Denise de Abreu Pereira

Comparative proteomic analysis of whole saliva from chronic periodontitis patients

Chronic periodontal disease is a chronic inflammatory process affecting tooth supporting tissues in the presence of pathogenic bacterial biofilm. There is some evidence for changes in the protein composition of whole saliva from chronic periodontitis patients, but there have been no studies using a proteomic approach. Hence, the aim of this study was to compare the protein profiles of unstimulated whole saliva from patients with periodontitis and healthy subjects by two complementary approaches (2D-gel electrophoresis and liquid chromatography). Protein spots of interest were analyzed by MALDI-TOF-TOF, and the data was complemented by an ESI-Q-TOF experiment. The analyses revealed that subjects with periodontal disease have increased amounts of blood proteins (serum albumin and hemoglobin) and immunoglobulin, and they have a lower abundance of cystatin compared to the control group. A higher number of protein spots were observed in the periodontitis group, of which most were identified as alpha-amylase. This higher number of alpha-amylase variants seems to be caused by hydrolysis by cysteine proteases under such inflammatory conditions. This approach gives novel insights into alterations of salivary protein in presence of periodontal inflammation and may contribute to the improvement of periodontal diagnosis.

Analysis of the salivary proteome in gingivitis patients

BACKGROUND AND OBJECTIVE Gingivitis is a disease that is characterized by inflammation of the gingival tissue, which can progress to periodontitis and tooth loss. Although many studies have attempted to identify salivary proteins that are associated with the disease, this is the first study to use a proteomic approach to analyze and compare the proteomic profile of whole saliva from gingivitis patients and healthy controls. MATERIAL AND METHOD To analyze the saliva proteome, two-dimensional gel electrophoresis and liquid chromatography were used, followed by mass spectrometry. RESULTS The analyses showed that gingival inflammation was associated with increased amounts of blood proteins (serum albumin and hemoglobin), immunoglobulin peptides and keratins. In the control group, salivary cystatins, which were detected using capillary Liquid Chromatography on line to electrospray ionization Quadrupole Time-of-flight mass spectrometry, appeared to be more abundant. CONCLUSION This approach provides novel insight into profiles of the salivary proteome during gingival inflammation, which may contribute to improvements in diagnosis.

Renal Cell Carcinoma and Proteomics

Renal cell carcinoma (RCC) represents 3% of adult malignancies. About 30% of RCC patients develop metastatic disease. So far, drugs cannot significantly increase the survival of these patients. We present a recent review of proteomics and RCC. Proteomic technologies have been used in the research to discover new markers of RCC that might increase survival. Furthermore, newly discovered markers cannot increase patient survival, rather their prognostic value supporting therapeutic decisions or new agents targeted at these new markers. More research is required to develop proteomic technologies and biomarkers for identification and validation.

Urine screening by Seldi-Tof, followed by biomarker identification, in a Brazilian cohort of patients with Renal Cell Carcinoma (RCC)

PURPOSE To screen proteins/peptides in urine of Renal Cell Carcinoma (RCC) patients by SELDI-TOF (Surface Enhanced Laser Desorption Ionization - Time of Flight) in search of possible biomarkers. MATERIAL AND METHODS Sixty-one urines samples from Clear Cell RCC and Papillary RCC were compared to 29 samples of control urine on CM10 chip. Mass analysis was performed in a ProteinChip Reader PCS 4,000 (Ciphergen Biosystems, Fremont, CA) with the software Ciphergen Express 3.0. All chips were read at low and at high laser energy. For statistical analysis the urine samples were clustered according to the histological classification (Clear Cell and Papillary Carcinoma). For identification urine was loaded on a SDS PAGE gel and bands of most interest were excised, trypsinized and identified by MS/MS. Databank searches were performed in Swiss-Prot database using the MASCOT search algorithm and in Profound. RESULTS Proteins that were identified from urine of controls included immunoglobulin light chains, albumin, secreted and transmembrane 1 precursor (protein K12), mannan-binding lectin-associated serine protease-2 (MASP-2) and vitelline membrane outer layer 1 isoform 1. Identification of immunoglobulins and isoforms of albumin are quite common by proteomics and therefore cannot be considered as possible molecular markers. K12 and MASP-2 play important physiological roles, while vitellite membrane outer layer 1 role is unknown since it was never purified in humans. CONCLUSIONS The down expression of Protein K-12 and MASP-2 make them good candidates for RCC urine marker and should be validated in a bigger cohort including the other less common histological RCC subtypes.

Steady-state kinetic mechanism of Thermoanaerobium brockii alcohol dehydrogenase: A study of discrimination between alternative kinetic models

Two steady-state kinetic mechanisms have been proposed for the oxidation of 2-propanol catalyzed by Thermoanaerobium brockii alcohol dehydrogenase (TBADH): the sequential ordered BiBi mechanism and the Theorell-Chance BiBi mechanism. Discrimination between these kinetic mechanisms was achieved by analyzing the inhibition produced by acetone, the first product of the reaction sequence in relation to the second substrate of the enzyme (2-propanol). Two types of experimental data were used: a data set combining initial rate experiments in the absence of products with data involving inhibition by acetone in relation to 2-propanol as variable substrate; and, data sets just containing product inhibition experiments by acetone with 2-propanol as variable substrate. The results obtained strongly suggest that the kinetic mechanism of TBADH is described by the Theorell-Chance BiBi kinetic model.

Proteomic analysis reveals differentially secreted proteins in the urine from patients with clear cell renal cell carcinoma

OBJECTIVE The aim of this study was to evaluate the differentially secreted protein profile in the urine from patients with clear cell renal cell carcinoma (ccRCC) using mass spectrometry-based methods. Urine composition can reflect kidney physiology and can be used to detect markers for renal diseases. Moreover, characterization of the secretome is likely to assist in the investigation of new drugs for biological targets and diagnose the ccRCC at an early stage. METHODS AND MATERIALS Urine samples from patients were divided according to Fuhrman degree (FI-IV), which was associated with the cellular differentiation as good prognosis (GP) and poor prognosis (PP). Healthy individuals were used as the control group (CG). We used both qualitative and quantitative mass spectrometry-based analyses that involved the following approaches: 1-dimensional gel electrophoresis combined with liquid chromatography mass spectrometry in tandem (1DE LC-MS/MS), in-solution digestion combined with label-free 1-dimensional LC-MS(E) (1D LC-MS(E)), and bidimensional gel electrophoresis combined with matrix-assisted laser desorption/ionization time of flight in tandem (2DE MALDI-TOF/TOF) or combined with LC-MS/MS. RESULTS All the strategies allowed the identification of 354 proteins from the CG, GP, and PP groups. Qualitative experiments using 1DE LC-MS/MS analysis detected different protein profiles, and 224 proteins were identified in all groups. The label-free MS(E) quantitative analysis identified 113 proteins and generated novel information on secreted protein profiles, including 49 up-secreted proteins in the urine from patients with ccRCC and 40 down-secreted proteins related to the CG. Proteins such as kininogen-1, uromodulin, apolipoprotein D, polyubiquitin, and CD59 glycoprotein were down secreted according to the groups CG>GP>PP. In contrast, apolipoprotein A, fibrinogen, and haptoglobin were up secreted in patient groups. The same expression profile observed for kininogen-1, apolipoprotein D, fibrinogen, and haptoglobin was corroborated by 2DE LC-MS/MS or 2DE MALDI-TOF/TOF analyses. These 2 strategies also showed 13 differentially secreted proteins among the 3 groups. CONCLUSIONS The proteins kininogen-1, apolipoprotein D, fibrinogen, and haptoglobin presented similar quantitative protein profiles according to MS(E) and 2DE approaches. The latter proteins were up secreted and the former ones were down-regulated. The strategies used proved to be valuable in identifying proteins that were differentially secreted in urine from patients with RCC.

Kinetic mechanism of the oxidation of 2-propanol catalyzed by Thermoanaerobium brockii alcohol dehydrogenase

Abstract The reaction of oxidation of 2-propanol to acetone in the presence of NADP catalyzed by Thermoanaerobium brockii alcohol dehydrogenase (TBADH) has been studied for gaining insight into the coupled-substrate approach that has been extensively used for NADPH regeneration in preparative-scale reductions catalyzed by this enzyme. The data obtained in initial velocity experiments in the absence of products as well as those involving product inhibition and dead-end inhibition by pyrazole suggest that the reaction mechanism is of the Theorell-Chance BiBi type and in which the coenzymes bind to the free form of the enzyme. The seven kinetic parameters that characterize this kinetic model were estimated by non-linear regression analysis using the appropriate rate equations. The kinetic mechanism proposed in the present work is fully compatible with the coupled-substrate approach used for regeneration of NADPH in reduction reactions catalyzed by TBADH.

CD26/DPPIV cell membrane expression and DPPIV activity in plasma of patients with acute leukemia

CD26/DPPIV (dipeptidil peptidase IV) displays an array of diverse functional properties, with a role in the development of several human cancers. This enzyme is found mainly anchored in the membrane of cells although it also has an enzymatically active plasma isoform. The regulation of biological activities of cytokines by DPP IV activity has a potential role in the homeostatic regulation of hematopoiesis. In this study, we analyzed the CD26 antigen cell membrane expression by flow cytometry and the DPPIV activity in plasma of patients of acute leukemia. The results showed that the plasma DPPIV activity is significantly higher in leukemia patients and could be 100% inhibited by Januvia™ (Merck Sharp & Dohme) a selective DPPIV inhibitor. Although CD26 expression on immune cells were not leukemia-dependent the analysis of the correlation between CD26 expression and the DPPIV plasma activity were statistically significant (p < 0.01) in acute lymphoid leukemia (B-ALL and T-ALL).

Proteomics analysis of tissue samples from patients with squamous cell carcinoma of the penis and positive to human papillomavirus.

ABSTRACT Purpose: The aim of this study was to identify possible protein biomarkers and/or candidates for therapeutic targets in tissues of patients with SCCP, infected by HPV, applying one dimensional electrophoresis (1DE), followed by direct mass spectrometry (MS) analysis. Materials and Methods: Tissues from 10 HPV positive patients with SCCP and from 10 patients with HPV negative non-tumorous penile foreskins were analyzed applying 1D electrophoresis, followed by analysis with direct mass spectrometry (MS). Results: Sixty-three different proteins were identified in the first group and 50 in the second group. Recognition was possible for 28 proteins exclusively detected in Group 1 and 21 proteins presented only in Group 2. Conclusion: Some proteins in the first group are directly involved in the development of other types of cancer, and therefore, suitable for analysis. Complement C3 protein is a strong candidate for evaluating SCCP patients.

Measurement of HER2 in Saliva of Women in Risk of Breast Cancer

HER2 amplification can be present in ductal carcinoma in situ (DCIS). The aim of the present study was to test the feasibility of measuring soluble HER2 in the saliva of patients at risk of breast cancer towards early diagnosis and prognosis. Women with lesions classified as 4 according to BIRADS and women with spontaneous nipple discharge (NAF) were recruited for this study. Quantification of soluble HER2 in saliva was performed using the enzyme immunoassay ELISA. Median values of HER2 were quantified in saliva of the control groups and in the patient groups. The statistical test nonparametric Mann–Whitney was applied for the evaluation of median differences. Although the medians increased with the severity of the clinical status, no significant difference was found in all possibilities (p > 0.05) when comparing the medians among the patients groups. Interestingly, inter-individual HER2 quantity variations in the saliva were detected in this study in some subjects from each group. Considering possible inter-individual variations, research on saliva-based circulating HER2 has to be reinforced to ensure its correct application in diagnosis, treatment and in follow-up of breast cancer patients. Older and current issues surrounding the controversy about the appropriate methods for HER2 evaluation are discussed.