N-glycoprotein analysis discovers new up-regulated glycoproteins in colorectal cancer tissue.

Colorectal cancer is one of the leading causes of death due to cancer worldwide. Therefore, the identification of high-specificity and -sensitivity biomarkers for the early detection of colorectal cancer is urgently needed. Post-translational modifications, such as glycosylation, are known to play an important role in cancer progression. In the present work, we used a quantitative proteomic technique based on (18)O stable isotope labeling to identify differentially expressed N-linked glycoproteins in colorectal cancer tissue samples compared with healthy colorectal tissue from 19 patients undergoing colorectal cancer surgery. We identified 54 up-regulated glycoproteins in colorectal cancer samples, therefore potentially involved in the biological processes of tumorigenesis. In particular, nine of these (PLOD2, DPEP1, SE1L1, CD82, PAR1, PLOD3, S12A2, LAMP3, OLFM4) were found to be up-regulated in the great majority of the cohort, and, interestingly, the association with colorectal cancer of four (PLOD2, S12A2, PLOD3, CD82) has not been hitherto described.

Development of nervous systems to metamorphosis in feeding and non-feeding echinoid larvae, the transition from bilateral to radial symmetry.

The development of nervous system (NS) in the non-feeding vestibula larva of the sea urchin, Holopneustes purpurescens, and the feeding echinopluteus larva of Hemicentrotus pulcherrimus was examined by focusing on fate during metamorphosis. In H. purpurescens, the serotonergic NS (SerNS) appeared simultaneously and independently in larval tissue and adult rudiment, respectively, from 3-day post-fertilization. In 4-day vestibulae, an expansive aboral ganglion (450 x 100 mum) was present in the larval mid region that extended axons toward the oral ectoderm. These axons diverged near the base of the primary podia. An axonal bundle connected with the primary podia and the rim of vestopore on the oral side. Thus, the SerNS of the larva innervated the rudiment at early stage of development of the primary podia. This innervation was short-lived, and immediately before metamorphosis, it disappeared from the larval and adult tissue domains, whereas non-SerNS marked by synaptotagmin remained. The NS of 1-month post-fertilization plutei of H. pulcherrimus comprised an apical ganglion (50 x 17 mum) and axons that extended to the ciliary bands and the adult rudiment (AR). A major basal nerve of serotonergic and non-serotonergic axons and a minor non-serotonergic nerve comprised the ciliary band nerve. In 3-month plutei, axonal connection among the primary podia in the neural folds completed. The SerNS never developed in the AR. Thus, there was distinctive difference between feeding- and non-feeding larvae of the above sea urchins with respect to SerNS and the AR.

Nervous system development in feeding and nonfeeding asteroid larvae and the early juvenile.

Larval and juvenile nervous systems (NS) of three asterinid sea stars with contrasting feeding and nonfeeding modes of development were characterized using the echinoderm-specific synaptotagmin antibody. In the feeding bipinnaria and brachiolaria larvae of Patiriella regularis, the species with ancestral-type development, an extensive NS was associated with the ciliary bands (CBs) and attachment complex. Lecithotrophic planktonic (Meridastra calcar) and benthic (Parvulastra exigua) brachiolariae lacked CBs and the associated NS, but had an extensive NS in the attachment complex. The similarity in the distribution and morphology of synaptotagmin immunoreactive neurons and the anatomy of the NS in the attachment complex of these closely related sea stars suggests conservation of neurogenesis in settlement-stage larvae regardless of larval feeding mode. Nerve cells were prominent on the brachia of all three species. In advanced brachiolariae the larval nervous system was localized to the adhesive disc as the larval body resorbed during metamorphosis. The structures and tissues that contained larval neurons degenerated during metamorphosis. There was no evidence that the larval NS persists through metamorphosis. In juvenile development, synaptotagmin IR was first evident in the NS of the tube feet. As the central nervous system developed, synaptotagmin IR reflected the histological organization of the adult NS. The juvenile NS formed de novo with a temporal lapse between histogenesis and synaptotagmin IR. We evaluated the ontogeny of NS organization in the change in body plan from the bilateral larva to the radial juvenile.

Identification of different mutational profiles in cancers arising in specific colon segments by next generation sequencing.

The objective of this study was to investigate the mutational profiles of cancers arising in different colon segments. To this aim, we have analyzed 37 colon cancer samples by use of the Ion AmpliSeq™ Comprehensive Cancer Panel. Overall, we have found 307 mutated genes, most of which already implicated in the development of colon cancer. Among these, 15 genes were mutated in tumors originating in all six colon segments and were defined "common genes" (i.e. APC, PIK3CA, TP53) whereas 13 genes were preferentially mutated in tumors originating only in specific colon segments and were defined "site-associated genes" (i.e. BLNK, PTPRD). In addition, the presence of mutations in 10 of the 307 identified mutated genes (NBN, SMUG1, ERBB2, PTPRT, EPHB1, ALK, PTPRD, AURKB, KDR and GPR124) were found to be of clinical relevance. Among clinically relevant genes, NBN and SMUG1 were identified as independent prognostic factors that predicted poor survival in colon cancer patients. In conclusion, the findings reported here indicate that tumors arising in different colon segments present differences in the type and/or frequency of genetic variants, with two of them being independent prognostic factors that predict poor survival in colon cancer patients.

Identification of copy number alterations in colon cancer from analysis of amplicon-based next generation sequencing data.

The objective of this study was to determine the feasibility to detect copy number alterations in colon cancer samples using Next Generation Sequencing data and to elucidate the association between copy number alterations in specific genes and the development of cancer in different colon segments. We report the successful detection of somatic changes in gene copy number in 37 colon cancer patients by analysis of sequencing data through Amplicon CNA Algorithm. Overall, we have found a total of 748 significant copy number alterations in 230 significant genes, of which 143 showed CN losses and 87 showed CN gains. Validation of results was performed on 20 representative genes by quantitative qPCR and/or immunostaining. By this analysis, we have identified 4 genes that were subjected to copy number alterations in tumors arising in all colon segments (defined "common genes") and the presence of copy number alterations in 14 genes that were significantly associated to one specific site (defined "site-associated genes"). Finally, copy number alterations in ASXL1, TSC1 and IL7R turned out to be clinically relevant since the loss of TSC1 and IL7R was associated with advanced stages and/or reduced survival whereas copy number gain of ASXL1 was associated with good prognosis.

Gating competence of constitutively open CLC-0 mutants revealed by the interaction with a small organic Inhibitor.

Opening of CLC chloride channels is coupled to the translocation of the permeant anion. From the recent structure determination of bacterial CLC proteins in the closed and open configuration, a glutamate residue was hypothesized to form part of the Cl--sensitive gate. The negatively charged side-chain of the glutamate was suggested to occlude the permeation pathway in the closed state, while opening of a single protopore of the double-pore channel would reflect mainly a movement of this side-chain toward the extracellular pore vestibule, with little rearrangement of the rest of the channel. Here we show that mutating this critical residue (Glu166) in the prototype Torpedo CLC-0 to alanine, serine, or lysine leads to constitutively open channels, whereas a mutation to aspartate strongly slowed down opening. Furthermore, we investigated the interaction of the small organic channel blocker p-chlorophenoxy-acetic acid (CPA) with the mutants E166A and E166S. Both mutants were strongly inhibited by CPA at negative voltages with a >200-fold larger affinity than for wild-type CLC-0 (apparent KD at -140 mV approximately 4 micro M). A three-state linear model with an open state, a low-affinity and a high-affinity CPA-bound state can quantitatively describe steady-state and kinetic properties of the CPA block. The parameters of the model and additional mutagenesis suggest that the high-affinity CPA-bound state is similar to the closed configuration of the protopore gate of wild-type CLC-0. In the E166A mutant the glutamate side chain that occludes the permeation pathway is absent. Thus, if gating consists only in movement of this side-chain the mutant E166A should not be able to assume a closed conformation. It may thus be that fast gating in CLC-0 is more complex than anticipated from the bacterial structures.

Structural requisites of 2-(p-chlorophenoxy)propionic acid analogues for activity on native rat skeletal muscle chloride conductance and on heterologously expressed CLC-1.

(1) The 2-(p-chlorophenoxy)propionic acid (CPP) modulates in a stereoselective manner the macroscopic chloride conductance (gCl), the electrical parameter sustained by the CLC-1 channel, of skeletal muscle. In order to determine the structural requirements for modulating native gCl and to identify high-affinity ligands, the effects of newly synthesised CPP analogues have been evaluated on gCl of rat EDL muscle fibres by means of the two-microelectrode current-clamp technique. (2) Each type of the following independent modification of CPP structure led to a three- to 10-fold decrease or to a complete lack of gCl-blocking activity: replacement of the electron-attractive chlorine atom of the aromatic ring, substitution of the oxygen atom of the phenoxy group, modification at the chiral centre and substitution of the carboxylic function with a phosphonate one. (3) The analogues bearing a second chlorophenoxy group on the asymmetric carbon atom showed a significant gCl-blocking activity. Similar to racemate CPP, the analogue with this group, spaced by an alkyl chain formed by three methylenic groups, blocked gCl by 45% at 100 micro M. (4) These latter derivatives were tested on heterelogously expressed CLC-1 performing inside-out patch-clamp recordings to further define how interaction between drug and channel protein could take place. Depending on the exact chemical nature of modification, these derivatives strongly blocked CLC-1 with K(D) values at -140 mV ranging from about 4 to 180 micro M. (5) In conclusion, we identified four molecular determinants pivotal for the interaction with the binding site on muscle CLC-1 channels: (a) the carboxylic group that confers the optimal acidity and the negative charge; (b) the chlorophenoxy moiety that might interact with a hydrophobic pocket; (c) the chiral centre that allows the proper spatial disposition of the molecule; (d) an additional phenoxy group that remarkably stabilises the binding by interacting with a second hydrophobic pocket.

Characterization and expression of a sea star otx ortholog (Protxß1/2) in the larva of Patiriella regularis.

A transcript of otx from the sea star Patiriella regularis (Protxß1/2) was characterized and its expression in early bipinnaria larvae was documented by whole mount in situ hybridization (WMISH). The nucleotide sequence exhibited 94% identity with Amotxß1/2 from the closely related species Patiria miniata. Protxß1/2 was expressed strongly in the developing archenteron in the future fore and mid-gut regions. This was followed by expression of Protxß1/2 in the developing enterocoels, mesodermal derivatives. This suggests a role for Protx in endomesoderm development. In coelom development, Protxß1/2 was first expressed in the left coelom. Subsequently expression was evident in the right coelom, but localization was never as strong as in the left coelom. This asymmetry in Protxß1/2 expression in the coeloms was evident up to the stage when they started to extend posteriorly. These data indicate that Protxß1/2 may have a role in coelom development, particularly in the left coelom, a definitive adult structure.

Avaliação clínica longitudinal de restaurações de resina composta em lesões cervicais não cariosas utilizando técnicas direta e semidireta: estudo randomizado / Clinical longitudinal evaluation of composite resin restorations in non-carious cervical lesions using direct and direct-indirect techniques: a randomized study

O objetivo desse estudo clínico randomizado boca dividida foi avaliar longitudinalmente a efetividade de restaurações de resina composta de lesões cervicais não cariosas realizadas pelas técnicas direta e semidireta. Foram selecionados 30 pacientes voluntários com necessidade de restaurações cervicais do tipo classe V. Cada paciente recebeu duas restaurações, uma realizada pela técnica direta e outra através da técnica semidireta, totalizando 60 restaurações. Após a realização das restaurações, foi feita uma avaliação inicial imediata (baseline), após 7 dias, 6, 12 e 24 meses, por meio dos critérios USPHS modificado. Cada paciente foi avaliado a cada retorno por dois examinadores calibrados. A análise dos dados foi realizada através de estatística descritiva por meio de porcentagem de sucesso das restaurações de acordo com os critérios estudados e os escores obtidos. Para análise inferencial foi realizado o teste T Student para avaliar as diferenças entre extensão, profundidade e tempo. Os testes Qui-Quadrado/Fisher foram utilizados para comparação das taxas entre os grupos após cada período (p<0,05). Os resultados obtidos foram avaliados por testes de sobrevida e taxa anual de falha (Kaplan-Meier). Em relação ao tempo, foi observada diferença estatisticamente significante, sendo a técnica direta 21,8 min (± 14,50) mais rápida que a técnica semi direta 35,3 min (± 19,89). Das 60 restaurações realizadas, 1 restauração direta foi perdida por falha de retenção e nenhum paciente faltou ao retorno em 7 dias. Com 6 meses, 4 restaurações foram perdidas por falta de retenção na técnica direta e 5 restaurações foram perdidas pelo mesmo motivo na técnica semi-direta. Somente 1 paciente se ausentou. No retorno de 12 meses, 2 restaurações foram perdidas e 2 pacientes ausentaram-se em ambas as técnicas. E com 24 meses, 2 pacientes não compareceram ao retorno e nenhuma restauração falhou pelo critério retenção pela técnica direta. Na técnica semi-direta, 1 paciente ausentou-se e 1 restauração foi perdida por falta de retenção. O sucesso cumulativo da técnica direta foi de 99%, 93,1%, 88,5% e 88,5% nos períodos de 7 dias, 6, 12 e 24 meses respectivamente. Na técnica semi-direta o sucesso cumulativo foi de 100%, 92,8%, 88,4% e 83,7% nos períodos de 7 dias, 6, 12 e 24 meses respectivamente. Conclui-se que, independente da técnica empregada, ambas são boas opções restauradoras e possuem altas taxas de sucesso cumulativo nos períodos estudados. O tempo de trabalho foi superior na técnica semidireta que na técnica direta. Com o passar do tempo houve redução da sensibilidade dental em ambas as técnicas. Houve trauma gengival imediatamente após os procedimentos restauradores realizados com as duas técnicas, porém houve redução do mesmo no decorrer dos períodos avaliados(AU)

The purpose of this randomized split-mouth clinical study was to longitudinally evaluate the effectiveness of composite resin restorations of non-carious cervical lesions performed by direct and semi-direct techniques. A total of 30 volunteers with a need for class V cervical restorations were selected. Each patient received two restorations, one performed by the direct technique and the other by the direct-indirect technique, totaling 60 restorations. Assessment at baseline, 7 days, 6, 12 and 24 months, we performed using the modified USPHS criteria. Each patient was evaluated at return by two calibrated examiners. Data analysis was performed through descriptive statistics analysis using percentage of success of the restorations according to the criteria studied and scores obtained. For inferential analysis, the Student T test was used to evaluate the differences between extension, depth and time. Chi-Square/Fisher tests were used to compare rates between groups after each period (p <0.05). The results were evaluated by survival and annual failure rates (Kaplan-Meier). Differences were detected regarding to time, in which direct and direct-indirect procedures last 21.8(± 14.50) and 35.3 (± 19.89) minutes, respectively. Of the 60 restorations performed, 1 direct restoration was lost due to retention failure and no patient was missing the return in 7 days. At 6 months, 4 restorations were lost due to lack of retention in the direct technique and 5 restorations were lost for the same reason in the direct-indirect technique. Only 1 patient was absent. At 12 months return, 2 restorations were lost and 2 patients were absent in both techniques. And at 24 months, 2 patients did not attend the return and no restoration failed by the retention criterion by the direct technique. In the direct-indirect technique, 1 patient was absent and 1 restoration was lost due to lack of retention. The cumulative success of the direct technique was 99%, 93.1%, 88.5% and 88.5% in the 7-day, 6th, 12th and 24thmonths periods respectively. In the direct-indirect technique, cumulative success was 100%, 92.8%, 88.4% and 83.7% in the 7-day, 6, 12 and 24-month periods, respectively. It is concluded that, regardless of the technique employed, both are good restorative options and have high cumulative success rates in the studied periods. Working time was longer in the direct-indirect technique than in the direct technique. There was reduction of dental sensitivity in both techniques. There was gingival trauma immediately after the restorative procedures performed by the two techniques, with trauma reduction with the along the evaluated periods (AU)

Engrailed is expressed in larval development and in the radial nervous system of Patiriella sea stars.

We documented expression of the pan-metazoan neurogenic gene engrailed in larval and juvenile Patiriella sea stars to determine if this gene patterns bilateral and radial echinoderm nervous systems. Engrailed homologues, containing conserved En protein domains, were cloned from the radial nerve cord. During development, engrailed was expressed in ectodermal (nervous system) and mesodermal (coeloms) derivatives. In larvae, engrailed was expressed in cells lining the larval and future adult coeloms. Engrailed was not expressed in the larval nervous system. As adult-specific developmental programs were switched on during metamorphosis, engrailed was expressed in the central nervous system and peripheral nervous system (PNS), paralleling the pattern of neuropeptide immunolocalisation. Engrailed was first seen in the developing nerve ring and appeared to be up-regulated as the nervous system developed. Expression of engrailed in the nerve plexus of the tube feet, the lobes of the hydrocoel along the adult arm axis, is similar to the reiterated pattern of expression seen in other animals. Engrailed expression in developing nervous tissue reflects its conserved role in neurogenesis, but its broad expression in the adult nervous system of Patiriella differs from the localised expression seen in other bilaterians. The role of engrailed in patterning repeated PNS structures indicates that it may be important in patterning the fivefold organisation of the ambulacrae, a defining feature of the Echinodermata.

Molecular modeling of p-chlorophenoxyacetic acid binding to the CLC-0 channel.

Molecular simulation techniques were applied to predict the interaction of the CLC-0 Cl(-) channel and the channel-blocking molecule p-chlorophenoxyacetic acid (CPA). A three-dimensional model of the CLC-0 channel was constructed on the basis of the homology with the bacterial Cl(-) channel StCLC, the structure of which has been solved by X-ray crystallography. Docking of the CPA molecule was obtained by using a geometric recognition algorithm, yielding 5000 possible conformations. By restraining the simulation to those conformations in which CPA is near the intracellular mouth of the channel, the CPA-protein complex models were reduced to three sets of conformations, which are interconvertible within 2 ns when molecular dynamics is applied to the system. Point mutations of CLC-0 at three different positions predicted to interact with CPA in these configurations did, however, not greatly alter CPA inhibition, suggesting a deeper final binding location. In the model, binding of CPA to a more internal position in the ionic pathway was obtained by applying a constant force vector to CPA, pushing it toward the center of the channel. This technique allowed us to outline the possible intrachannel pathway of CPA and to describe qualitatively the binding sites and energy barriers of this pathway. The consistency of the obtained models and the experimental data indicates that the CLC-0-CPA complex model is reasonable and can be used in further biological studies, such as rational design of blocking agents of and mutagenesis of CLC Cl(-) channels.

Molecular determinants of differential pore blocking of kidney CLC-K chloride channels.

The highly homologous Cl(-) channels CLC-Ka and CLC-Kb are important for water and salt conservation in the kidney and for the production of endolymph in the inner ear. Mutations in CLC-Kb lead to Bartter's syndrome and mutations in the small CLC-K subunit barttin lead to Bartter's syndrome and deafness. Here we show that CLC-Ka is blocked by the recently identified blocker 2-(p-chlorophenoxy)-3-phenylpropionic acid of the rat channel CLC-K1 with an apparent K(D) approximately 80 microM. We also found that DIDS (4,4'-diisothiocyanatostilbene-2,2'-disulphonic acid), a generic Cl(-) channel blocker, inhibits CLC-Ka (K(D) approximately 90 microM). Surprisingly, the highly homologous channel CLC-Kb is fivefold to sixfold less sensitive to both compounds. Guided by the crystal structure of bacterial CLC proteins, we identify two amino acids, N68/D68 and G72/E72, in CLC-Ka and CLC-Kb, respectively, that are responsible for the differential drug sensitivity. Both residues expose their side chains in the extracellular pore mouth, delineating the probable drug binding site. These novel CLC-K channel blockers are promising lead compounds for the development of new diuretic drugs.