Clinical proteomics最新文献

Integrating functional proteomics and next-generation sequencing (NGS) offers a comprehensive approach to unraveling the molecular intricacies of breast cancer. This study investigates the functional interplay between genomic alterations and protein expression in Taiwanese breast cancer patients. By analyzing 61 breast cancer samples using tandem mass tag (TMT) labeling and mass spectrometry, coupled with whole-exome sequencing (WES) or targeted sequencing, we identified key genetic mutations and their impact on protein expression. Notably, pathogenic variants in BRCA1, BRCA2, PTEN, and PIK3CA were found to be clinically relevant, potentially guiding targeted therapy decisions. Additionally, we discovered trans correlations between specific gene alterations (FANCA, HRAS, PIK3CA, MAP2K1, JAK2) and the expression of 22 proteins, suggesting potential molecular mechanisms underlying breast cancer development and progression. These findings highlight the power of integrating proteomics and NGS to identify potential therapeutic targets and enhance personalized medicine strategies for Taiwanese breast cancer patients.

Background: The standard "7 + 3" induction results in 30% of de novo acute myeloid leukemia (AML) patients not achieving complete remission (CR). We aimed to utilize the Olink^® platform to compare the bone marrow plasma proteomic profiles of newly diagnosed de novo AML patients who did and did not achieve CR following "7 + 3" induction treatment.

Methods: This prospective study included 43 untreated AML patients, stratified into CR (n = 29) and non-CR (n = 14) groups based on their response to "7 + 3" induction therapy. We employed the Olink^® Explore-384 Inflammation platform for proteomic analysis to investigate differences in bone marrow plasma protein levels between the CR and non-CR groups.

Results: Proteomic analysis demonstrated that the CR group exhibited significantly higher bone marrow plasma levels of ARTN and CCL23 than did the non-CR group. Immunohistochemical staining confirmed a higher proportion of tissue samples with intense staining for ARTN (25.40% vs. 7.05%, p = 0.013) and CCL23 (24.14% vs. 14.29%, p = 0.039) in the CR group. These findings were corroborated by bulk-RNA-seq, which indicated significantly elevated mRNA expression levels of ARTN (1.93 vs. -0.09; p = 0.003) and CCL23 (1.50 vs. 0.12; p = 0.021) in the CR group. The Human Protein Atlas provided external support for our findings.

Conclusions: The results suggest that ARTN and CCL23 may serve as biomarkers for predicting responsiveness to the "7 + 3" induction in untreated AML. Using an enzyme-linked immunosorbent assay to identify the roles of ARTN and CCL23 in predicting AML chemosensitivity may enhance clinical applicability in the future.

Background: Medwakh smoking has radically expanded among youth in the Middle East and around the world. The rising popularity of medwakh/dokha usage is linked to the onset of several chronic illnesses including cardiovascular diseases and cancers. Medwakh smoking is reported to increase the risk of inflammation in the lower respiratory tract owing to oxidative burden. To date, there are no reported studies investigating the impact of medwakh smoking on salivary protein profile. The current study aims to elucidate alterations in the salivary proteome profile of medwakh smokers.

Methods: Saliva samples collected from 33 medwakh smokers and 30 non-smokers were subjected to proteomic analysis using UHPLC-ESI-QTOF-MS. Saliva samples were further subjected to validatory experiments involving analysis of inflammatory cytokine profile using LEGENDplex™ Human Essential Immune Response Panel.

Results: Statistical analysis revealed alterations in the abundance of 74 key proteins including immune mediators and inflammatory markers in medwakh smokers (Accession: PXD045901). Proteins involved in building oxidative stress, alterations in cell anchorage, and cell metabolic processes were enhanced in medwakh smokers. Salivary immune response evaluation further validated the proteome findings, revealing significantly higher levels of IL-1β, IL-12p70, IL-23, IFN-γ (Th1 cytokines), IL-6 (Th2 cytokine), and MCP-1 (chemokine) in medwakh smokers. In addition, a substantial increase in abundance of involucrin suggesting a plausible stratified squamous cell differentiation and increased cell lysis in the oral cavity of medwakh smokers akin to chronic obstructive pulmonary diseases (COPD). The protein-metabolite joint pathway analysis further showed significantly enriched differentially expressed proteins and metabolites of glycolysis/gluconeogenesis, pentose phosphate, fructose and mannose, nicotinate and nicotinamide, and glutathione metabolism pathways among medwakh smokers.

Conclusions: The findings of the study provide valuable insights on potential perturbations in various key immune molecules, cytokines, and signaling pathways among medwakh smokers. Medwakh smokers displayed elevated inflammation, increased oxidative stress and defective antioxidant responses, dysregulated energy metabolism, and alterations in proteins related to cell adhesion, migration, differentiation, and proliferation. The findings of study underscore the urgent need for comprehensive public health interventions among youth by raising awareness, implementing effective smoking cessation programs, and promoting healthy lifestyle to safeguard the well-being of individuals and communities worldwide.

Our objective is to determine the protein and complements constituents of Cord blood Platelet-rich plasma (CB-PRP), based on the hypothesis that it contains beneficial components capable of arresting or potentially decelerating the advancement of atrophic age-related macular degeneration (dry-AMD), with the support of radiomics. Two distinct pools of CB-PRP were assessed, each pool obtained from a total of 15 umbilical cord-blood donors. One aliquot of each pool respectively was subjected to proteomic analysis in order to enhance the significance of our findings, by identifying proteins that are shared between the two sample pools and gaining insights into the pathways they are associated with. The bioinformatics analysis was developed using Reactome software. Three-hundred-seven (307) distinct proteins were found. Two hundred fifteen (215) of the elements mentioned above are shared by both pools. Seventy (70) elements are exclusive to pool S1, while pool S2 contains 22. We detected 109 representative and statistically significant pathways out of 549. We found proteins related to the immune system, signal transduction, vesicle-mediated transport, cell-cell communication, hemostasis, cellular responses to stimuli, cell cycle, and developmental biology. The analysis showed the presence of P15692-12, representing VEGF factor A, long form. With over 200 proteins, the CB-PRP can increase the immune response, including BCR, CD-22, FCGR, phospholipids, IL-10, FCGR-3A, and others. Discovering crucial trophic and complement-regulating variables is highly significant for potential applications in dry AMD. Our future research will examine the effects of intravitreal CB-PRP on dry-AMD eyes.

Background: The therapeutic potential of mesenchymal stem cells (MSCs) may be partly attributed to their secretion growth factors, cytokines and chemokines. In various preclinical studies, the use of MSC-conditioned media (CM) has demonstrated promising potential for promoting vascular repair.

Methods: To gain a comprehensive understanding of the variations in conditioned media derived from different sources of mesenchymal stem cells (MSCs) including umbilical cord, adipose and bone marrow, we investigated their reparative effects on human umbilical vein endothelial cells (HUVECs) subjected to damage induced by high glucose. Initially, the secreted proteins from the three types of MSCs were assessed using the bicinchoninic acid (BCA) method. Subsequently, we examined the influence of different type of MSC secreted proteins on the proliferation of HUVECs under high glucose conditions. Following this, transwell migration experiments were conducted to evaluate the impact of MSC source on the migration of HUVECs damaged by high glucose. We further compared the effects of adding secreted proteins from the three types of MSCs on the tube formation ability of HUVECs subjected to high glucose damage. Finally, tandem mass tag (TMT) labeling quantitative proteomics was performed to analyze differently expressed proteins in the secreted proteins of three type MSC by using LC-MS/MS.

Results: In this study, we observed a significantly higher secretion of proteins from umbilical cord mesenchymal stem cells (UMSCs) compared to adipose-derived stem cells (ADSCs). Subsequently, we found that the of proliferation HUVECs was significantly improved with supplementing the three MSCs secreted proteins under high glucose medium. Notably, the reparative effects of bone marrow mesenchymal stem cells (BMSCs) and UMSCs were superior to those of ADSCs. Afterwards, UMSCs exhibited the strongest ability to repair cell migration when HUVECs damaged by high glucose. Moreover, all three MSCs' secreted proteins exhibited the ability to enhance tube formation. Importantly, the UMSCs' secretome showed the most pronounced improvement in tube formation, as evidenced by the evaluation of parameters such as the number of nodes, the number of branches, and total length. These findings suggest that the UMSCs' secretome plays a crucial role in biological processes such as vasculature development, cell adhesion, and tissue remodeling. Additionally, the BMSCs' secretome was found to promote vascular development. The results collectively indicate the diverse therapeutic potential of MSC secretomes in influencing various aspects of cellular function and tissue repair.

Conclusion: In conclusion, this study offers a valuable reference for the selection of more suitable sources of mesenchymal stem cells (MSCs) in the treatment of diabetic cardiovascular disease.

Background: Pancreatic cancer is a highly aggressive tumor with a poor prognosis due to a low early detection rate and a lack of biomarkers. Most of pancreatic cancer is pancreatic ductal adenocarcinoma (PDAC). Alterations in the N-glycosylation of plasma immunoglobulin G (IgG) have been shown to be closely associated with the onset and development of several cancers and could be used as biomarkers for diagnosis. The study aimed to explore intact N-glycosylation profile of IgG in patients with PDAC and find relation between intact N-glycosylation profile of IgG and clinical information such as diagnosis and prognosis.

Methods: In this study, we employed a well-evaluated approach (termed GlycoQuant) to assess the site-specific N-glycosylation profile of human plasma IgG in both healthy individuals and patients with pancreatic ductal adenocarcinoma (PDAC). The datasets generated and analyzed during the current study are available in the ProteomeXchange Consortium ( http://www.proteomexchange.org/ ) via the iProX partner repository, with the dataset identifier PXD051436.

Results: The analysis of rapidly purified IgG samples from 100 patients with different stages of PDAC, in addition to 30 healthy controls, revealed that the combination of carbohydrate antigen 19 - 9 (CA19-9), IgG1-GP05 (IgG1-TKPREEQYNSTYR-HexNAc [4]Hex [5]Fuc [1]NeuAc [1]), and IgG4-GP04 (IgG4-EEQFNSTYR- HexNAc [4]Hex [5]Fuc [1]NeuAc [1]) can be used to distinguish between PDAC patients and healthy individuals (AUC = 0.988). In addition, cross validation of the diagnosis model showed satisfactory result.

Conclusions: The study demonstrated that the integrated quantitative method can be utilized for large-scale clinical N-glycosylation research to identify novel N-glycosylated biomarkers. This could facilitate the development of clinical glycoproteomics.

Radiation-induced lung injury (RILI) is a common adverse effect of radiation therapy that negatively affects treatment progression and the quality of life of patients. Identifying biomarkers for RILI can provide reference for the prevention and treatment of RILI in clinical practice. In this study, to explore key proteins related to RILI, we constructed a rat model of RILI and analyzed RILI tissues and normal lung tissues using tandem mass spectrometry labeling and quantitative proteomics technology. We used Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, Gene Ontology (GO) enrichment and protein-protein interaction (PPI) networks for bioinformatics analysis of Differentially expressed proteins (DEPs). The results identified 185 differentially expressed proteins in lung tissue from the RILI group compared with the controls, including 110 up-regulated proteins and 75 down-regulated proteins. GO analysis showed that the differentially expressed proteins were involved oxidation-reduction process, cellular biosynthetic processes and extracellular matrix. KEGG results demonstrated that the differentially expressed proteins were mainly involved in the PI3K-Akt, ECM receptor interactions, arachidonic acid metabolism, glutathione metabolism and other pathways. These results on the functions and signaling pathways of the differentially expressed proteins provide a theoretical basis for further study of the mechanism of RILI.

Background: Tuberculosis (TB) diagnostic monitoring is paramount to clinical decision-making and the host biomarkers appears to play a significant role. The currently available diagnostic technology for TB detection is inadequate. In the present study, we aimed to identify biomarkers for diagnosis of pulmonary tuberculosis (PTB) using urinary metabolomic and proteomic analysis.

Methods: In the study, urine from 40 PTB, 40 lung cancer (LCA), 40 community-acquired pneumonia (CAP) patients and 40 healthy controls (HC) was collected. Biomarker panels were selected based on random forest (RF) analysis.

Results: A total of 3,868 proteins and 1,272 annotated metabolic features were detected using pairwise comparisons. Using AUC ≥ 0.80 as a cutoff value, we picked up five protein biomarkers for PTB diagnosis. The five-protein panel yielded an AUC for PTB/HC, PTB/CAP and PTB/LCA of 0.9840, 0.9680 and 0.9310, respectively. Additionally, five metabolism biomarkers were selected for differential diagnosis purpose. By employment of the five-metabolism panel, we could differentiate PTB/HC at an AUC of 0.9940, PTB/CAP of 0.8920, and PTB/LCA of 0.8570.

Conclusion: Our data demonstrate that metabolomic and proteomic analysis can identify a novel urine biomarker panel to diagnose PTB with high sensitivity and specificity. The receiver operating characteristic curve analysis showed that it is possible to perform non-invasive clinical diagnoses of PTB through these urine biomarkers.

Background: The effect of varying brain ventricular volume on the cerebrospinal fluid (CSF) proteome has been discussed as possible confounding factors in comparative protein level analyses. However, the relationship between CSF volume and protein levels remains largely unexplored. Moreover, the few existing studies provide conflicting findings, indicating the need for further research.

Methods: Here, we explored the association between levels of 88 pre-selected CSF proteins and ventricular volume derived from magnetic resonance imaging (MRI) measurements in 157 cognitively healthy 70-year-olds from the H70 Gothenburg Birth Cohort Studies, including individuals with and without pathological levels of Alzheimer's disease (AD) CSF markers (n = 123 and 34, respectively). Both left and right lateral, the inferior horn as well as the third and the fourth ventricular volumes were measured. Different antibody-based methods were employed for the protein measurements, with most being analyzed using a multiplex bead-based microarray technology. Furthermore, the associations between the protein levels and cortical thickness, fractional anisotropy, and mean diffusivity were assessed.

Results: CSF levels of many brain-derived proteins correlated with ventricular volumes in A-T- individuals, with lower levels in individuals with larger ventricles. The strongest negative correlations with total ventricular volume were observed for neurocan (NCAN) and neurosecretory protein VGF (rho = -0.34 for both). Significant negative correlations were observed also for amyloid beta (Ab) 38, Ab40, total tau (t-tau), and phosphorylated tau (p-tau), with correlation ranging between - 0.34 and - 0.28, while no association was observed between ventricular volumes and Ab42 or neurofilament light chain (NfL). Proteins with negative correlations to ventricular volumes further demonstrated negative correlations to mean diffusivity and positive correlation to fractional anisotropy. However, only weak or no correlations were observed between the CSF protein levels and cortical thickness. A + T + individuals demonstrated higher CSF protein levels compared to A-T- individuals with the most significant differences observed for neurogranin (NRGN) and synuclein beta (SNCB).

Conclusions: Our findings suggest that the levels of many brain-derived proteins in CSF may be subjected to dilution effects depending on the size of the brain ventricles in healthy individuals without AD pathology. This phenomenon could potentially contribute to the inter-individual variations observed in CSF proteomic studies.

Background: The vitreous humor serves as a window into the physiological and pathological processes of the eye, particularly the retina. Diabetic retinopathy (DR), a leading cause of blindness, involves hyperglycemia-induced damage to retinal cells, leading to ischemia and elevated nitric oxide levels, culminating in vascular proliferation. Rhegmatogenous retinal detachment (RD) results from a break in the neuroretina, triggering ischemia, photoreceptor death, and cellular proliferation. Proliferative vitreoretinopathy (PVR) further complicates these conditions through fibrous proliferation. Despite their prevalence and potential for blindness, our understanding of the molecular mechanisms underlying these vitreoretinal diseases is incomplete.

Methods and results: To elucidate disease mechanisms and identify potential therapeutic targets, we conducted a comparative proteomic analysis of vitreous samples from DR, RD, and macular pucker (P) patients, which were chosen as controls. LC-MS analysis identified 988 quantifiable proteins, with distinct clustering observed among disease groups. Differential expression analysis revealed 202 proteins in RD vs. P and 167 in DR vs. P, highlighting distinct proteomic signatures. Enrichment analysis identified glucose metabolism as an altered process in both diseases, suggesting common pathways despite differing etiologies. Notably, aldo-keto reductase family 1 member B1 (AKR1B1) has emerged as a potential key player in both DR and RD, indicating its role in glucose metabolism and inflammation. In silico drug screening identified diclofenac, an approved ophthalmic non-steroidal anti-inflammatory drug (NSAID), as a potential therapeutic agent targeting AKR1B1.

Conclusion: Our study revealed distinct proteomic signatures and common pathways in vitreoretinal diseases, highlighting AKR1B1 as a potential therapeutic target. Using diclofenac during diagnosis and postoperative care for diabetic retinopathy or rhegmatogenous retinal detachment may reduce complications, lower costs, and improve quality of life. Future research will focus on confirming AKR1B1's role in vitreoretinal diseases and understanding diclofenac's mechanism of action.