Research projects

Biopsy-based prediction and prognosis in inflammatory bowel disease

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.I n 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.

Investigation of the local immune system regulation in COVID-19

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 

Glycolipid-sensing by Natural Killer T cells

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. 

Molecular mechanisms of lipid-induced inflammation

Group Freigang Cardiovascular diseases, particularly atherosclerosis-related diseases, remain the leading cause of death worldwide. While first clinical trials demonstrated the beneficial effects of anti-inflammatory therapies in CVD patients, a better understanding of the molecular mechanisms of vascular inflammation will be critical to develop more effective treatment strategies. Recent advances in the field of immunometabolism generated strong interest in delineating metabolic pathways that influence macrophage responses in atherosclerosis. In this project, we study mechanisms of IL-1–driven vascular inflammation that are linked to metabolic perturbation and mitochondrial dysfunction.

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

Immune regulation by oxidized lipids

Group Freigang Exposure of cellular membranes to reactive oxygen species creates a broad range of distinct oxidized phospholipid (OxPL) species that may actively modulate cellular signaling processes and immune responses. We have previously described cyclo-pentenone-containing OxPLs and their isoprostanes as pro-resolving lipid mediators. This project investigates the OxPL-signaling in myeloid cells during atherogenesis and microbial infection using functionalized lipid probes and a novel oxidative stress reporter.



Cyclopentenone-containing oxidized phospholipids inhibit the production of the pro-inflammatory cytokine IL-6 by macrophages

Functional changes in local T cells during onset vs. remission vs. relapse of colitis

Group Müller Understanding the mechanisms that drive remission and relapsing of intestinal inflammation is a prerequisite for treating patients with inflammatory bowel diseases. We have recently established a reversible, relapsing-remitting mouse model of colitis with reproducible onset of intestinal inflammation, induction of remission and repeated flares of inflammation (Brasseit et al., Mucosal Immunol 2016). In this model we monitor the composition of the intestinal microbiota during relapsing – remitting colitis and define its consequences on the metabolic profile in the feces and the host. Furthermore, we investigate how these changes influence the host immune response and vice versa. An ultimate goal is to identify strategies to specifically extend the remission period, or even prevent a further relapse of disease.

In the healthy intestine, luminal bacteria are separated by a mucus layer (green) from the epithelium (blue), containing mucus-secreting goblet cells (green) and the lamina propria, containing numerous immune cells

Functional plasticity and retention of tissue-resident TRM cells in the intestinal mucosa

Group Müller Understanding the functions and the regulation of intestinal T cell subsets is one of our long-standing research objectives. Some of these T cells in the intestine represent the prototypical example of tissue-resident T cells due to their resident location at a barrier site, and their limited capacity to recirculate. Currently, we investigate the regulation of intestinal resident T cells in the protective immunity against pathogens (e.g. infection with Listeria monocytogenes), but also their contribution to the development of chronic inflammatory disorders. In particular, we investigate the molecular mechanisms that regulate their tissue-resident phenotype, and assess how distinct functional activities of this T cell subset may either result in protective immunity, or inflammatory pathologies.

Intestinal tissue resident T cells show a unique molecular signature which is distinct from the core transcriptome in their circulating counterparts

TREM-1 as an amplifier of inflammation in immunosurveillance and immunopathologies

Group Müller TREM-1 (Triggering Receptor Expressed on Myeloid Cells-1) is an activating innate immune receptor on neutrophils and monocytes/macrophages. We previously described a critical pathogenic role for TREM-1 not only in acute, but also in chronic inflammation, notably, in inflammatory bowel diseases (Schenk et al., J Immunol 2005, J Clin Invest 2007). We generated a Trem1-/- mouse (Weber et al. PLoS Pathog 2014) to determine the Trem1 mediated effects in the pathogenesis of atherosclerosis (Zysset et al., Nat Comms 2016) and on the development of colitis-associated colorectal carcinoma (Saurer and Zysset et al., Sci Rep 2017). Current research interests include the involvement of TREM-1 in neurological disorders, such as stroke (Liu et al., Nat Immunol 2019), neurodegenerative disorders, and in infections with intracellular pathogens such as Listeria monocytogenes.

TREM-1-activation on monocytes leads to an enhanced lipid uptake (red droplets) when cultured in the presence of dyslipidemic serum from ApoE-/- mice, maintained on a high fat/high cholesterol diet


Role of cytokine signaling for immunopathology and tumor development

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). 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

mRNA splicing and epithelial integrity

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)

Cross-talk between innate and adaptive immunity

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 that is responsible for memory. In this project, we use different murine models to better understand how innate immune cells modulate adaptive immune responses in dependence on the inflammatory environment, in infectious (e.g. after infection with a pathogen; Cardoso Alves, EMBO Reports, 2020) or sterile (e.g. for tumor surveillance) situations.


TRAIL programs NK cells by blocking the production of inflammatory messengers (IFNγ) but promoting the formation of cell toxins (GZMB). NK cells lacking TRAIL produce more IFNγ but less GZMB, which results in greater antivirus CD8+ T cell response in infected mice

Influence of neoadjuvant therapy on the immune profile of esophageal adenocarcinomas

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

Highly multiplex, spatially resolved immunophenotyping of PDAC for biomarker discovery

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)

Tumor budding in gastrointestinal neoplasms

Group Lugli The main aim of the GIPAR 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.  

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

Clinical, pathological and molecular characterization of adult medulloblastomas for targeted therapy: a multicenter cohort study including primary and relapse cases

Group Vassella Medulloblastomas are the most common aggressive brain tumours of childhood, molecularly defined by different groups and subtypes. Though medulloblastoma is a rare disease, it has been also described in post-pubertal and adult patients. However, due to lack of studies exclusively on adult medulloblastomas, the therapeutic approach of these patients mostly relies on pre-existing data from studies focused on medulloblastomas of the paediatric population. On these grounds, and considering that adult patients do not present a satisfying clinical outcome post-therapy, we aim to investigate 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 the development of a molecular risk-adjusted targeted therapy.   

Overview of the molecular subgroups and subtypes of pediatric medulloblastoma (Cavalli FMG, et al. Intertumoral Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. Jun 12 2017)

Epigenetic changes in PanNETs

Group Perren Almost, half of Pancreatic Neuro-endocrine Tumors (PanNETs) shows mutation in MEN1, DAXX or ATRX. All the three genes encode for proteins which are involved in epigenetic regulation. Based on DNA methylation we identified subgroups of PanNETs with: specific cell of origin, genetic background and clinical outcome. Notably, we demonstrated that MEN1/DAXX/ATRX mutated tumors originated from alpha pancreatic cells and that they have an increased risk of relapse.
We focus on understanding the epigenetic changes along PanNET progression and their impact of pathways activation.


Top: Phyloepigenetic analysis of PanNET human samples and normal alpha and beta-cell samples.  Bottom: Progression model hypothesis based on epigenetic and genetic evolution

Precision medicine approach for PanNET treatment

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 PanNET patients which resemble features of original tumor tissue and which can be used for in vitro drug screenings. We are currently assessing the utility of PanNET tumoroids to predict patient therapy response and to identify novel epigenetic treatment options. Also, we aim at identifying specific molecular profiles through DNA sequencing, methylation- and gene expression analysis to predict therapy response in vitro and on the patients.


Patient-derived Tumoroids from PanNET patients are utilized for in vitro pharmacotyping and molecular profiling

Metabolic changes in PanNET

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. 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 of tumor development by modern mass spectrometry, fluorescence microscopy and RNAseq data will delineate these metabolic and test novel therapeutic strategies.      


Tissue mass spectrometry (top) identified five metabolic PanNET. Fluorescence microscopy measured mitochondrial activity (middle) and lipid storage (bottom) in PanNET cells

Unravel the functions of autophagy in breast cancer motility

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 breast cancer subtypes or 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

PU.1 and alternative splicing

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 RNA 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

Reducing FASN expression facilitates AML differentiation

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)

Generation of potent cross-presenting Dendritic Cells (DC) for tumor immunotherapy

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

Dendritic cells and their co-stimulatory properties for cytotoxic T cells in melanoma

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.

Molecular characterization of recurrent glioblastoma

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

Role of serine-threonine phosphatases in temozolomide resistance of 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

Tumor Budding in Colorectal Cancer

Group Zlobec Tumor buds are linked to aggressive tumor behaviour and poor prognosis. One of our objectives is to standardize the assessment and reporting of tumor budding in routine diagnostics. This was the main incentive for our group to initiate and organize the first International Tumor Budding Consensus Conference (ITBCC) which took place in 2016. The proceedings of the ITBCC were published in the journal ‘Modern Pathology’ in 2017 and have since been integrated in reporting protocols of major societies such as the College of American Pathologists. One of our ongoing projects is to validate the ITBCC recommendations on large colorectal cancer cohorts, also in collaboration with the International Budding Consortium (IBC). Other aspects of our research are focused on further characterization of tumor buds in primary colorectal cancer and colorectal liver metastases within the tumor microenvironment. Our ultimate goal is to find targets that can be used against tumor buds in a therapeutic setting.

Tumor buds in colorectal cancer (H&E staining, 40x)

The epigentic landscape of CDX2

Group Zlobec Up to 20% of colorectal cancers have decreased expression or complete loss of CDX2 protein. CDX2 loss is associated with microsatellite instability, high-level CpG island methylation and BRAF mutation, features consistent with the serrated pathway. Our functional studies show that hypermethylation of the CDX2 promoter is a major reason for this loss and can be recovered with DNMTi treatment. Together with the group of Prof. M. Tschan, we investigate genetic and epigenetic modifications of CDX2 using CRISPR/Cas9 technology.


A) Positive expression of CDX2 protein in colorectal cancer. B) Loss of CDX2 has a significant negative impact on patient outcome (Kaplan-Meier curve, log-rank test)

Digital pathology and machine learning

Group Zlobec Our group uses digital pathology and machine learning to investigate clinically relevant scenarios in colorectal cancer and the tumor budding/microenvironment using histopathological images and ngTMAⓇ. We apply deep learning to identify genotype-phenotype correlations (post-doc work by Dr. HG. Nguyen) and develop algorithms for future validation and use in diagnostic routine (PhD project A. Khan). Together with the lab of Prof. J.-P- Thiran (EPFL), we develop computational methods for prognosis classification (PhD project C. Abbet) and with Prof. A. Fischer (UniFribourg/HESO) apply graph-representations and geometric deep learning to understand the tumor microenvironment (PhD project L. Studer). Our numerous Master students in Bioinformatics (MSc) and Medicine  (MMed) work on interdisciplinary projects, all on the basis of histological images.


Example of p53 in an endometrial cancer within an ngTMA experiment