Transcriptomic analysis across liver diseases reveals disease-modulating activation of constitutive androstane receptor in cholestasis

Background & Aims: Liver diseases are caused by many factors, such as genetics, nutrition, and viruses. Therefore, it is important to delineate transcriptomic changes that occur in various liver diseases. Methods: We performed high-throughput sequencing of mouse livers with diverse types of injuries, including cholestasis, diet-induced steatosis, and partial hepatectomy. Comparative analysis of liver transcriptome from mice and human samples of viral infections (HBV and HCV), alcoholic hepatitis (AH), non-alcoholic steatohepatitis (NASH), and biliary atresia revealed distinct and overlapping gene profiles associated with liver diseases. We hypothesised that discrete molecular signatures could be utilised to assess therapeutic outcomes. We focused on cholestasis to test and validate the hypothesis using pharmacological approaches. Results: Here, we report significant overlap in the expression of inflammatory and proliferation-related genes across liver diseases. However, cholestatic livers were unique and displayed robust induction of genes involved in drug metabolism. Consistently, we found that constitutive androstane receptor (CAR) activation is crucial for the induction of the drug metabolic gene programme in cholestasis. When challenged, cholestatic mice were protected against zoxazolamine-induced paralysis and acetaminophen-induced hepatotoxicity. These protective effects were diminished upon inhibition of CAR activity. Further, drug metabolic genes were also induced in the livers from a subset of biliary atresia patients, but not in HBV and HCV infections, AH, or NASH. We also found a higher expression of CYP2B6, a CAR target, in the livers of biliary atresia patients, underscoring the clinical importance of our findings. Conclusions: Comparative transcriptome analysis of different liver disorders revealed specific induction of phase I and II metabolic genes in cholestasis. Our results demonstrate that CAR activation may lead to variations in drug metabolism and clinical outcomes in biliary atresia. (C) 2020 The Author(s). Published by Elsevier B.V. on behalf of European Association for the Study of the Liver (EASL).

Protein engineering approaches for direct antigen targeting in CD8+ T cell inducing vaccines

Vasiliki Panagiotou

Effective vaccine design and public vaccination programs have led to the eradication of several diseases and protected millions of people from deadly infections. However, intracellular infections remain a challenge and their eradication requires the activation of cytolytic mechanisms. CD8+ T cells promote effector mechanisms for infected cell killing subsequent to their priming by antigen-presenting cells. Their activation occurs upon detection of intracellular antigen in a pathway that many current subunit vaccine technologies are trying to approach by cross-presentation. Advances in CD8+ T cell-inducing subunit vaccines include direct targeting of antigens to cross-presenting cells and are studied in this thesis. Antigen delivery to the appropriate cell type for cross-presentation to CD8+ T cells can occur with fusion antibodies. Our laboratory has previously demonstrated that antigens bearing an erythrocyte-binding antibody domain (TER119) target the liver. We used this technology to fuse TER119 and ovalbumin (OVA) antigen with the BBOX domain of the high mobility group box 1 (HMGB1) danger signal and co-administer it with CpG-B adjuvant in a hepatic vaccine context. In liver vaccines, activation of local cytotoxic responses represents an important challenge. Erythrocyte-mediated OVA delivery with adjuvants resulted in cytotoxic CD8+ T lymphocyte (CTL) activation with memory formation in the liver and protection was provided after infection with Listeria monocytogenes. Another method for antigen targeting is through a cross-presenting dendritic cell (DC) subset, called CD8+ DCs. Recent studies in mice showed successful vaccination against OVA fused to XCL1 ligand, which binds CD8+ DCs. To attract CD8+ DCs to the site of injection for increased antigen uptake, we co-injected XCL1-OVA with a fusion protein consisting of XCL1 and the extracellular matrix (ECM) binding domain of placenta growth factor-2 (PlGF-2123-144), called XCL1-PlGF. XCL1-PlGF binds extracellular matrix at the injection site and attracts CD8+ DCs locally. In the context of prophylactic and therapeutic vaccination, the combination of two fusion proteins (XCL1-OVA and XCL1-PlGF) enhanced cytotoxicity and prolonged survival against B16-OVA melanoma. Finally, antigen transport via biomaterial delivery platforms was evaluated as an alternative method to deliver antigens to immunologically relevant sites. Our laboratory and others have shown that nanoscale carriers promote CTL responses in vaccination. Here we present a cationic micelle vaccination platform in which OVA and adjuvant (CpG-B and/or MPLA) loading is mediated by non-covalent molecular encapsulation and adsorption. Following a prime and double boost vaccination, CTL responses were raised in the spleen and lymph nodes of vaccinated mice, along with antigen-specific antibody production. These findings highlight the advantages of the micelle carrier platform in vaccine applications. Overall, this thesis presents novel techniques to target antigens to the appropriate cell compartments, facilitating CTL activation in vaccination either by direct targeting of antigen fused to antibodies and chemokines, or antigen delivery with polymeric vehicles. These platforms for optimized delivery seek to improve current approaches and impact the design of new strategies in CD8+ T cell inductive vaccination.

EPFL2016

The role and transcriptional regulation of FAM46A in adipocyte differentiation

Ann-Kristin Hov

Obesity is currently a leading global health concern. Treatments include undergoing a weight-loss regimen. However, successful weight-loss is variable, where the heritability of obesity is considered part of the cause. This patient variability to weight-loss was addressed by Carayol et al. (2017), where protein plasma level changes was associated to genetic variability and changes in BMI under a low-calorie diet intervention. A highly significant association region was found to regulate downstream gene FAM46A; coding for a nucleotidyl-transferase protein. Loss of function mutations in FAM46A have previously been discovered in multiple human diseases, such as osteogenesis imperfecta. However, there is a lack of understanding of FAM46Aâs function, especially in the context of adipose tissue and metabolism. This thesis aimed to follow up on the Carayol et al. study by investigating the transcriptional regulation of FAM46A and how the associated region is influencing this regulation, as well as how FAM46A is involved in adipose tissue function. When mapping the physical DNA interaction network around the associated region using chromosome conformation capture (3C) in human subcutaneous adipocytes (SGBS cells), no interactions between the FAM46A promoter and selected loci of the associated region were found. Interestingly, significant interaction peaks downstream of the promoter overlapped with regions of open chromatin and were enriched for transcription factor (TF) motifs that are involved in stem cell differentiation and TGFÎ² signalling. SMAD4, part of the TGFÎ² signalling pathway, binds to this region, indicating a potential regulator of FAM46A. To address FAM46Aâs potential role in adipocyte function, FAM46A expression was disrupted in vitro in differentiating adipocytes. Reduction of FAM46A expression in SGBS cells resulted in decreased expression of PPARG and CEBPA, the master regulators of adipogenesis, complemented by a reduction in lipid accumulation. Follow up studies in murine mesenchymal stem cells where Fam46a was over-expressed were controversial as this led to a decrease in adipogenic markers (Adipoq and PPARðŸ). Overall, disruption of FAM46A expression led to opposing changes in adipogenic potential, suggesting the requirement for a more stable cell system to study FAM46A in vitro. To further characterise the role of Fam46a, metabolic phenotyping of a Fam46a knockout (KO) mouse model under hyper-caloric stress was performed in collaboration with the IMG in Prague. This model revealed a significantly smaller mouse, and increased plasma alkaline phosphatase, as previously observed. When fed a high-fat diet, KO mice had reduced overall fat mass, improved glucose clearance and reduced adipocyte size in both subcutaneous and visceral white adipose tissue (subWAT/visWAT) depots. Transcriptomic analysis of these two depots revealed an up-regulation of genes expressed in ribosome related pathways in the subWAT, whereas the visWAT showed the up-regulation of fatty acid metabolism pathways, suggesting that the KO adipose tissue is more metabolically active. Other down-regulated pathways involved stem cell differentiation and BMP/TGFÎ²-signalling. In conclusion, this study found the possible regulation of the FAM46A promoter by TFs involved in adipogenesis regulation, such as SMAD proteins, as well as strengthening its possible functional involvement in TGFÎ² signalling by enrichment of this pathway in KO studies.

EPFL2021

The role and transcriptional regulation of FAM46A in adipocyte differentiation

Ann-Kristin Hov

EPFL2021

Protein engineering approaches for direct antigen targeting in CD8+ T cell inducing vaccines

Vasiliki Panagiotou

EPFL2016