Research

ESR 1: Fatemeh Asgari

The role of TIR8 and PTX3 in sepsis induced immunosuppression

Objectives: PTX3 is a key component of the humoral innate immunity identified by ICH, induced by cytokines and microbes at sites of infection by stromal and immune cells. TIR8/SIGIRR is a member of the IL-1R like receptor family acting intracellularly to inhibit IL-1R like receptors and TLR signalling, cloned by ICH and associated with infections and inflammation.

At Humanitas Research Institute, we will evaluate the involvement of TIR8 and PTX3 in the pathogenesis of sepsis, taking advantage of gene-targeted mice generated by ICH. Available models include murine sepsis associated with infections caused by diverse microbes, e.g. Pseudomonas aeruginosa, Streptococcus pneumoniae, Aspergillus fumigatus, Klebsiella pnaumoniae, and Staphylococcus aureus, and tolerance models. These models will be used to compare the susceptibility and the inflammatory response of immunocompetent, PTX3- and TIR8-deficient mice, and to address the mechanisms underlying defective resistance to infections and exacerbated inflammation or immunosuppression. Recombinant PTX3 will be used to perform treatment. Moreover, we have two separate domains of the molecule and mutants to investigate their interaction with microbial components and address the functional parts of PTX3. TIR8 activating and inhibitory antibodies are under development and will be used to modulate the functional activity of TIR8, through in vitro and in vivo studies.

Host: Instituto Clinico Humanitas, Milan, Italy

Supervisor: Prof. A. Mantovani, MD, PhD; Prof. Cecilia Garlanda, DVM, PhD (cecilia.garlanda@humanitasresearch.it)

ESR3: Berke Gürkan

The role of IRAK-M in sepsis induced immunosuppression

 Objectives: IRAK-M has emerged as a key player in sepsis induced immunosuppression. ESR2 will (1) Obtain insight into the distribution and regulation of IRAK-M expression in vivo, (2) Determine the binding sites involved in the interactions of IRAK-M with IRAK-1 and IRAK-4, (3) Determine the impact of IRAK-M deficiency in sepsis and (4) Determine the effect of IRAK-M inhibition in sepsis. IRAK-M gene-targeted mice are available at the AMC. Murine models of sepsis of infectious origin will be used. The approach will include the study of the role of IRAK-M in the following aspects: inflammatory response to the pathogen; the interplay of both molecules with cellular receptors; the prophylactic and therapeutic potential of IRAK-M in murine models of sepsis (B. pseudomallei, S. pneumoniae, E. coli). The project will generate insight in the role of IRAK-M in different infection models and thus identify potential pathologies that may benefit from treatment with IRAK-M inhibitors. A plural competence in cellular and molecular biology is  highly desirable for this position.

Host: Academic Medical Center, University of Amsterdam (AMC, UvA), Center for Experimental and Molecular Medicine (CEMM).

Supervisors: Dr. Kees van ‘t Veer, Dr. Joost Wiersinga

ESR5: Elena Karakike

Development of microRNAs as biomarkers in sepsis

Objectives: The aim of this project is to link the microRNAome with distinct septic transcription patterns characteristic of sepsis immunosuppression. More precisely, at a first stage analysis will run in samples available from the large biobank of the Hellenic Sepsis Study Group. Analysis will run to well-characterize which microRNAs can be used as indicators of the anti-inflammatory nature of the host taking into consideration the specific patient phenotype. Then a prospective study will run at a second stage with two aims: a) to validate the findings of the first stage particularly as related to specific phenotypes; and b) daily collection of samples trying to identify how the change of the kinetics of circulating microRNAs is related with final outcome in specific sepsis phenotypes and how it can develop to improve decision making.

Host: National and Kapodistrian University of Athens, 4^th Department of Internal Medicine

Supervisor: Evangelos J. Giamarellos-Bourboulis, MD, PhD

ESR 7: Charlotte Théroude

Functional studies of MDSC in sepsis

Objectives: To evaluate the biological functions of myeloid-derived suppressor cells (MDSC) subpopulations cell-sorted based either on established immunophenotyping or using markers identified in collaboration with ESR6. Analyses will be performed using MDSC, from healthy donors and sepsis patients, stimulated or not with microbial products or pathogens acting through various classes of pattern recognition receptors. All parameters will be compared to biological and clinical parameters, the occurrence of nosocomial infections and the outcome of septic patients.

 Host: Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland

Supervisor: PD-Dr Thierry Roger; Prof Thierry Calandra

ESR 9: Miranda Melis

Evaluation of theranostic biomarkers in sepsis.

 Objectives: The failure of multiple immunomodulatory trials in sepsis is arguably due to a one-size-fits-all strategy. A personalized approach, whereby the right patient can be targeted to receive the drug at optimal dose and dosing period, offers a far better chance of success. The lab has developed reproducible and sophisticated long-term rat models of peritonitis with advanced monitoring that allow early prognostication by a variety of physiological or biological tests. Modulation of the abnormal poor-prognosis signature through targeted intervention by a number of putative agents modulating immune response, adrenergic stress, or metabolism may result in improved outcomes. ESR 9 will test such approaches and, on identification of suitable candidates, assist in developing point-of-care test panels using various platforms. The ESR will learn in vivo physiological techniques, including advanced instrumentation, echocardiography, indirect calorimetry and tissue perfusion monitoring, and a variety of standard (ELISA, Western, FACS) and advanced (such as nanotechnology, microdialysis) ex vivo techniques.

Host: University College London, UK

Supervisor: Prof. Mervyn Singer

ESR11: Chloe Albert

New immune functional assay coupled with transcriptomic analysis for the characterization of the altered immune status observed in septic patients

Define a new immune functional assay (IFA) coupled with transcriptomic analysis to characterize the altered immune status observed in septic patients

The project consist of the development and optimization of an immune functional assay (IFA), in order to characterize the altered immune status observed in septic patients. Septic patients develop an early dominant hyper-inflammatory response followed by a partially overlapping immuno-suppressive phase. The hyper-inflammatory phase can lead to early death by organ dysfunction, resolved toward homeostasis or either enter a long-lasting immunosuppressive state. To drive therapeutic decisions, an IFA should be designed to deliver results in very short time and with limited sample handling. To meet these clinical constraints, such assay will be performed as follows i) use of whole blood to avoid the time-consuming isolation of a specific cell population, ii) stimulation with a yet to be determine stimuli within a 4 hour incubation time and iii) transcriptomic read-outs obtained with rapid and sensitive methods such as quantitative Polymerase Chain Reaction and RNA Sequencing.

First of all, a selection of stimuli will be performed based on immuno-modulatory properties, well-chemically defined characteristics and accessibility to the compound. Then a drug screening will be set up using several ex vivo models mimicking altered state of immunity, to choose the stimuli with the most discriminant immune-modulatory characteristics.
In a second step, RNA sequencing technique and/or alternative molecular techniques will be optimized and transcriptomic markers will be selected to define a confident immune response. The relevant read out able to discriminate fold-changes in the transcriptomic profile as well as differentially expressed markers, will be combined into a multiplexed PCR based assay compatible with clinical settings. The combination of stimuli and related read out will defined the IFA prototype.
In a third part, basic research will be performed to understand the mechanism of action of the compounds. This will be looked at the cellular level, i.e. which cell populations take part in the observed response to the drug, and at the molecular level, i.e. which receptors and associated pathways are involved in drug response.
Last, this prototype will be validated by assessing its ability to stratify septic patients compare to classical methods and that would allow to adapt a suitable treatment to each patient.

Host: bioMerieux, Medical Diagnostic Discovery Department, Marcy l’Etoile (Lyon) France.

Supervisors: François Mallet; Sophie Assant

ESR13: Harjeet Singh

Whole blood molecular assays to quantitate sepsis induced immunosuppression

Objectives: Molecular signatures derived from blood leukocytes provide more information about the nature and severity of the inflammatory response and the magnitude of organ injury than traditional single protein or gene biomarkers.  These signatures can be used for identifying patients at risk of dying and/or sepsis complications, thereby allowing individualised preventive or therapeutic interventions. The main objective of ESR13’s project is to identify molecular signatures within blood leukocytes that are able: (1) to quantitate sepsis induced immunosuppression, (2) to identify patients at high risk of developing sepsis and (3) to stratify the individual patient with respect to risk of dying. Work will include an -omnics approach: DNA methylation patterns, epigenetic signatures and metabolomics. Our previously identified whole blood leukocyte gene expression patterns of survivors and non-survivors of septic shock will be incorporated in a custom array and subsequently in a PCR based bedside assay will be tested in independent sepsis patient cohorts. Tentative projects include validating previous findings obtained from our adults sepsis cohorts in pediatric sepsis and in tropical sepsis (e.g. in patients with melioidosis). Affinity with clinical work and competence in molecular biology as well as computational biology is desirable for this position.

Host: Academic Medical Center, University of Amsterdam (AMC, UvA), Center for Experimental and Molecular Medicine (CEMM).

Supervisors: Dr. Brendon Scicluna, Prof. Tom van der Poll,  Dr. Joost Wiersinga

ESR 15: CHristos Oikonomou

Analytics to identify biomarkers for sepsis diagnosis or treatment

Objectives: This work will focus on the exploration of sepsis data, such as from the MARS study, to identify factors which seem to be more diagnostic of the onset of sepsis or benefits of treatment. This will involve the study, implementation, and application of a variety of data analytics tools which do statistical factor identification. Other more novel machine learning tools will also be explored for their usefulness in the sepsis context. The project will include a theoretical and empirical assessment with computer experiment of the comparative benefits of several analytics methods for their appropriateness for their use with data related to sepsis diagnosis and treatment.

Host: INSEAD, Fontainebleau, France

Supervisor: Prof. Stephen Chick, PhD