Biomedical research relies increasingly on large collections of data sets and knowledge whose generation, representation and analysis often require large collaborative and interdisciplinary efforts. This dimension of 'big data' research calls for the development of computational tools to manage such a vast amount of data, as well as tools that can improve communication and access to information from collaborating researchers and from the wider community. Whenever research projects have a defined temporal scope, an additional issue of data management arises, namel...

BACKGROUND: The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets. Here, we present DC-ATLAS, a novel and versatile resource for the interpretation of high-throughput data generated perturbing the si...

Dep. Dermatology, University Hospital Erlangen Expected completion: January 2010 To improve the routine monitoring of tumour-specific T-cell subsets by multicolour flow cytometry, we established a protocol for the combination of multimer staining and intracellular cytokine staining. After antigenic stimulation, human cytolytic T lymphocyte (CTL) exhibit a decrease in their binding to human leukocyte antigen (HLA)-peptide tetramers, since CTLs lose the colocalization of the T cell receptor (TCR) with CD8. It has been suggested by the group of Pierre van der Brug...

Despite the immunogenic nature of malignant melanoma and the reported induction of vaccine-induced cellular immune responses, limited clinical success has been achieved so far. The maturation status of the dendritic cells (DC) plays a pivotal role in their capacity to induce tumor-eradicating T cells. Recently, we have shown that so-called ‘TriMixDC’ have an improved T cell stimulatory capacity in vitro (Bonehill et al, Mol. Ther.). These TriMixDC are immature DCs (iDC) electroporated with mRNAs encoding CD40ligand (CD40L), CD70, a constitutive active form of...

I started my Ph.D in the lab of Federica Sallusto, Ph.D at the Institute for Research in Biomedicine, Bellinzona in November 2005. During the first part of my Ph.D I was mainly focused on the development of a novel assay to examine the repertoire of human naïve CD4+ and CD8+ T cells. The second part was then devoted to the validation and application of this method. After 3 ½ years of working on that project, I plan to defend my Ph.D next spring (April 2009). During vaccinations or in the course of natural infections a small number of antigen-specific T cells e...

Early in life, thymic export establishes the size and the diversity of the human naive T-cell pool. Yet, on puberty thymic activity drastically decreases. Because the overall size of the naive T-cell pool decreases only marginally during ageing, peripheral postthymic expansion of naive T cells has been postulated to account partly for the maintenance of T-cell immunity in adults. So far, the analysis of these processes had been hampered by the inability to distinguish recent thymic emigrants from proliferated, peripheral, naive T cells. However, recently, CD31 ha...

A number of soluble factors and the interaction between dendritic cells, T cells and other cell types of the immune system determine the magnitude and quality of the individual’s response to vaccination. Knowledge about this complex interplay is especially important for experimental therapies using dendritic cells, e.g in cancer patients with a disturbed immune system due to previous therapeutic administration of anti-proliferative drugs. We have analysed different aspects of the initiation of immune responses by dendritic cells: 1.In cooperation with R. Geig...

I have been registered as a PhD student at the Karolinska Institute on the 31th of May, 2007 and expect to finish my PhD in June 2011. Project 1 - Preparation and immunomontioring of a clinical trial in patients with advanced melanoma ? collaboration with Carl Figdor Patients will receive a DC vaccination regimen (3 vaccinations at weekly intervals) followed by 3 adoptive transfers of autologous in vitro expanded T cells. This novel approach combines in vivo priming by the DC vaccine with passive immunotherapy by lymphocyte infusion. Patients will undergo surg...

Predicted finish date for my PhD: February 2010 Our projects focuses on computational methods for the reconstruction of signalling pathways and the integration of gene expression data with existing biological information. In particular we target the response of dendritic cells to pathogenic and non pathogenic yeasts on a whole genome scale. At the same time our role in DC-THERA is to collaborate with bioinformaticians and with experimentalists for the solution of genomics problems that require highly interdisciplinary skills. We are also involved in the develop...

Peripheral T cell tolerance, mediated by antigen-presenting steady state dendritic cells, is thought to significantly contribute to the prevention of autoimmunity. We set out to analyze the involvement of FoxP3+ regulatory T-cells, which are known to be important for maintenance of self-tolerance, in dendritic cell-induced peripheral tolerance of T-cells. Most autoreactive T cells are deleted in the thymus. Peripheral autoreactive T cells are controlled by peripheral tolerance, which acts through unresponsiveness/anergy, regulation/suppression and deletion. CD4+...

My PhD project relates to the Tripartite motif (TRIM) proteins, which have been shown to be involved in many cellular functions including cell differentiation, apoptosis, cytokine signalling and some have antiviral activity. I have performed a comprehensive analysis of expression of TRIM molecules in cells of the innate and adaptive immune system. The cells used for my study include macrophages, myeloid and plasmacytoid dendritic cells (DC), and a panel of CD4+T cells (naïve T cells, Th1, Th2, and CD25+T regulatory cells and IL-10 T regulatory cells). My work u...

The objective of our work was to identify genes involved in the function of mature DCs by comparing genes expressed by DC before and after maturation. Immature and mature dendritic cells were purified from spleens at ULB. The transcriptomes of both populations were analyzed and compared at the University of Milano and the data were sent back to us. Interestingly, the gene STAT4 was the most upregulated during maturation (by 30-fold). We therefore compared the antigen-presenting-cell function of DC from WT versus STAT-4 KO mice but the results did not reveal anay...

The tyrosine kinase inhibitors sorafenib and sunitinib are approved for the treatment of patients with malignant diseases. To analyze the possible use of these compounds in combination with immunotherapeutic approaches, we analyzed the effects of both inhibitors on the immunostimulatory capacity of human dendritic cells (DCs) and the induction of primary immune responses in vivo. Sorafenib, but not sunitinib, inhibits function of DCs, characterized by reduced secretion of cytokines and expression of CD1a, major histocompatibility complex, and costimulatory molecu...

I will finish my PhD probably in 2010. Abstract: Toll-like receptors (TLRs) are important receptors of the innate immune system able to respond to molecular patterns borne by microbial and viral pathogens. TLR3, TLR7 and TLR9 form a subset of TLRs that are localized intracellularly and can recognize nucleic acids to initiate antiviral immune responses. Among these TLRs, TLR7 is triggered by viral or bacterial single stranded RNA (ssRNA) and mediates responses to RNA viruses. However, self-RNA can in some instances also activate TLR7, leading to the development o...

Interferon-producing killer dendritic cells (IKDCs) have been described as possessing the lytic potential of NK cells and the antigen-presenting capacity of dendritic cells (DCs). In this study, we examine the lytic function and antigen-presenting capacity of mouse spleen IKDCs, including those found in DC preparations. IKDCs efficiently killed NK cell targets, without requiring additional activation stimuli. However, in our hands, when exposed to protein antigen or to MHC class II peptide, IKDCs induced little or no T cell proliferation relative to conventional ...

The importance of conventional dendritic cells (cDCs) in the processing and presentation of antigen is well established, but the contribution of plasmacytoid dendritic cells (pDCs) to these processes, and hence to T cell immunity, remains unclear. Here we showed that unlike cDCs, pDCs continued to synthesize major histocompatibility complex (MHC) class II molecules and the MHC class II ubiquitin ligase MARCH1 long after activation. Sustained MHC class II-peptide complex formation, ubiquitination and turnover rendered pDCs inefficient in the presentation of exogen...

Toll-like receptors exist as highly conserved pathogen sensors throughout the animal kingdom and they represent a key family of molecules bridging the ancient innate and adaptive immune systems. The first molecules of adaptive immunity appeared in the cartilaginous fishes and, with these, major histocompatibility proteins and cells expressing these molecules, and thus, by definition, the advent of antigen-presenting cells and the "professional" antigen-presenting cells, the dendritic cells. Dendritic cells themselves are highly specialized subsets of cells with t...

Poxviruses such as the causative agent of smallpox have developed multiple strategies to suppress immune responses, including the suppression of DC activation. Since poxviruses are large DNA viruses, we hypothesized that their detection by DCs may involve the endosomal DNA recognition receptor TLR9. Indeed, we have shown here that DC recognition of ectromelia virus (ECTV), the causative agent of mousepox, completely depended on TLR9. The importance of TLR9 was highlighted by the fact that mice lacking TLR9 showed drastically increased susceptibility to infection ...

The development of functionally specialized subtypes of dendritic cells (DCs) can be modeled through the culture of bone marrow with the ligand for the cytokine receptor Flt3. Such cultures produce DCs resembling spleen plasmacytoid DCs (pDCs), CD8(+) conventional DCs (cDCs) and CD8(-) cDCs. Here we isolated two sequential DC-committed precursor cells from such cultures: dividing 'pro-DCs', which gave rise to transitional 'pre-DCs' en route to differentiating into the three distinct DC subtypes (pDCs, CD8(+) cDCs and CD8(-) cDCs). We also isolated an in vivo equi...