Urine as a source for clinical proteome analysis: From discovery to clinical application

The success of clinical proteome analysis should be assessed based on the clinical impact following implementation of findings. Although there have been several technological advancements in mass spectrometry in the last years, these have not resulted in similar advancements in clinical proteomics. In addition, application of proteomic biomarkers in clinical diagnostics and practical improvement in the disease management is extremely rare. In this review, we discuss the relevant issues associated with identification of robust biomarkers of clinical value. Urine appears to be an ideal source of biomarkers, for theoretical, methodological, and practical reasons. Therefore, this review is focused on the search for biomarkers in urine within the last decade. Urine can be used for non-invasive assessment of a variety of diseases including those affecting the urogenital tract and also other pathologies such as cardiovascular disease or appendicitis. We also discuss the importance of data validation, an essential step in translating biomarkers into the clinical practice. Furthermore, we examine several examples of apparently successful proteomic biomarker discovery studies and their implications for disease diagnosis, prognosis, and therapy evaluation. We also discuss some current challenges in this field and reflect on future research prospects. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.     

The Role of Podoplanin in the Biology of Differentiated Thyroid Cancers

Podoplanin (PDPN), a mucin-type transmembrane glycoprotein specific to the lymphatic system is expressed in a variety of human cancers, and is regarded as a factor promoting tumor progression. The purpose of this study was to elucidate the molecular role of PDPN in the biology of thyroid cancer cells. PDPN expression was evaluated in primary thyroid carcinomas and thyroid carcinoma cell lines by RT-qPCR, Western blotting, IF and IHC. To examine the role of podoplanin in determining a cell''s malignant potential (cellular migration, invasion, proliferation, adhesion, motility, apoptosis), a thyroid cancer cell line with silenced PDPN expression was used. We observed that PDPN was solely expressed in the cancer cells of 40% of papillary thyroid carcinoma (PTC) tissues. Moreover, PDPN mRNA and protein were highly expressed in PTC-derived TPC1 and BcPAP cell lines but were not detected in follicular thyroid cancer derived cell lines. PDPN knock-down significantly decreased cellular invasion, and modestly reduced cell migration, while proliferation and adhesion were not affected. Our results demonstrate that PDPN mediates the invasive properties of cells derived from papillary thyroid carcinomas, suggesting that podoplanin might promote PTC progression.     

Anticonvulsant Effectiveness and Neurotoxicity Profile of 4-butyl-5-[(4-chloro-2-methylphenoxy)methyl]-2,4-dihydro-3H-1,2,4-triazole-3-thione (TPL-16) in Mice

Neurochemical Research - Protective (antiseizure) effects of 4-butyl-5-[(4-chloro-2-methylphenoxy)-methyl]-2,4-dihydro-3H-1,2,4-triazole-3-thione (TPL-16) and acute neurotoxic effects were...     

N-Methylated Analogs of hIAPP Fragments 18–22, 23–27, 33–37 Inhibit Aggregation of the Amyloidogenic Core of the Hormone

Amylin (hIAPP) aggregation leads to the formation of insoluble deposits and is one of the factors in the development of type II diabetes. The aim of this research was to find N-methylated analogs of the aggregating amylin fragments 18–22, 23–27, and 33–37, which would not themselves be susceptible to aggregation and would inhibit the aggregation of the amyloidogenic cores of the hormone. None of the analogs of fragment 18–22 containing one or two N-methylated amino acid residues showed any tendency to aggregate. Only the peptide H−F(N−Me)GA(N−Me) IL−OH ( 6 ) derived from the 23–27 hIAPP hot spot did not form fibrous structures. All analogs of the 33–37 amylin fragment were characterized by the ability to form aggregates, despite the presence of N-methylated amino acids in their structures. N-Methylated peptides 1 – 5 demonstrated inhibitory properties against the aggregation of fragment 18–22. Aggregation of the amyloidogenic core of 23–27 was significantly inhibited by N-methylated peptides 1 – 3 derived from the (18–22) H−HSSNN−OH fragment and by the H−F(N-Me)GA(N−Me)IL−OH ( 6 ) fragment derived from the 23–27 amylin hot spot. Fragment (33–37) H−GSNTY−NH₂ was found to be inhibited in the presence of N-methylated peptides 1 – 3 derived from the 18–22 fragment and by the double methylated peptide H−F(N−Me)GA(N−Me)IL−OH ( 6 ). Research on the possibility of using N-methylated analogs of amyloidogenic amylin cores as inhibitors of hormone aggregation is ongoing, with a focus on finding the minimum concentration of N-methylated peptides capable of inhibiting the aggregation of hIAPP hot spots.     

Selection of bacteria capable of dissimilatory reduction of Fe(III) from a long-term continuous culture on molasses and their use in a microbial fuel cell

Ferric ion-respiring microorganisms (FRMs) are a group of prokaryotes that use Fe(III) as well as other metals as terminal electron acceptors in the process of anaerobic respiration. Special attention is paid to a biotechnological significance of FRMs because of their potential role in electricity production in microbial fuel cells (MFCs) where the terminal acceptor of the electrons during anaerobic respiration is not a ferric ion but the anode. One of the best known FRMs is the Shewanellaceae family. Most of the Shewanella species have been isolated from marine environments. In this report, sugar beet molasses and ferric oxide were successfully used in the selection of a bacterial consortium capable of dissimilatory Fe(III) reduction in a long-term continuous culture. The inoculum was a sample of eutrophic lake bottom sediment. Among the bacteria present in this culture were representatives of the Enterobacteriaceae, and the genera Pseudomonas, Arcobacter, and Shewanella. Two non-marine Fe(III)-reducing Shewanella-related clones named POL1 and POL2 were isolated. The abilities of the POL1 and POL2 isolates to metabolize a panel of 190 carbon sources were examined using a BIOLOG assay. The results confirmed the abilities of the shewanellas to utilize a broad range of carbon substrates. The utility of the POL1 and POL2 isolates in H-type MFCs operating on pyruvate or molasses was demonstrated. The operation of the MFC with shewanellas cultured on molasses was shown for the first time. A two-stage character of the fuel cell polarization curves, not previously noted in Shewanella MFC studies, was observed.     

Malate plays a crucial role in starch metabolism, ripening, and soluble solid content of tomato fruit and affects postharvest softening

Despite the fact that the organic acid content of a fruit is regarded as one of its most commercially important quality traits when assessed by the consumer, relatively little is known concerning the physiological importance of organic acid metabolism for the fruit itself. Here, we evaluate the effect of modifying malate metabolism in a fruit-specific manner, by reduction of the activities of either mitochondrial malate dehydrogenase or fumarase, via targeted antisense approaches in tomato (Solanum lycopersicum). While these genetic perturbations had relatively little effect on the total fruit yield, they had dramatic consequences for fruit metabolism, as well as unanticipated changes in postharvest shelf life and susceptibility to bacterial infection. Detailed characterization suggested that the rate of ripening was essentially unaltered but that lines containing higher malate were characterized by lower levels of transitory starch and a lower soluble sugars content at harvest, whereas those with lower malate contained higher levels of these carbohydrates. Analysis of the activation state of ADP-glucose pyrophosphorylase revealed that it correlated with the accumulation of transitory starch. Taken together with the altered activation state of the plastidial malate dehydrogenase and the modified pigment biosynthesis of the transgenic lines, these results suggest that the phenotypes are due to an altered cellular redox status. The combined data reveal the importance of malate metabolism in tomato fruit metabolism and development and confirm the importance of transitory starch in the determination of agronomic yield in this species.     

Cryopreservation of mononuclear cells before extracorporeal photochemotherapy does not impair their anti-proliferative capabilities

Background aimsThe clinical benefits of extracorporeal photochemotherapy (ECP) are well recognized, but its clinical use is limited by logistical difficulties, especially because of the need to perform repeated aphereses. The cryopreservation of mononuclear cells could allow maintenance of the ECP schedule while reducing the number of aphereses. The aim of this work was to assess whether previous cryopreservation impairs the immunomodulatory function of ECP-treated peripheral blood mononuclear cells (PBMC).MethodsFresh or previously cryopreserved PBMC were exposed to ECP and added on day 0 into a mixed leukocyte reaction. Proliferation of alloreactive lymphocytes was measured by carboxyfluorescein succinimidyl ester (CFSE) dye dilution. Apoptosis was quantified by annexin–7AAD staining.ResultsECP-induced apoptosis was slightly increased in cryopreserved cells but the kinetics of apoptosis were similar to fresh cells. Lymphocytes stimulated in the presence of ECP-treated PBMC displayed a significant decrease in proliferation. The suppression was enforced when ECP-treated cells had been activated previously by allogeneic stimulation. Cryopreservation before ECP exposure did not impact apoptosis triggering or anti-proliferative properties of ECP-treated cells.ConclusionsCryopreservation before ECP does not impair the immunomodulatory effects of treated cells. These data warrant investigation of the clinical use of cryopreserved PBMC for ECP.