PROTAC-driven Protein degradation by Proteasome during Antigen Processing and Presentation (ProAPP)

Project Information

ProAPP

Grant agreement ID: 101065466

DOI

10.3030/101065466

Project closed

EC signature date 8 June 2022

Start date 1 August 2022

End date 31 October 2024

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 189 687,36

Coordinated by

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Germany

Periodic Reporting for period 1 - ProAPP (PROTAC-driven Protein degradation by Proteasome during Antigen Processing and Presentation (ProAPP))

Reporting period: 2022-08-01 to 2024-10-31

Summary of the context and overall objectives of the project

PROteolysis TArgeting Chimeras (PROTACs) are a new type of drug that can target and destroy specific proteins in the body that are involved in diseases. They work by tagging unwanted proteins for destruction by the cell's waste disposal system, known as the ubiquitin-proteasome system. The waste disposal system also plays a role in the immune system. It helps create a set of peptides, which are small pieces of proteins that the immune system uses to recognize and fight infections/cancer.

However, it is still unclear what would happen when increasing the activity of the waste disposal system can have on the immune system. This could have both good and bad effects on the immune system, like improving immunity or causing autoimmune diseases, where the body attacks itself. The drugs might change the balance of peptides, which could affect the immune system. The goal of the research is to understand how these drugs impact the balance of proteins and peptides in the cell and how they might affect the immune system. The research focuses on a specific protein called KRas, which is often altered in cancer. Understanding how PROTACs affect this protein could help us learn more about their potential as cancer treatments.

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

A PROTAC targeting the KRas oncoprotein (PROTAC-KRas) was tested in KRAS-mutated lung cancer cell line models. High KRas degradation was exhibited by one lung cancer cell line and one pancreatic cancer cell line in response to the drug. The effective concentration of PROTAC-KRas that achieved significant KRas degradation while maintaining cell viability was determined. Kinetic analyses of RNA sequencing and proteomics were conducted under these optimized treatment conditions. Specific degradation of the KRas protein was confirmed over the course of treatment.

The antigen processing and presentation pathway was impacted by PROTAC-KRAS, as revealed by proteomic analyses. The susceptibility of the KRas protein to proteasome-mediated degradation was established with these purified proteasomes. The proteasomes' capacity to degrade a variety of proteins in in vitro conditions was demonstrated in collaboration.

The immunopeptidome, consisting of peptides presented on the cell surface for immune recognition, was collected by collaborators. The integration of data from transcriptome, proteome, and immunopeptidome is currently being explored to understand the impact of PROTAC-KRAS on antigen presentation.

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)

The study intends to provide a better fundamental understanding of how the cells respond to PROTAC-KRas from several aspects from which cellular pathways were affected, changes proteasome-derived peptide repertoire to the changes in immune recognition, thus, provide insights into the suitability of PROTAC-KRas application as a therapeutic approach for anti-cancer therapies.

From the transcriptomic and proteomic datasets, we observed that the PROTAC-KRas specifically drive the degradation of KRas. Besides, the degradation of KRas resulted in changes in biological pathways, for instance, the antigen processing and presentation pathway. Together with the immunopeptidome, these layers of multi-omics dataset can be used to understand both the effect of KRas as well as PROTAC.