Specific MHC-I Peptides Are Induced Using PROTACs

Abstract

Peptides presented by the class-I major histocompatibility complex (MHC-I) are important targets for immunotherapy. The identification of these peptide targets greatly facilitates the generation of T-cell-based therapeutics. Herein, we report the capability of proteolysis targeting chimera (PROTAC) compounds to induce the presentation of specific MHC class-I peptides derived from endogenous cellular proteins. Using LC-MS/MS, we identified several BET-derived MHC-I peptides induced by treatment with three BET-directed PROTAC compounds. To understand our ability to tune this process, we measured the relative rate of presentation of these peptides under varying treatment conditions using label-free mass spectrometry quantification. We found that the rate of peptide presentation reflected the rate of protein degradation, indicating a direct relationship between PROTAC treatment and peptide presentation. We additionally analyzed the effect of PROTAC treatment on the entire immunopeptidome and found many new peptides that were displayed in a PROTAC-specific fashion: we determined that these identifications map to the BET pathway, as well as, potential off-target or unique-to-PROTAC pathways. This work represents the first evidence of the use of PROTAC compounds to induce the presentation of MHC-I peptides from endogenous cellular proteins, highlighting the capability of PROTAC compounds for the discovery and generation of new targets for immunotherapy.

Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition

“…IFN-γ-induced pMHC alterations are distinct from palbociclib. Previous work has demonstrated that CDK4/6 inhibition stimulates IFN signaling, augmenting antigen presentation levels 15 . We also observed upregulation of IFN-γ response genes with low-dose palbociclib treatment, as well as increased expression of genes relating to antigen presentation (Figs.…”

“…Traditional data-dependent acquisition (DDA) methods to profile pMHC repertoires using mass spectrometry (MS) are well documented [10][11][12] , but quantitative methods have critical limitations. Specifically, most common relative quantification pMHC methods lack a normalization strategy to account for variations in sample input and processing [13][14][15][16][17][18] . Peptide losses during processing vary across peptide sequences, concentrations, and samples, underscoring the need for normalization 19,20 .…”

Could PROTACs Protect Us From COVID-19?

“…This suggests that PROTAC-mediated ubiquitination of the viral protein could stimulate the presentation of viral peptides to MHC-I and favor the development of host T-cell therapeutic activity against the viral protein. In fact, this capability has already been reported for PORTACs [4] . These findings mechanistically imply that by leveraging the ubiquitin proteasome system, antiviral PROTACs have the potential of achieving a dual function: 1) degradation of the viral target protein ( Fig.…”

“…The ternary complex forms when the PROTAC engages both intended targets, the POI and E3 ligase. This binding activity brings the two proteins together and engages them with PROTAC-mediated protein-protein-interactions [4] . For the ternary complex to be productive, the protein interface must have the following structural requirements or features: 1) minimization of PPIs that cause steric hinderance or electrostatic clashes along the newly formed protein interface 5 , 6 ; 2) maximization of PPIs that promote structural complementarity at the new protein interface 5 , 6 ; and 3) recruitment of the adequate E3 ligase in a proper binding orientation that facilitates target POI ubiquitination [7] .…”

Significance of Selective Protein Degradation in the Development of Novel Targeted Drugs and Its Implications in Cancer Therapy

“…However, a recent study identified the “side effects” of PROTAC in degrading target proteins, such as the emergence of class I major histocompatibility complex peptides during PROTAC‐mediated BET degradation. [ 153 ] In addition, acquired resistance to PROTACs was confirmed in different cells, limiting the clinical application of PROTAC. [ 154 ]…”