Ensemble transcript interaction networks: A case study on Alzheimer's disease

Systems biology techniques are a topic of recent interest within the neurological field. Computational intelligence (CI) addresses this holistic perspective by means of consensus or ensemble techniques ultimately capable of uncovering new and relevant findings. In this paper, we propose the application of a CI approach based on ensemble Bayesian network classifiers and multivariate feature subset selection to induce probabilistic dependences that could match or unveil biological relationships. The research focuses on the analysis of high-throughput Alzheimer's disease (AD) transcript profiling. The analysis is conducted from two perspectives. First, we compare the expression profiles of hippocampus subregion entorhinal cortex (EC) samples of AD patients and controls. Second, we use the ensemble approach to study four types of samples: EC and dentate gyrus (DG) samples from both patients and controls. Results disclose transcript interaction networks with remarkable structures and genes not directly related to AD by previous studies. The ensemble is able to identify a variety of transcripts that play key roles in other neurological pathologies. Classical statistical assessment by means of non-parametric tests confirms the relevance of the majority of the transcripts. The ensemble approach pinpoints key metabolic mechanisms that could lead to new findings in the pathogenesis and development of AD

Sensitization profiles and cross-reactivity among plant allergens. Molecular mechanisms of food allergy development and the role of enhancers

La prevalencia de las alergias está aumentando desde mediados del siglo XX, y se estima que actualmente afectan a alrededor del 2-8 % de la población, pero las causas de este aumento aún no están claras. Encontrar el origen del mecanismo por el cual una proteína inofensiva se convierte en capaz de inducir una respuesta alérgica es de vital importancia para prevenir y tratar estas enfermedades. Aunque la caracterización de alérgenos relevantes ha ayudado a mejorar el manejo clínico y a aclarar los mecanismos básicos de las reacciones alérgicas, todavía queda un largo camino para establecer el origen de la alergenicidad y reactividad cruzada. El objetivo de esta tesis ha sido caracterizar las bases moleculares de la alergenicidad tomando como modelo dos familias de panalergenos (proteínas de transferencia de lípidos –LTPs- y taumatinas –TLPs-) y estudiando los mecanismos que median la sensibilización y la reactividad cruzada para mejorar tanto el diagnóstico como el tratamiento de la alergia. Para ello, se llevaron a cabo dos estrategias: estudiar la reactividad cruzada de miembros de familias de panalérgenos; y estudiar moléculas-co-adyuvantes que pudieran favorecer la capacidad alergénica de dichas proteínas. Para estudiar la reactividad cruzada entre miembros de la misma familia de proteínas, se seleccionaron LTPs y TLPs, descritas como alergenos, tomando como modelo la alergia a frutas. Por otra parte, se estudiaron los perfiles de sensibilización a alérgenos de trigo relacionados con el asma del panadero, la enfermedad ocupacional más relevante de origen alérgico. Estos estudios se llevaron a cabo estandarizando ensayos tipo microarrays con alérgenos y analizando los resultados por la teoría de grafos. En relación al estudiar moléculas-co-adyuvantes que pudieran favorecer la capacidad alergénica de dichas proteínas, se llevaron a cabo estudios sobre la interacción de los alérgenos alimentarios con células del sistema inmune humano y murino y el epitelio de las mucosas, analizando la importancia de moléculas co-transportadas con los alérgenos en el desarrollo de una respuesta Th2. Para ello, Pru p 3(LTP y alérgeno principal del melocotón) se selección como modelo para llevarlo a cabo. Por otra parte, se analizó el papel de moléculas activadoras del sistema inmune producidas por patógenos en la inducción de alergias alimentarias seleccionando el modelo kiwi-alternaria, y el papel de Alt a 1, alérgeno mayor de dicho hongo, en la sensibilización a Act d 2, alérgeno mayor de kiwi. En resumen, el presente trabajo presenta una investigación innovadora aportando resultados de gran utilidad tanto para la mejora del diagnóstico como para nuevas investigaciones sobre la alergia y el esclarecimiento final de los mecanismos que caracterizan esta enfermedad. ABSTRACT Allergies are increasing their prevalence from mid twentieth century, and they are currently estimated to affect around 2-8% of the population but the underlying causes of this increase remain still elusive. The understanding of the mechanism by which a harmless protein becomes capable of inducing an allergic response provides us the basis to prevent and treat these diseases. Although the characterization of relevant allergens has led to improved clinical management and has helped to clarify the basic mechanisms of allergic reactions, it seems justified in aspiring to molecularly dissecting these allergens to establish the structural basis of their allergenicity and cross-reactivity. The aim of this thesis was to characterize the molecular basis of the allergenicity of model proteins belonging to different families (Lipid Transfer Proteins –LTPs-, and Thaumatin-like Proteins –TLPs-) in order to identify mechanisms that mediate sensitization and cross reactivity for developing new strategies in the management of allergy, both diagnosis and treatment, in the near future. With this purpose, two strategies have been conducted: studies of cross-reactivity among panallergen families and molecular studies of the contribution of cofactors in the induction of the allergic response by these panallergens. Following the first strategy, we studied the cross-reactivity among members of two plant panallergens (LTPs , Lipid Transfer Proteins , and TLPs , Thaumatin-like Proteins) using the peach allergy as a model. Similarly, we characterized the sensitization profiles to wheat allergens in baker's asthma development, the most relevant occupational disease. These studies were performed using allergen microarrays and the graph theory for analyzing the results. Regarding the second approach, we analyzed the interaction of plant allergens with immune and epithelial cells. To perform these studies , we examined the importance of ligands and co-transported molecules of plant allergens in the development of Th2 responses. To this end, Pru p 3, nsLTP (non-specific Lipid Transfer Protein) and peach major allergen, was selected as a model to investigate its interaction with cells of the human and murine immune systems as well as with the intestinal epithelium and the contribution of its ligand in inducing an allergic response was studied. Moreover, we analyzed the role of pathogen associated molecules in the induction of food allergy. For that, we selected the kiwi- alternaria system as a model and the role of Alt a 1 , major allergen of the fungus, in the development of Act d 2-sensitization was studied. In summary, this work presents an innovative research providing useful results for improving diagnosis and leading to further research on allergy and the final clarification of the mechanisms that characterize this disease.

Occupational allergic multiorgan disease induced by wheat flour

Bakers are repeatedly exposed to wheat flour (WF) and may develop sensitization and occupational rhinoconjunctivitis and/or asthma to WF allergens.1 Several wheat proteins have been identified as causative allergens of occupational respiratory allergy in bakery workers.1 Testing of IgE reactivity in patients with different clinical profiles of wheat allergy (food allergy, wheat-dependent exercise-induced anaphylaxis, and baker's asthma) to salt-soluble and salt-insoluble protein fractions from WF revealed a high degree of heterogeneity in the recognized allergens. However, mainly salt-soluble proteins (albumins, globulins) seem to be associated with baker's asthma, and prolamins (gliadins, glutenins) with wheat-dependent exercise-induced anaphylaxis, whereas both protein fractions reacted to IgE from food-allergic patients.1 Notwithstanding, gliadins have also been incriminated as causative allergens in baker's asthma.2 We report on a 31-year-old woman who had been exposed to WF practically since birth because her family owned a bakery housed in the same home where they lived. She moved from this house when she was 25 years, but she continued working every day in the family bakery. In the last 8 years she had suffered from work-related nasal and ocular symptoms such as itching, watery eyes, sneezing, nasal stuffiness, and rhinorrhea. These symptoms markedly improved when away from work and worsened at work. In the last 5 years, she had also experienced dysphagia with frequent choking, especially when ingesting meats or cephalopods, which had partially improved with omeprazole therapy. Two years before referral to our clinic, she began to have dry cough and breathlessness, which she also attributed to her work environment. Upper and lower respiratory tract symptoms increased when sifting the WF and making the dough. The patient did not experience gastrointestinal symptoms with ingestion of cereal products. Skin prick test results were positive to grass (mean wheal, 6 mm), cypress (5 mm) and Russian thistle pollen (4 mm), WF (4 mm), and peach lipid transfer protein (6 mm) and were negative to rice flour, corn flour, profilin, mites, molds, and animal dander. Skin prick test with a homemade WF extract (10% wt/vol) was strongly positive (15 mm). Serologic tests yielded the following results: eosinophil cationic protein, 47 ?g/L; total serum IgE, 74 kU/L; specific IgE (ImmunoCAP; ThermoFisher, Uppsala, Sweden) to WF, 7.4 kU/L; barley flour, 1.24 kU/L; and corn, gluten, alpha-amylase, peach, and apple, less than 0.35 kU/L. Specific IgE binding to microarrayed purified WF allergens (WDAI-0.19, WDAI-0.53, WTAI-CM1, WTAI-CM2, WTAI-CM3, WTAI-CM16, WTAI-CM17, Tri a 14, profilin, ?-5-gliadin, Tri a Bd 36 and Tri a TLP, and gliadin and glutamine fractions) was assessed as described elsewhere.3 The patient's serum specifically recognized ?-5-gliadin and the gliadin fraction, and no IgE reactivity was observed to other wheat allergens. Spirometry revealed a forced vital capacity of 3.88 L (88%), an FEV1 of 3.04 L (87%), and FEV1/forced vital capacity of 83%. A methacholine inhalation test was performed following an abbreviated protocol,4 and the results were expressed as PD20 in cumulative dose (mg) of methacholine. Methacholine inhalation challenge test result was positive (0.24 mg cumulative dose) when she was working, and after a 3-month period away from work and with no visits to the bakery house, it gave a negative result. A chest x-ray was normal. Specific inhalation challenge test was carried out in the hospital laboratory by tipping WF from one tray to another for 15 minutes. Spirometry was performed at baseline and at 2, 5, 10, 15, 20, 30, 45, and 60 minutes after the challenge with WF. Peak expiratory flow was measured at baseline and then hourly over 24 hours (respecting sleeping time). A 12% fall in FEV1 was observed at 20 minutes and a 26% drop in peak expiratory flow at 9 hours after exposure to WF,