Current group members
I obtained my Master in Biology at the University of Geneva, working in the laboratory of Prof. Katharina Strub on Alu sequences and RNA-protein interactions, in the Cell Biology Department. I then wanted to focus on host-pathogen interactions, since I have always been fascinated by bacteria and how the host cell fights the infection. I therefore joined the lab of Thierry Soldati for my PhD in 2013, as part of the “International PhD Program in Basic and Applied Molecular Life Sciences”.
Understanding the role of vacuolins and their possible partners in the biogenesis of the Mycobacterium niche, and RNA-seq as a high throughput tool to monitor the transcriptional response during infection
Vacuolins are closely related to the mammalian flotillin/reggie proteins, which were shown to be involved in diverse mechanisms, such as the translocation of Glut4 transporters to the plasma membrane and more recently in E-cadherin and TfR recycling. Reggies/flotillins were also shown to interact with Rab11 and SNX4, known to be involved in recycling. In the lab, I am investigating the role of vacuolins and their possible partners in Dictyostelium, in the specific context of an infection with Mycobacterium marinum, a close cousin of the human pathogen Mycobacterium tuberculosis. Using my experience with RNA, I am also working in setting up an RNA-sequencing-based method to monitor the transcriptional response of both the host and the pathogen during an infection. We will then use this method to characterize the putative modes of action of different compounds identified by the drug screening and that have an effect during the infection, by comparing the transcriptional profiles.
I read Biology at the University of Geneva where, after being awarded an Excellence Master Fellowship grant, I performed a MSc
with option Genetics, Development and Evolution in the Department of Molecular Biology. There, as a member of David Shore’s Laboratory, using the budding yeast as a model system, I studied the nucleosome dynamics in growth-related gene promoter regions. In 2016, immediately after earning the MSc, I joined the group of Thierry Soldati engaging in a PhD research project with the aim to further the insights on the early effectors involved in Dictyostelium discoideum (Dicty) cell-autonomous defense response against pathogenic bacteria.
I am interested in Dicty’s early response factors involved in pathogen detection and stress signal transduction. Presently, I am gearing up to address Dicty factors involved in pathogen detection and stress signal transduction. For this, I will start by identification of the sub-cellular location of candidate factors through the GFP-tagging approach and live confocal microscopy. In a complementary study, employing a proximity-dependent biotinylation technique, ubiquitin-ligase complexes co-localizing with bacteria containing vacuoles, will be used as a “Trojan horse” in order to spot neighboring upstream and downstream acting factors. In addition, I will analyse on a genome-wide scale RNA-seq-generated expression patterns of various Dicty strains, in different conditions, shortly after the onset of infection with different pathogen strains. The goal would be to develop models in which the addition, the removal or the interaction of various host and pathogen factors would allow to predict in silico the outcomes of infections holding complex, not intuitive mechanisms.
I pursued a M.Sc. in clinical microbiology during which my major research focus was the identification of virulence genes and characterization of antibiotic resistance in H. pylori. The major focus of my thesis and my first postdoctoral studies was to characterize bacterial pathogenesis in Brucella. I did a second postdoctoral study at the EMBL were my research focused on the molecular and biochemical characterization of a post-translational modification in M. tuberculosis.
Characterization of anti-microbial target pathways in Mycobacterium using NGS techniques
I joined the Soldati group in November 2016, and I am interested in the characterization of anti-infective drugs against mycobacteria using high throughput NGS techniques. Dual RNA-sequencing is used to decipher a signature of the global state of the host-pathogen system. Specifically, our aim is to obtain full transcriptional profiles of Dictyostelium interacting with M. marinum and with anti-infective compounds. Once the putative mode of action identified, we will validate the major pathways of drug interference with infection by using a palette of standard biological assays.
I graduated from the University of Grenoble, France, with a Biology Master in Immunology, Microbiology and Infectious Disease. I did my internship at the Institute of Structural Biology with Dr Pascal Fender, and we focused on adenoviruses and their interaction with the Desmoglein 2 Receptor. I then wanted to go toward host-pathogen interactions in order to gain a better understanding of how the host cell can fight the infection. I therefore joined the group of Thierry Soldati for my PhD in September 2017, as part of the "International PhD Program in Life Sciences".
Single-cell dynamics of host-pathogen interactions
In the lab, we study the host and pathogen factors involved in mycobacterial infection by using the macrophage surrogate D. discoideum as a host. Intrinsic cellular defences play an important role during infection, and I am particularly interested by their roles in the establishment of the replication niche, its breakdown and the restriction of cytosolic bacteria. Furthermore, to get a deeper understanding of the mechanisms of mycobacterial infection, we need to characterize the infection process at the single cell level. This is why I am also studying the dynamics of the host-pathogen relation using a microfluidics system allowing the capture and observation of infected cell and a long-term integration and quantification of infection parameters.
I obtained my BSc and MSc at the University of Konstanz (DE). I worked at the Human and Environmental Toxicology group of Prof. Daniel Dietrich, where I focused on microcystins, a family of potent liver toxins produced by cyanobacteria and a potential threat to many water supply systems. Throughout my master’s studies I also worked in the Neurobiology lab of Dr. Einat Couzin-Fuchs and the MPI for Ornithology on active sensing in cockroaches, which propelled my enthusiasm for computer-aided workflows.
(1) Genome-wide characterisation of novel anti-tuberculosis compounds and study of their mode of action
(2) Image-based analysis of collective streaming behaviour in Dictyostelium
For my PhD, I wanted to bring together my two major scientific interests. I joined the group of Prof. Soldati to (1) discover novel active compounds against mycobacteria infections by using the amoeba D. discoideum as a 3R host model, and (2) to study the collective behaviour of D. discoideum during its developmental cycle. For the latter, I will collaborate with the group of Prof. Giovanna Di Marzo Serugendo (UNIGE), who is interested in bioinspired and autonomous algorithms.
After working on an acido-resistance system in Brucella microti and on the diversity of marine amoeba and their association with bacteria, I started an MSc in Microorganism-Host and Environment Interaction. During my first year, I completed an internship at the IRIM-CNRS, in Montpellier (FR), where I studied the role of phosphoinositides in the infection by the pathogenic intracellular bacterium Coxiella burnetii. Thus, I developed a strong interest for bacterial infection and their intracellular development. To continue in this field, I joined the group of Thierry Soldati to work on Mycobacterium marinum infection.
To study M. marinum infection the lab uses the social amoeba Dictyostelium discoideum as a model. Using this infection model, the role of vacuolins (homologues of the mammalian flotillins) was investigated and it was found that these host proteins are important for the infectious cycle of the bacteria. Along this line, the aim of my Master project is to compare the process of M. marinum infection in D. discoideum and BV-2 murine microglial cells. First, I will aim at confirming the role of flotillins in the infection of BV-2 cells and, in a second part, I will characterise the maturation of the Mycobacterium-Containing Vacuole in BV-2 cells compared to the MCV in Dictyostelium.
My interest in scientific research emerged during the period of my degree in Molecular and Cellular Biotechnology at University of L’Aquila (Italy). I started an internship for my Master’s degree project at Telethon Institute of Genetics and Medicine in Pozzuoli (Naples), in the lab of Prof. Maria Antonietta De Matteis, where I worked on a research project focused on the biogenesis of cellular stress granules with Sodium Arsenite as cellular stress inducer, analyzing the response of the secretory pathway COPII and the The TRAnsport Protein Particle (TRAPP), implicated in many human diseases. I joined the group of Prof. Soldati for my PhD because the use of D. discoideum as model host organism has a wide range of applications, many fundamental signal transduction pathways are shared with mammals and it’s an excellent platform to study membrane organization status, intracellular trafficking and signalling outcomes.
The role of the D. discoideum discoidins during M. marinum infection
Galectins are a family of 15 mammalian lectins with affinity for β-galactoside sugars that share a characteristic carbohydrate recognition domain and functions in signaling and endocytosis. Some galectins recognize the surface of various pathogens and have been proposed to have a direct antibacterial effect. In D. discoideum only discoidins share molecular and biological characteristics with galectins and they recognize self and non-self-glycoconjugates. There are two discoidin proteins, DscI and DscII, which share 48% sequence identity. DscI comprises three isoforms (DscA, DscC and DscD), whereas DscII has only one isoform (DscE). Discoidins are localized to the vicinity of pathogenic mycobacteria and required the induction of damage in the MCV membrane, which suggested a role during infection. For my PhD I would like to deepen further the Host response to vacuolar escape and better dissect the role of discoidins in the autophagic pathway.
Krikor Bared Eblighatian
I started my MSc studies in chemical biology after obtaining a BSc in biochemistry at the University of Geneva. Having background both in chemistry and biochemistry, I was interested in working on an interdisciplinary master project that involves both fields. During my bachelor studies, I had the opportunity to do a summer internship in the Soldati lab to study membrane repair mechanisms in Dictyostelium discoideum upon sterile damage and during Mycobacterium marinum infection.
Using and optimizing Flipper probes to label the MCV in D. discoideum and to measure membrane tension upon hyperosmotic shock, upon sterile damage and during M. marinum infection.
Fluorescent membrane tension reporter (Flipper-TR) is a novel planarizable push-pull probe which has mechanosensitive properties that allow the live imaging of membrane tension with fluorescent lifetime imaging microscopy (FLIM). It has been developed by Prof. Matile’s lab and already been used in other labs to demonstrate the dependence of certain biological functions on membrane tension in mammalian cells. Furthermore, different organelle-specific Flipper probes have already been developed. The aim of my project is to find the best Flipper probe to label Mycobacterium Containing Vacuole (MCV) in D. discoideum. Optimizing the existing options by synthetizing probes with modified headgroups for better targeting to MCV will be a part of the project. Successfully labeling the MCV at different stages of M. marinum infection with Flipper probe will allow the study of membrane damage and repair mechanisms as well as investigating if membrane tension has a role in activating ESCRT and autophagy machineries. A part of the project will be carried out in Prof. Matile’s lab.
I obtained a PhD in the host-pathogen interactions field from the University Lyon 1 in France. My PhD works discovered one of the targets of the LegK2 protein kinase, a Legionella pneumophila effector secreted in the host cell during infection. I then joined the Agaisse Lab in Charlottesville (USA) for a post-doctorate on the characterization of Shigella flexneri dissemination mechanisms. One of my projects explored the host side, studying the role of the mammalian protein WIPF2, whereas my other project focused on a Shigella effector. To continue to increase my knowledge in the host-pathogen field, I joined the Soldati group in March 2020 for a new post-doctoral study.
Mechanistic aspect of host membrane repair during mycobacterial infection
My project focuses on the membrane damage/repair step occurring during mycobacterial infection. During MCV establishment, the vacuole undergoes several damage events and repair of damage is a crucial step for a successful infection. The team previously showed that the autophagy and the ESCRT system are two pathways involved in this mechanism but the interplay between them is not yet understood. My aim is to elucidate the interplay between autophagy and ESCRT upon MCV damage, as well as to identify the bacterial components generating damage. The signaling cascade triggered by these events will also be explored.