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PubMed2026

Phosphoproteomic Analysis of GAP50-Deficient Parasites Reveals the Inner Membrane Complex Is Involved in Ion Regulation in Toxoplasma gondii.

The Alveolata group of organisms is characterized by a vesicular structure located beneath the plasma membrane. In apicomplexa, this structure is known as the inner membrane complex (IMC). The IMC acts as a scaffold during the budding of the daughter parasite and is utilized as a rigid base for the glideosome. In this study, we discovered that the phosphatase activity of GAP50 is crucial for its function in the biogenesis of the IMC. Through further phosphoproteomic analysis of parasites lacking GAP50, we identified that an NIPA family transporter is localized in the IMC. Knocking out TgNIPA1 significantly impairs the robust growth of the parasites. Additionally, expressing TgNIPA1 in a Salmonella strain lacking magnesium transporters could rescue the growth phenotype of bacteria under low magnesium conditions, indicating that it functions as an active magnesium transporter. Our results strongly suggest that the flattened vesicles of the IMC may play important roles in ion regulation in T. gondii.

Toxoplasma↗
PubMed2025

Phosphoproteomics analysis provides novel insight into the mechanisms of extreme desiccation tolerance of the desert moss Syntrichia caninervis.

Syntrichia caninervis is a model species for research on desiccation tolerance (DT) because it is capable of rapidly responding to drastic changes in water conditions. Phosphorylation, a key post-translational modification process that is rapid and reversible, enables the rapid regulation of protein functions, aiding plants to quickly adapt to changing environments. Modifications to phosphorylation may play a crucial role in the DT of S. caninervis, although no studies have been published. Here, we report a 4D label-free high-resolution dynamic proteomic and phosphoproteomic analysis of S. caninervis during dehydration and rehydration, allowing for the quantification of 2854 proteins and 1177 phosphoproteins, including 1447 differentially expressed proteins (DEPs) and 699 differentially phosphorylated proteins (DPPs). Among the phosphoproteins, 36.5% displayed changes in protein abundance. The proteomic and phosphoproteomic changes involved proteins (DEPs and DPPs) that were mainly involved in photosynthesis, glutathione metabolism, the citrate cycle, and the biosynthesis of secondary metabolism pathways during dehydration. During rehydration, DEPs and DPPs were mainly associated with processes related to ribosome and energy metabolism. In summary, during dehydration, phosphorylation mainly regulates signal transduction and metabolic processes, allowing plants to adapt to a loss of water. During rehydration, phosphorylation controls repair and recovery mechanisms, restoring metabolic activity and reestablishing cellular functions. ScDHAR1, a protein involved in glutathione metabolism, was differentially phosphorylated at two serine sites (S29 and S218) in response to desiccation. Further analysis revealed that phosphorylation of S29/S218 in ScDHAR1 significantly increased its enzymatic activity, thereby enhancing the DT of S. caninervis in situ. This work establishes a phosphoprotein database for a DT moss. These findings not only broaden our understanding of S. caninervis DT but also fill knowledge gaps in the field of phosphoproteomics in DT mosses, while providing valuable data resources for future related research.

Phosphoproteins↗
PubMed2026

Phosphoproteomic Analysis of Cortical Tissue from Mice Lacking Both CaMKIIα and CaMKIIβ Identifies Novel In Vivo Substrates.

Ca2+/calmodulin-dependent protein kinase II (CaMKII) plays a critical role in calcium signaling. Several studies have shown that mice with single Camk2a or Camk2b gene knockouts are viable, yet exhibit distinct phenotypes, whereas the double knockout of both genes is lethal. These findings indicate that each gene can have distinct roles and that they also partially compensate for each other in yet unknown essential brain functions. In order to provide insight into potential novel CaMKII functions, we performed parallel phosphoproteomic analyses on nonstimulated cortex tissues from inducible Camk2a and Camk2b double knockout (Camk2af/f;Camk2bf/f;CAG-CreESR) mice and from wild type mice. A total of 5622 phosphorylated peptides derived from 2080 proteins were identified. Phosphorylation at serine/threonine residues in 130 proteins was downregulated in the double knockout mice, including residues in 113 proteins that have not previously been identified as potential CaMKII substrates. Comparison of amino acid sequences surrounding the downregulated phosphorylation residues provided new insights into the CaMKII-substrate consensus sequences in vivo. This data set provides an important resource for future studies examining novel roles for CaMKII in the brain.

Animals↗
PubMed2026

Phosphoproteomic analysis in a mouse model reveals ERK signaling as a key modulator of inflammatory response in nasal mucosa associated with childhood allergic rhinitis.

Childhood allergic rhinitis (AR) is a multifactorial condition arising from the interplay between genetic predisposition and environmental exposures. Although protein phosphorylation is widely recognized as a key regulator of gene expression across various physiological and pathological states, its global alterations in the nasal mucosa of pediatric patients with AR and their subsequent impact on mucosal function and inflammatory pathways remain incompletely characterized. Our study aimed to elucidate the molecular mechanisms underlying nasal mucosa dysfunction induced by pediatric AR. Our analysis revealed 3,861 proteins encompassing a total of 15,491 phosphorylation sites. Specifically, we detected 441 downregulated phosphorylation sites on 584 proteins and 531 upregulated phosphorylation sites on 722 proteins in the nasal mucosa of the AR group. Our proteomics findings suggest that the dysregulation of immune activation and metabolic regulation may contribute to AR pathophysiology. Through pathway analysis of the identified phosphorylation sites, we found Extracellular Signal-Regulated Kinase (ERK) signaling emerged as an important pathway; notably, upregulation of ERK1/2 phosphorylation was observed as a significant marker associated with AR. Importantly, targeting ERK inhibitors presents a potential therapeutic strategy for modulating key inflammatory response signaling pathways in the context of AR, although this finding is derived from preclinical mouse models and requires rigorous validation in human pediatric nasal mucosal tissues before any clinical translation can be considered. Collectively, these findings highlight that elucidating the molecular mechanisms underlying AR-induced nasal mucosal dysfunction in the mouse model may inform the novel therapeutic targets for pediatric allergy-related diseases. Overall, elucidating these mechanisms has substantial implications for developing targeted interventions aimed at mitigating inflammation associated with allergic rhinitis.

Animals↗
PubMed2026

High-Fat Diet and a High Amyloid Load Interact to Induce PKC-α Dependent Synaptic Insulin Resistance.

A plethora of studies suggest that a high-fat diet in combination with a high amyloid load causes synaptic insulin resistance and is a risk factor for Alzheimer's disease. Our understanding of the underlying mechanisms is still fragmented. To gain new insights, we conducted integrated proteomic and phosphoproteomic profiling of hippocampal synaptosomes from WT and a transgenic mouse line with a high amyloid load (heterozygous TBA2.1 mice) that show no overt signs of neurodegeneration and dementia. Mice were fed with a regular or high-fat diet. Data-independent acquisition quantified over 5400 proteins, revealing a stable synaptic proteome across conditions. However, the combination of high amyloid load and high-fat diet triggered coordinated remodeling of lipid metabolism pathways, particularly mitochondrial and peroxisomal fatty acid catabolism. Phosphoproteomic analysis showed pronounced activation of lipid- and stress-responsive kinases, including protein kinase C-α, along with increased inhibitory phosphorylation of insulin receptor substrates (IRS1/2). In vitro experiments indicate that blocking protein kinase C-α indeed prevents synaptic insulin resistance in primary neurons. The findings suggest that this proteomic workflow, combined with kinase pathway analysis, can reveal nodal points for interventions in a complex disease state with a trajectory to Alzheimer's disease.

Animals↗
PubMed2026

Integrated multi-omics profiling identifies aging-related molecular signatures and convergent interferon signaling in systemic lupus erythematosus.

BACKGROUND: Systemic lupus erythematosus (SLE) is characterized by chronic immune activation and molecular alterations that overlap with aging-related biological processes. However, how these alterations are organized across molecular layers and whether they converge on shared regulatory networks remain incompletely understood. METHODS: We performed an integrative multi-omics analysis combining in-house proteomic and phosphoproteomic data from 130 patients with SLE and 90 healthy controls (HCs) and publicly available transcriptomic datasets comprising 1,461 SLE patients. Proteins and phosphorylation sites were annotated using established aging-related gene resources. Differential protein abundance and phosphorylation changes were analyzed across disease-status and disease-activity comparisons. Nominal P-value thresholds were used for exploratory feature selection, whereas FDR-adjusted P values were used to assess robustness after multiple-testing correction. Kinase-substrate enrichment, transcription factor annotation, and cell-type-resolved transcriptomic comparison were used to explore potential regulatory programs. RESULTS: We identified 128 nominally altered proteins annotated to aging-related biological processes, including genomic instability, mitochondrial dysfunction, and epigenetic alterations. Phosphoproteomic analysis revealed 36 nominally altered phosphorylation sites, including previously unreported sites in IFI16 (S153, S780) and PKCδ (S507, S664). Clustering analysis demonstrated heterogeneous protein co-regulation patterns across disease states. Kinase activity inference suggested altered activity of TBK1 and IKKβ. TF analysis further highlighted STAT1, RELA, and PML as potential central nodes within the inferred regulatory network. Notably, these multi-omic alterations were not randomly distributed but showed convergence toward shared signaling pathways, particularly those related to interferon responses. CONCLUSIONS: This integrative multi-omics study identifies inflammatory and interferon-dominated molecular alterations in SLE PBMCs that overlap with aging-related biological processes and converge on shared regulatory networks. These findings provide a hypothesis-generating framework for investigating the intersection between chronic immune activation and aging-related molecular remodeling in SLE.

Humans↗
PubMed2026

Opposing kinase signaling may underlie the inverse relationship between cancer and Alzheimer's disease.

Cancer and Alzheimer's disease (AD) are leading causes of mortality and exhibit an inverse relationship, where AD patients have reduced cancer risk and vice versa. However, the molecular basis of this relationship remains poorly understood. We reanalyzed published proteomic and phosphoproteomic datasets to investigate this relationship. Differentially abundant proteins were identified in lung adenocarcinoma and glioblastoma samples relative to controls and compared with proteins altered in AD brains, revealing 37 proteins with opposing abundance patterns. Protein-protein interaction and pathway analyses revealed enrichment in kinase signaling and phosphorylation pathways. Phosphoproteomic analysis identified 52 differentially phosphorylated sites with opposing patterns, while kinase-substrate enrichment analysis identified 44 kinases with opposing inferred activity profiles. Integration of kinase activity and phosphosite data identified 29 kinase-phosphosite pairs, including 4 prioritized pairs with opposing patterns relevant to both diseases. Across seven independent cancer cohorts, 17 of 20 statistically significant phosphosite-cohort comparisons (85%) were concordant with the discovery findings, supporting reproducibility of the prioritized phosphosites. Together, these findings highlight opposing kinase signaling as a prominent feature of the inverse relationship and suggest potential biomarkers and therapeutic targets. This study provides a novel systems-level framework for investigating inverse relationships, supported by an R Shiny application for data exploration (https://advscancer.shinyapps.io/advscancer/). SIGNIFICANCE: This study presents an integrated proteomic and phosphoproteomic framework for investigating the inverse relationship between cancer and Alzheimer's disease (AD). By integrating differential protein abundance, phosphosite phosphorylation, inferred kinase activity, and curated kinase-substrate relationships, we identified opposing signaling patterns and prioritized four kinase-phosphosite pairs. Independent evaluation across seven CPTAC cancer cohorts supported the reproducibility of the prioritized phosphosite patterns. These findings provide insight into molecular processes potentially associated with the inverse relationship between cancer and AD, identify candidate biomarkers and therapeutic targets, and demonstrate the value of systems-level, data-driven approaches for investigating shared and opposing disease processes.

Humans↗
PubMed2026

Phosphoproteomic Profiling of Early-Stage Non-Small Cell Lung Cancer Provides Preliminary Evidence of Phosphorylation-Regulated Rho GTPase Signaling Driving Cytoskeletal Remodeling, Angiogenesis, and Cell Cycle Progression.

Non-small cell lung cancer (NSCLC) is the primary cause of cancer-related deaths worldwide. This can be attributed to the difficulty in early detection and the limited efficacy of available treatments, partly due to an incomplete understanding of the disease biology. Identification of key proteins involved in early-stage progression and understanding the underlying mechanisms can greatly contribute to the development of diagnostic and treatment strategies for NSCLC. Quantitative phosphoproteomic analysis was done on paired tumor tissues and adjacent normal lung tissues from early-stage NSCLC adenocarcinoma (LUAD) patients to allow for the identification of proteins with differential phosphorylation and their associated pathways. A total of 6483 phosphoproteins were identified, with 1229 proteins having significantly higher phosphorylation and 701 proteins having significantly lower phosphorylation in the tumor tissues. All MS data were deposited in ProteomeXchange with the identifier PXD071583. Function enrichment analysis showed that the differentially phosphorylated proteins and phosphosites were primarily involved in Rho GTPase signaling and cytoskeleton remodeling. Analysis of protein interaction networks suggests that the predicted kinase activity likely drives malignant transformation in NSCLC LUAD, presumably through Rho GTPase-mediated angiogenesis and cell cycle progression. More importantly, this study identified several protein phosphosites with differential phosphorylation and inferred kinase-phosphosite activities that have not previously been reported in NSCLC LUAD.

Humans↗
PubMed2026

H-NOX and NosP Regulate Flagellar Protein and Virulence Factor Production in Vibrio cholerae.

The ability of Vibrio cholerae to transition between motile and sessile forms in the environment and in the host is critical to its survival and virulence. The molecular cues, sensor proteins, and signaling pathways mediating these transitions are highly complex and often overlapping. Nevertheless, a detailed understanding of them is critical for understanding the persistence and pathogenesis of this deadly pathogen. Nitric oxide (NO) functions as an important signaling molecule in many bacteria, affecting biofilm formation, motility, and virulence, often through interaction with heme protein sensors. The genome of V. cholerae encodes two such sensors called H-NOX and NosP. Here we constructed a Δhnox/nosP mutant and employed a multi-omics methodology that combines tandem-mass-tag (TMT)-based quantitative proteomics, phosphoproteomics, and targeted metabolomics to investigate the function of these sensors. A set of 258 proteins was differentially expressed in the mutant that included many proteins involved in flagellar biosynthesis and motility as well as critical virulence factors, iron acquisition systems, and metabolic enzymes. Many of the identified genes are also part of the ferric uptake regulator (Fur) regulon and iron-dependent transcriptional repression of several Fur targets was disrupted. Phosphoproteomics analysis also revealed proteins involved in motility and virulence as differentially phosphorylated in the mutant strain. In most cases, these phosphoproteins have not been previously observed and provide a wealth of new targets for investigating mechanisms of V. cholerae signaling. Taken together, this work illustrates a role for H-NOX and NosP in promoting factors important for infection while suppressing those important for environmental survival, suggesting a function in priming the organism for infection and/or maintaining the infectious phenotype.

Journal Article↗
PubMed2025

KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics.

SUMMARY: Proteome-wide datasets of phosphorylated peptides, either measured in a condition of interest or in response to perturbations, are increasingly becoming available for model organisms across the evolutionary spectrum. We introduce KINAID (KINase Activity and Inference Dashboard), an interactive and extensible tool written in Dash/Plotly, that predicts kinase-substrate interactions, uncovers and displays kinases whose substrates are enriched amongst phosphorylated peptides, interactively illustrates kinase-substrate interactions, and clusters phosphopeptides targeted by similar kinases. KINAID is the first tool of its kind that can analyze data from not only Homo sapiens but also 10 additional model organisms (including Mus musculus, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae). We demonstrate KINAID's utility by applying it to recently published S. cerevisiae phosphoproteomics data. AVAILABILITY AND IMPLEMENTATION: Webserver is available at https://kinaid.princeton.edu; open-source python library is available at https://github.com/Singh-Lab/kinaid; archive is available at https://doi.org/10.24433/CO.8460107.v1.

Proteomics↗
PubMed2025

Phosphoproteomics delineates hepatocellular carcinoma subtypes and pinpoints therapeutic targets.

BACKGROUND AND AIMS: Only a minority of patients could benefit from systemic therapy owing to the high heterogeneity of HCC. Therefore, a deeper understanding of the pathogenesis of HCC is essential for precision therapy. Genomic and proteomic studies of HCC have enhanced our understanding of HCC. However, the phosphoproteomic characterization of HCC remains poorly understood. APPROACH AND RESULTS: We conducted an in-depth analysis of a clinical cohort of HCC using high-coverage phosphoproteomic. Effective therapeutic targets were validated using liver cancer cell lines and HCC patient-derived xenograft mouse models that correspond to the phosphoproteomic subtypes of HCC. Phosphoproteomic analysis classified HCC into 3 subtypes, A, B, and C, with increasing malignancy and correlation with clinical features, including patient prognosis, tumor staging, serum alpha-fetoprotein levels, tumor thrombus, and tumor size. Phosphoproteomic subtyping deeply reflected the biological characteristics and clinical features of patients with HCC​​​​​​. The profiles of HCC-dysregulated kinase activities inferred from the different phosphoproteomic subtypes consistently identify increased kinase activity related to cell proliferation. Subtype-C HCC patients showed the most significant dysregulation, indicating a potential therapeutic target. The corresponding drug, bosutinib, demonstrated efficacy in inhibiting the growth of subtype C tumors in liver cancer cell lines and HCC patient-derived xenograft mouse models representative of the phosphoproteomic HCC subtypes. CONCLUSIONS: Our study provides a comprehensive exploration of the phosphoproteomic landscape of HCC, establishing new subtypes that match clinical features and identifying potential therapeutic targets for the most malignant C subtype.

Carcinoma, Hepatocellular↗
PubMed2026

Astrocyte reactivity by alcohol dependence in the central amygdala.

Astrocytes play essential roles in maintaining brain homeostasis and in contributing to synaptic functions, but, in response to injury, infection, or disease, astrocytes can downregulate their homeostatic and physiological functions while increasing neuroinflammatory responses. The central amygdala (CeA) is important for stress responsivity and the development of alcohol (ethanol) dependence. Using a multi-omics approach in Aldh1l1-EGFP/Rpl10a mice and the chronic intermittent ethanol two-bottle choice (CIE-2BC) model, we have characterized the translational response of CeA astrocytes, as well as the proteomic and phosphoproteomic changes in ethanol dependent, non-dependent, and naïve mice. We identified astrocyte-specific alterations in neuroimmune functions and antioxidant/oxidative stress pathways in ethanol dependent mice as well as cytoskeletal plasticity related pathways in non-dependent mice. Proteomic analysis showed down-regulation of astrocyte physiological functions in dependent animals while phosphoproteomic analysis identified pathways associated with cytoskeleton remodeling in both dependent and non-dependent mice. Reconstructions of astrocyte morphologies demonstrated increased CeA astrocyte complexity in dependent and non-dependent groups compared to naïve mice. The astrocyte-specific activation of neuroimmune and antioxidant pathways, down-regulation of homeostatic functions, alteration in protein phosphorylation-mediated cytoskeleton remodeling, and increased astrocyte morphological complexity demonstrate that ethanol dependence induces astrocyte reactivity in the CeA consistent with both adaptive and maladaptive changes. These findings highlight the role of CeA astrocytes in the progression from alcohol intake to dependence and represent a first step toward identifying astrocyte-specific therapeutic strategies to treat Alcohol Use Disorder (AUD) aimed at potentiating reactive astrocyte adaptive changes and inhibiting maladaptive responses.

Animals↗
PubMed2026

Host Proteome Remodeling During Group A Streptococcus Skin Infection.

Group A Streptococcus (Streptococcus pyogenes, GAS) is a bacterial pathogen that commonly causes local infections in humans and can lead to invasive diseases. GAS infections trigger complex host immune and tissue responses, yet how these processes are coordinated over time and across different tissues remains poorly understood. To explore the spectrum of GAS infection, we examined responses in a skin infection model at multiple proteome levels, characterizing local and distant tissues with variable infection responses. We map changes in canonical innate and adaptive immune signaling while uncovering new mechanisms in the context of skin infection. We uncover the robust and time-dependent expression of one family of proteins, chitinase-like proteins, that coincides with immune cell infiltration of local tissues. Because immunomodulatory networks are tightly regulated through post-translational modifications, we integrated global proteomic data with cytokine signaling and key phosphoproteome changes. This analysis revealed correlations between mTOR and kinase signaling pathways that diverge at local and systemic tissues. Our systems-based approach provides a rigorous evaluation of a GAS skin infection, characterizing host proteome remodeling across experimental groups and individual mice.

Animals↗
PubMed2026

Hepatic metabolic adaptation to endurance exercise: temporal and sex differences by multiomics integration and validation.

BACKGROUND: Although endurance exercise benefits liver health, sex-specific adaptive trajectories remain unclear. This study mapped dynamic liver adaptation in males and females during prolonged training and identified underlying molecular programs. METHODS: Using publicly available time-resolved liver multi-omics data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we established a computational pipeline for differential analysis of transcriptomic, proteomic, phosphoproteomic, and metabolomic data with FDR correction, followed by FGSEA pathway enrichment. Kinase activities were inferred through ortholog mapping and PhosphoSitePlus. Cross-omics co-expression networks were constructed using WGCNA and topological overlap to link omics features with physiological phenotypes. For experimental validation, liver tissues were collected from endurance-trained Sprague-Dawley rats, and key nodes were confirmed by Western blotting, qRT-PCR, and immunofluorescence/immunohistochemical staining. Public scRNA-seq data were further integrated to map multi-omics signals to single-cell resolution and assess functional changes in specific cell types. RESULTS: The hepatic response to exercise stress was stage-specific, shifting from early transcriptional activation to later proteomic and metabolic remodeling. Multi-omics integration revealed distinct sex-associated adaptive trajectories: males were more strongly associated with energy metabolism, redox-related programs, and amino acid/organic acid catabolism, whereas females showed prominent membrane lipid remodeling, proteostasis -related programs, and mitochondrial/ribosomal translational features. Single-cell analysis showed that tissue remodeling occurred without major lineage turnover, instead involving altered communication among pre-existing cell communities. Validation of PPP1R3G identified a protein-dominant exercise-responsive marker, supporting the contribution of post-transcriptional or protein-level regulation. CONCLUSIONS: Hepatic adaptation to endurance stress follows a cross-omics evolutionary pattern with sex-specific reprogramming of energy supply and homeostatic maintenance. This time-resolved framework clarifies how exercise improves liver function and supports sex-oriented metabolic interventions and therapeutic target discovery.

Animals↗
PubMed2026

Anti-inflammatory and phosphorylation effects of CFTR modulator triple therapy in cystic fibrosis.

CFTR modulators like elexacaftor-tezacaftor-ivacaftor (ETI) improve morbidity in cystic fibrosis (CF), but their systemic effects on young children are not yet clear. We hypothesize that ETI has anti-inflammatory effects and reverse disease-associated molecular signatures in children with CF. This exploratory pilot study evaluates the cellular mechanisms of ETI on peripheral immune cells in children (<12 years) with CF using a multi-omics approach. Seventeen children with CF (median age 8.7 years, 26% female) and 12 controls (median age 9.6 years, 42% female) were included for blood RNA-sequencing, proteomics and phosphoproteomics. Baseline pathway enrichment analysis revealed systemic inflammation, transmembrane transporter deficiencies, reduced protein kinase, and GTPase activity. Three months post-ETI, anti-inflammatory effects, epigenetic modulation, and increased protein kinase activity were observed, indicating partial reversal of cellular abnormalities. ETI modified systemic inflammatory, epigenetic, and phosphorylation pathways in young children with CF, offering insights into CF pathology and potential biomarkers for treatment monitoring.

cystic fibrosis↗
PubMed2025

Tonic signaling of the B-cell antigen-specific receptor is a common functional hallmark in chronic lymphocytic leukemia cell phosphoproteomes at early disease stages.

B-cell chronic lymphocytic leukemia (B-CLL) is characterized by highly heterogeneous genomic alterations and altered signaling pathways, with limited studies on its proteome. Our study presents a comprehensive analysis of the proteome and phosphoproteome in B-CLL and CLL-like monoclonal B-cell lymphocytosis (MBL) primary cells. Using high-resolution mass spectrometry, we identified 2970 proteins and 316 phosphoproteins across five tumor samples, including 55 newly identified phosphopeptides (ProteomeXchange-PXD005997). Our multifaceted approach also integrated protein microarrays and western blotting for further data validation in a new patient cohort of 14 patients. Despite sharing 73% of their proteomes, the phosphoproteomes varied significantly among samples, independent of cytogenetic alterations and immunoglobulin heavy variable cluster (IGHV) mutational status. We identified common functional hallmarks in B-CLL and MBL phosphoproteomes, notably tonic signaling (low-level, constitutive signaling) of the B-cell antigen-specific receptor (BCR) and nuclear factor NF-kappa-B (NF-k&#x3b2;)/signal transducer and activator of transcription 3 (STAT3) pathways. Nine phosphoproteins involved in BCR signaling were further validated, showing a high correlation with early disease stages. Our study advances the field by providing a detailed perspective on the proteome and phosphoproteome of B-CLL cells, revealing signaling pathways crucial for disease development and progression. Integrating diverse proteomics techniques and identifying novel phosphopeptides offers new insights into CLL biology, potentially informing future therapeutic strategies and biomarker development for early diagnosis and personalized treatment.

Humans↗
PubMed2026

Emerging Trends in Mass Spectrometry-Based Quantitative Proteome and Phosphoproteome Profiling in Maize.

Maize (Zea mays) is both an agronomically important crop and a reference model organism that has enabled the dissection of the molecular basis of plant development and environmental responses. Mass spectrometry-based proteomics provides a powerful approach to identify and quantify proteins and their post-translational modifications, facilitating the discovery of molecular mechanisms underlying complex biological processes. Unlike the study of gene expression using transcriptomics, analysis of the proteome and phosphoproteome provides direct measurement of proteins, which are responsible for driving or regulating nearly all cellular processes, thus offering a more complete picture of the cell's functional state. Over the past two decades, advancements in mass spectrometry have enabled large-scale profiling of protein abundance and phosphorylation sites in maize, improving our understanding of various biological phenomena. Here, we briefly summarize some of the major biological insights gained from maize proteome and phosphoproteome studies, and provide an overview of mass spectrometry sample preparation and acquisition/analysis workflows for the quantitative and reproducible analysis of protein abundance and phosphorylation dynamics in maize.

Zea mays↗
PubMed2026

Proteomic and Phosphoproteomic Signatures Link Molecular Remodeling to Behavioral Outcomes Following Elderberry and DHA Supplementation in Aging Mice.

Background: Aging is a risk factor for Alzheimer's disease and related dementias, which are associated with synaptic dysfunction and cognitive decline. Elderberry (Sambucus spp.) is rich in anthocyanins with antioxidant and anti-inflammatory properties. Docosahexaenoic acid (DHA), an essential fatty acid, plays a key role in neuronal membrane integrity during brain aging. However, it remains unclear whether elderberry and DHA exert overlapping or distinct effects on brain aging and how these relate to molecular signaling. This study aimed to characterize molecular signatures induced by dietary supplementation and to determine their relationships with behavioral outcomes. Methods: 44-week-old male C57BL/6J mice were randomly assigned to control, elderberry, DHA, or combined diets for 12 weeks. Behavioral testing assessed anxiety-like behavior, spatial learning and memory. Brain tissues underwent proteomic and phosphoproteomic profiling and fatty-acid analysis. Data were analyzed using Ingenuity Pathway Analysis to identify enriched pathways, upstream regulators, and functional associations. Results: Elderberry as well as DHA supplementation induced targeted remodeling of the proteome and phosphoproteome, with pathway enrichment involving synaptogenesis, glutamatergic signaling, and long-term potentiation. Upstream-regulator analysis predicted elderberry-associated CDK5 signaling, accompanied by reduced MAPT/Tau phosphorylation at selected sites, whereas DHA supplementation was associated with CAMK-related signaling. DHA supplementation altered fatty-acid composition, increasing the n-3/n-6 ratio. Elderberry reduced anxiety-like behavior and improved target-directed search during the Barnes maze probe test. Molecular signatures were examined in relation to the measured behavioral outcomes. Conclusions: Elderberry and DHA are associated with distinct molecular networks related to synaptic function and behavioral outcomes in the aging male mouse brain. These findings support further investigation of elderberry and DHA as dietary interventions targeting molecular and behavioral features of brain aging.

Animals↗