Tracking Prostate Carcinogenesis over Time through Urine Proteome Profiling in an Animal Model: An Exploratory Approach.
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ABSTRACT:
SUBMITTER: Moreira-Pais A
PROVIDER: S-EPMC9315930 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The urgent need for new tools for the early diagnosis of prostate cancer (PCa) has prompted us to investigate the proteomic profile of urine during the course of prostate carcinogenesis. Using an established animal model of prostate adenocarcinoma, we performed a comprehensive analysis of the proteomic profile of urine from healthy animals and animals with adenocarcinoma at two time points. At the second time point of prostate carcinogenesis, the incidence of pre-neoplastic and neoplastic lesions was 100%. GeLC-MS/MS and subsequent bioinformatic analysis revealed several proteins involved in prostate carcinogenesis. Increased levels of retinol-binding protein 4 and decreased levels of cadherin-2 appear to be characteristic of early stages of the disease, whereas increased levels of enolase-1 and T-kininogen 2 and decreased levels of isocitrate dehydrogenase 2 describe more advanced stages. With increasing age, urinary levels of clusterin and corticosteroid-binding globulin increase and neprilysin levels decrease, all of which appear to play a role in prostatic hyperplasia or carcinogenesis. The present exploratory analysis could be considered an important starting point for studies targeting specific human urinary proteins for the early detection of age-related maladaptive changes in the prostate that may lead to cancer.
2022-08-12 | PXD034432 | Pride
Project description:Numerous metabolic profiling pipelines have been developed to characterize the composition of human biofluids and tissues, the vast majority of these being for studies in adults. To accommodate limited sample volume and to take into account the compositional differences between adult and infant biofluids, we developed and optimized sample handling and analytical procedures for studying urine from newborns. A robust pipeline for metabolic profiling using NMR spectroscopy was established, encompassing sample collection, preparation, spectroscopic measurement, and computational analysis. Longitudinal samples were collected from five infants from birth until 14 months of age. Methods of extraction and effects of freezing and sample dilution were assessed, and urinary contaminants from breakdown of polymers in a range of diapers and cotton wool balls were identified and compared, including propylene glycol, acrylic acid, and tert-butanol. Finally, assessment of urinary profiles obtained over the first few weeks of life revealed a dramatic change in composition, with concentrations of phenols, amino acids, and betaine altering systematically over the first few months of life. Therefore, neonatal samples require more stringent standardization of experimental design, sample handling, and analysis compared to that of adult samples to accommodate the variability and limited sample volume.
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Project description:Background:Hashtags are widely used for communication in online media. As a condensed version of information, they characterize topics and discussions. For their analysis, we apply methods from network science and propose novel tools for tracing their dynamics in time-dependent data. The observations are characterized by bursty behaviors in the increases and decreases of hashtag usage. These features can be reproduced with a novel model of dynamic rankings. Hashtag communities in time:We build temporal and weighted co-occurrence networks from hashtags. On static snapshots, we infer the community structure using customized methods. On temporal networks, we solve the bipartite matching problem of detected communities at subsequent timesteps by taking into account higher-order memory. This results in a matching protocol that is robust toward temporal fluctuations and instabilities of the static community detection. The proposed methodology is broadly applicable and its outcomes reveal the temporal behavior of online topics. Modeling topic-dynamics:We consider the size of the communities in time as a proxy for online popularity dynamics. We find that the distributions of gains and losses, as well as the interevent times are fat-tailed indicating occasional, but large and sudden changes in the usage of hashtags. Inspired by typical website designs, we propose a stochastic model that incorporates a ranking with respect to a time-dependent prestige score. This causes occasional cascades of rank shift events and reproduces the observations with good agreement. This offers an explanation for the observed dynamics, based on characteristic elements of online media.
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Project description:Development of noninvasive, reliable biomarkers for lung cancer diagnosis has many clinical benefits knowing that most of lung cancer patients are diagnosed at the late stage. For this purpose, we conducted proteomic analyses of 231 human urine samples in healthy individuals (n=33), benign pulmonary diseases (n=40), lung cancer (n=33), bladder cancer (n=17), cervical cancer (n=25), colorectal cancer (n=22), esophageal cancer (n=14), and gastric cancer (n=47) patients collected from multiple medical centers. By random forest modeling, we nominated a list of urine proteins that could separate lung cancers from other cases. With a feature selection algorithm, we selected a panel of five urinary biomarkers (FTL: Ferritin light chain; MAPK1IP1L: Mitogen-Activated Protein Kinase 1 Interacting Protein 1 Like; FGB: Fibrinogen Beta Chain; RAB33B: RAB33B, Member RAS Oncogene Family; RAB15: RAB15, Member RAS Oncogene Family) and established a combinatorial model that can correctly classify the majority of lung cancer cases both in the training set (n=46) and the test sets (n=14-47 per set) with an AUC ranging from 0.8747 to 0.9853. A combination of five urinary biomarkers not only discriminates lung cancer patients from control groups but also differentiates lung cancer from other common tumors. The biomarker panel and the predictive model, when validated by more samples in a multi-center setting, may be used as an auxiliary diagnostic tool along with imaging technology for lung cancer detection.
| S-EPMC5952250 | biostudies-literature
Project description:ObjectiveProstate cancer (PCa) is one of the most common malignant tumors, accounting for 20% of total tumors ranked first in males. PCa is usually asymptomatic at the early stage and the specificity of the current biomarkers for the detection of PCa is low. The present study evaluates circulating tumor DNA (ctDNA) in blood or urine, which can be used as biomarkers of PCa and the combination of these markers may increase the sensitivity and specificity of the detection of PCa.MethodsTissue, blood, and urine samples were collected from patients with PCa. All prostate tissue specimens underwent pathological examination. A hybrid-capture-based next-generation sequencing assay was used for plasma and urinary ctDNA profiling. Sequencing data were analyzed by an in-house pipeline for mutation calling. Mutational profiles of PCa and BPH were compared in both plasma and urine samples. Associations of detected mutations and clinical characteristics were statistically analyzed.ResultsA significant association of mutation allele frequencies (MAFs) in the blood samples with patients with metastatic PCa rather than patients with primary PCa, and MAFs are changed after treatment in patients with PCa. Further, the number of mutations in urine is not associated with clinical characteristics of PCa patients, but the frequencies of mutation alleles in the urine are associated with patient age. Comparison of cfDNA aberration profiles between urine and blood reveals more alterations in urine than in blood, including TP53, AR, ATM, MYC, and SPOP mutations.ConclusionThis work provides the potential clinical application of urine, in addition to blood, as a powerful and convenient non-invasive approach in personalized medicine for patients with PCa.
| S-EPMC8984469 | biostudies-literature
Project description:In response to myocardial infarction (MI), neutrophils (PMNs) are early responders that initiate the inflammatory reaction. Because macrophages and fibroblasts show polarization states after MI, we hypothesized PMNs also undergo phenotypic changes over the MI time course. The objective of the current study was to map the continuum of polarization phenotypes in cardiac neutrophils over the first week of MI. C57BL/6J male mice (3-6 months old) underwent permanent coronary artery ligation to induce MI, and PMNs were isolated from the infarct region at days 1, 3, 5, and 7 after MI. Day 0 served as a no MI negative control. Aptamer proteomics was performed on biological replicates (n = 10-12) for each time point. Day (D)1 MI neutrophils had a high degranulation profile with increased matrix metalloproteinase (MMP) activity. D3 MI neutrophil profiles showed upregulation of apoptosis and induction of extracellular matrix (ECM) organization. D5 MI neutrophils further increased their ECM reorganization profile. D7 MI neutrophils had a reparative signature that included expression of fibronectin, galectin-3, and fibrinogen to contribute to scar formation by stimulating ECM reorganization. Of note, fibronectin was a key modulator of degranulation, as it amplified MMP-9 release in the presence of an inflammatory stimulus. Our results indicate that neutrophils selectively degranulate over the MI time course, reflective of both their intrinsic protein profiles as well as the ECM environment in which they reside. MMPs, cathepsins, and ECM proteins were prominent neutrophil degranulation indicators.
| S-EPMC6695384 | biostudies-literature
Project description:Biochemical networks mediating normal lung morphogenesis and function have important implications for ameliorating morbidity and mortality in premature infants. Although several transcript-level studies have examined normal lung development, corresponding protein-level analyses are lacking. Here we performed proteomics analysis of murine lungs from embryonic to early adult ages to identify the molecular networks mediating normal lung development. We identified 8,932 proteins, providing a deep and comprehensive view of the lung proteome. Analysis of the proteomics data revealed discrete modules and the underlying regulatory and signaling network modulating their expression during development. Our data support the cell proliferation that characterizes early lung development and highlight responses of the lung to exposure to a nonsterile oxygen-rich ambient environment and the important role of lipid (surfactant) metabolism in lung development. Comparison of dynamic regulation of proteomic and recent transcriptomic analyses identified biological processes under posttranscriptional control. Our study provides a unique proteomic resource for understanding normal lung formation and function and can be freely accessed at Lungmap.net.
| S-EPMC6087896 | biostudies-literature
Project description:BackgroundChina issued strict nationwide guidelines to combat the COVID-19 outbreak in January 2020 and gradually loosened the restrictions on movement in early March. Little is known about how these disease control measures affected the 600 million people who live in rural China. The goal of this paper is to document the quarantine measures implemented in rural China outside the epicenter of Hubei Province and to assess the socioeconomic effect of the measures on rural communities over time.MethodsWe conducted three rounds of interviews with informants from 726 villages in seven provinces, accounting for over 25% of China's overall rural population. The survey collected data on rural quarantine implementation; COVID-19 infections and deaths in the survey villages; and effects of the quarantine on employment, income, education, health care, and government policies to address any negative impacts. The empirical findings of the work established that strict quarantine measures were implemented in rural villages throughout China in February.ResultsThere was little spread of COVID-19 in rural communities: an infection rate of 0.001% and zero deaths reported in our sample. However, there were negative social and economic outcomes, including high rates of unemployment, falling household income, rising prices, and disrupted student learning. Health care was generally accessible, but many delayed their non-COVID-19 health care due to the quarantine measures. Only 20% of villagers received any form of local government aid, and only 11% of villages received financial subsidies. There were no reports of national government aid programs that targeted rural villagers in the sample areas.ConclusionsBy examining the economic and social effects of the COVID-19 restrictions in rural communities, this study will help to guide other middle- and low-income countries in their containment and restorative processes. Without consideration for economically vulnerable populations, economic hardships and poverty will likely continue to have a negative impact on the most susceptible communities.
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Project description:Time series profiling is a powerful approach for obtaining information on protein expression dynamics and prevailing biochemical pathways. To date, such information could only be obtained at the mRNA level using mature and highly parallel technologies such as microarray gene expression profiling. The generation of time series data at the protein level has lagged due to the lack of robust and highly reproducible methodologies. Using a combination of SILAC strategy, SDS-PAGE and LC-MS/MS, we demonstrate successful monitoring of expression levels of the same set of proteins across different time points within the ER compartment of human primary fibroblast cells when exposed to ER stress inducers tunicamycin and thapsigargin. Data visualization was facilitated using GeneSpring GX analysis platform that was designed to process Affymetrix microarray data. This software also facilitated the generation of important parameters such as data normalization, calculation of statistical values to extract significant changes in protein expression, and the cross comparison of data sets.
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Project description:Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers in the literature-curated database. Forty-three percentage of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.
| S-EPMC8076675 | biostudies-literature