Journal of Proteome Research最新文献

Diabetic cardiomyopathy (DCM), a severe complication of type 2 diabetes mellitus (T2DM), lacks specific and effective biomarkers for early diagnosis. This study constructed a plasma-specific spectral library by integrating proteomic and nonenzymatic glycation data from eight pretreatment workflows via data-dependent acquisition. Data-independent acquisition was then applied to profile plasma proteomes and glycation modifications in controls, DM patients, and DCM patients, revealing clear disparities in protein abundance and glycation modification patterns among the three groups. Functional enrichment analysis indicated that these differentially expressed proteins and modified peptides were involved primarily in immune responses, inflammatory processes, and metabolic pathways. Subsequently, parallel reaction monitoring was used to validate the proteins and glycation sites with significant changes. Specific peptides of complement 5 and specific glycation modifications on human serum albumin demonstrated a strong capacity to discriminate DCM from DM, achieving the highest area under the curve values of 0.97 in receiver operating characteristic analyses, underscoring their promising potential as DCM biomarkers. In conclusion, integrated proteomic and glycation modification analysis revealed candidate biomarkers for DCM diagnosis and offered novel insights into DCM pathogenesis.

Vitronectin (VTN) is a multifunctional glycoprotein that promotes cell adhesion and survival signaling through interactions with integrins. Elevated serum VTN levels have recently emerged as diagnostic and prognostic markers for hepatocellular carcinoma (HCC), yet its mechanistic role in HCC progression remains unclear. Here, we show that VTN knockdown in HCC cells has minimal effects on cell migration and viability, raising the possibility that VTN may promote tumor progression by shaping the tumor microenvironment rather than via cell-intrinsic mechanisms. To investigate this, we conducted secretome profiling after VTN knockdown in HCC cells, identifying 756 secreted proteins. Functional enrichment analysis revealed critical biological pathways and protein-protein interaction modules potentially regulated by VTN. Notably, a subset of proteins downregulated upon VTN silencing was associated with poor HCC prognosis. Using Parallel Reaction Monitoring (PRM) proteomics, we validated that the pro-tumorigenic cytokines CXCL5 and CXCL8 were significantly decreased following VTN knockdown. These findings indicate that VTN promotes expression of cytokines involved in HCC progression, implicating autocrine and paracrine mechanisms in its tumor-promoting effects.

The survival rates of high-grade serous ovarian cancer have not improved in the last three decades, despite extensive research into the molecular determinants of chemoresistance that could inform personalized therapies. This systematic review synthesizes proteomic studies that have used varied sample types, including cell lines, serum, plasma, and ascites, to propose molecular markers of response to treatment regimens consisting of platinum-based chemotherapeutics, taxanes, doxorubicin, and combinations thereof. Gene ontology analyses of differentially expressed proteins across all studies highlight key biological functions, such as heat shock response, cell adhesion, and cell migration. Frequently implicated protein families include keratins, annexins, thioredoxin-related proteins, and SERPINs. We evaluate methodological rigor, orthogonal validation attempts, and adherence to MIAPE data reporting standards to contextualize current knowledge and promote reproducibility in future studies. Collectively, this review underscores proteomics as a promising tool for the prediction of chemotherapy response in high-grade serous ovarian cancer, while emphasizing the need for prospective, standardized approaches that align with data reporting guidelines.

The air–liquid interface (ALI) model using Calu-3 cells has been used to model lung diseases. In ALI, Calu-3 polarizes and changes to a mucus-producing cell. Polarized Calu-3 similarity with primary cells has been proven; however, no studies have been focusing on the pathways differentially expressed in ALI. Here, we profiled the proteome and transcriptome of Calu-3 from submerged (nonpolarized) to ALI (polarized) conditions, and in the omics data, we observed an increase in cell replication in the nonpolarized condition while polarized cells presented higher activation of cellular energy production, protein maturation and recycle, and expression of immune molecules. Moreover, the omics findings showed upregulation of different biological processes related to the protein quality control system and antigen processing presentation in polarized cells. Immunoblot and fluorescence microscopy confirmed increased expression of bronchial epithelium integrity components such as mucus and tight junctions in polarized cells and revealed a characteristic protein expression and cellular organization found in normal lung epithelium. Furthermore, SARS-CoV-2 infection in polarized cells revealed increased cell death associated with the higher expression of ACE2. The differences observed in this study give us a better understanding of how ALI can mimic human bronchial-epithelial cells and its applications in different contexts of lung diseases.

Numerous genetic variants have been identified by genome-wide association studies as being associated with colorectal cancer (CRC) risk. Metabolome-wide association analysis was performed for 187 CRC-associated genetic variants using genomic data and untargeted ¹H nuclear magnetic resonance urine metabolomics from 1951 Airwave Health Monitoring Study participants. We identified statistically significant associations between seven CRC single-nucleotide polymorphisms (SNPs) and urinary metabolites. This included SNPs within or close to RHPN2 with sucrose (P = 1.2 × 10^–7), SLC6A18 with amino acids (P = 6.9 × 10^–5 with tyrosine, P = 9.9 × 10^–5 with leucine), and MAP2K5 and BMP2 with gut microbial metabolites (P = 1.6 × 10^–4 and P = 4.4 × 10^–4). The most significant correlation was followed by functional experiments in Caco-2 colon cancer cells. CRISPR-mediated knockout of a 48-nt RHPN2 intronic region containing rs10411210 in colon cancer cells compromised cell growth. RNA sequencing was performed in the two sets of clones (3 edited and 3 unedited) followed by pathway enrichment, and gene ontology analysis depicted extensive deregulation of genes (448 up- and 195 downregulated) involved in cell division and several metabolic processes. Overall, these findings demonstrate that integrating genetic and metabolomic data highlights the importance of the RHPN2 intronic locus in CRC potentially through metabolic processes affecting excretion of dietary and other metabolites.

Recent advances in mass spectrometry permit unbiased proteome profiling of thousands of proteins from single cells using both label-free and labeling approaches. However, a major limitation of unbiased approaches is missing data, which worsens as the sample size increases. In addition, the reproducible measurement of post-translational modifications (PTMs) at the single cell level, particularly those present at a lower stoichiometry than their unmodified counterparts, poses an even greater challenge. To overcome this limitation, we developed a targeted strategy that combines tandem mass tag (TMT) multiplexing with SureQuant-based triggered MS/MS using super heavy TMT-labeled peptides that are 9 Da heavier than the TMTpro tags as triggers. To demonstrate the feasibility of our approach, we established a method quantifying four PTMs on the histone H3 protein (i.e., K14ac, K23ac, K27me, K27me3, and K79me) at single-cell resolution. We demonstrated robustness in quantitation compared to conventional approaches of data-dependent acquisition and standard parallel reaction monitoring. Further, we applied this strategy to single cells and revealed cellular heterogeneity in histone PTMs. Overall, we developed a targeted strategy with improved sensitivity and throughput for analyzing PTMs in single cells, which we expect will be broadly applicable to multiple types of PTMs while enabling focused analysis.

Hexavalent uranium (U(VI)) is widely found in nature and has an impact on human lung health. In this study, the proteomic changes in lung epithelial BEAS-2B cells exposed to U(VI) were evaluated using DIA (Data-Independent Acquisition) proteomics. BEAS-2B cells cultured in vitro were exposed to 0, 200, 400, and 700 mg/L U(VI) for 24 h, and differential proteins were identified by classification, KEGG pathway enrichment, and GO enrichment analysis. Furthermore, oxidative stress levels were measured, and five proteins were screened for validation. The results indicated that the number of differential proteins increased with the increase of the U(VI) dose. The differentially expressed proteins (DEPs) identified in the GJL vs Control comparison were significantly enriched in several KEGG pathways, including the PI3K-Akt signaling pathway, pathways in cancer, cell cycle, lysosome, and JAK-STAT signaling pathway. The DEPs related to the nucleoplasm, nucleus, and cytoskeleton were found to be enriched in several biological processes, including the cell cycle, positive regulation of transcription by RNA polymerase II, cell division, and cell migration. Differential proteins involve multiple organelles, and their functions are mostly related to protein binding. Furthermore, the ROS level increased, and the GSH was reduced. The expressions of STAT3, N-cadherin, and CDK2 proteins were down-regulated, and the expressions of GPX3 and TNFSF10B were up-regulated. This study provides a comprehensive understanding of the molecular mechanisms underlying U(VI)-induced pulmonary epithelial cytotoxicity.

Ulcerative colitis (UC) is a multifactorial inflammatory bowel disease (IBD) with increasing incidence worldwide. Current treatments, including NSAIDs and corticosteroids, provide partial symptom relief but are associated with significant side effects, highlighting the need for novel therapies with improved safety profiles. Given the role of oxidative stress and inflammation in driving tissue damage during colitis, natural compounds with antioxidant and anti-inflammatory properties represent promising therapeutic candidates. Thinned apples (TA), an agricultural byproduct, were identified as a valuable source of polyphenols (TAP) with demonstrated anti-inflammatory and antioxidant activities in a cell-based inflammation model. This study evaluates TAP’s therapeutic potential in a DNBS-induced colitis mouse model using label-free quantitative proteomics. Proteomic analysis revealed modulation of key pathways affected by TAP treatment, including: (i) activation of antioxidant defense mechanisms; (ii) reversal of DNBS-induced alterations, specifically ferroptosis and heme-toxicity; (iii) suppression of immune responses; and (iv) attenuation of ulcerative features, with downregulation of proteins involved in coagulation, inflammation, and angiogenesis. Overall, TAP showed significant therapeutic effects by targeting oxidative stress and inflammation, supporting its use as a polyphenol-rich extract in health products for UC. Moreover, repurposing TA as a bioactive extract offers an innovative strategy for industrial applications in therapeutic development.

Nonmuscle invasive bladder cancer (NMIBC) represents a significant clinical challenge due to its high recurrence and progression rates. We aimed to characterize proteomic differences between matched pairs of tumor and control bladder tissues in NMIBC to identify potential biomarkers and underlying molecular mechanisms. Methods: Data-independent analysis proteomics experiments were conducted in paired samples from 45 patients with NMIBC, comprising 45 tumor and 45 control tissues. Tumor and nontumor results were compared using a paired Student’s t test. Proteins detected in at least 50% of the samples were used. Results: A total of 188 differentially abundant detected proteins were identified, along with 11 proteins exclusively detected in tumor tissues, including SPINT1, TXNDC12, GTF2F1, COPZ1, RS25, PTK2, LSR, SNRNP40, NCOA5, SEC63, and CD2AP. The protein interaction network analysis among this set of proteins revealed AGR2, FLNA, TPM1, and CALD1. Additionally, CNDP2 and CTSD expression were inversely correlated with tumor recurrence and progression risk respectively, while EPS8L2 and KRT7 levels were associated with tumor staging. Conclusions: Our study identified specific proteins as potential NMIBC biomarkers and drug targets. The identified proteins, particularly those linked to tumor recurrence and staging, warrant further validation to assess their clinical utility in NMIBC diagnosis, prognosis, and treatment strategies.