intensity projection of collagen visualisation using 3D open top light sheet microscopy. Middle: spatial transcriptomics analysis of tumour budding. Bottom: digitial image analysis of fibrous structures from H&E

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.  By incorporating text feedback along with image predictions, vision-language models can be used to train a new model by learning from human feedback. The ultimate goal is to improve the overall performance of MetAssist, resulting in an accurate nodal screening tool to assist pathologists in their routine clinical work.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