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Background: Abdominal aortic aneurysm (AAA) is a disease of high prevalence in old age, and its incidence gradually increases with increasing age. There were few studies about differences in the circulatory system in the incidence of AAA, mainly because younger patients with AAA are fewer and more comorbid nonatherosclerotic factors., Method: We induced AAA in ApoE -/- male mice of different ages (10 or 24 weeks) and obtained plasma samples. After the top 14 most abundant proteins were detected, the plasma was analyzed by a proteomic study using the data-dependent acquisition (DDA) technique. The proteomic results were compared between different groups to identify age-related differentially expressed proteins (DEPs) in the circulation that contribute to AAA formation. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) network analyses were performed by R software. The top 10 proteins were determined with the MCC method of Cytoscape, and transcription factor (TF) prediction of the DEPs was performed with iRegulon (Cytoscape)., Results: The aortic diameter fold increase was higher in the aged group than in the youth group ( p < 0.01). Overall, 92 DEPs related to age and involved in AAA formation were identified. GO analysis of the DEPs showed enrichment of the terms wounding healing, response to oxidative stress, regulation of body fluid levels, ribose phosphate metabolic process, and blood coagulation. The KEGG pathway analysis showed enrichment of the terms platelet activation, complement and coagulation cascades, glycolysis/gluconeogenesis, carbon metabolism, biosynthesis of amino acids, and ECM-receptor interaction. The top 10 proteins were Tpi1, Eno1, Prdx1, Ppia, Prdx6, Vwf, Prdx2, Fga, Fgg, and Fgb, and the predicted TFs of these proteins were Nfe2, Srf, Epas1, Tbp, and Hoxc8., Conclusion: The identified proteins related to age and involved in AAA formation were associated with the response to oxidative stress, coagulation and platelet activation, and complement and inflammation pathways, and the TFs of these proteins might be potential targets for AAA treatments. Further experimental and biological studies are needed to elucidate the role of these age-associated and AAA-related proteins in the progression of AAA., Competing Interests: The authors declare that they have no competing interests., (© 2022 Ren et al.)

Introduction : Abdominal aortic aneurysm (AAA) is a common, complex, and life-threatening disease. Currently, the pathogenesis of AAA is not well understood. No biomarkers or specific drugs are available for AAA in clinical applications. Proteomics is a powerful tool in biomarker discovery, exploration of pathogenesis, and drug target identification. Areas covered : We review the application of mass spectrometry-based proteome analysis in AAA patients within the last ten years. Differentially expressed proteins associated with AAA were identified in multiple sample sources, including vascular tissue, intraluminal thrombus, tissue secretome, blood, and cells. Some potential disease biomarkers, pathogenic mechanisms, or therapeutic targets for AAA were discovered using proteome analysis. The challenges and prospects of proteomics applied to AAA are also discussed. Expert opinion : Since most of the previous proteomic studies used relatively small sample sizes, some promising biomarkers need to be validated in multicenter cohorts to accelerate their clinical application. With the rapid development of mass spectrometry technology, modification-specific proteomics and multi-omics research in the future will enhance our understanding of the pathogenesis of AAA and promote biomarker discovery and drug development for clinical translation.

Urine, reflecting many changes in the body, is a better source than blood for biomarker discovery. However, even under physiological conditions, the urine proteome often varies. Understanding how various regulating factors affect urine proteome helps link changes to urine proteome with urinary biomarkers of physiological conditions as well as corresponding diseases. To evaluate the possible impact of α1-adrenergic receptor on urine proteome, this study investigated effects of the specific inhibitor prazosin on the urine proteome in a rat model by using tandem mass tagging and two-dimensional liquid chromatography-tandem mass spectrometry. A total of 775 proteins were identified, approximately half of which were influenced by prazosin treatment, indicating that the sympathetic nervous system exerts a significant impact on urine proteome. Eight significantly changed proteins were previously annotated as urinary candidate biomarkers. Angiotensinogen, haptoglobin, and beta-2 microglobulin, which were reported to be associated with blood pressure, were validated via Western blot. Prazosin is widely used in clinical practice; thus, these protein changes should be considered when studying corresponding diseases such as hypertension, post-traumatic stress disorder and benign prostatic hyperplasia. The related physiological activities of α1-receptors, controlling blood pressure and fear response might significantly affect the urine proteome and warrant further biomarker studies., Competing Interests: The authors have declared that no competing interests exist.

Urinary proteomics is emerging as a potent tool for detecting sensitive and non-invasive biomarkers. At present, the comparability of urinary proteomics data across diverse liquid chromatography−mass spectrometry (LC-MS) platforms remains an area that requires investigation. In this study, we conduct a comprehensive evaluation of urinary proteome across multiple LC-MS platforms. To systematically analyze and assess the quality of large-scale urinary proteomics data, we develop a comprehensive quality control (QC) system named MSCohort, which extracted 81 metrics for individual experiment and the whole cohort quality evaluation. Additionally, we present a standard operating procedure (SOP) for high-throughput urinary proteome analysis based on MSCohort QC system. Our study involves 20 LC-MS platforms and reveals that, when combined with a comprehensive QC system and a unified SOP, the data generated by data-independent acquisition (DIA) workflow in urine QC samples exhibit high robustness, sensitivity, and reproducibility across multiple LC-MS platforms. Furthermore, we apply this SOP to hybrid benchmarking samples and clinical colorectal cancer (CRC) urinary proteome including 527 experiments. Across three different LC-MS platforms, the analyses report high quantitative reproducibility and consistent disease patterns. This work lays the groundwork for large-scale clinical urinary proteomics studies spanning multiple platforms, paving the way for precision medicine research. Urinary proteomics offers sensitive, non-invasive biomarkers, but cross-platform LC-MS data comparability requires investigation. Here, the authors evaluate 20 LC-MS platforms, developing MSCohort, a QC system with 81 metrics, and a unified SOP, paving the way for precision medicine research. [ABSTRACT FROM AUTHOR]

Introduction: Cardiovascular diseases (CVDs) are the leading causes of mortality and morbidity worldwide, making early diagnosis and effective treatment essential. As a promising and noninvasive research method, urine proteomics shows excellent potential to identify reliable urinary biomarkers that could enhance prediction, prevention, and prognosis in patients with CVD. Areas covered: This review summarizes recent advancements in urinary protein biomarker profiling using urine proteomic techniques to identify potential CVD biomarkers. Additionally, it highlights potential disease biomarkers for the early detection, risk stratification, and monitoring of CVD, including hypertension, atherosclerosis, coronary artery disease, angina, myocardial infarction, heart failure, preeclampsia, and vasculitis. A literature search was conducted through Pubmed, Scopus, Google Scholar, and Web of Science. The period is January 2009 to February 2024. Expert opinion: Over the past decade, urinary proteomics has been employed in CVD research, with the potential to facilitate the discovery of novel disease biomarkers and the exploration of prospective therapeutic targets. Proteomics-based multicenter cohort studies should be conducted in the future to gain deeper insights into the pathophysiological mechanisms of CVD, accelerate the identification of potential biomarkers for disease prediction, diagnosis, and treatment, and facilitate their clinical translation. [ABSTRACT FROM AUTHOR]

A study conducted on rhesus macaques aimed to explore the co-pathogenic mechanism of the Delta variant of SARS-CoV-2 and the original virus. The study found that SARS-CoV-2 infection in the macaques induced typical characteristics of COVID-19 in their livers. Proteomic and phosphoproteomic analysis revealed changes in protein synthesis, metabolism, autophagy, and ferroptosis in the infected livers. The findings suggest that the hepatobiliary system can be influenced by COVID-19 infection, and understanding the biological processes and pathological mechanisms can help identify potential therapeutic targets. [Extracted from the article]

Aortic aneurysm and dissection (AAD) is a life-threatening disease worldwide. Recently, fluoroquinolones have been reported to significantly increase the risk of AAD. This study aimed to investigate the potential functional mechanism and molecular targets of fluoroquinolones in relation to AAD by an integrated proteomic and network pharmacology strategy. A total of 1351 differentially expressed proteins were identified in human aortic vascular smooth muscle cells (VSMCs) after ciprofloxacin (CIP) stimulation. The functional analysis emphasized the important roles of metabolism, extracellular matrix homeostasis, mitochondrial damage, focal adhesion, and apoptosis in CIP-stimulated VSMCs. CIP targets were predicted with online databases and verified by molecular docking. Protein–protein interaction (PPI) analysis and module construction of the 34 potential CIP targets and 37 selected hub molecules after CIP stimulation identified four critical target proteins in the module: PARP1, RAC1, IGF1R and MKI67. Functional analysis of the PPI module showed that the MAPK signalling pathway, focal adhesion, apoptosis, regulation of actin cytoskeleton, and PI3K-Akt signalling pathway were significantly enriched. Our results will provide novel insights into the pathogenic mechanism of fluoroquinolones in aortic diseases. [ABSTRACT FROM AUTHOR]

Objective: We aimed to explore and identify candidate protein biomarkers of cryoglobulinemia (CGE) in disease control patients with negative cryoglobulin (DC) or healthy controls (HCs). Methods: The tandem mass tag (TMT)-labeled serum quantitative proteomics approach was used to identify differentially expressed proteins between the CGE and DC groups. Ingenuity pathway analysis was used for functional annotation of differentially expressed proteins. Biomarker candidates were validated in another cohort using the parallel reaction monitoring (PRM) method. Apolipoprotein A1 (APOA1), apolipoprotein CIII (APOC3), adiponectin, and proprotein convertase subtilisin/kexin type-9 (PCSK9), which represent key proteins involved in the cholesterol metabolism pathway, were further verified in an increased number of samples by enzyme-linked immunosorbent assay (ELISA). Results: A total of 1004 proteins were identified, of which 109 proteins were differentially expressed between the CGE and DC groups. These differentially expressed proteins were primarily involved in hepatic fibrosis/hepatic stellate cell activation and immune/inflammation-related pathways. In the disease and biofunction analysis, these proteins were mainly associated with the adhesion of blood cells, leukocyte migration, cholesterol transport, and transport of lipids. Twelve candidate biomarkers were validated by PRM-based proteomics, and proteins involved in the cholesterol metabolism pathway were further verified. APOA1, APOC3, adiponectin and PCSK9 concentrations were increased in CGE patients compared with healthy controls (P=0.0123, 0.1136, 0.5760, and 0.0019, respectively). Conclusion: This report describes the first application of a TMT-PRM-ELISA workflow to identify and validate CGE-specific biomarkers in serum. APOA1 and PCSK9 have been confirmed to be increased in CGE patients, demonstrating that proteins involved in cholesterol metabolism are also implicated in the development of CGE. These findings contribute to pathogenesis research and biomarker discovery in CGE. [ABSTRACT FROM AUTHOR]

Cryptococcus neoformans is an invasive human fungal pathogen that causes more than 181,000 deaths each year. Studies have demonstrated that pulmonary C. neoformans infection induces innate immune responses involving copper, and copper detoxification in C. neoformans improves its fitness and pathogenicity during pulmonary C. neoformans infection. However, the molecular mechanism by which copper inhibits C. neoformans proliferation is unclear. We used a metallothionein double-knockout C. neoformans mutant that was highly sensitive to copper to demonstrate that exogenous copper ions inhibit fungal cell growth by inducing reactive oxygen species generation. Using liquid chromatography-tandem mass spectrometry, we found that copper down-regulated factors involved in protein translation, but up-regulated proteins involved in ubiquitin-mediated protein degradation. We propose that the down-regulation of protein synthesis and the up-regulation of protein degradation are the main effects of copper toxicity. The ubiquitin modification of total protein and proteasome activity were promoted under copper stress, and inhibition of the proteasome pathway alleviated copper toxicity. Our proteomic analysis sheds new light on the antifungal mechanisms of copper. [ABSTRACT FROM AUTHOR]

Urine is a promising biomarker source for clinical proteomics studies. Regional physiological differences are common in multi-center clinical studies. In this study, we investigate whether significant differences are present in the urinary proteomes of individuals from different regions in China. In this study, morning urine samples were collected from healthy urban residents in three regions of China (Haikou, Xi'an and Xining) and urinary proteins were preserved using a membrane-based method (Urimem). The urine proteomes of 27 normal samples were analyzed using LC-MS/MS and compared among three regions. Functional annotation of the differential proteins among the three areas was analyzed using the DAVID online database, and pathway enrichment of the differential urinary proteins was analyzed using KEGG. We identified 1898 proteins from Urimem samples using label-free proteome quantification, of which 56 urine proteins were differentially expressed among the three regions (P < 0.05). Hierarchical clustering analysis showed that inter-regional differences caused less significant changes in the urine proteome than inter-sex differences. After gender stratification, 16 differential proteins were identified in male samples and 84 differential proteins were identified in female samples. Among these differential proteins, several proteins have been previously reported as urinary disease biomarkers. Urimem will facilitate urinary protein storage for large-scale urine sample collection. Regional differences are a confounding factor influencing the urine proteome and should be considered in future multi-center biomarker studies. [ABSTRACT FROM AUTHOR]

Urine is a better source than plasma for biomarker studies, as it can accumulate all changes in the body. Various candidate urinary biomarkers of physiological condition, kidney disease and even brain dysfunction, have been detected in urine; however, urine has rarely been used to reflect cardiac diseases. In this study, urine at day 0, 14, 21 and 28 were collected from the myosin-induced autoimmune myocarditis rat models. The candidate urinary biomarkers were then characterized using the isobaric tandem mass tag labeling approach coupled with offline two-dimensional reverse-phase liquid chromatography and high-resolution mass spectrometry. Compared with controls, forty-six urinary proteins were significantly changed in the myocarditis rats; among them, ten had previously been associated with myocarditis, twelve corresponding gene products had annotated as mainly cardiovascular network genes by the Ingenuity Pathway Analysis, four urinary proteins were validated by western blot, thirteen were reported in previous urine proteome studies of other diseases and twenty-six were reported the first time to be related to myocarditis. Significance This is the first study to use isobaric tandem mass tag labeling approach in the urine proteome analysis of experimental autoimmune myocarditis. These findings may provide clues for the pathogenesis of myocarditis. And the study showed that urine can be a good source of myocarditis biomarkers. [ABSTRACT FROM AUTHOR]

Despite advances in cancer treatments, early diagnosis of cancer is still the most promising way to improve outcomes. Without homeostatic control, urine reflects systemic changes in the body and can potentially be used for early detection of cancer. In this study, a tumor-bearing rat model was established by subcutaneous injection of Walker 256 cells. Urine samples from tumor-bearing rats were collected at five time points during cancer development. Dynamic urine proteomes were profiled using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Several urine proteins that changed at multiple time points were selected as candidate cancer biomarkers and were further validated by multiple reaction monitoring (MRM) analysis. It was found that the urinary protein patterns changed significantly with cancer development in a tumor-bearing rat model. A total of 10 urinary proteins (HPT, APOA4, CO4, B2MG, A1AG, CATC, VCAM1, CALB1, CSPG4, and VTDB) changed significantly even before a tumor mass was palpable, and these early changes in urine could also be identified with differential abundance at late stages of cancer. Our results indicate that urine proteins could enable early detection of cancer at an early onset of tumor growth and monitoring of cancer progression. [ABSTRACT FROM AUTHOR]

Biomarkers are the measurable changes associated with physiological or pathophysiological processes. Urine, unlike blood, lacks mechanisms for maintaining homeostasis: it is therefore an ideal source of biomarkers that can reflect systemic changes. Urinary proteome and metabolome have been studied for their diagnostic capabilities, ability to monitor disease and prognostic utility. In this review, the effects of common physiological conditions such as gender, age, diet, daily rhythms, exercise, hormone status, lifestyle and extreme environments on human urine are discussed. These effects should be considered when biomarker studies of diseases are conducted. More importantly, if physiological changes can be reflected in urine, we have reason to expect that urine will become widely used to detect small and early changes in pathological and/or pharmacological conditions. [ABSTRACT FROM PUBLISHER]

Apolipoprotein knockout (ApoE−/−) and CD57BL/6J mouse models of angiotensin II (Ang II)-induced abdominal aortic aneurysm (AAA) are commonly used in AAA research. However, the similarities and differences in the molecular mechanisms of AAA in these two genotypes have not been reported. In our study, we analyzed proteomics data from ApoE−/− and CD57BL/6J mouse models of Ang II-induced AAA and control mice by LC–MS/MS. Gene set enrichment analysis (GSEA) of differentially abundance proteins (DAPs) in the ApoE−/− or CD57BL/6J mouse groups was performed in R software, and infiltration of immune cells in groups was assessed. DAP that showed the same trend in abundance in ApoE−/− and CD57BL/6J mice (S-DAP) were identified and subjected to GO enrichment, KEGG pathway, and connectivity map (CMap) analyses. The protein–protein interaction (PPI) network of the S-DAP was drawn, the key S-DAP were identified by MCODE, and the transcription factors (TFs) of crucial S-DAP were predicted by iRegulon in Cytoscape. Male ApoE−/− and CD57BL/6J mouse models of Ang II-induced AAA are commonly used in AAA research, and extracellular matrix organization is associated with AAA in both of these models. However, there are some differences between the mechanisms underlying AAA in these two genotypes, and these differences need to be considered when studying AAA and selecting models. Our research provided the first insight into the similarity and differential mechanisms of Ang II infused AAA models using ApoE−/− and CD57BL/6J mice. This study might provide the some advises for the selection of Ang II infused AAA models for further AAA researches. [Display omitted] • This study provides a first insight on the mechanism of Ang II infused AAA models in ApoE−/− and CD57BL/6J mice based on proteomic. • The Infiltration of immune cells of CD57BL/6J AAA model were differently abundance in resting CD4+ memory T cells, activated CD4+ memory cells, regulatory T cells (Tregs), resting NK cells, and neutrophils, while Neutrophils was differently abundance in ApoE−/− model. • The DEPs of two Ang II infused AAA models mostly enriched on extracellular matrix pathway. • Beclometasone, Nitrofurantoin, and Milrinone might suppress to AAA formation. [ABSTRACT FROM AUTHOR]