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17 Nov 2021

Peak peptides: paving the way for investigating new cancer immunotherapies.

Peak Peptides

The field of targeted cancer immunotherapy is exciting and offers promise for greatly improving treatments for many cancers. One highly promising tool is T cell bispecific antibodies (TCB), which recognise oncogene antigens (Ags) presented on the MHC-1 molecules on the surface of cancer cells, and cell surface markers from T cells. These bi-specific antibodies, therefore, bring the T cells and cancer cells into close proximity, resulting in cancer cell destruction. However, this method is limited to the availability of Ags with high tumour specificity and sufficient epitope density on cancer cell surfaces.

For this reason, the groups of Andrea Romagnani and Yvonne Nagel from Roche in Basel, Switzerland, aimed to increase the abundance of Ag peptides from oncoproteins on cell surface MHC-I receptors in tumour cell lines in their recent publication. The teams used proteolysis-targeting chimaeras (PROTACs), also known as degraders, which are hetero-bi-functional molecules consisting of an E3 ligase-binding ligand connected via a linker to a ligand specific to the target protein. Therefore degraders hijack endogenous E3 ligase bringing it into close proximity with the target protein resulting in proteasome degradation of the target protein. An increase in Ags of the target protein is then available for trafficking to the cell surface for MHC presentation.

The researchers targeted the breakdown of the Bromo- and Extra-Terminal (BET) protein BRD4, which plays important roles in transcriptional regulation, epigenetics, and cancer. They identified five novel MHC-I binding peptide antigens from BRD4. To use a proteomics approach overseen by senior principal scientist Axel Ducret also at Roche, the team enlisted the help of CRB and ordered our highly purified custom PEAKTM Peptides. Our PEAKTM Peptides are isotopically labelled with the customer’s chosen residue and are analysed for net peptide content as standard, allowing for precise peptide quantification. The team ordered PEAKTM Peptides of the two most abundant MHC-I binding peptides identified, QEFGADVRL (QEFGADV-[U-13C6,15N4-Arg]-L-acid) and AEALEKLFL (AEALE-[U-13C6,15N2-Lys]-LFL-acid), which allowed them to determine the relative peptide abundance from the ratio of light (unlabelled, experimental sample) to over heavy (isotopically labelled standard) signal using MHC I-associated peptide proteomics (MAPPs) a technique which utilises powerful mass spectrometry.

Using this method, the researchers demonstrated that PROTACs targeting bromo- and extraterminal domain proteins increase the abundance of target-derived peptide Ags on MHC I in both liquid and solid tumours. With the help of CRB, they demonstrated that targeted protein degradation is a promising strategy in immuno-oncology to enhance an immune response against specific Ags and that this can be combined with a TCB in a cancer immunotherapy setting.

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Massafra et al., (2021). Proteolysis-Targeting Chimeras Enhance T Cell Bispecific Antibody-Driven T Cell Activation and Effector Function through Increased MHC Class I Antigen Presentation in Cancer Cells. J Immunol. PMID: 34215653

Zengerle et al., (2015). Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4. ACS Chemical Biology. 10(8): 1770-7. PMID: 26035625