Investigating inflammatory signaling by combining phospho- and ubiquitin proteomics with CRISPR/Cas9 technology

Project Information

Cytokineproteomics

Grant agreement ID: 746329

DOI

10.3030/746329

Project closed

EC signature date 22 February 2017

Start date 1 March 2017

End date 28 February 2019

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 159 460,80

EU contribution

€ 159 460,80

Coordinated by

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Germany

Periodic Reporting for period 1 - Cytokineproteomics (Investigating inflammatory signaling by combining phospho- and ubiquitin proteomics with CRISPR/Cas9 technology)

Reporting period: 2017-03-01 to 2019-02-28

Summary of the context and overall objectives of the project

Cytokines are implicated in many disease settings. Successful therapeutic targeting of cytokine signalling is challenging: whereas targeting one cytokine in most inflammatory diseases is not sufficient to prevent inflammation, this can already be enough to induce many side effects due to multifunctional roles of cytokines. There is an urgent need to better understand the regulation of cytokine signaling to design more efficient anti-inflammatory therapies. This can only be achieved by investigating the signalling interplay of multiple cytokines, which has been poorly studied due to its complexity.

Signal transduction of cytokine signalling pathways occur through posttranslational modifications (PTMs) of signalling components. To investigate signaling crosstalk it is important to capture and analyse those PTMs in an unbiased, system-based manner. Mass spectrometry-based proteomics has matured remarkably in the last years and now provides a comprehensive discovery tool to address diverse biological questions. To analyse signaling events we enrich for posttranslational modification, which are subsequently analysed in a highly quantitative fashion. Thereby we aim to identify crucial signaling events for cytokine signaling in isolation and in context of other cytokines. These findings will give more insights into cytokine signaling and might provide more suitable drug targets. Targeting downstream signaling events instead of inhibiting cytokine pathways upstream (e.g. TNF inhibition) could be a potential approach to reduce treatment toxicity.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The tumor necrosis factor (TNF) and interferon gamma (IFNγ) are pleiotropic, pro-inflammatory cytokines predominantly produced by the same cell types, which are T-cells and macrophages. To obtain a global view on phosphorylation events regulated upon TNF and IFNγ stimulation compared to single treatments we enriched for phosphopeptides. While TNF induced several hundreds of significant changes in phosphorylation events compared to the unstimulated control, IFNγ had a minor effect. Co-stimulation showed small differences to TNF single stimulation. We, however, identified phosphorylations on two major IFNγ signalling components, which are regulated by TNF only and could present a potential mode of regulation of IFNγ signaling by TNF.

We conducted further analyses of the TNF phosphoproteome in myeoloid cells and investigated its kinetics, from very early time points of one minute to one hour of stimulation. Thereby we required the generation of a deep library acquired by DDA, which allowed identification of DIA acquired MS2 spectra. We detected up to 20,000 phosphopeptides per sample and identified a range of phosphorylations on E3 ligases, kinases and transcription factor that are significantly regulated by TNF in a time dependent manner. Several of these candidates are critical for TNF signaling or have been implicated in other innate immune signaling pathways.
Also RIPK3, a kinase essential for TNF-induced necroptosis has been found regulated in response to TNF. We investigated the impact of RIPK3 on the phosphoproteome upon TNF stimulation and induction of TNF-induced apoptosis and necroptosis. Therefore we firstly generated U937 cells deficient for RIPK3 using the CRISPR/Cas9 system. These cells were stimulated accordingly and phosphopeptides were enriched. The analysis revealed RIPK3 dependent phosphorylations of several proteins.

We also analysed the phosphoproteome of myeloid cells undergoing TNF-induced apoptosis and necroptosis for 15 minutes and 3 hours. At the early 15 min time point was no significant difference between the phosphoproteomes of TNF and TNF-induced apoptosis and necroptosis. After 3 hours of stimulation TNF-induced apoptosis induced phosphorylation on many proteins involved in the DNA damage response as a result of caspase activity at this later time point. This was not detected in TNF-induced necroptosis when caspases are inhibited. Consistently, we detected upregulation of phosphorylations in apoptosis compared to necroptosis and control on three sites of the caspase inhibitor XIAP, a key player in TNF signalling.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

With this study we aim to gain novel insights into cytokine signaling. Our goal is to uncover intracellular crosstalks between different pro-inflammatory and anti-inflammatory cytokines that are simultaneously expressed during pathological conditions and act on the same cell types. This should help to uncover novel regulators or regulatory signaling events that are potential therapeutic targets to correct compromised signalling. These candidates can be screened for small molecule inhibitors/activators, which would be economically superior to expensive antibody therapies (e.g. anti TNF blocking antibodies) that are up to now the most effective treatments used against inflammatory disease. Antibody therapies frequently cause side effects by targeting major cytokines directly and thereby blocking their activity completely. Targeting downstream components might still retain normal cytokine activity while counteracting pathological signalling.

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