Plasma marker proteins associated with the progression of lung cancer in obese mice fed a high-fat diet

Integrative Multianalytical Model Based on Novel Plasma Protein Biomarkers for Distinguishing Lung Adenocarcinoma and Benign Pulmonary Nodules

Given the pressing clinical problem of making a decision in diagnosis for subjects with pulmonary nodules, we aimed to discover novel plasma protein biomarkers for lung adenocarcinoma (LUAD) and benign pulmonary nodules (BPNs) and then develop an integrative multianalytical model to guide the clinical management of LUAD and BPN patients. Through label-free quantitative plasma proteomic analysis (data are available via ProteomeXchange with identifier PXD046731), 12 differentially expressed proteins (DEPs) in LUAD and BPN were screened. The diagnostic abilities of DEPs were validated in two independent validation cohorts. The results showed that the levels of three candidate proteins (PRDX2, PON1, and APOC3) were lower in the plasma of LUAD than in BPN. The three candidate proteins were combined with three promising computed tomography indicators (spiculation, vascular notch sign, and lobulation) and three traditional markers (CEA, CA125, and CYFRA21-1) to construct an integrative multianalytical model, which was effective in distinguishing LUAD from BPN, with an AUC of 0.904, a sensitivity of 81.44%, and a specificity of 90.14%. Moreover, the model possessed impressive diagnostic performance between early LUADs and BPNs, with the AUC, sensitivity, specificity, and accuracy of 0.868, 65.63%, 90.14%, and 82.52%, respectively. This model may be a useful auxiliary diagnostic tool for LUAD and BPN by achieving a better balance of sensitivity and specificity.

Proteomic responses reveal the differential effects induced by cadmium in mussels Mytilus galloprovincialis at early life stages

Cadmium (Cd) has become an important metal contaminant and posed severe risk on the organisms in the coastal environments of the Bohai Sea. Marine mussel Mytilus galloprovincialis is widely distributed along the Bohai coast and consumed as seafood by local residents. Evidences indicate that the early stages of marine organisms are more sensitive to metal contaminants. In this study, we applied two-dimensional electrophoresis-based proteomics to characterize the biological effects of Cd (50 μg L(-1)) in the early life stages (D-shape larval and juvenile) of mussels. The different proteomic responses demonstrated the differential responsive mechanisms to Cd exposure in these two early life stages of mussels. In details, results indicated that Cd mainly induced immune and oxidative stresses in both D-shape larval and juvenile mussels via different pathways. In addition, the significant up-regulation of triosephosphate isomerase and metallothionein confirmed the enhanced energy demand and mobilized detoxification mechanism in D-shape larval mussels exposed to Cd. In juvenile mussels, Cd exposure also induced clear apoptosis. Overall, this work suggests that Cd is a potential immune toxicant to mussel M. galloprovincialis at early life stages.

A bayesian integrative model for genetical genomics with spatially informed variable selection

We consider a Bayesian hierarchical model for the integration of gene expression levels with comparative genomic hybridization (CGH) array measurements collected on the same subjects. The approach defines a measurement error model that relates the gene expression levels to latent copy number states. In turn, the latent states are related to the observed surrogate CGH measurements via a hidden Markov model. The model further incorporates variable selection with a spatial prior based on a probit link that exploits dependencies across adjacent DNA segments. Posterior inference is carried out via Markov chain Monte Carlo stochastic search techniques. We study the performance of the model in simulations and show better results than those achieved with recently proposed alternative priors. We also show an application to data from a genomic study on lung squamous cell carcinoma, where we identify potential candidates of associations between copy number variants and the transcriptional activity of target genes. Gene ontology (GO) analyses of our findings reveal enrichments in genes that code for proteins involved in cancer. Our model also identifies a number of potential candidate biomarkers for further experimental validation.

Hypothermia activates adipose tissue to promote malignant lung cancer progression

Microenvironment has been increasingly recognized as a critical regulator of cancer progression. In this study, we identified early changes in the microenvironment that contribute to malignant progression. Exposure of human bronchial epithelial cells (BEAS-2B) to methylnitrosourea (MNU) caused a reduction in cell toxicity and an increase in clonogenic capacity when the temperature was lowered from 37°C to 28°C. Hypothermia-incubated adipocyte media promoted proliferation in A549 cells. Although a hypothermic environment could increase urethane-induced tumor counts and Lewis lung cancer (LLC) metastasis in lungs of three breeds of mice, an increase in tumor size could be discerned only in obese mice housed in hypothermia. Similarly, coinjections using differentiated adipocytes and A549 cells promoted tumor development in athymic nude mice when adipocytes were cultured at 28°C. Conversely, fat removal suppressed tumor growth in obese C57BL/6 mice inoculated with LLC cells. Further studies show hypothermia promotes a MNU-induced epithelial-mesenchymal transition (EMT) and protects the tumor cell against immune control by TGF-β1 upregulation. We also found that activated adipocytes trigger tumor cell proliferation by increasing either TNF-α or VEGF levels. These results suggest that hypothermia activates adipocytes to stimulate tumor boost and play critical determinant roles in malignant progression.

Responses of Mytilus galloprovincialis to bacterial challenges by metabolomics and proteomics

Pathogens can cause diseases and lead to massive mortalities of aquaculture animals and substantial economic loss. In this work, we studied the responses induced by Micrococcus luteus and Vibrio anguillarum in gill of mussel Mytilus galloprovincialis at protein and metabolite levels. Metabolic biomarkers (e.g., amino acids, betaine, ATP) suggested that both M. luteus and V. anguillarum induced disturbances in energy metabolism and osmotic regulation. The unique and some more remarkably altered metabolic biomarkers (threonine, alanine, aspartate, taurine, succinate) demonstrated that V. anguillarum could cause more severe disturbances in osmotic regulation and energy metabolism. Proteomic biomarkers (e.g., goose-type lysozyme 2, matrilin, ependymin-related protein, peptidyl-prolyl cis-trans isomerases) indicated that M. luteus caused immune stress, and disturbances in signaling pathways and protein synthesis. However, V. anguillarum mainly induced oxidative stress and disturbance in energy metabolism in mussel gills indicated by altered procollagen-proline dioxygenase, protein disulfide isomerase, nucleoside diphosphate kinases, electron transfer flavoprotein and glutathione S-transferase. This work confirmed that an integration of proteomics and metabolomics could provide an insightful view into the effects of pathogens to the marine mussel M. galloprovincialis.

Proteomic and metabolomic responses of clam Ruditapes philippinarum to arsenic exposure under different salinities

Arsenic (As) contamination is a severe problem in the intertidal zones of the Bohai Sea (China) with wide salinity variation. In the present study, we combined proteomics and metabolomics to characterize the differential responses of arsenic in clam Ruditapes philippinarum under different salinities (31.1, 23.3 and 15.6 psu). Both proteomic and metabolomic responses indicated that varying salinities could significantly affect the toxicological responses of clams to As. Metabolic biomarkers revealed that the environmentally relevant arsenic (20 μg L(-1)) exposure induced disturbance in energy metabolism and/or osmotic regulation under different salinities, whereas protein biomarkers indicated oxidative stress, cellular injury and apoptosis and disturbance in energy metabolism. In addition, the up-regulated proteins including ATP synthase, succinyl-CoA synthetase and nucleoside diphosphate kinase were validated by related metabolites, succinate and ATP, which confirmed the disturbance in energy metabolism in clam gills at low salinity (15.6 psu). These findings provide important insights into toxicological effects of environmental contaminant at molecular levels using combined proteomics and metabolomics.

High-throughput screening of tumor metastatic-related differential glycoprotein in hepatocellular carcinoma by iTRAQ combines lectin-related techniques

Glycoproteomics is an important aspect in the research of cancer biomarker discovery. The objective of our study is to screen the profile of serum glycoproteins in hepatocellular carcinoma (HCC) patients and to discover differentially expressed glycoproteins in HCC with or without metastasis. We collected serum from HCC patients and divided them into two groups (non-metastatic HCC group and metastatic HCC group) according to 2002 UICC TNM staging system. Wheat germ agglutinin (WGA) lectin was used to enrich the serum glycoproteins by lectin affinity chromatography. The enriched glycoproteins were labeled with mass-balanced isobaric tags (iTRAQ) and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Two differential glycoproteins were validated by Western blot and biochemical methods, respectively. Fifteen differential serum glycoproteins with WGA affinity were identified (p < 0.05). Among them, nine proteins were up-regulated (>1.5-folds) and six were down-regulated (<0.5-folds) in HCC patients with metastasis. Expression of alpha-1-antitrypsin (SERPINA1) and apolipoprotein A-I (APOA1) was validated by Western blot and biochemical methods, respectively (p < 0.05). Our study has obtained a set of HCC metastasis-associated glycoproteins which may serve as novel prognostic candidates and potential therapeutic targets for HCC metastasis. SERPINA1 might act as a potential glycoprotein biomarker of HCC metastasis.