Changes In Proteomic Profile Research Articles

Proteome profile changes in SH-SY5y neuronal cells after treatment with neurotrophic factors

Artemin, one of glial cell line-derived neurotrophic factors (GDNFs) supports sensory neuron. Although a role of artemin and GDNF as neurite outgrowth regulators in early neuron development has been suggested, the immediate effects of artemin and GDNF on neuronal cells have not been elucidated. Here, we investigated artemin and GDNF actions on the neuronal cell proteome. To identify immediate-early protein changes by artemin and GDNF in neuronal cells, we used a differential proteomics approach in SH-SY5y human neuronal cells treated with artemin or GDNF for 1 h. Eleven proteins that changed after both artemin and GDNF treatment were identified using two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight tandem mass spectroscopy. The calcium ion-binding chaperone calreticulin and calcium/calmodulin-binding nuclear matrix protein matrin 3 showed common quantitative differences after both artemin and GDNF treatment. Cytoskeletal proteins also showed quantitative profile differences, which are functionally relevant to cytoskeletal rearrangement leading to the neurite elongation in neurons. These protein changes were detected in neuronal cells without accompanying changes in mRNA levels. These results suggest that immediate changes induced by artemin and GDNF are related to cytoskeletal protein level changes without transcriptional regulation.

Radiation-related Changes in Serum Proteome Profiles Detected by Mass Spectrometry in Blood of Patients Treated with Radiotherapy Due to Larynx Cancer

Radiation-related Changes in Serum Proteome Profiles Detected by Mass Spectrometry in Blood of Patients Treated with Radiotherapy Due to Larynx Cancer

OP36.09: Changes in amniotic fluid and umbilical cord serum proteomic profiles in fetuses with intrauterine growth restriction and Doppler velicimetry abnormalities

Objectives: The aim of this study is to evaluate three dimensional cerebroplacental ratio (CPR 3D) using 3D power Doppler angiography (3D PDA) in the intrauterine monitoring of the growth restricted fetuses (IUGR). Methods: Cerebroplacental ratio (CPR), the ratio between PI of MCA and PI of umbilical artery (UA), is a better predictor for adverse outcome than a single vessel considered alone. We defined CPR 3DPDA as the ratio between vascular indices of a region of fetal brain (ROI) and the vascular indices of the placenta using 3DPDA methodology. The ROI evaluated were a ‘frontal zone’, sprinkled mainly by anterior cerebral artery, obtained tracing a contour passing through the anterior side of cavum septum pellucido (CSP) surrounding part of temporal and frontal bone. Then a second ROI obtained tracing a contour from temporal bones of the width of CSP included (’temporal zone’) sprinkled by middle cerebral artery MCA. We considered 3DPDA vascular indexes (VI = vascularisation FI = flow, VFI = vascularisation and flow). We enrolled 33 IUGR fetuses and 81 adeguate for gestational age, as control cases (24–38 weeks). IUGR fetuses were divided into 2 groups: group 1, IUGR with normal flussimetry of umbilical artery (UA) and MCA; group 2, IUGR with abnormal UA-PI (mean > 2 SD) and abnormal MCA-PI (PI < 2 SD). We calculated the 2D CPR and the CPR 3D of the frontal and temporal cerebral zones for all vascular indexes. Results: Values of 2D CPR were in accordance with the expected ones. CPR 3D, applying VI and VFI, both in frontal and temporal zone demonstrated a statistically significant different values compared with control cases. Conclusions: CPR 3D can be considered a new parameter: it demonstrates the vascular redistribution in frontal and temporal zones during the ‘brain sparing effect’ in IUGR fetuses also in the group of IUGR fetuses without bidimensional pathological flussimetry.

Proteomic Analysis of Honeybee (Apis mellifera L.) Pupae Head Development

The honeybee pupae development influences its future adult condition as well as honey and royal jelly productions. However, the molecular mechanism that regulates honeybee pupae head metamorphosis is still poorly understood. To further our understand of the associated molecular mechanism, we investigated the protein change of the honeybee pupae head at 5 time-points using 2-D electrophoresis, mass spectrometry, bioinformatics, quantitative real-time polymerase chain reaction and Western blot analysis. Accordingly, 58 protein spots altered their expression across the 5 time points (13–20 days), of which 36 proteins involved in the head organogenesis were upregulated during early stages (13–17 days). However, 22 proteins involved in regulating the pupae head neuron and gland development were upregulated at later developmental stages (19–20 days). Also, the functional enrichment analysis further suggests that proteins related to carbohydrate metabolism and energy production, development, cytoskeleton and protein folding were highly involved in the generation of organs and development of honeybee pupal head. Furthermore, the constructed protein interaction network predicted 33 proteins acting as key nodes of honeybee pupae head growth of which 9 and 4 proteins were validated at gene and protein levels, respectively. In this study, we uncovered potential protein species involved in the formation of honeybee pupae head development along with their specific temporal requirements. This first proteomic result allows deeper understanding of the proteome profile changes during honeybee pupae head development and provides important potential candidate proteins for future reverse genetic research on honeybee pupae head development to improve the performance of related organs.

Proteomic patterns analysis with multivariate calculations as a promising tool for prompt differentiation of early stage lung tissue with cancer and unchanged tissue material

BackgroundLung cancer diagnosis in tissue material with commonly used histological techniques is sometimes inconvenient and in a number of cases leads to ambiguous conclusions. Frequently advanced immunostaining techniques have to be employed, yet they are both time consuming and limited. In this study a proteomic approach is presented which may help provide unambiguous pathologic diagnosis of tissue material.MethodsLung tissue material found to be pathologically changed was prepared to isolate proteome with fast and non selective procedure. Isolated peptides and proteins in ranging from 3.5 to 20 kDa were analysed directly using high resolution mass spectrometer (MALDI-TOF/TOF) with sinapic acid as a matrix. Recorded complex spectra of a single run were then analyzed with multivariate statistical analysis algorithms (principle component analysis, classification methods). In the applied protocol we focused on obtaining the spectra richest in protein signals constituting a pattern of change within the sample containing detailed information about its protein composition. Advanced statistical methods were to indicate differences between examined groups.ResultsObtained results indicate changes in proteome profiles of changed tissues in comparison to physiologically unchanged material (control group) which were reflected in the result of principle component analysis (PCA). Points representing spectra of control group were located in different areas of multidimensional space and were less diffused in comparison to cancer tissues. Three different classification algorithms showed recognition capability of 100% regarding classification of examined material into an appropriate group.ConclusionThe application of the presented protocol and method enabled finding pathological changes in tissue material regardless of localization and size of abnormalities in the sample volume. Proteomic profile as a complex, rich in signals spectrum of proteins can be expressed as a single point in multidimensional space and than analysed using advanced statistical methods. This approach seems to provide more precise information about a pathology and may be considered in futer evaluation of biomarkers for clinical applications in different pathology. Multiparameter statistical methods may be helpful in elucidation of newly expressed sensitive biomarkers defined as many factors "in one point".

Proteomic analysis of plasma derived from platelet buffy coats during storage at room temperature. An application of ProteoMiner™ technology

The present study was aimed at revealing new insights into the analysis of storage-related processes occurring in the supernatants of platelet concentrates (PCs) derived from pooled buffy coats suspended in whole plasma. To reduce the dynamic range of plasma protein concentrations and access low-abundance proteins, we made use of a solid-phase combinatorial peptide ligand library, known under the trade name of ProteoMiner™. Afterwards, two-dimensional electrophoresis (2-DE) was coupled with mass spectrometry (MS) to reveal changes in proteomic profiles. Several storage-induced protein alterations were identified including changes to major plasma proteins. In particular, a precursor of the secretory form of clusterin was shown to accumulate during storage of PC supernatants, together with platelet-derived tropomyosin, suggesting a progressive loss of platelet integrity. Platelet-released proteins following activation have also been detected (alpha-1-B-glycoprotein, kininogen-1, and serpin proteinase inhibitor 8). Moreover, specific protein fragments (vitronectin, plakoglobin, hornerin, and apolipoprotein A-IV) were found to be modulated upon storage, possibly indicating a time-dependent buffy-coat PC deterioration. Globally, our findings provided the disclosure of unique proteins in PC supernatants with respect to previous studies conducted in similar experimental conditions, suggesting ProteoMiner enrichment technology to be a possible complementary tool in the identification of diagnostically relevant proteins as age/quality biomarkers of therapeutic products.

Differential proteomics of plant development

In this mini-review, recent advances in plant developmental proteomics are summarized. The growing interest in plant proteomics continually produces large numbers of developmental studies on plant cell division, elongation, differentiation, and formation of various organs. The brief overview of changes in proteome profiles emphasizes the participation of stress-related proteins in all developmental processes, which substantially changes the view on functional classification of these proteins. Next, it is noteworthy that proteomics helped to recognize some metabolic and housekeeping proteins as important signaling inducers of developmental pathways. Further, cell division and elongation are dependent on proteins involved in membrane trafficking and cytoskeleton dynamics. These protein groups are less prevalently represented in studies concerning cell differentiation and organ formation, which do not target primarily cell division. The synthesis of new proteins, generally observed during developmental processes, is followed by active protein folding. In this respect, disulfide isomerase was found to be commonly up-regulated during several developmental processes. The future progress in plant proteomics requires new and/or complementary approaches including cell fractionation, specific chemical treatments, molecular cloning and subcellular localization of proteins combined with more sensitive methods for protein detection and identification.

Radiation-related Changes in Serum Proteome Profiles Detected by Mass Spectrometry in Blood of Patients Treated with Radiotherapy Due to Larynx Cancer

The study aimed to detect features of human serum proteome that were associated with exposure to ionizing radiation. The analyzed group consisted of 46 patients treated with radical radiotherapy for larynx cancer; patients were irradiated with total doses in a range from 51 to 72 Gy. Three consecutive blood samples were collected from each patient: before the start, 2 weeks after the start, and 4-6 weeks after the end of radiotherapy. The low-molecular-weight fraction of the serum proteome (2,000-13,000 Da) was analyzed by the MALDI-ToF mass spectrometry. Proteome profiles of serum samples collected before the start of radiotherapy and during the early stage of the treatment were similar. In marked contrast, mass profiles of serum samples collected several weeks after the end of the treatment revealed clear changes. We found that 41 out of 312 registered peptide ions changed their abundance significantly when serum samples collected after the final irradiation were compared with samples collected at the two earlier time points. We also found that abundances of certain serum peptides were associated with total doses of radiation received by patients. The results of this pilot study indicate that features of serum proteome analyzed by mass spectrometry have potential applicability as a retrospective marker of exposure to ionizing radiation.

One-dimensional proteomic mapping of embryos danio rerio

In the present study, a proteomic technology combining one-dimensional gel electrophoresis (1DE) with subsequent mass spectrometry (MALDI-TOF-PMF) has been successfully applied for revelation of changes in the protein profile of zebrafish (Danio rerio) 52 hpf embryos. Prior to 1DE separation of zebrafish embryonic proteins, the procedure for obtaining embryos homogenate was optimized by ultrasonic treatment. A total of 84 proteins, including 15 vitellogenins, were identified. It was shown that growing of zebrafish embryos in the medium with doxorubicin (DOX) stimulated Caspase-3 induction and promoted the disappearance of cardiac troponins, both these findings being consistent with literature data on doxorubicin-induced cardiotoxicity. The 1DE-based proteomic mapping approach proposed herein enabled not only to identify proteins but also to register those changes in embryos' proteomic profile that were caused by doxorubicin.

Changes in the leaf proteome profile of Mentha arvensis in response to Alternaria alternata infection

Plant pathogenic fungi cause important yield losses in crops. A proteomic approach was used to study the changes in the leaf proteome profile of the plant Mentha arvensis infected with a necrotrophic fungus, Alternaria alternata. High-resolution two-dimensional gel electrophoresis (2-DE) followed by colloidal Coomassie staining and mass spectrometric analysis was used to identify highly abundant proteins differentially expressed in response to fungal infection. From a total of 210 reproducibly detected and analyzed spots, the intensity of sixty-seven spots was altered, and forty-five of them were successfully identified by matrix assisted laser desorption/ionization time of flight-mass spectrometry (MALDI TOF/TOF MS/MS). Fifty-six percent of the identified proteins belonged to energy and metabolism whereas 29% were stress and defense related. Taken together, the results allow to assess changes at the proteomic level in the host due to the defense response. Results show an initial defense response, not strong enough to overcome the pathogenesis, which may be similar to other susceptible plant-pathogen interactions; however, cross-talks between various defense pathways, regulatory networks and physiological conditions are other important aspects to be considered.

Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease

Because of its availability, ease of collection, and correlation with physiology and pathology, urine is an attractive source for clinical proteomics/peptidomics. However, the lack of comparable data sets from large cohorts has greatly hindered the development of clinical proteomics. Here, we report the establishment of a reproducible, high resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins, ranging from 800 to 17,000 Da, using samples from 3,600 individuals analyzed by capillary electrophoresis coupled to MS. All processed data were deposited in an Structured Query Language (SQL) database. This database currently contains 5,010 relevant unique urinary peptides that serve as a pool of potential classifiers for diagnosis and monitoring of various diseases. As an example, by using this source of information, we were able to define urinary peptide biomarkers for chronic kidney diseases, allowing diagnosis of these diseases with high accuracy. Application of the chronic kidney disease-specific biomarker set to an independent test cohort in the subsequent replication phase resulted in 85.5% sensitivity and 100% specificity. These results indicate the potential usefulness of capillary electrophoresis coupled to MS for clinical applications in the analysis of naturally occurring urinary peptides.

PROTEOMIC ANALYSIS OF POST-HEMORRHAGIC SHOCK MESENTERIC LYMPH

Recent studies have documented the association of mesenteric lymphatic route with adult respiratory distress syndrome and multiple organ failure after hemorrhagic shock. However, the mediators and mechanisms of the toxic effects of mesenteric lymph remain unclear. This study aimed to identify mediators or biomarkers in the mesenteric lymph through comparative proteomic analysis. Fourteen mature male Sprague-Dawley rats were randomly divided and subjected to trauma (laparotomy) plus hemorrhagic shock or trauma plus sham shock. Mesenteric lymph samples were collected before shock and at 3 h after resuscitation from hemorrhagic shock (or sham shock). To investigate changes in proteome profiles between preshock and 3-h postshock (or 3-h post-sham shock) mesenteric lymph samples, two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry were performed. We found a more than 2-fold change in abundance of 31 protein spots in the lymph samples. Mass spectrometry analyses identified 12 distinct proteins. Four proteins were consistently upregulated in the 3-h postshock lymph samples, including serum albumin precursor, two isoforms of cytoplasmic actin, complement C3 precursor, and major urinary protein precursor. Two proteins, including haptoglobin and one unidentified protein, were consistently downregulated. The deregulation of these proteins was confirmed by Western blots. Most of these altered proteins are functionally implicated in tissue inflammation. The findings of this study provide a starting point for investigating the functions of these proteins in hemorrhagic shock-induced lung injury and hold great promise for the development of potential therapeutic interventions.

Canonical and alternate functions of the microRNA biogenesis machinery

The canonical microRNA (miRNA) biogenesis pathway requires two RNaseIII enzymes: Drosha and Dicer. To understand their functions in mammals in vivo, we engineered mice with germline or tissue-specific inactivation of the genes encoding these two proteins. Changes in proteomic and transcriptional profiles that were shared in Dicer- and Drosha-deficient mice confirmed the requirement for both enzymes in canonical miRNA biogenesis. However, deficiency in Drosha or Dicer did not always result in identical phenotypes, suggesting additional functions. We found that, in early-stage thymocytes, Drosha recognizes and directly cleaves many protein-coding messenger RNAs (mRNAs) with secondary stem-loop structures. In addition, we identified a subset of miRNAs generated by a Dicer-dependent but Drosha-independent mechanism. These were distinct from previously described mirtrons. Thus, in mammalian cells, Dicer is required for the biogenesis of multiple classes of miRNAs. Together, these findings extend the range of function of RNaseIII enzymes beyond canonical miRNA biogenesis, and help explain the nonoverlapping phenotypes caused by Drosha and Dicer deficiency.

Quantitative Proteomic Profiling of Matched Normal and Tumor Breast Tissues

Proteomic analysis of breast cancer tissue has proven difficult due to its inherent histological complexity. This pilot study presents preliminary evidence for the ability to differentiate adenoma and invasive carcinoma by measuring changes in proteomic profile of matched normal and disease tissues. A dual lysis buffer method was used to maximize protein extraction from each biopsy, proteins digested with trypsin, and the resulting peptides iTRAQ labeled. After combining, the peptide mixtures they were separated using preparative IEF followed by RP nanoHPLC. Following MALDI MS/MS and database searching, identified proteins were combined into a nonredundant list of 481 proteins with associated normal/tumor iTRAQ ratios for each patient. Proteins were categorized by location as blood, extracellular, and cellular, and the iTRAQ ratios were normalized to enable comparison between patients. Of those proteins significantly changed (upper or lower quartile) between matched normal and disease tissues, those from two invasive carcinoma patients had >50% in common with each other but <22% in common with an adenoma patient. In invasive carcinoma patients, several cellular and extracellular proteins that were significantly increased (Periostin, Small breast epithelial mucin) or decreased (Kinectin) have previously been associated with breast cancer, thereby supporting this approach for a larger disease-stage characterization effort.

Proteomic Analysis of Interstitial Fluid in Bone Marrow Identified That Peroxiredoxin 2 Regulates H2O2 Level of Bone Marrow during Aging

Hematopoiesis in bone marrow declines during aging owing to alteration of the hematopoietic niche. However, due to difficult accessibility and other complexities, senescence-related alteration of the hematopoietic niche is largely unknown. The interstitial fluid of bone marrow (IFBM), a pivotal component of the hematopoietic niche, includes soluble secretory factors that are present between bone marrow cells. To characterize the proteomic profile changes of IFBM during aging, we analyzed the IFBMs of young, adult, and senescent rats using 2-DE combined with ESI/MALDI-Q-TOF MS. Finally, 31 differentially expressed proteins involved in multiple biological functions were identified. Peroxiredoxin 2 (Prx2), down-regulated during aging, was further analyzed and demonstrated that it is produced by bone marrow stromal cells. Interestingly, higher levels of hydrogen peroxide (H(2)O(2)) were detected in the bone marrow with lower Prx2 expression. Moreover, exogenous Prx2 reduced the intracellular H(2)O(2) level in bone marrow stromal cells in vitro. Therefore, Prx2 is implied in the regulation of H(2)O(2) production in the bone marrow during aging. Our data characterized the dynamic protein profiles of the bone marrow microenvironment during aging and we provided clues to elucidate the mechanism of creating a low ROS level in the hematopoietic niche.

Protein expression during the embryonic development of a gastropod

Despite the potential use of gastropod embryos in basic and applied research, little is known about their protein expression. We examined, for the first time, changes in proteomic profile during embryonic development of Pomacea canaliculata from an embryo without a shell (stage II) to an embryo with a fully formed shell (stage III) to understand the roles that proteins play in critical developmental events, such as the formation of shell, operculum and heart, and the differentiation of head and foot. To analyze protein expression during development, we used 2-DE to detect, MS to analyze, and de novo peptide sequencing followed by MS-BLAST to identify the proteins. The de novo cross-species protein identification method was adopted because of a lack of genomic and proteomic data in the whole class of Gastropoda. 2-DE detected approximately 700 protein spots. Among the 125 spots that were abundant, 52% were identified, a marked improvement over the conventional direct MS-BLAST method. These proteins function in perivitelline fluid utilization, shell formation, protein synthesis and folding, and cell cycle and cell fate determination, providing evidence to support that this embryonic period is a period of dynamic protein synthesis and metabolism. The data shall provide a basis for further studies of how gastropod embryos respond to natural and human-induced changes in the environment.

Identification of serum proteins as prognostic and predictive markers of colorectal cancer using surface enhanced laser desorption ionization-time of flight mass spectrometry

Colorectal cancer (CRC) is the second most common cause of cancer related death. Prognosis is highly dependent on stage at diagnosis making early detection mandatory. This study aimed to identify novel disease specific biomarkers of CRC, validate our previously identified biomarkers of CRC and identify serum biomarkers predicting treatment response and for monitoring. Serum of patients with metastatic CRC was collected, according to a predefined schedule, prior to start of standard first-line chemotherapy with oxaliplatin and capecitabine and serially before each 3 weekly treatment cycle and analyzed for proteomic profile by standardized SELDI-TOF MS. Serum proteomic mass spectrometry data of all subjects were processed using the tbimass R-package and proteomic profiles of CRC patients were compared with those of matched normal control subjects. Furthermore, changes in proteomic profiles during the course of chemotherapy were recorded according to treatment response. In total, 42 patients with advanced CRC were treated and mean follow-up was 13.5 months. The response rate was 50% and the median overall survival 19.5 months (95% CI: 16-23). By comparing CRC patients and healthy controls we identified 13 potential biomarkers of CRC (m/z 2.0-31.9 kDa) whereas two proteins, m/z 14060 and 28100 Da (apolipoprotein A-I), were highly significant (p<0.0001). Comparison of responding and non-responding patients identified 6 proteins potentially predicting response, where of m/z 3330 Da was significant (p=0.007). Serial analysis identified 2 proteins, m/z 2022 and 28100 Da, that changed during chemotherapy in accordance with response. We identified 13 m/z values discriminating between CRC patients and healthy controls, including the previously identified apolipoprotein A-I as a candidate biomarker for CRC and treatment monitoring.

Abstract 4589: Changes in proteomic profiles with age in male rats using the iTRAQ approach

Abstract Aging is an important risk factor for many diseases including prostate cancer (PC). Enhanced risk for disease may, in part, be due to aging-related changes in the proteome. Thus, a better knowledge of the changes in protein levels occurring with age would help in the early detection of the disease, as well as in monitoring chemopreventive intervention. In the present study we used male F344 rats, a commonly used aging and PC model, and compared protein levels in the blood plasma of young (4 months), mature (12 months), old (18 months) and very old (24 months) rats by a proteomic approach known as isobaric Tag for Relative and Absolute Quantitation (iTRAQ). In this multi-plex non-gel based technique samples can be simultaneously labeled with isobaric tagging reagents for quantitation and identification by mass spectrometry. Plasma samples were pooled from three animals and 50 μg of protein from each group was labeled for a 4-plex iTRAQ analysis. A total of seventy nine proteins were identified, thirty one with &amp;gt;99% confidence. Among those, the levels of thirteen proteins were changed significantly (p&amp;lt;0.05) with age and five of which with &amp;gt;99% confidence including serotransferrin, hemopexin, fetuin-A, fetuin-B and α-1-acid glycoprotein. Both age-specific and growth-development related changes were observed throughout the life span with maximum changes (either increases or decreases) being observed at 18 months. The results of this study show that age indeed can influence the expression profile of plasma proteins. The relationship of these proteins to PC is currently being investigated by analyzing their levels in different lobes of the prostate gland. Supported in part by R01 CA 127729-01 Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4589.

Serum proteomics and disease-specific biomarkers of patients with advanced gastric cancer

Gastric cancer is a commonly diagnosed solid tumor which is associated with a dismal prognosis making early diagnosis essential. Thus, this study aimed to identify novel biomarkers in gastric cancer. Serum of patients with advanced gastric cancer was collected according to a predefined schedule: prior to first-line chemotherapy with epirubicin (50 mg/m(2), day 1), cisplatin (60 mg/m(2), day 1) and capecitabine (1,000 mg/m(2), twice daily on days 1-14). The serum was collected serially before the treatment cycles and then analyzed by SELDI-TOF MS. Normal control subjects were matched according to age, gender and serum collection. Serum proteomic mass spectrometry data of all subjects were processed using the tbimass R-package and compared. We analyzed i) whether proteomic profile changes were associated with a response to chemotherapy and survival, and ii) whether changes in proteomic profiles occurring during the time period of chemotherapy were associated with tumor response. In total, 82 patients with adenocarcinoma of the stomach (mean age 57 years, males 69.5%) were treated with a mean number of five chemotherapy cycles. The overall tumor response rate, complete and partial remission combined, was 37%, median time to progression was 7 months (95% CI, 6-8) and median overall survival 11 months (95% CI, 9.5-12). By comparing 77 serum samples of patients with normal matched controls, we identified 32 proteins which discriminated the two groups. By selecting the most differentiating proteins, we built a classification model that correctly categorized 81% of the gastric cancer patients and 90% of the normal controls. Furthermore, we found a statistically significant correlation between the pre-treatment intensity of serum amyloid-α (SAA) and overall survival in gastric cancer patients, whereby a low intensity of SAA predicted a longer patient survival. A classification model, based on the 32 most discriminating proteins differentiating gastric cancer from normal controls, correctly classified subjects with relatively high sensitivity and specificity.

Pharmacological Modulation of Genome and Proteome Alterations in Mice Treated with the Endocrine Disruptor Bisphenol A

Among endocrine disruptors, the xenoestrogen bisphenol A (BPA) is of particular interest due to the very high production and widespread environmental contamination. We recently demonstrated that the oral administration of BPA to mice results in the formation of DNA adducts not only in liver but also in mammary tissue. The present study aimed at evaluating the modulation of BPA-related DNA adducts and proteome alterations by the chemopreventive agents budesonide (BUD) and phenethyl isothiocyanate (PEITC). Swiss ICR (CD-1) mice received, for 8 days, BPA with the drinking water and either chemopreventive agent with the diet. We measured DNA adducts by (32)P postlabeling and 656 proteins by antibody microarray. BPA induced the formation, with similar patterns, of DNA adducts in liver and in mammary tissue. Moreover, BPA dysregulated 13 proteins in mammary tissue, mostly in the sense of upregulation, including estrogen receptor-beta and proteins involved in cell proliferation, inhibition of apoptosis, tissue remodeling, inflammation, stress response, and glutathione synthesis. PEITC significantly inhibited the formation of BPA-induced DNA adducts, but only at the highest dose tested, and BUD was totally ineffective. The chemopreventive agents modulated a variety of BPA-induced changes in proteome profiles. However, as shown by both hierarchical cluster analysis and principal component analysis, BUD and especially PEITC were not able to restore the physiological situation in BPA-treated mice. Therefore, the in vivo use of proteome analysis proves to be a sensitive tool for the early prediction not only of protective effects but also of adverse effects of chemopreventive agents.