Introduction
The adaptive immune system provides a specialized and formidable defense system
against infected and transformed cells through the ability of immune cells to recognize
and respond to specific antigens, which are often presented as peptides on the surface
of host cells. Major histocompatibility complex (MHC) molecules, and the peptides they
present, are pivotal to orchestrating this detection system. 1 MHC molecules are divided
into two main classes: class I and class II. 2 While both classes are critical for immune
function, MHC class I (MHC-I) molecules are the primary vehicle in presenting peptides
to cytotoxic T cells.3
MHC-I molecules are expressed on the surface of nearly all nucleated cells and present
a diverse array of peptides derived from protease digestion of intracellular proteins.4 Once
displayed on the surface of the host cells, this peptide-MHC complex (pMHC) engages
with cytotoxic T cells, a subset of T lymphocytes specialized in identifying and eliminating
peptides that are not recognized as “self”. 5 This designation of self vs non-self is
paramount to the proper function of the adaptive immune system. The circulating T cell
repertoire is shaped by a negative selection process in the thymus, where T cell receptors
(TCRs) that bind self-peptides are eliminated from future propagation. 6 As a result, the
remaining T cells in circulation can potentially recognize peptides that were absent from
the negative selection process.7
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Traditionally, non-self peptides are derived from pathogens (e.g., bacteria, fungi, and
viruses) or transformed cells from genetic lesions that yield new protein sequences.
However, non-self-peptides can be more broadly defined as any peptide sequence that
has an altered chemical composition relative to endogenous expression. 8 Even a single
amino acid alteration can drastically affect the TCR recognition of a peptide, potentially
altering the activity of the immune response. 9 Therefore, understanding the impact of
amino acid modifications on MHC-I-presented peptides is necessary for elucidating how
the immune system responds to infections, cancers, and in autoimmunity.
It was recently revealed that most PTMs can escape negative selection due to their low
abundance throughout the lifetime of the thymus, suggesting that PTM modified peptides
may play a role in immune-related diseases. 12 PTMs, such as phosphorylation,
glycosylation, and ubiquitination, can alter the structure and function of proteins, including
those that are later processed into peptides for presentation. 13 One of the ways these
modifications can affect the immune response is by altering peptide binding affinity to
MHC-I or its recognition by TCRs. 14 Recently, we systematically assessed the impact of
enzymatic PTMs by synthesizing modified peptides and assessing their MHC-I binding
and T cell recognition relative to unmodified counterparts and found that they can play a
significant role in altering these interactions.15
A less appreciated form of PTMs arises from non-enzymatic chemical entities. While
some of these modifications are native and regulated (e.g., certain forms of cysteine
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oxidation which occur during oxidative bursts), many non-enzymatic alterations are poorly
controlled and, therefore, can generate a pool of non-self peptides. 18 Notably, whereas
enzymatic PTMs are often reversible through specific “eraser” enzymes, non-enzymatic
PTMs have not been reported to be natively reversed. 19 In most cases, non-enzymatic
PTMs result from electrophilic chemical species reacting with nucleophilic amino acids
(e.g., cysteine, arginine, lysine, histidine, tyrosine, and, to a lesser extent, aspartic acid
and glutamic acid). The sources of these electrophiles are diverse, with well-
characterized examples naturally formed in healthy cells including reactive oxygen
species (ROS), reactive nitrogen species (RNS), oxidative byproducts of glycolysis, and
non-native short-chain fatty acids that are activated to acetyl-co-enzyme A adducts. 20
The consequences of amino acid modifications on peptide presentation are multifaceted.
First, they can affect the stability of the peptide-MHC (pMHC) complex. The binding
affinity between a peptide and MHC-I is a critical determinant of whether a peptide will be
effectively presented to T cells. Amino acid modifications can either enhance or disrupt
this binding, thereby influencing the stability of the complex and the likelihood of T cell
recognition.22, 23 Second, these modifications can directly impact the interaction between
the presented peptide and the TCRs of cytotoxic T cells. Because TCRs are finely tuned
to recognize specific pMHC combinations, any alteration in the peptide sequence due to
amino acid modifications can potentially disrupt recognition and compromise immune
response against the infected or transformed cell. 24 Furthermore, the presence of
modified peptides can lead to the activation of autoimmune responses, where the immune
system mistakenly targets healthy, self-cells. 25 Collectively, these non-enzymatic
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modifications generate a chemically distinct pool of peptides that can escape negative
selection, potentially altering immune recognition. In particular, these modified peptides
may inadvertently trigger autoimmune pathologies, causing the immune system to target
healthy cells.21
To investigate the role non-enzymatic PTMs play in antigen presentation through MHC-I,
we determined the effects of non-enzymatic PTMs on the pMHC-I complex stability and
T cell recognition. We also explored the effects that non-enzymatic PTMs have on
peptides presented in the context of cancer cells. Finally, we developed a novel
enrichment strategy to identify MHC-I associated peptides bearing non-enzymatic
modifications to improve detection of chemically modified peptides presented on MHC-I
molecules.
Results
indicate that non-enzymatic PTMs can induce significant changes in the binding
affinity of ovaWT to H-2Kb.
Next, we evaluated how non-enzymatic PTMs affect T cell recognition of their target
ligand. RMA-S cells were incubated with 5 M peptide and co-cultured with B3Z T cells,
which express a TCR specific for ovaWT presented by H-2K b and contain a -
galactosidase reporter gene under the control of an IL-2 inducible promoter. Upon
recognition of its cognate ligand, B3Z activation induces -galactosidase expression,
which can be quantified on a plate reader via the enzymatic conversion of chlorophenol
red -D galactopyranoside (CPRG) to chlorophenol red.38
As previously mentioned, position 7 of ovaWT is a solvent-exposed residue that plays a
key role in TCR interactions. Despite its minimal effects on H-2K b affinity, modifications
at position 7 (ovaK7formyl, ovaK7aad, ovaK7hcit, and ovaK7lac) eliminated T cell activation
(Figure 1D ). This likely reflects the loss of the lysine side chain’s positive charge, as
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previous studies have shown that charge alterations at TCR-contact residues can
eliminate TCR recognition. 15, 39 Similarly, both asparagine modifications ( ovaN4D and
ovaN4Diso) abolished T cell activation, further supporting the critical role of charge and
side-chain chemistry in TCR engagement (Figure 1D).
Interestingly, the sulfonic acid-modified variant ovaE6CSO3 restored T cell activation
relative to the inactive ovaE6C (Figure 1D). We attribute this response to the negatively
charged sulfonic acid moiety mimicking the native glutamate residue. This finding
suggests that certain non-enzymatic PTMs can functionally resemble canonical amino
acids, potentially contributing to T cell cross-reactivity. Overall, these results demonstrate
that non-enzymatic PTMs can influence both pMHC stability and T cell recognition,
highlighting their potential to modulate antigen presentation and immune responses.
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Figure 2. (A) Chemical structure of the unmodified and modified cancer-associated
peptides. Dose-response analysis of the RMA-S stabilization assay for methionine
oxidation (B), asparagine deamidation (C), or cysteinylation (D). RMA-S cells were
incubated with the indicated concentration of peptide and analyzed via flow cytometry
for H-2Kb expression.
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Non-Enzymatic PTMs on Cancer-Associated Peptides Influence MHC-I Binding
Affinity
To examine the role of non-enzymatic PTMs in the presentation of cancer-associated
peptides, we sought to synthesize modified peptides previously identified as being
displayed on cancer cells. Kacen et al. developed a mass spectrometry-based platform
that helped identify that non-enzymatic modifications constituted the majority of modified
MHC-I-associated peptides and play a role in altering the cancer immunopeptidome. 22
The primary non-enzymatic modifications identified in their study included oxidation,
deamidation, and cysteinylation. However, mass spectrometry alone cannot fully
resolve the functional impact of these modifications on pMHC binding. To address this,
we synthesized both unmodified and modified variants of peptides reported to be
presented in cancer cells.22
We aimed to observe how modifications at various positions in the peptide may
influence peptide binding to H-2Kb by using the RMA-S stabilization assay. Accordingly,
we synthesized peptides bearing the aforementioned modifications at multiple positions
along the peptide chain (Figure 2A). For cancer-associated peptides 1 (KGMNYTVRL,
ca1) and cancer-associated peptide 2 (SAPENAVRM, ca2), methionine oxidation at
positions 3 or 9, respectively, disrupted display on H-2Kb (Figure 2B). Increasing the
degree of methionine oxidation from ca1oxide to ca1oxone also demonstrated a greater
decrease in display on RMA-S cells. Additionally, deamidation at position 2 of ca3
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(INFDFPKL) to make ca3isoasp caused a >100-fold decrease in peptide display on RMA-
S cells, further suggesting that backbone modifications may have a substantial negative
impact on H-2Kb affinity (Figure 2C). In contrast, cysteinylation at positions 1 of ca4
(CGYEFTSKL) to make ca4cystine or position 7 of ca5 (VAYEYLCHL) to make ca5cystine
resulted in minimal changes to pMHC-I affinity (Figure 2D). These results are also
consistent with prior reports showing that cysteinylated peptides can be presented as
immunodominant forms in viral infections and as HY antigens.40,41 Overall, these results
demonstrate that non-enzymatic PTMs can modulate MHC-I display in endogenously
presented peptides, and it potentially represent an immune evasion mechanisms by
reducing the display of potentially immunogenic epitopes on the surface of cancer cells.
Identification of Peptide Acylation Sites Displayed on MHC-I
We next aimed to develop a chemical enrichment strategy to identify non-enzymatically
modified peptides presented on MHC-I molecules. Identifying modified peptides remains
a considerable analytical challenge due to their typically low stoichiometric abundance
within complex cellular environments, the structural diversity and unpredictability of
PTMs, the complex fragmentation patterns, and the modification-induced effects on the
ionization efficiency.42 43 44 To overcome these limitations, we reasoned that a targeted
pull-down approach would allow for selective enrichment and identification of modified
species.
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To achieve selective capture of a specific non-enzymatic PTM, we utilized a thioester-
based alkyne chemical probe ( 1) developed by the Meier group, which was previously
shown to label sites of non-enzymatic acylation. 45 Probe 1 reacts covalently with
nucleophilic residues at sites of non-enzymatic acylation and contains an alkyne handle
to enable bioorthogonal conjugation and enrichment ( Figure 3A ). We postulated that
labeling with 1 would allow specific tagging and isolation of modified peptides.
First, we confirmed cellular incorporation of 1 by treating MDA-MB-231 cells with
increasing concentrations of 1. Cells were subsequently reacted with FAM-N 3 through a
copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction and analyzed by flow
cytometry, revealing a concentration-dependent increase in fluorescence and confirming
successful probe labeling ( Figure 3B). Consistent with these results, fluorescent SDS-
PAGE analysis of lysates from cells treated with 1 demonstrated robust incorporation of
1 into protein targets (Figure 3C).
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Figure 3 (A) Schematic representation of labeling sites of non-enzymatic modifications
by probe 1. (B) Flow cytometry analysis of MDA-MB-231 cells treated with the indicated
concentration of 1 followed by a reaction FAM-N3 in the presence of CuSO4, ascorbic
acid, and THPTA. (C) In-gel fluorescence analysis of 1-treated MDA-MB-231 cells after
labeling with FAM-N3 in the presence of CuSO4, ascorbic acid, and THPTA and
resolved by SDS-PAGE (D) Schematic of the chemical enrichment workflow using 1.
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Peptides from the immunopeptidome of 1-treated cells were reacted with DADPS-biotin
azide and enriched on streptavidin beads prior to LC-MS/MS analysis. Representative
LC-MS/MS spectra of modified peptides RKSPRPAGP (E) and EKNKQNKTKL (F).
Detected b+ ion fragments are shown in blue, and y+ ion fragments are shown in pink.
After validating efficient cellular and proteomic labeling, we applied this approach to
isolate modified MHC-I peptides (Figure 3D). Approximately 2 x 108 MDA-MB-231 cells
were treated with 1 for 6 h, followed by isolation of MHC-I-associated peptides by
immunoaffinity purification. 46,47 The enriched peptide fractions were conjugated to an
acid-cleavable dialkoxydiphenylsilane (DADPS)-biotin azide linker via CuAAC reaction,
enabling selective capture of probe-modified peptides on streptavidin-functionalized
beads. Bound peptides were then released under acidic conditions and identified by LC-
MS/MS.
Using this workflow, we identified two MHC-I associated peptides bearing the modification
introduced by 1 (Figure 3E-F). Notably, both peptides originated from nuclear proteins
implicated in DNA damage and repair, suggesting that nuclear repair enzymes may be
particularly susceptible to non-enzymatic acylation or more abundantly displayed on
MHC-I. These results also demonstrate the feasibility of chemically tagging proteins with
a bioorthogonal handle to enrich modified peptide targets from the immunopeptidome.
More broadly, this approach establishes a chemical proteomics framework for the direct
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identification of non-enzymatically modified peptides presented by MHC-I, which may play
underappreciated roles in immune surveillance and tumor immunogenicity.
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