New approaches to open problems in gene expression microarray data

In the past decade, the advent of efficient genome sequencing tools and high-throughput experimental biotechnology has lead to enormous progress in the life science. Among the most important innovations is the microarray tecnology. It allows to quantify the expression for thousands of genes simultaneously by measurin the hybridization from a tissue of interest to probes on a small glass or plastic slide. The characteristics of these data include a fair amount of random noise, a predictor dimension in the thousand, and a sample noise in the dozens. One of the most exciting areas to which microarray technology has been applied is the challenge of deciphering complex disease such as cancer. In these studies, samples are taken from two or more groups of individuals with heterogeneous phenotypes, pathologies, or clinical outcomes. these samples are hybridized to microarrays in an effort to find a small number of genes which are strongly correlated with the group of individuals. Eventhough today methods to analyse the data are welle developed and close to reach a standard organization (through the effort of preposed International project like Microarray Gene Expression Data -MGED- Society [1]) it is not unfrequant to stumble in a clinician's question that do not have a compelling statistical method that could permit to answer it.The contribution of this dissertation in deciphering disease regards the development of new approaches aiming at handle open problems posed by clinicians in handle specific experimental designs. In Chapter 1 starting from a biological necessary introduction, we revise the microarray tecnologies and all the important steps that involve an experiment from the production of the array, to the quality controls ending with preprocessing steps that will be used into the data analysis in the rest of the dissertation. While in Chapter 2 a critical review of standard analysis methods are provided stressing most of problems that In Chapter 3 is introduced a method to adress the issue of unbalanced design of miacroarray experiments. In microarray experiments, experimental design is a crucial starting-point for obtaining reasonable results. In a two-class problem, an equal or similar number of samples it should be collected between the two classes. However in some cases, e.g. rare pathologies, the approach to be taken is less evident. We propose to address this issue by applying a modified version of SAM [2]. MultiSAM consists in a reiterated application of a SAM analysis, comparing the less populated class (LPC) with 1,000 random samplings of the same size from the more populated class (MPC) A list of the differentially expressed genes is generated for each SAM application. After 1,000 reiterations, each single probe given a "score" ranging from 0 to 1,000 based on its recurrence in the 1,000 lists as differentially expressed. The performance of MultiSAM was compared to the performance of SAM and LIMMA [3] over two simulated data sets via beta and exponential distribution. The results of all three algorithms over low- noise data sets seems acceptable However, on a real unbalanced two-channel data set reagardin Chronic Lymphocitic Leukemia, LIMMA finds no significant probe, SAM finds 23 significantly changed probes but cannot separate the two classes, while MultiSAM finds 122 probes with score >300 and separates the data into two clusters by hierarchical clustering. We also report extra-assay validation in terms of differentially expressed genes Although standard algorithms perform well over low-noise simulated data sets, multi-SAM seems to be the only one able to reveal subtle differences in gene expression profiles on real unbalanced data. In Chapter 4 a method to adress similarities evaluation in a three-class prblem by means of Relevance Vector Machine [4] is described. In fact, looking at microarray data in a prognostic and diagnostic clinical framework, not only differences could have a crucial role. In some cases similarities can give useful and, sometimes even more, important information. The goal, given three classes, could be to establish, with a certain level of confidence, if the third one is similar to the first or the second one. In this work we show that Relevance Vector Machine (RVM) [2] could be a possible solutions to the limitation of standard supervised classification. In fact, RVM offers many advantages compared, for example, with his well-known precursor (Support Vector Machine - SVM [3]). Among these advantages, the estimate of posterior probability of class membership represents a key feature to address the similarity issue. This is a highly important, but often overlooked, option of any practical pattern recognition system. We focused on Tumor-Grade-three-class problem, so we have 67 samples of grade I (G1), 54 samples of grade 3 (G3) and 100 samples of grade 2 (G2). The goal is to find a model able to separate G1 from G3, then evaluate the third class G2 as test-set to obtain the probability for samples of G2 to be member of class G1 or class G3. The analysis showed that breast cancer samples of grade II have a molecular profile more similar to breast cancer samples of grade I. Looking at the literature this result have been guessed, but no measure of significance was gived before.

The immunogenicity of chemically derived zwitterionic polysaccharides

Bacterial capsular polysaccharides (PS) which naturally contain zwitterionic charge motifs (ZPS) possess specific immunostimulatory activity, leading to direct activation of antigen-presenting cells (APCs) through Toll-like receptor 2 (TLR2) and of T cells in co-culture systems. When administered intraperitoneally, ZPS and bacteria expressing them are involved in the induction or regulation of T-cell dependent inflammatory processes such as intra-abdominal abscess formation. Moreover it has been published that ZPSs are processed to low molecular weight carbohydrates and presented to T cells through a pathway similar to that used for protein antigens. These findings were in contrast with the paradigm according to which polysaccharides are T-independent antigens unable to be presented in association with MHC class II molecules and unable to induce a protective immune response. For this reason in glycoconjugate vaccines polysaccharides often need to be conjugated to a carrier protein to induce protection. The aim of our work was to generate vaccine candidates with antigen and adjuvant properties in one molecule by the chemical introduction of a positive charge into naturally anionic PS from group B streptococcus (GBS). The resulting zwitterionic PS (ZPS) has the ability to activate human and mouse APCs, and in mixed co-cultures of monocytes and T cells, ZPS induce MHC II-dependent T-cell proliferation and up-regulation of activation markers. TLR2 transfectants show reporter gene transcription upon incubation with ZPS and these stimulatory qualities can be blocked by anti-TLR2 mAbs or by the destruction of the zwitterionic motif. However, in vivo, ZPS used alone as vaccine antigen failed to induce protection against GBS challenge, a result which does not confirm the above mentioned postulate that ZPS are T-cell dependent Ags by virtue of their charge motif. Thus to make ZPS visible to the immune system we have conjugated ZPS with a carrier protein. ZPS-glycoconjugates induce higher T cell and Ab responses to carrier and PS, respectively, compared to control PS-glycoconjugates made with the native polysaccharide form. Moreover, protection of mothers or neonate offspring from lethal GBS challenge is better when mothers are immunized with ZPS-conjugates compared to immunization with PS-conjugates. In TLR2 knockout mice, ZPS-conjugates lose both their increased immunogenicity and protective effect after vaccination. When ZPS are co-administered as adjuvants with unconjugated tetanus toxoid (TT), they have the ability to increase the TT-specific antibody titer. In conclusion, glycoconjugates containing ZPS are potent vaccines. They target Ag to TLR2-expressing APCs and activate these APCs, leading to better T cell priming and ultimately to higher protective Ab titers. Thus, rational chemical design can generate potent novel PS-adjuvants with wide application, including glycoconjugates and co-administration with unrelated protein Ags.

New polymeric materials for vascular surgery

The dramatic impact that vascular diseases have on human life quality and expectancy nowadays is the reason why both medical and scientific communities put great effort in discovering new and effective ways to fight vascular pathologies. Among the many different treatments, endovascular surgery is a minimally-invasive technique that makes use of X-ray fluoroscopy to obtain real-time images of the patient during interventions. In this context radiopaque biomaterials, i.e. materials able to absorb X-ray radiation, play a fundamental role as they are employed both to enhance visibility of devices during interventions and to protect medical staff and patients from X-ray radiations. Organic-inorganic hybrids are materials that combine characteristics of organic polymers with those of inorganic metal oxides. These materials can be synthesized via the sol-gel process and can be easily applied as thin coatings on different kinds of substrates. Good radiopacity of organic-inorganic hybrids has been recently reported suggesting that these materials might find applications in medical fields where X-ray absorption and visibility is required. The present PhD thesis aimed at developing and characterizing new radiopaque organic-inorganic hybrid materials that can find application in the vascular surgery field as coatings for the improvement of medical devices traceability as well as for the production of X-ray shielding objects and garments. Novel organic-inorganic hybrids based on different polyesters (poly-lactic acid and poly-ε-caprolactone) and polycarbonate (poly-trimethylene carbonate) as the polymeric phase and on titanium oxide as the inorganic phase were synthesized. Study of the phase interactions in these materials allowed to demonstrate that Class II hybrids (where covalent bonds exists between the two phases) can be obtained starting from any kind of polyester or polycarbonate, without the need of polymer pre-functionalization, thanks to the occurrence of transesterification reactions operated by inorganic molecules on ester and carbonate moieties. Polyester based hybrids were successfully coated via dip coating on different kinds of textiles. Coated textiles showed improved radiopacity with respect to the plain fabric while remaining soft to the touch. The hybrid was able to coat single fibers of the yarn rather than coating the yarn as a whole. Openings between yarns were maintained and therefore fabric breathability was preserved. Such coatings are promising for the production of light-weight garments for X-ray protection of medical staff during interventional fluoroscopy, which will help preventing pathologies that stem from chronic X-ray exposure. A means to increase the protection capacity of hybrid-coated fabrics was also investigated and implemented in this thesis. By synthesizing the hybrid in the presence of a suspension of radiopaque tantalum nanoparticles, PDMS-titania hybrid materials with tunable radiopacity were developed and were successfully applied as coatings. A solution for enhancing medical device radiopacity was also successfully investigated. High metal radiopacity was associated with good mechanical and protective properties of organic-inorganic hybrids in the form of a double-layer coating. Tantalum was employed as the constituent of the first layer deposited on sample substrates by means of a sputtering technique. The second layer was composed of a hybrid whose constituents are well-known biocompatible organic and inorganic components, such as the two polymers PCL and PDMS, and titanium oxide, respectively. The metallic layer conferred to the substrate good X-ray visibility. A correlation between radiopacity and coating thickness derived during this study allows to tailor radiopacity simply by controlling the metal layer sputtering deposition time. The applied metal deposition technique also permits easy shaping of the radiopaque layer, allowing production of radiopaque markers for medical devices that can be unambiguously identified by surgeons during implantation and in subsequent radiological investigations. Synthesized PCL-titania and PDMS-titania hybrids strongly adhered to substrates and show good biocompatibility as highlighted by cytotoxicity tests. The PDMS-titania hybrid coating was also characterized by high flexibility that allows it to stand large substrate deformations without detaching nor cracking, thus being suitable for application on flexible medical devices.

Celiachia e difetti dello smalto in età evolutiva: correlazione tra periodo di esposizione al glutine, forme cliniche di celiachia e aplotipo HLA

The association between celiac disease (CD) and dental enamel defects (DED) is well known. AIM: This study was designed to investigate the prevalence of DED in CD children and to specifically find a possible correlation between DED and gluten exposure period, CD clinical forms, HLA class II haplotype. MATERIALS AND METHODS: This study was designed as a matched case-control study: 374 children were enrolled (187 celiac and 187 non celiac). Data about age at CD diagnosis, CD clinical form and HLA haplotype were recorded. RESULTS: DED were detected in 87 celiac subject while no dental lesions were found in the remaining 100 patients; in 187 healthy controls enamel lesion were significantly less frequent (5.3 % versus 46.5% ; p<0.005).We found a correlation between DED and gluten exposure period, since among CD patients the mean age at CD diagnosis was significantly (p= 0.0004) higher in the group with DED (3.41± 1.27) than without DED (1.26± 0.7). DED resulted more frequent in atypical and silent forms than in the typical one. The presence of HLA DR 52-53 and DQ7 antigens significantly increased the risk of DED (p=0.0017). CONCLUSIONS: Our results confirmed a possible correlation between CD clinical form, age at CD diagnosis, HLA antigens and DED. The origin of DED in CD children is due to multifactorial events and further studies are needed to investigate other determinants.

Caratteristiche ortopediche-ortodontiche in pazienti affetti da Sindrome di Nooan

La sindrome di Noonan (SN) è una patologia a trasmissione autosomica dominante caratterizzata da bassa statura, difetti cardiaci congeniti, dismorfia facciale. In letteratura sono stati pubblicati pochi case reports riguardanti le condizioni orali-facciali in pazienti affetti da SN. Obiettivo. Individuare patologie di pertinenza ortopedico-ortodontica caratteristiche della sindrome utilizzando un campione di pazienti con diagnosi di SN. Metodi. Un gruppo di 10 pazienti affetti da SN è stato sottoposto a esame obiettivo extraorale ed intraorale, ortopantomografia, teleradiografia latero-laterale, impronte delle arcate dentarie. Le misurazioni sulle TLL sono state effettuate sulla base dell'analisi MBT; i valori palatali provengono dai modelli di studio dell’arcata superiore. È stata utilizzato il test t-Student per mettere a confronto il gruppo di studio e il gruppo di controllo riguardo le misure cefalometriche e i valori palatali. Risultati. Nel gruppo di studio sono state rilevate anomalie di numero (un dente deciduo soprannumerario e una agenesia di un dente permanente). Il test t-Student rivela differenze statisticamente significative per 7 variabili cefalometriche su 13 e per 2 variabili palatali. Conclusioni. Basandosi su questo studio è possibile concludere che i pazienti con SN mostrano II classe scheletrica di tipo mandibolare, crescita iperdivergente, tendenza al morso aperto scheletrico, palatoversione degli incisivi superiori, palato stretto. Questi risultati possono fornire informazioni utili sia per la diagnosi di SN sia per la pianificazione del corretto trattamento ortodontico.

Ecological genetics and conservation genomics of wolf (Canis lupus)

In the present work, we apply both traditional and Next Generation Sequencing (NGS) tools to investigate some of the most important adaptive traits of wolves (Canis lupus). In the first part, we analyze the variability of three Major Histocompatibility Complex (MHC) class II genes in the Italian wolf population, also studying their possible role in mating choice and their influence on fitness traits. In the second section, as part of a larger canid genome project, we will exploit NGS data to investigate the transcript-level differences between the wolf and the dog genome that can be correlated to domestication.