Palmitoylation is a key post-translational modification regulating viral replication, yet its regulatory mechanism in Dengue virus (DENV) infection remains elusive. This study aimed to elucidate the underlying regulatory function of palmitoylation and zinc finger Asp-His-His-Cys (ZDHHC) proteins in DENV replication and identify palmitoylated DENV proteins. We explored the function of palmitoylation in DENV replication using the palmitoylation inhibitor 2-bromopalmitate (2BP) and enhancer palmitic acid (PA), combined with qRT-PCR, western blot, confocal immunofluorescence microscopy, co-immunoprecipitation, and acyl-biotin exchange (ABE) assays. We found that 2BP promoted DENV replication, while PA inhibited it. Further analyses showed that 2BP and PA exerted no significant effects on DENV adsorption, internalization, or the interactions between E protein and the structural proteins prM/C that are essential for viral assembly. ABE assays verified that the DENV E protein is palmitoylated, with no such modification detected in prM and C proteins. Mass spectrometry and site-directed mutagenesis further revealed that the DENV E protein is palmitoylated at three cysteine residues: Cys74, Cys302, and Cys333. ZDHHC11, a characterized regulator of Zika virus E protein palmitoylation, directly interacted with DENV E protein and catalyzed its palmitoylation. Functionally, knockdown of ZDHHC11 enhanced DENV replication, while overexpression suppressed it. These findings deepen our understanding of flavivirus-host interaction mechanisms and provide a theoretical basis for the development of broad-spectrum anti-flavivirus therapies.
The dendritic cell-targeting peptide (DCP) trimer sequence has previously shown to enhance specific IgG induction. This study aims to investigate the expression of rabies virus glycoprotein (RVG) in eukaryotic cells through cloning in the pCDNA3.1 + vector, alongside the fusion of a DCP. The DCP trimer sequence was fused to the C-terminal of the RVG to improve the immune response. The construct was designed to include a His-tag for protein purification and an enterokinase (EK) cleavage site for separation of the tag from the recombinant protein. The RVG gene was amplified from the rabies virus genome via RT-PCR, and cloning was performed using BamHI and EcoRI restriction enzymes. The recombinant plasmid (RVG- pCDNA3.1+) was transfected into BHK-21 cells using lipofection, and the expression of the recombinant protein was confirmed through SDS-PAGE and western blotting using anti-His antibodies. The His-tagged recombinant protein was purified using Ni-NTA resin. Immunogenicity of the recombinant protein was investigated through mouse inoculation and analysis of the serum samples using RFFIT and ELISA methods. The results indicated successful cloning and expression of the RVG-DCP fusion protein in eukaryotic cells, with potential applications in rabies vaccine development. The results suggests a novel method for enhancing the immunogenicity of viral glycoproteins through the use of dendritic cell-targeting peptides.
Few studies have reported that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein may suppress cancer cell growth. Here, we investigated the effect of the SARS-CoV-2 spike protein in A549 lung cancer cells using recombinant spike protein (SP), spike protein transfection (SPT), and pseudo-SARS-CoV-2 virus (PSV). To evaluate its anticancer effects and associated molecular changes, we performed RNA sequencing, colony formation, immunofluorescence, cell viability, migration, FACS, western blotting, 3D spheroid, molecular docking, siRNA knockdown, qRT-PCR, apoptosis assays, and computational interaction analyses. Spike protein significantly inhibited the long-term growth of A549 cells. Among the delivery methods, PSV showed the most potent anticancer effect, followed by SPT and SP, as evidenced by reduced migration, spheroid growth, and increased sub-G1 arrest. RNA-Seq identified two differentially expressed lncRNAs, with MEG3 upregulated and BCYRN1 downregulated following spike-related treatment. Functional experiments showed that BCYRN1 knockdown or MEG3 overexpression reproduced key spike protein-induced antiproliferative and pro-apoptotic effects, including increased cleaved caspase-3 expression. Computational analyses suggested possible interactions between the Spike protein and these lncRNAs. In addition, actinomycin D (ActD) chase experiments indicated altered transcript dynamics of MEG3 and BCYRN1 under spike-related conditions. Collectively, these findings suggest that SARS-CoV-2 spike protein exerts antitumor activity in A549 cells and may contribute to the regulation of MEG3 and BCYRN1. Further studies, including formal rescue and biochemical interaction assay, will be required to establish causality and direct molecular mechanisms.
Interactomics aims at identifying and characterizing in a comprehensive way the complete set of protein-protein interactions that occur within a cell, tissue, or organism. In this chapter, we cover the most relevant experimental and computational approaches that are used in the field to assess the interactome of a specific protein or of all the proteins in a defined compartment. We address their applicability as well as their advantages and disadvantages. We then describe the different databases available to researchers interested in dissecting protein-protein interactions and finally briefly summarize the several attempts that have been made to identify the human interactome, i.e., the complete set of protein interactions that occur within a human cell.
Protein secondary structure prediction represents an important intermediate step between a protein's linear amino acid sequence and its three-dimensional structure, with broad implications for synthetic biology, drug development, and disease research. Although experimental techniques such as X-ray crystallography provide highly accurate structural information, they are labor-intensive, time-consuming, and costly, which has motivated the development of computational alternatives. Early machine-learning approaches to this problem were limited in their ability to capture complex sequence-structure relationships. The introduction of convolutional and recurrent neural networks improved hierarchical feature extraction, and predictive performance advanced further with transformer-based architectures such as AlphaFold2. This review outlines recent advances in hybrid model design, benchmark datasets, and evaluation metrics for protein secondary structure prediction. We also discuss current methodological limitations, including data dependency and dataset bias, and outline future directions such as cross-species validation, uncertainty-aware modeling, and the still-emerging potential of incorporating heterogeneous biological data into next-generation PSSP frameworks.
Aptamers, as single-stranded DNA (ssDNA) or RNA oligonucleotides, are pivotal in biosensing due to their high affinity. However, excessive lengths of these nucleic acid probes can impair their binding affinity and target recognition efficiency. Traditional optimization methods, such as static structural modeling, fail to capture the dynamic interactions between aptamers and biological macromolecules. Therefore, optimizing aptamer length to enhance affinity while maintaining effective target recognition is crucial. Here, we employed 600ns molecular dynamics (MD) simulations using the amberff14sb and parmbsc1 force fields, alongside molecular mechanics/generalized Born surface area (MM/GBSA) free energy calculations to optimize the binding affinity of a ssDNA aptamer targeting the hemagglutinin-neuraminidase (HN) protein-a critical surface receptor of Newcastle disease virus (NDV) responsible for viral attachment and entry. By systematically truncating the aptamer sequence guided by normalized criteria to eliminate length bias, we identified a 10-nucleotide variant (fqh-2) that exhibited a hydrogen bond efficiency ratio (HBER) of 1.055 and a binding free energy efficiency ratio (BFEER) of -5.124 kcal/mol, reflecting enhanced interactions with the HN protein. Furthermore, a graphene oxide (GO)-based fluorescence quenching assay confirmed a threefold increase in binding affinity for the optimized aptamer, aligning with computational predictions. This study not only provides a dynamic structure-guided framework for aptamer optimization but also lays a theoretical foundation for further advancements in optimizing and tailoring aptamers for specific applications.
Limitations in genome editing of avian species, including chicken, due to the inaccessibility of one-cell zygotes, have led to the manipulation of primordial germ cells (PGCs) as the primary approach for generating genetically engineered birds. Although plasmid-mediated delivery of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) has been widely used, it has several limitations, including delayed nuclease activation, increased off-target effects, cytotoxicity, and the inability to apply in vivo selection strategies. Collectively, these limitations highlight the need to develop strategies that achieve high on-target activity at the initial editing step. In this study, we compared plasmid- and ribonucleoprotein (RNP)-mediated CRISPR/Cas9 delivery in Leghorn male hepatoma (LMH) cells and in PGCs targeting three loci: deleted in azoospermia like (DAZL), chicken vasa homologue (CVH), and stimulated by retinoic acid 8 (STRA8). RNP delivery showed comparable or higher cell viability and editing efficiency than plasmid delivery in both cell types. Insertion/deletion (indel) profiling revealed broader and more diverse mutation patterns with RNPs, consistent with a shift in repair pathway engagement toward microhomology-mediated end joining (MMEJ), which favors larger deletions. Off-target analysis further showed substantially reduced off-target editing and high specificity with RNP delivery. Together, these findings demonstrate that RNP delivery improves efficiency, reduces cytotoxicity, and improves precision, providing a more reliable platform for chicken genetic engineering.
In the absence of a definitive gold standard for diagnosing latent tuberculosis infection (LTBI) in healthcare workers (HCWs), alternative specific biomarkers are needed. This longitudinal cohort study with baseline testing evaluated the diagnostic performance of stimulated plasma interferon-γ inducible protein 10 (IP-10) for LTBI detection among HCWs in a high tuberculosis (TB)-burden setting, using interferon-γ release assays (IGRAs) as the reference standard. The study was conducted at Songklanagarind Hospital, Thailand, between 2021 and 2024, and included 64 healthy HCWs. Serum and stimulated plasma samples were collected, and IP-10 and IFN-γ concentrations were measured by ELISA. Nine HCWs (14.0%) were LTBI-positive. Stimulated plasma IP-10, but not serum IP-10, showed significant correlations with IFN-γ levels in TB1 (r = 0.719) and TB2 (r = 0.768; p < 0.0001) tubes. At cut-off values of ≥ 2,980.0 pg/mL for TB1 and ≥ 3,108.0 pg/mL for TB2, sensitivity was 100%, specificity was 96.0% and 94.5%, and overall accuracy was 96.8% and 95.3%, respectively. Based on either IGRA or stimulated plasma IP-10 cut-off levels, five of nine LTBI cases declined treatment; among these, one individual (20.0%) progressed to active pulmonary TB 16 months later. Stimulated plasma IP-10 shows high diagnostic performance for LTBI detection among HCWs and may serve as an alternative for LTBI screening in high-TB-incidence with universal BCG vaccination.
Exercise provides significant benefits for most women, but adverse effects on reproduction can and do occur. Increased frequency, duration, and intensity of exercise are associated with a higher risk of female infertility. In particular, exercise-induced reproductive dysfunction is linked to alterations in the hypothalamic-pituitary-gonadal (HPG) axis. However, the role of meteorin-like protein (metrnl), as an exercise-induced myokine, in female reproductive function and the HPG axis is not yet fully understood. In this study, we investigated the effects of metrnl, compared with a swimming exercise protocol, on sexual motivation and the HPG axis in female rats. Female rats with regular estrous cycles were randomly allocated into three groups (n = 9 per group), and subjected to deionized water (1 mL/kg), metrnl (1 µg/day) or swimming-based moderate-intensity exercise (30 min/day, 5 days/week) for about 19 consecutive days. The results showed that metrnl administration reduced the time spent near the male rat and the male preference ratio, indicators of sexual motivation. It also decreased hypothalamic GnRH expression (in the median eminence and preoptic area), serum concentrations of reproductive hormones (follicle-stimulating hormone and anti-Müllerian hormone), and the numbers of ovarian follicles (primordial and primary follicles), similar to the effects observed after the swimming exercise protocol. Furthermore, metrnl concentrations in serum remained unchanged in female rats treated with metrnl and exercise. In conclusion, metrnl treatment reduced sexual incentive motivation and altered HPG axis regulation in female rats. These findings suggest that exercise-induced metrnl may be a potential exerkine associated with changes in female sexual motivation and HPG axis regulation due to exercise.
Extreme high temperatures significantly threaten insect development and reproduction. Small heat shock proteins (sHSPs) are crucial for thermal adaptation, but their specific roles in reproduction and heat stress response remain incompletely understood. This study investigates SfHSP19.8, a testis-enriched sHSP in the fall armyworm (Spodoptera frugiperda), to elucidate its function. Testis-specific expression of SfHSP19.8 occurred during the 6th- instar larval and pupal stages. Homozygous knockout mutants were generated using CRISPR/Cas9 technology. Transcriptomic analysis of 6th-instar larval testes revealed dysregulation of genes in steroid hormone biosynthesis and detoxification pathways. However, knockout did not impair adult male fertility, testis morphology or sperm count under standard conditions. SfHSP19.8 expression was strongly induced by heat shock across developmental stages. Mutants exhibited severely compromised thermotolerance under heat stress, including complete egg hatching failure, high larval mortality, prolonged larval development, and reduced adult longevity and reproductive fitness. These findings demonstrate that SfHSP19.8 is essential for systemic thermotolerance across life stages and maintains reproductive function specifically under thermal challenge, while being dispensable for basal male reproduction under optimal conditions. SfHSP19.8 represents a potential target for pest control strategies in the context of future climate warming. © 2026 Society of Chemical Industry.
Heart failure (HF) is a major complication of metabolic dysfunction-associated steatotic liver disease (MASLD). The C-reactive protein-triglyceride glucose index (CTI), which reflects systemic inflammation and insulin resistance, is linked to cardiovascular outcomes, but its predictive value for HF in MASLD patients remains unclear. We aimed to evaluate the baseline and cumulative CTI (CumCTI) in relation to incident HF and explore blood pressure as a potential mediator. We included 26,499 participants with MASLD from the Kailuan Study. The baseline and CumCTI values were calculated and examined for associations with HF via Cox regression. Restricted cubic splines were used to assess dose‒response patterns. Predictive performance was evaluated using C-index, reclassification metrics, time-dependent ROC curves, and calibration analyses. During a median follow-up of 16.0 years, 1,158 HF events occurred. A higher CTI was independently associated with increased HF risk (HR for Q4 vs. Q1: 1.78; 95% CI: 1.48-2.11; P < 0.001), with each 1-SD increase corresponding to a 27% greater risk (HR 1.27; 95% CI: 1.19-1.35). CumCTI showed stronger associations with HF and modestly improved model discrimination and reclassification compared with conventional risk factors. Time-dependent ROC analyses showed slight increases in AUC at 5 and 10 years after adding CumCTI (0.782 to 0.783 and 0.763 to 0.767, respectively), with good calibration between predicted and observed risks. Mediation analysis indicated that systolic and diastolic blood pressure explained only a small proportion of the CTI-HF association. Associations were stronger for CumCTI in participants aged < 60 years. These findings suggest that a higher CTI, especially cumulative exposure, is independently associated with HF risk in MASLD and may provide complementary information for cardiovascular risk assessment.
To assess the combination of high dose interleukin 2 (HD IL2) and nivolumab in patients with checkpoint inhibitor-refractory melanoma or renal cell carcinoma (RCC), we performed a single-arm, Simon two-stage phase II trial for patients with unresectable stage III or IV melanoma or any histology RCC. The primary endpoint was overall response rate (ORR); secondary endpoints were adverse events and progression-free survival (PFS), defined as time to radiographic or clinical progression, whichever occurred first. Five patients enrolled, three with melanoma and two with RCC. Median age at registration was 47 (35-77) years. Two patients (40%) had treated or asymptomatic brain metastases, and one (20%) had liver metastases. Median prior lines of systemic therapy per patient were 3 (2-5). Patients completed a median of 1 (0.5-3) treatment cycle, involving two admissions for HD IL2 administration and two doses of nivolumab. ORR was 20%. Median PFS was 1.4 (0.8-45.0) months. Time to next therapy for each living patient was 2.5 and 45.6 months for local modalities, and 2.0, 2.3, and 45.9 months for systemic therapies. Adverse events reflected the known toxicity of HD IL2. One treatment-related death occurred, leading to trial termination. The combination of HD IL2 and nivolumab resulted in a durable response in one of five patients with PD-1-refractory advanced melanoma or RCC. Use of HD IL2 remains limited by its toxicity; augmented IL2 formulations and administration strategies are needed. ClinicalTrials.gov ID: NCT03889782 (Registered 6/16/2019; https://clinicaltrials.gov/study/NCT03889782).
Multispecificity involves high-affinity binding to multiple related ligands while preserving discrimination against other ligands. The binding of tick evasins to human CC chemokines exemplifies key principles of multispecific binding: a rigid core recognising conserved features of all targets, with flexible peripheral regions enabling discrimination within the target family.
Individuals with phenylketonuria (PKU), caused by different variants of the phenylalanine hydroxylase gene, need to restrict their intake of phenylalanine. This study evaluated dietary patterns and physical activity levels in children with different PKU phenotypes compared to healthy controls. Eighty-two children were recruited (22 classic PKU [cPKU], 21 BH4-responsive PKU, 19 hyperphenylalaninemia, and 20 controls). Anthropometric data, dietary intake, biochemical markers, and physical activity were assessed. Classic PKU (cPKU) subjects exhibited higher carbohydrate and sugar intake than other PKU phenotypes and controls. Notably, 42% of carbohydrate and 17% of sugar intake was from special low-protein foods, and 20% of carbohydrate and 29% of sugar intake was from protein substitutes. Compared to controls, the cPKU group was less physically active and reported a higher frequency of sweet consumption. Ninety percent of PKU had good metabolic control and carbohydrate intake was significantly correlated with HOMA-IR; however, after adjusting for age, only a trend remained (p = 0.08). Participants in the PKU group following a low natural protein diet consumed more carbohydrate and sugars than those on a normal-protein diet. Multivariate regression analysis showed that the low natural protein diet group was significantly associated with higher levels of vitamin B12, linoleic acid, α-linolenic acid, eicosapentaenoic acid, and docosahexaenoic acid, and with lower levels of total cholesterol and HDL-C compared to the normal-protein diet group. In conclusion, children with PKU, particularly those with classical PKU following low-protein diets, showed higher carbohydrate intake and distinct micronutrient and lipid profiles compared with healthy controls.
Food allergy (FA) is an immune-related condition, mainly characterized by hypersensitivity to food allergens in children and adults. Clinical proteomics is among the first medical disciplines supported by novel technologies, on the basis of which it becomes possible to understand FA from a therapeutic point of view. Within this chapter, three subdisciplines of proteomics will be covered: discovery clinical proteomics, targeted clinical proteomics, and clinical proteomics-based systems biology. Discovery clinical proteomics refers to the analysis of protein expression aiming at biomarker identification and knowledge about disease mechanisms which bring out completely new proteins connected to FAs. In targeted clinical proteomics, proteins that were identified in the exploratory studies are followed up so as to increase sensitivity for biomarkers detection in diagnostics. Proteomic-based systems biology is a means by which proteomics data can be integrated with other "omics" technologies for simulating immune response pathways governing biological systems and identifying therapeutic targets. Over the years, it has been possible to study what causes diseases, find new markers, and customize drug prescriptions according to protein results obtained from patients. Clinical proteomics has provided insight on immune responses, allergen diversity, and treatment possibilities in relation to FAs. It provides a detailed mapping of protein alterations as a result of allergens that are responsible for essential interactions with the immune system. In turn, clinical proteomics helps individualized medicine through identifying specific proteins signatures in patients enabling customized treatment approaches that will enhance its efficacy while mitigating any ill-effect. In this way, basic research is supposed to be united with clinical practice to offer novel opportunities for diagnosing, monitoring, and managing food allergic conditions that impact positively on outcomes leading to better life quality for patients.
Cellular senescence plays a crucial role in respiratory diseases. Nitrogen dioxide (NO2), a major air pollutant, causes multi-system toxicity, primarily affecting the respiratory system. However, the association between NO2 and pulmonary senescence remains unclear. This study systematically explored the association between NO2 exposure and premature pulmonary senescence using animal and cellular models. Rats were exposed for 45 days (4 h/day) to filtered air, 0.5 ppmV, or 5.0 ppmV NO2. Human bronchial epithelial (HBE) cells were treated with 0 or 120 μmol/L NaNO3, a stable metabolite of NO2, for 96 h. HBE cells exhibited hallmark senescence phenotypes, including elevated reactive oxygen species (ROS), increased expression of senescence-associated proteins (Fibronectin 1 (Fn1), Clusterin (CLU), senescence Marker Protein 30 (SMP30)), elevated β-galactosidase (β-gal) activity, increased developmentally regulated GTP-binding protein 1 (DRG1) and cyclin-dependent protein kinase 5 (CDK5) expression, and G1-phase cell cycle arrest. Treatment with the ROS inhibitor N-acetylcysteine (NAC), si-DRG1, or a CDK5 inhibitor alleviated these effects. Co-immunoprecipitation assays revealed that NaNO3 promoted the interaction between DRG1 and CDK5 during senescence. The study demonstrated that NO2/NaNO3 induces bronchial epithelial cellular senescence, contributing to pulmonary senescence via ROS-dependent upregulation of DRG1 and CDK5 expression and interaction. Targeting the ROS-DRG1/CDK5 axis may represent a therapeutic strategy for environmental pollutant-induced premature respiratory senescence and provide new insights for the management of related disorders.
In Salmonella Typhimurium (S. Typhimurium), yiiD encodes a two-domain protein, with one domain having bona fide malonyl-ACP decarboxylase activity, and the other showing sequence similarity to Gcn5-type acetyltransferases (GNATs). Recent work on this enzyme was motivated by the essentiality of its decarboxylase domain to initiation of fatty acid biosynthesis in a strain devoid of β-ketoacyl-[acyl-carrier-protein, ACP] synthase III (FabH) activity. A function for the putative GNAT domain has not been established. We find that a ∆yiiD strain has an unconventional, slow-growth lag phenotype during growth on succinate that is only weakly dependent on YiiD decarboxylase activity, implicating the putative GNAT domain. The ∆yiiD mutation suppresses the effect of a ∆rpoS mutation that is known to shorten the lag phase during growth on succinate, suggesting the function of the YiiD protein may also be regulatory. Isolation of spontaneous suppressor mutations in a ∆yiiD strain revealed changes in the promoter of cpdA, the gene encoding cyclic-AMP phosphodiesterase. Exogenous addition of cAMP to the medium fully abrogated the ∆yiiD phenotype, and intracellular cAMP measurements revealed that the ∆yiiD strain fails to accumulate cAMP during lag phase, with levels about half of those measured in the wildtype strain. During the lag phase, the ∆yiiD strain was also measured to have increased expression of the adenylate cyclase gene, cyaA, implying that the mechanism altering cAMP levels occurs posttranscriptionally. We conclude YiiD function is necessary for early cAMP accumulation during transitions into some non-phosphotransferase system (non-PTS) growth conditions. We suggest changing the name of the YiiD protein to LcmM (for lipid and carbon metabolism modulator) to encapsulate its roles in S. Typhimurium physiology.
Endoplasmic reticulum associated degradation (ERAD) plays pivotal role in protein homeostasis and quality control in normal and cancer cells, yet the regulatory mechanism of ERAD remains elusive, especially regarding its ubiquitination function mediated by hydroxymethylglutaryl reductase degradation protein 1 (HRD1). Here, we report that Sel-1 Suppressor of Lin-12-Like 3 (SEL1L3) protein resided on the ER membrane can effectively prevent HRD1-mediated ERAD process via dual mechanisms: SEL1L3 disrupts SEL1L-HRD1 complex by mutually exclusively interacting with SEL1L and HRD1 respectively, resulting in concomitant prevention of substrate degradation; on the other hand, SEL1L3 can accelerate HRD1 protein degradation. Biologically, SEL1L3 inhibits colorectal cancer (CRC) cell growth and migration, which counteracts the oncogenic activity of HRD1; moreover, we identify STING as a HRD1 substrate and a critical downstream effector mediating tumor suppression activity of SEL1L3. Collectively, these data demonstrate that SEL1L3 is a critical regulator of ERAD and exerts a potent tumor-suppressing function, and that the SEL1L3/HRD1/STING axis plays a crucial role in CRC growth and migration.
PROTACs, also called proximity-inducing agents, are chimeric molecules composed of a ligand for protein of interest (POI), an E3 ligase ligand and a linker connecting them. PROTACs have transformed the therapeutic landscape by enabling an event-driven strategy to degrade disease-associated proteins previously regarded as undruggable. The unique event-driven mechanism of PROTACs allows selective protein degradation with greater potency and lower drug resistance than conventional occupancy-based inhibitors. Despite their advantages, challenges such as high molecular weight, low permeability, poor pharmacokinetic properties restrict their clinical applications. To overcome these limitations, AI-driven technologies are being utilised to generate novel, chemically valid PROTACs. This review highlights the drawbacks of conventional computational methods and explores emerging AI-driven tools applied to multiple areas of PROTAC research, such as target (POI) selection (DeepUSI, DrugnomeAI), linker generation (AIMLinker, DiffLinker), activity prediction (AI-DPAPT, DeepPROTAC), POI degradability assessment (PrePROTAC, MAPD), ternary complex modelling (ProFlow), PROTAC generation (PROTAC-RL), and ADME property estimation (MT-GNN). It also outlines current challenges such as data scarcity, reproducibility issues, inadequate model generalizability, emphasizing the need for hybrid models or integrated AI techniques to mitigate these limitations.
Proteomics is an already established transformative tool for dissecting the molecular mechanisms underlying plant immunity and pathogen virulence. As crop losses due to plant diseases intensify under climate change, understanding these interactions at the protein level has become essential for sustainable crop improvement. Advances in mass spectrometry, bioinformatics, and quantitative proteomics have expanded the capacity to characterize dynamic changes in host and pathogen proteomes, enabling the identification of defense-related proteins, signaling networks, effector targets, and pathogenicity determinants. This chapter synthesizes recent proteomic insights across major crops as soybean, tomato, rice, grapevine, maize, and wheat, highlighting how proteome profiling has revealed key regulators of pathogen-associated molecular pattern (PAMP)-triggered and effector-triggered immunity, pathogen infection strategies, and the impact of biocontrol agents and priming compounds. Case studies illustrate how proteomics uncovers cultivar-specific responses, subcellular reprogramming, and protein networks critical for resistance. We further explore how proteomics informs biotechnology, from identifying candidate genes for breeding and genome editing to supporting safety assessments of engineered crops.