Study of glycosidic changes in lung cancer: potential effectors in hematogenous metastasis

RESUMO: O cancro do pulmão (LC), uma das principais causas de mortalidade relacionada com cancro em Portugal, pode levar à formação de metástases hematogénicas. A adesão das células tumorais ao endotélio é considerada um dos passos fundamentais envolvidos na metástase. Em células sanguíneas, esta adesão é mediada por ligandos de E-selectina (E-SL), glicoproteínas ou glicolípidos decorados principalmente com sialyl-Lewis x (sLex) e sialyl-Lewis a (sLea). Tem sido descrito a expressão destes antigénios em LC, contudo o seu papel funcional em permitir a adesão das células de LC ao endotélio é ainda pouco compreendido. Foram analisadas amostras emparelhadas normais e tumorais de pacientes com cancro de pulmão de não-pequenas células (NSCLC) e três linhas celulares de LC. Immunoblotting assays com anti-sLex/sLea e molécula quimérica de E-selectina demonstraram que tecidos tumorais de LC sobreexpressam significativamente E-SL e resultados de citometria de fluxo demonstraram uma expressão elevada de E-SL nas linhas celulares. Para compreender o mecanismo da sobreexpressão de E-SL em tecidos tumorais e linhas celulares de LC, foi analisada a expressão de genes envolvidos na biossíntese de E-SL, nomeadamente FUT3, FUT4, FUT6, FUT7, ST3GAL3, ST3GAL4, ST3GAL6, β4GALT1, GCNT1 e GALNT3. Observou-se a sobreexpressão das fucosiltransferases FUT3, FUT6 e FUT7 em tecidos tumorais de LC e FUT3 em linhas celulares de LC, sendo que neste último, esta expressão é correlacionada com um aumento da adesão das células de LC às selectinas endoteliais. Foi observado que uma baixa expressão de FUT4 em tecidos tumorais está associada com estadios menos avançados de NSCLC. Foram analisadas ainda proteínas decoradas com sLex/sLea, tendo-se identificado como E-SL o antigénio carcinoembrionário em NSCLC. Em resumo, esta tese contribuiu para uma melhor compreensão das alterações glicosídicas e moléculas que podem influenciar a progressão tumoral do LC, podendo permitir identificar futuramente novos biomarcadores de diagnóstico/prognóstico e potenciais alvos terapêuticos para o NSCLC.--------------------------ABSTRACT: Lung cancer (LC), one of the major causes of mortality related to cancer in Portugal, may lead to hematogenous metastasis. Adhesion of cancer cells to endothelium is considered one of the crucial steps involved in metastasis. In blood cells, this adhesion is initiated by endothelial selectin ligands (E-SL) that are glycoproteins or glycolipids decorated mostly with sialyl-Lewis x (sLex) and sialyl-Lewis a (sLea). While LC has been described as expressing these sialyl Lewis antigens, its functional role in allowing LC adhesion to endothelium is still poorly understood. We analyzed paired tumor and normal tissues samples from non-small cell lung cancer (NSCLC) patients and three LC cell lines. Immunoblotting assays with anti-sLex/sLea and E-selectin chimera demonstrated that LC tumor tissues significantly overexpress E-SL and flow cytometry results indicated that E-SL are also abundantly expressed in LC cell lines. To understand the mechanism behind the overexpression of E-SL in LC tissues and cell lines, we analyzed the expression of genes involved in its biosynthesis, namely FUT3, FUT4, FUT6, FUT7, ST3GAL3, ST3GAL4, ST3GAL6, β4GALT1, GCNT1 and GALNT3. It was observed the overexpression of fucosyltransferases FUT3, FUT6 and FUT7 in LC tumor tissues and FUT3 in LC cell lines, being this last one correlated with an increased reactivity of the LC cells to endothelial selectins. It was described that low expression of FUT4 in tumor tissues is correlated with early stages of NSCLC. We also analyzed scaffolds proteins of sLex/sLea and it was identified the carcinoembryonic antigen as an E-SL in NSCLC. In summary, this thesis contributed to a better understanding of the glycosidic changes and molecules that can influence tumor progression of LC, allowing identifying in the future new diagnosis/prognosis biomarkers and potential therapeutic targets for NSCLC.

Assessment of a novel Cu (II) complex as a potential anticancer agent

Widely used in cancer treatment, chemotherapy still faces hindering challenges, ranging from severe induced toxicity to drug resistance acquisition. As means to overcome these setbacks, newly synthetized compounds have recently come into play with the basis of improved pharmacokinetic/pharmacodynamic properties. With this mind-set, this project aimed towards the antiproliferative potential characterization of a group of metallic compounds. Additionally the incorporation of the compounds within a nanoformulation and within new combination strategies with commercial chemotherapeutic drugs was also envisaged. Cell viability assays presented copper (II) compound (K4) as the most promising, presenting an IC50 of 6.10 μM and 19.09 μM for HCT116 and A549 cell line respectively. Exposure in fibroblasts revealed a 9.18 μM IC50. Hoechst staining assays further revealed the compound’s predisposition to induce chromatin condensation and nuclear fragmentation in HCT116 upon exposure to K4 which was later demonstrated by flow cytometry and annexin V-FITC/propidium iodide double staining analysis (under 50 % cell death induction). The compound further revealed the ability to interact with major macromolecules such as DNA (Kb = 2.17x105 M-1), inducing structural brakes and retardation, and further affecting cell cycle progression revealing delay in S-phase. Moreover BSA interactions were also visible however not conclusive. Proteome profiling revealed overexpression of proteins involved in metabolic activity and underexpression of proteins involved in apoptosis thus corroborating Hoechst and apoptosis flow cytometry data. K4 nanoformulation suffered from several hindrances and was ill succeeded in part due to K4’s poor solubility in aqueous buffers. Other approaches were considered in this regard. Combined chemotherapy assays revealed high cytotoxicity for afatinib and lapatinib strategies. Lapatinib and K4 proteome profiling further revealed high apoptosis rates, high metabolic activity and activation of redundant proteins as part of compensatory mechanisms.

Design of bio-inspired ionic liquids for protein stabilisation

Ionic Liquids (ILs) consist in organic salts that are liquid at/or near room temperature. Since ILs are entirely composed of ions, the formation of ion pairs is expected to be one essential feature for describing solvation in ILs. In recent years, protein - ionic liquid (P-IL) interactions have been the subject of intensive studies mainly because of their capability to promote folding/unfolding of proteins. However, the ion pairs and their lifetimes in ILs in P-IL thematic is dismissed, since the action of ILs is therefore the result of a subtle equilibrium between anion-cation interaction, ion-solvent and ion-protein interaction. The work developed in this thesis innovates in this thematic, once the design of ILs for protein stabilisation was bio-inspired in the high concentration of organic charged metabolites found in cell milieu. Although this perception is overlooked, those combined concentrations have been estimated to be ~300 mM among the macromolecules at concentrations exceeding 300 g/L (macromolecular crowding) and transient ion-pair can naturally occur with a potential specific biological role. Hence the main objective of this work is to develop new bio-ILs with a detectable ion-pair and understand its effects on protein structure and stability, under crowding environment, using advanced NMR techniques and calorimetric techniques. The choline-glutamate ([Ch][Glu]) IL was synthesized and characterized. The ion-pair was detected in water solutions using mainly the selective NOE NMR technique. Through the same technique, it was possible to detect a similar ion-pair promotion under synthetic and natural crowding environments. Using NMR spectroscopy (protein diffusion, HSQC experiments, and hydrogen-deuterium exchange) and differential scanning calorimetry (DSC), the model protein GB1 (production and purification in isotopic enrichment media) it was studied in the presence of [Ch][Glu] under macromolecular crowding conditions (PEG, BSA, lysozyme). Under dilute condition, it is possible to assert that the [Ch][Glu] induces a preferential hydration by weak and non-specific interactions, which leads to a significant stabilisation. On the other hand, under crowding environment, the [Ch][Glu] ion pair is promoted, destabilising the protein by favourable weak hydrophobic interactions , which disrupt the hydration layer of the protein. However, this capability can mitigates the effect of protein crowders. Overall, this work explored the ion-pair existence and its consequences on proteins in conditions similar to cell milieu. In this way, the charged metabolites found in cell can be understood as key for protein stabilisation.

Chlorite Dismutase from perchlorate reducing bacteria. A potential biocatalyst to eliminate chlorinated species from polluted water resources and industrial wastes

Magnetospirillum (M.) sp. strain Lusitani, a perchlorate reducing bacteria (PRB), was previously isolated from a wastewater treatment plant and phylogenetic analysis was performed to classify the isolate. The DNA sequence of the genes responsible for perchlorate reduction and chlorite dismutation was determined and a model was designed based on the physiological roles of the proteins involved in the pcr-cld regulon. Chlorite dismutase (Cld) was purified from Magnetospirillum sp. strain Lusitani cells grown in anaerobiosis in the presence of perchlorate. The protein was purified up to electrophoretic grade using HPLC techniques as a 140 kDa homopentamer comprising five ~28 kDa monomers. Steady-state kinetic studies showed that the enzyme follows a Michaelis-Menten model with optimal pH and temperature of 6.0 and 5°C, respectively. The average values for the kinetic constants KM and Vmax were respectively 0.56 mM and 10.2 U, which correspond to a specific activity of 35470 U/mg and a turnover number of 16552 s-1. Cld from M. sp. strain Lusitani is inhibited by the product chloride, but not by dioxygen. Inhibition constants KiC= 460 mM and KiU= 480 mM indicated that sodium chloride is a weak mixed inhibitor of Cld, with a slightly stronger competitive character. The X-ray crystallography structure of M. sp. strain Lusitani Cld was solved at 3.0 Å resolution. In agreement with cofactor content biochemical analysis, the X-ray data showed that each Cld monomer harbors one heme b coordinated by a histidine residue (His188), hydrogen-bonded to a conserved glutamic acid residue (Glu238). The conserved neighboring arginine residue (Arg201) important for substrate positioning, was found in two different conformations in different monomers depending on the presence of the exogenous ligand thiocyanate. UV-Visible and CW-EPR spectroscopies were used to study the effect of redox agents, pH and exogenous ligands on the heme environment.

The potential field method and the nonlinear attractor dynamics approach: what are the differences?

One of the most popular approaches to path planning and control is the potential field method. This method is particularly attractive because it is suitable for on-line feedback control. In this approach the gradient of a potential field is used to generate the robot's trajectory. Thus, the path is generated by the transient solutions of a dynamical system. On the other hand, in the nonlinear attractor dynamic approach the path is generated by a sequence of attractor solutions. This way the transient solutions of the potential field method are replaced by a sequence of attractor solutions (i.e., asymptotically stable states) of a dynamical system. We discuss at a theoretical level some of the main differences of these two approaches.

Prediction of drug targets in human pathogens

The identification of new and druggable targets in bacteria is a critical endeavour in pharmaceutical research of novel antibiotics to fight infectious agents. The rapid emergence of resistant bacteria makes today's antibiotics more and more ineffective, consequently increasing the need for new pharmacological targets and novel classes of antibacterial drugs. A new model that combines the singular value decomposition technique with biological filters comprised of a set of protein properties associated with bacterial drug targets and similarity to protein-coding essential genes of E. coli has been developed to predict potential drug targets in the Enterobacteriaceae family [1]. This model identified 99 potential target proteins amongst the studied bacterial family, exhibiting eight different functions that suggest that the disruption of the activities of these proteins is critical for cells. Out of these candidates, one was selected for target confirmation. To find target modulators, receptor-based pharmacophore hypotheses were built and used in the screening of a virtual library of compounds. Postscreening filters were based on physicochemical and topological similarity to known Gram-negative antibiotics and applied to the retrieved compounds. Screening hits passing all filters were docked into the proteins catalytic groove and 15 of the most promising compounds were purchased from their chemical vendors to be experimentally tested in vitro. To the best of our knowledge, this is the first attempt to rationalize the search of compounds to probe the relevance of this candidate as a new pharmacological target.

Protein-based nanodevices for therapeutic applications

Tese de Doutoramento em Biologia Molecular e Ambiental (área de especialização em Biologia Celular e Saúde).

Novel strategies to combat gram-negative bacterial pathogens using bacteriophage proteins

Dissertação de mestrado em Bioengenharia

Effect of arginine vasopressin on the canine epicardial coronary artery: experiments on V1-receptor-mediated production of nitric oxide

OBJECTIVE: To determine whether arginine vasopressin releases endothelium-derived nitric oxide (EDNO) from the epicardial coronary artery. METHODS: We studied segments of canine left circumflex coronary arteries suspended in organ chambers to measure isometric force. The coronary artery segments were contracted with prostaglandin F2alpha (2 x 10-6M) and exposed to a unique, strong arginine vasopressin concentration (10-6M) or titrated concentrations (10-9 a 10-5 M). RESULTS: The unique dose of arginine vasopressin concentration (10-6M) induced transient, but significant (p<0.05), relaxation in arterial segments with endothelium, and an increase, not significant, in tension in arteries without endothelium. Endothelium-dependent relaxation to arginine vasopressin was inhibited by Ng-monomethyl-L-arginine (L-NMMA, 10-5M) or N G-nitro-L-arginine (L-NOARG) (10-4M), 2 inhibitors of nitric oxide synthesis from L-arginine. Exogenous L-arginine (10-4M), but not D-arginine (10-4M), reversed the inhibitory effect of L-NMMA on vasopressin-mediated vasorelaxation. Endothelium dependent relaxation to vasopressin was also reversibly inhibited by the vasopressin V1-receptor blocker d(CH2)5Try(Me) arginine vasopressin (10-6M) (n=6, P<0.05). CONCLUSION: Vasopressin acts through V1 endothelial receptors to stimulate nitric oxide release from L-arginine.

Importancia del Ca2+ en la fisiología espermática: modulación de su actividad por progesterona y proteínas del plasma seminal. Importance of calcium in sperm physiology: its regulation by progesterone and proteins from the seminal plasma.

El objetivo general del proyecto es estudiar el efecto de la progesterona y de algunas proteínas del plasma seminal sobre la actividad del Ca2+ en diferentes procesos fisiológicos que ocurren en el espermatozoide, los cuales están estrechamente relacionados con la capacidad fertilizante de esta célula. La progesterona, principal esteroide secretado por las células del cumulus oophorus, ejerce su efecto a través de un receptor no-genómico provocando aumento en el calcio intracelular de los espermatozoides y, consecuentemente, promoviendo la capacitación, la respuesta quimiotáctica y la exocitosis acrosomal. Pese a estas observaciones, los mecanismos a través de los cuales la progesterona estimula fenómenos tan diversos en el espermatozoide son aún desconocidos. Tampoco se conoce con exactitud el papel funcional y los mecanismos de acción de algunas proteínas del plasma seminal que interaccionan y se unen a los espermatozoides, con alta especificidad, durante la eyaculación. Por lo tanto, resulta altamente interesante profundizar los estudios sobre las propiedades funcionales de las proteínas caltrin (calcium transport inhibitor) y ß-microseminoprotein (MSP) del plasma seminal de mamíferos, las cuales responden a las características mencionadas. Los estudios hasta ahora realizados han dado cuenta de que caltrin inhibe la incorporación de Ca2+ extracelular, previene la exocitosis acrosomal espontánea y promueve la unión espermatozoide-zona pelúcida. También hay datos preliminares que sugieren un efecto inhibitorio sobre la movilidad hiperactivada de los espermatozoides. Respecto a MSP, sólo se sabe que inhibe la exocitosis acrosomal espontánea y que su contenido, en el plasma seminal, guarda una relación inversa con la fertilidad. Por todo lo expuesto, se propone estudiar los mecanismos de acción de la progesterona y las proteínas caltrin y MSP sobre los procesos fisiológicos antes indicados. Para ello, se estudiarán las variaciones de Ca2+ intracelular en espermatozoides individuales sometidos a diferentes tratamientos (gradientes de progesterona, capacitación en presencia y ausencia de caltrin y/o MSP, etc.), usando video microscopía de fluorescencia y análisis computarizado de imágenes. También se examinará la influencia de estas moléculas sobre la interacción de gametas y la fertilización.

Estudio de los mecanismos moleculares involucrados en la inmunosupresión observada durante la infección con Trypanosoma cruzi: Rol de la vía PD-1/PD1-L y E3 ubiquitina ligasas. Molecular mechanismns involved in the immunosupression during Tryapanosoma cruzi infection. Role of PD1-PD1-L pathway and E3 ubiquitin ligases.

Trypanosoma cruzi es el agente causal de la enfermedad de Chagas, un problema de salud importante en América Latina, así como también en América Central, ya que causa infección crónica afectando a millones de personas [1]. Durante esta enfermedad se han descripto varias alteraciones de la respuesta inmune, entre ellas una severa inmunosupresión durante la etapa aguda de la infección, tanto en humanos como en ratones. Células T provenientes de ratones infectados activadas in vitro, muestran reducción en la respuesta proliferativa a mitógenos, característica de un estado de inmunosupresión [2-4]. La falla del sistema inmune durante estadios tempranos de la infección probablemente colabore con la diseminación y el establecimiento del parásito. Un gran número de estudios se han focalizado en la identificación de mecanismos moleculares responsables del fenómeno de inmunosupresión, entre los mecanismos citados se ha demostrado presencia de células supresoras [5-9], factores inmunosupresores presentes en el parásito [2, 3, 10-13], producción excesiva de óxido nítrico [14], disminuida producción de IL-2 y reducida expresión del receptor de IL2 en células de bazo de animales infectados [9, 15-17]. Muchos de estos mecanismos han sido exhaustivamente investigados, sin embargo no está del todo claro si existen mecanismos adicionales involucrados en la inmunosupresión de la célula T. Adicionalmente, en los últimos años nuevas moléculas que median la regulación negativa de la célula T, entre las cuales están PD-1/PD1-L [18], arginasa [19] y E3 ubiquitina ligasas [20-22], han sido reportadas durante inmunosupresión en diversas infecciones. Trypanosoma cruzi, the etiological agent of Chagas’ disease, is parasite causing chronic infections in human and other mammalian species. There is an important immunosupresion during the acute phase of the infection that contribute to the dissemination and installation of the parasite. Several studies have been focused on identifying the mechanisms involved in the immunosupresion; however it is not clear if there are additional mechanisms implicated. In addition, during the last years new molecules involved in the negative T cell regulation such as PD-1/PD1-L pathway and E3 ubiquitin ligases (E3-Ub-Lig) have been reported. It has been demonstrated, that E3-Ub-Lig control the amount and localization of intracellular signal mediators, limiting T cell activation. Moreover, these mechanisms mediate the immunosupresion observed during several infections leading to the persistence of the pathogen in the host. In this project the role of E3-Ub-Lig on the T cell immunosupresion and hipo-response mechanisms observed during T. cruzi infection will be studied. On the other hand, it has been reported that some pathogens release proteins with E3-Ub-Lig activity modifying the ubiquitination process to promote their survival and replication in the host. Recently, a protein with E3-Ub-Lig activity was identified in T. cruzi, however its target molecule has not been discovered yet. Therefore, one of the aims of this project consists on studying different potential target molecules for this novel E3-Ub-Lig. In addition, during the last years, important progress has been done about the biological rol of PD-1/PD1-L pathway on the regulation of the immune response in several infections. However, it is not well known how PD-1/PD1-L pathway transduces signals at intracelular level to block T cell response. Because of this, it is interesting to study if there is any relation between the PD-1/PD1-L pathway and E3-Ub-Lig on the mechanism of T cell immunosupression during T. cruzi infection.

The retinoid-related orphan receptor RORα promotes keratinocyte differentiation via FOXN1.

RORα is a retinoid-related orphan nuclear receptor that regulates inflammation, lipid metabolism, and cellular differentiation of several non-epithelial tissues. In spite of its high expression in skin epithelium, its functions in this tissue remain unclear. Using gain- and loss-of-function approaches to alter RORα gene expression in human keratinocytes (HKCs), we have found that this transcription factor functions as a regulator of epidermal differentiation. Among the 4 RORα isoforms, RORα4 is prominently expressed by keratinocytes in a manner that increases with differentiation. In contrast, RORα levels are significantly lower in skin squamous cell carcinoma tumors (SCCs) and cell lines. Increasing the levels of RORα4 in HKCs enhanced the expression of structural proteins associated with early and late differentiation, as well as genes involved in lipid barrier formation. Gene silencing of RORα impaired the ability of keratinocytes to differentiate in an in vivo epidermal cyst model. The pro-differentiation function of RORα is mediated at least in part by FOXN1, a well-known pro-differentiation transcription factor that we establish as a novel direct target of RORα in keratinocytes. Our results point to RORα as a novel node in the keratinocyte differentiation network and further suggest that the identification of RORα ligands may prove useful for treating skin disorders that are associated with abnormal keratinocyte differentiation, including cancer.

Nuclear factor I-C links platelet-derived growth factor and transforming growth factor beta1 signaling to skin wound healing progression.

Transforming growth factor beta (TGF-beta) and platelet-derived growth factor A (PDGFAlpha) play a central role in tissue morphogenesis and repair, but their interplay remain poorly understood. The nuclear factor I C (NFI-C) transcription factor has been implicated in TGF-beta signaling, extracellular matrix deposition, and skin appendage pathologies, but a potential role in skin morphogenesis or healing had not been assessed. To evaluate this possibility, we performed a global gene expression analysis in NFI-C(-/-) and wild-type embryonic primary murine fibroblasts. This indicated that NFI-C acts mostly to repress gene expression in response to TGF-beta1. Misregulated genes were prominently overrepresented by regulators of connective tissue inflammation and repair. In vivo skin healing revealed a faster inflammatory stage and wound closure in NFI-C(-/-) mice. Expression of PDGFA and PDGF-receptor alpha were increased in wounds of NFI-C(-/-) mice, explaining the early recruitment of macrophages and fibroblasts. Differentiation of fibroblasts to contractile myofibroblasts was also elevated, providing a rationale for faster wound closure. Taken together with the role of TGF-beta in myofibroblast differentiation, our results imply a central role of NFI-C in the interplay of the two signaling pathways and in regulation of the progression of tissue regeneration.

Mutational analysis of the highly conserved arginine within the Glu/Asp-Arg-Tyr motif of the alpha(1b)-adrenergic receptor: effects on receptor isomerization and activation.

We have suggested previously that both the negatively and positively charged residues of the highly conserved Glu/Asp-Arg-Tyr (E/DRY) motif play an important role in the activation process of the alpha(1b)-adreneric receptor (AR). In this study, R143 of the E/DRY sequence in the alpha(1b)-AR was mutated into several amino acids (Lys, His, Glu, Asp, Ala, Asn, and Ile). The charge-conserving mutation of R143 into lysine not only preserved the maximal agonist-induced response of the alpha(1b)-AR, but it also conferred high degree of constitutive activity to the receptor. Both basal and agonist-induced phosphorylation levels were significantly increased for the R143K mutant compared with those of the wild-type receptor. Other substitutions of R143 resulted in receptor mutants with either a small increase in constitutive activity (R143H and R143D), impairment (R143H, R143D), or complete loss of receptor-mediated response (R143E, R143A, R143N, R143I). The R413E mutant displayed a small, but significant increase in basal phosphorylation despite being severely impaired in receptor-mediated response. Interestingly, all the arginine mutants displayed increased affinity for agonist binding compared with the wild-type alpha(1b)-AR. A correlation was found between the extent of the affinity shift and the intrinsic activity of the agonists. The analysis of the receptor mutants using the allosteric ternary complex model in conjunction with the results of molecular dynamics simulations on the receptor models support the hypothesis that mutations of R143 can drive the isomerization of the alpha(1b)-AR into different states, highlighting the crucial role of this residue in the activation process of the receptor.

Ab initio modeling and molecular dynamics simulation of the alpha 1b-adrenergic receptor activation.

This work describes the ab initio procedure employed to build an activation model for the alpha 1b-adrenergic receptor (alpha 1b-AR). The first version of the model was progressively modified and complicated by means of a many-step iterative procedure characterized by the employment of experimental validations of the model in each upgrading step. A combined simulated (molecular dynamics) and experimental mutagenesis approach was used to determine the structural and dynamic features characterizing the inactive and active states of alpha 1b-AR. The latest version of the model has been successfully challenged with respect to its ability to interpret and predict the functional properties of a large number of mutants. The iterative approach employed to describe alpha 1b-AR activation in terms of molecular structure and dynamics allows further complications of the model to allow prediction and interpretation of an ever-increasing number of experimental data.