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Chemoproteomic strategies have revolutionized proteome annotation by targeting nucleophilic and redox-active side chains. However, the primary amides of asparagine (Asn) and glutamine (Gln) have long lacked robust chemical tools for proteome-wide interrogation. We report a chemoselective palladium-mediated dehydration that converts Asn/Gln amides to nitriles under mild aqueous conditions. This transformation enables the first proteome-wide mapping of chemically addressable Asn/Gln sites in lysates and living cells. Leveraging this reactivity, we establish an inverse chemoproteomic framework in which reduced nitrile formation reports PTM-mediated protection of Asn/Gln sites, including those impacted by deamidation and N-glycosylation. This approach reveals sites masked by post-translational modifications (PTMs), specifically those associated with deamidation and N-glycosylation. In yeast, this framework expanded the known N-glycoproteome, identifying numerous candidates missed by traditional glycopeptide enrichment due to low abundance or noncanonical motifs. Furthermore, comparative profiling in Candida albicans captured the dynamic remodeling of glycosylation patterns during morphogenesis. This dehydration-to-nitrile platform establishes a scalable handle on the amide proteome to map residue accessibility and PTM-linked site dynamics across biological states.

Myocardial ischemia-reperfusion (MIR) injury drives adverse remodeling and heart failure after ST-elevation myocardial infarction (STEMI), yet no therapy directly targets the fibrotic response. Here, we developed a good manufacturing practice-compatible extracellular vesicle (EV)-enriched secretome from bone marrow mesenchymal stromal cells and identified a laminin-521-based production strategy suitable for clinical translation. The EV-enriched secretome exhibited in vitro immunomodulatory activity, and in murine MIR-injury models, treatment preserved left ventricular ejection fraction, reduced platelet-derived growth factor receptor beta (PDGFR beta)-associated myofibroblast activation quantified by positron emission tomography (PET) imaging, attenuated fibrosis, and promoted reparative macrophage polarization. In a clinically relevant porcine ischemia-reperfus ion model, intracoronary administration was cardioprotective. We further developed a clinically approved PDGFR beta-targeted PET-imaging platform for longitudinal assessment of fibrotic activity in STEMI patients, where preliminary observations suggest that myofibroblast activation persists for up to 2 months after STEMI in selected patients. Together, these findings establish a translational therapeutic-diagnostic framework for individualized management of MIR injury.

Recent developments in mass spectrometry-based proteomics have established it as a robust tool for system-wide analyses essential for pathophysiological research. While post-mortem samples are a critical source for these studies, our understanding of how body decomposition influences the proteome remains limited. Here, we have revisited published data and conducted a clinically relevant time-course experiment in mice, revealing organ-specific proteome regulation after death, with only a fraction of these changes linked to protein autolysis. The liver and spleen exhibit significant proteomic alterations within hours post-mortem, whereas the heart displays only modest changes. Additionally, subcellular compartmentalization leads to an unexpected surge in proteome alterations at the earliest post-mortem interval (PMI). Additionally, we have conducted a comprehensive analysis of semi-tryptic peptides, revealing distinct consensus motifs for different organs, indicating organ-specific post-mortem protease activity. In conclusion, our findings emphasize the critical importance of considering PMI effects when designing proteomics studies, as these effects may significantly overshadow the impacts of diseases. Preferably, the samples should be taken in the operation room, especially for studies including subcellular compartmentalization or trans-organ comparison. In single-organ studies, the planning should involve careful control of PMI.

Understanding protein interactions in the presence of biological metabolites is critical for unraveling biological processes and advancing therapeutic interventions. This study focuses on alpha,beta-unsaturated carbonyls, particularly acrolein-derived protein modifications, unveiling a one-pot, four-step, selective chemistry that results in the formation of a heterocyclic alpha,beta-unsaturated carbonyl, termed 3-formyl-3,4-dehydropiperidino (FDP), exclusively on lysine residues. Remarkably, this chemistry transforms lysine, a nucleophile, into an electrophilic warhead. We demonstrate its versatility in late-stage peptide diversification, precision protein engineering, and homogeneous protein labeling with diverse payloads. Additionally, FDP-lysine smoothly transforms into another heterocycle, 3-methylpyridinium (3-MP) lysine via deoxygenation and aromatization in reagentless conditions. This transformation facilitates late-stage peptide functionalization and homogeneous engineering of proteins, with MP-lysine acting as a mass booster. Leveraging this chemistry, we discovered hyperreactive sites responsible for acrolein-induced modification through chemoproteomic profiling of FDP- and MP-modified proteins. Our findings revealed changes in protein-protein interactions mediated by FDP-modified proteins and uncovered similar to 1548 novel cross-linking partners of an FDP-modified protein.

Single-cell proteomics (SCPs) has advanced significantly, yet it remains largely unidimensional, focusing primarily on protein abundances. In this study, we employed a pulsed stable isotope labeling by amino acids in cell culture (pSILAC) approach to simultaneously analyze protein abundance and turnover in single cells (SC-pSILAC). Using a state-of-the-art SCP workflow, we demonstrated that two SILAC labels are detectable from similar to 4,000 proteins in single HeLa cells recapitulating known biology. We performed a large-scale time-series SC-pSILAC analysis of undirected differentiation of human induced pluripotent stem cells (iPSCs) encompassing 6 sampling times over 2 months and analyzed >1,000 cells. Protein turnover dynamics highlighted differentiation-specific co-regulation of protein complexes with core histone turnover, discriminating dividing and non-dividing cells. Lastly, correlating cell diameter with the abundance of individual proteins showed that histones and some cell-cycle proteins do not scale with cell size. The SC-pSILAC method provides a multidimensional view of protein dynamics in single-cell biology.

A major challenge in the field of mechanobiology relates to the lack of methods that enable the identification of mechanically active receptors, associated proteins, and the individual cells that display enhanced force generation. For example, potent T cell activation requires the transmission of biophysical forces between the T cell receptor (TCR) and its peptide-loaded major histocompatibility (pMHC) complex antigens. Interestingly, TCR-antigen interactions are highly dynamic, displaying a broad range of force magnitudes between different cells and even within the same cell. Therefore, methods that can chemically tag mechanically active T cells, TCRs, and their associated proteomes, or mechanomes are highly desirable. Such techniques may enable a deeper understanding of the mechanisms governing immune responses and may also have broad applications in immunotherapy. Herein, we report a technique dubbed mechano-ID, which allows for mechanically selective proximity tagging by leveraging DNA-based molecular force probes that recruit proximity tagging enzymes. We demonstrate mechano-ID tagging of T cells using microscopy and flow cytometry, with further confirmation by proteomics and Western blotting of mechanically active T cell receptors.

Chronic infections and cancer cause T cell dysfunction known as exhaustion. This cell state is caused by persistent antigen exposure, suboptimal co-stimulation and a plethora of hostile factors that dampen protective immunity and limit the efficacy of immunotherapies^1,2,3,4. The mechanisms that underlie T cell exhaustion remain poorly understood. Here we analyse the proteome of CD8⁺ exhausted T (T_ex) cells across multiple states of exhaustion in the context of both chronic viral infections and cancer. We show that there is a non-stochastic pathway-specific discordance between mRNA and protein dynamics between T effector (T_eff) and T_ex cells. We identify a distinct proteotoxic stress response (PSR) in T_ex cells, which we term T_ex-PSR. Contrary to canonical stress responses that induce a reduction in protein synthesis^5,6, T_ex-PSR involves an increase in global translation activity and an upregulation of specialized chaperone proteins. T_ex-PSR is further characterized by the accumulation of protein aggregates and stress granules and an increase in autophagy-dominant protein catabolism. We establish that disruption of proteostasis alone can convert T_eff cells to T_ex cells, and we link T_ex-PSR mechanistically to persistent AKT signalling. Finally, disruption of T_ex-PSR-associated chaperones in CD8⁺ T cells improves cancer immunotherapy in preclinical models. Moreover, a high T_ex-PSR in T cells from patients with cancer confers poor responses to clinical immunotherapy. Collectively, our findings indicate that T_ex-PSR is a hallmark and a mechanistic driver of T cell exhaustion, which raises the possibility of targeting proteostasis pathways as an approach for cancer immunotherapy.

SARS-CoV-2 encodes numerous virulence factors, yet their precise mechanisms of action remain unknown. We provide evidence that the SARS-CoV-2 nonstructural protein 15 (nsp15) enhances viral virulence by suppressing the production of viral double-stranded (dsRNA), a potent inducer of antiviral signaling. The viral variants lacking nsp15 endoribonuclease activity elicited higher innate immune responses and exhibited reduced replication in human stem cell-derived lung alveolar type II epithelial cells, as well as in the lungs of infected hamsters. Consistently, these variants caused significantly less weight loss and mortality compared to wild-type (WT) virus in K18-hACE2 mice. Mechanistically, the cells infected with nsp15 mutants accumulated more viral dsRNA, causing enhanced stimulation of the interferon pathway. Chemical inhibition of interferon signaling dampened immune responses to nsp15 mutants and restored their replication to levels similar to the WT virus. These findings indicate that the endoribonuclease activity of nsp15 contributes to viral virulence by limiting the accumulation of viral dsRNA, thereby allowing robust replication with reduced activation of the host innate immune response.

Methionine plays a critical role in various biological and cell regulatory processes, making its chemoproteomic profiling indispensable for exploring its functions and potential in protein therapeutics. Building on the principle of rapid oxidation of methionine, we report Copper(I)-Nitrene Platform for robust, and selective labeling of methionine to generate stable sulfonyl sulfimide conjugates under physiological conditions. We demonstrate the versatility of this platform to label methionine in bioactive peptides, intact proteins (6.5-79.5 kDa), and proteins in complex cell lysate mixtures with varying payloads. We discover ligandable proteins and sites harboring hyperreactive methionine within the human proteome. Furthermore, this has been utilized to profile oxidation-sensitive methionine residues, which might increase our understanding of the protective role of methionine in diseases associated with elevated levels of reactive oxygen species. The Copper(I)-Nitrene Platform allows labeling methionine residues in live cancer cells, observing minimal cytotoxic effects and achieving dose-dependent labeling. Confocal imaging further reveals the spatial distribution of modified proteins within the cell membrane, cytoplasm, and nucleus, underscoring the platform's potential in profiling the cellular interactome. Methionine plays an essential role in various biological and cell regulatory processes, making its chemoproteomic profiling necessary to understand its function. Here, the authors present Copper(I)-Nitrene Platform (CuNiP) for robust and selective labelling of methionine to generate highly stable sulfonyl sulfimide conjugates under physiological conditions.