Proteomics to characterize inflammasome activation
The discovery of the inflammasome protein complex in 2002 was a breakthrough in our understanding how the immune system triggers inflammation. We use cutting-edge proteomics techniques to characterize how the inflammasomes are regulated, and what are its molecular targets.
The inflammasomes are protein complexes of the innate immune system that induce inflammation in response to microbial infection and endogenous danger signals. Inflammasomes have a key role in the antimicrobial defense and in the development and pathology of atherosclerosis, diabetes, and neurodegenerative diseases. It is expected that treatments specifically targeting inflammasomes will have a major effect on human health in coming years.
Non-canonical caspase-4 inflammasome is the most recently identified inflammasome structure. It is activated by intracellular bacterial lipopolysaccharide (LPS). The signalling cascades regulating non-canonical inflammasome activity are still poorly understood. Further, the molecular targets of inflammasomes contributing to different diseases are not well known.
Extracellular vesicle (EV)-mediated release of proteins has an extremely important role in intercellular communication, both locally and systematically. Our recent results show that the non-canonical caspase-4 inflammasome also activates a robust vesicle-mediated protein secretion in human macrophages and endothelial cells. However, the intracellular molecular pathways that activate EV secretion in response to caspase-4 activation remain to be characterized.
We want to have a global view on the molecular events involved in the caspase-4 inflammasome regulation, and combine modern high-resolution mass spectrometry (MS)-based proteomics with functional experiments in our studies. Proteins are the key signaling molecules, and only through characterizing the proteome (including protein levels, modifications and interactions) in time and space we can start to understand in detail how the non-canonical inflammasome is regulated. MS-based proteomics has developed immensely during the last decade. Never before has it been possible to characterize globally and dynamically the inflammatory response in such a detail than what modern MS-based proteomics methods allow.
The project will address two major, unsolved questions in human immune response:
- what are the molecular mechanisms regulating non-canonical inflammasome activation?
- how is vesicle-mediated protein secretion linked to non-canonical inflammasome activation?
We will do in-depth proteomic characterization of cells and secreted EVs upon non-canonical inflammasome activation using mass spectrometry-based proteomics. This includes quantitative analysis of the proteome composition as well as analysis of proteins’ post-translational modifications. The obtained proteomics data will be analyzed with bioinformatics and based on these results we will design functional studies.
Studentens work plan
Cell culture (human macrophages and/or endothelial cells), cell stimulations, EV isolation
Proteome and phosphoproteome analysis of cellular samples and EVs together with personnel in the Proteomics Unit
Bioinformatic analysis of the proteomics data
Participate in writing a scientific article based on proteomics and bioinformatics data
About the Research environment
The research will be done in Department of Immunology under the supervision of Dr Tuula Nyman.
Dr Nyman is the project manager for National network of Advanced Proteomics Infrastructure and Head of Proteomics Unit in OUS/UiO Faculty of Medicine. We have excellent facilities and opportunities for most modern proteomics analysis.
The research team for the proposed project is highly multidisciplinary and participating groups have expertise on innate immunity, cardiovascular diseases, extracellular vesicles, proteomics, and bioinformatics and-statistics. Bringing groups with complementary areas of expertise together will ensure that all the necessary expertise is available to carry out the project successfully.