Author Correction: Early methionine availability attenuates T cell exhaustion
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SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data
<h4>Background</h4>Tumor neoantigens are key targets for personalized vaccines and T-cell therapies, yet most pipelines focus on neoantigens derived from SNV/small indel and often yield a limited number of high-quality candidates. SVs are prevalent in tumors …
Read PDFSerial Aqueous Humor Proteomics in Diabetic Macular Edema: Correlation of Novel Targets with Retinal Fluid Volume
<h4>Objective</h4>Diabetic macular edema (DME) with incomplete response to anti-VEGF therapy is a significant challenge. Here, we integrated advanced proteomics and an artificial intelligence (AI)-driven platform to elucidate molecular mechanisms associated with resistance to anti-VEGF treatment.<h4>Design</h4>Translational …
Read PDFFenofibrate attenuates hyperhomocysteinemia-potentiated thrombosis by restoring platelet fatty acid β-oxidation
Hyperhomocysteinemia (HHcy) is an independent risk factor for thrombotic cardiovascular events. We previously demonstrated that homocysteine (Hcy) amplifies platelet activation by promoting membrane remodeling and enhancing signaling through surface platforms such as integrin αIIbβ3 and …
Read PDFThe Activation of ARF1 Is Dynamically Regulated by its Palmitoylation
ARF1 plays a crucial role in maintaining the structure and function of the Golgi apparatus, yet the precise on-site regulatory mechanism governing ARF1 activation remains incompletely understood. Here, we have uncovered a novel regulatory mechanism …
Read PDFFrom proteomics to colloidal gold tests for urinary thrombomodulin: a prospective cohort study on accurate sepsis screening
<h4>Background</h4>To develop a new non-invasive screening method for sepsis by detecting urine samples.<h4>Methods</h4>A prospective study was conducted to collect urine samples from a cohort of 22 individuals diagnosed with sepsis and admitted to the Intensive …
Read PDFA Multi-omics PTM Atlas Reveals Key Insights into Metabolic Reprogramming in Colorectal Cancer
<h4>Background/aim</h4>Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, with limited effective targeted therapies. Metabolic reprogramming is a hallmark of cancer, and post-translational modifications (PTMs), such as phosphorylation, ubiquitination, and malonylation, play critical …
Read PDFMolecular characteristics of follicular fluid in advanced maternal age women with different ovarian reserves: a multi-omics study
BACKGROUND: Age-related diminished ovarian reserve (DOR) exhibits marked significant individual variation. Some women of advanced age with normal ovarian reserve (NOR) achieve better reproductive outcomes than age-matched DOR patients. OBJECTIVE: This study aimed to compare …
Read PDFProteomic Profiling of Endometrial Cancer Tissues Reveals Differential Expression of Proteomes in Obese Versus Non-Obese Patients
Endometrial cancer (EC) is the leading gynecological malignancy worldwide. Obesity is reported to be associated with 50% of EC cases. Significant gaps remain in investigating specific molecular mechanisms behind the obesity-driven EC. Women diagnosed with …
Read PDFMulti-omic analysis reveals nitric oxide dependent remodeling in classically activated macrophages and identifies negative regulation mediated by AKR1A1
Nitric oxide (NO•) is an important regulatory molecule in many biological processes, including immune response. During response to classical activation stimuli lipopolysaccharide (LPS) and interferon-γ (IFNγ), macrophages generate NO• via inducible nitric oxide synthase (iNOS). …
Read PDFPost-Transcriptional Modification Integration for Ligand-Receptor Cellular Network Inference
Cell-cell communications are widely explored to understand tissue homeostasis and diseases. Numerous computational tools have been developed to infer cellular interactions from transcriptomic or proteomic expression data. However, proteins often carry post-translational modifications (PTMs) that …
Read PDFIntegrated serum proteomic and liver genomic analyses identify molecular signatures associated with metabolic dysfunction-associated steatotic liver disease: a multi-cohort study
<h4>Background</h4>Circulating proteomics acts as an intermediate phenotype linking genetic susceptibility to MASLD. However, current evidence rarely establishes a direct concordance between serum protein levels and hepatic gene expression. We aimed to perform a multi-cohort joint …
Read PDFImproved red blood cell storage quality of blood from donors carrying the hypermorphic PIMT I120 variant
Protein-l-isoaspartate <i>O</i>-methyltransferase (PIMT), encoded by <i>PCMT1</i>, is a repair enzyme that corrects isoaspartyl lesions, preserving protein structure and function. While indispensable for neuronal integrity, its role in red blood cells (RBCs) and transfusion outcomes is …
Read PDFBBB dynamics: the lifespan perspective
Recent advances have shifted our understanding of the blood-brain barrier (BBB) not as a static wall, but as a dynamic and evolving system whose property is variable across the lifespan: acquisitive in early development, heterogeneous …
Read PDFEnergy metabolism alteration and gene expression reprogramming in a cell model of high fat load non-alcoholic fatty liver disease
BACKGROUND: Metabolic rewiring plays a crucial role in the energy metabolism of hepatocytes during steatosis. However, the precise alterations in energy metabolism remain unclear. The aim of this study was to investigate the effects of …
Read PDFImpact of single freeze-thaw cycles on human serum proteins: Implications for mass spectrometry biomarker validation
Validation of biomarkers for clinical diagnostics requires high-quality samples and standardized protocols. This study investigated the effect of a single freeze-and-thaw (FT) cycle on the quality of liquid nitrogen-stored clinical serum samples. Using mass spectrometry, …
Read PDFDeciphering Stiffness-Driven Changes in Colorectal Cancer by Proteomics
Tumor stiffening plays a pivotal role in cancer progression. Increased tumor stiffness, resulting from interactions between cancer cells and their surrounding microenvironment, alters the tumor's mechanical properties and significantly impacts cancer growth and metastasis, the …
Read PDFAppraisal of the Use of Proteomics Methodological Approaches and Technologies on Sheep and Goat Research and Clinical Work
This paper describes a detailed evaluation of published works, in which proteomics methodological approaches and technologies were used to advance knowledge about small ruminants. The specific objective of this assessment was the presentation of quantitative …
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