In quest’ultimi decenni si è assistito ad un notevole miglioramento nella terapia delle Leucemie Acute (LA) pediatriche, nonostante tutto si assiste oggi ad una fase di plateau della curva di sopravvivenza e le leucemie continuano a costituire la principale causa di morte pediatrica per malattia. Ulteriori progressi nel trattamento delle LA potrebbero essere ottenuti mediante studi di farmacogenomica che, identificando le componenti genetiche associate alla risposta individuale ai trattamenti farmacologici, consentono il disegno di terapie personalizzate e tumore-specifiche, ad alta efficacia e bassa tossicità per ciascun paziente. Il lavoro svolto è stato, dunque, finalizzato allo studio della farmacogenomica del farmaco antitumorale Clofarabina (CLO) nel trattamento delle LA pediatriche al fine di identificare marcatori genetici predittivi di risposta delle cellule leucemiche al farmaco, delucidare i meccanismi di resistenza cellulare ed individuare nuovi bersagli verso cui indirizzare terapie più mirate ed efficaci. L’analisi in vitro della sensibilità alla CLO di blasti provenienti da pazienti pediatrici affetti da Leucemia Acuta Linfoblastica (LAL) e Mieloide (LAM) ha consentito l’identificazione di due sottopopolazioni di cellule LAL ad immunofenotipo T a diversa sensibilità alla CLO. Mediante DNA-microarrays, si è identificata la “signature” genetica specificamente associata alla diversa risposta delle cellule LAL-T al farmaco. Successivamente, la caratterizzazione funzionale dei geni differenziali e l’analisi dei pathways hanno consentito l’identificazione specifica di potenziali biomarcatori di risposta terapeutica aprendo nuove prospettive per la comprensione dei meccanismi di resistenza cellulare alla CLO e suggerendo un nuovo bersaglio terapeutico per le forme LAL-T a bassa sensibilità al farmaco. In conclusione, nel lavoro svolto si sono identificati set di geni e pathways di rilievo biologico per la risposta delle cellule LAL-T alla CLO suggerendo marcatori genetici in grado di identificare i soggetti eleggibili per il trattamento o verso cui disegnare terapie innovative. Il lavoro è paradigma per l’applicazione della farmacogenomica in altre neoplasie. / Over the past decades, treatment of Acute Leukemia (AL) in children has improved dramatically. However, despite the remarkable progress in the treatment of AL, leukemia remaining the leading cause of death by disease in children. Advances in cure rates could be obtained by pharmacogenomics aimed at developing strategies to personalize treatment and tailor therapy to individual patients, optimizing efficacy and safety through better understanding of human genome variability and its influence on drug response. In this work, we studied the pharmacogenomics of the antitumoral agent Clofarabine (CLO) in pediatric AL in order to identify predictive markers of drug response of leukemic cells, to elucidate mechanisms of drug resistance and, finally, to discover new therapeutic targets for more specific and efficient curative approaches. In vitro sensitivity to CLO was performed on blasts from children affected by Acute Lymphoblastic and Myeloid leukemia (ALL and AML). We identified two T-ALL subgroups on the base of their CLO sensitivity. Gene Expression Profiling by DNA-microarrays allowed us to identify the genetic “signature” associated to T-ALL Clofarabine response. Moreover, analysis of the differentially expressed genes permitted the identification of potential biomarkers of drug resistance providing mechanistic insights into the pharmacological basis of T-ALL drug resistance and suggesting a new therapeutic target for the treatment of T-ALLs resistant to CLO. In conclusion, our study identified set of genes and pathways of biological relevance for T-ALL response to CLO suggesting genetic biomarkers able to identify patients that could benefit from CLO treatment or new targets to develop innovative therapeutic strategies. Our study could be a paradigm for the application of pharmacogenomic studies in other human cancers.

Il problema dell'antibiotico-resistenza è un problema di sanità pubblica per affrontare il quale è necessario un sistema di sorveglianza basato sulla raccolta e l'analisi dei dati epidemiologici di laboratorio. Il progetto di dottorato è consistito nello sviluppo di una applicazione web per la gestione di tali dati di antibiotico sensibilità di isolati clinici utilizzabile a livello di ospedale. Si è creata una piattaforma web associata a un database relazionale per avere un’applicazione dinamica che potesse essere aggiornata facilmente inserendo nuovi dati senza dover manualmente modificare le pagine HTML che compongono l’applicazione stessa. E’ stato utilizzato il database open-source MySQL in quanto presenta numerosi vantaggi: estremamente stabile, elevate prestazioni, supportato da una grande comunità online ed inoltre gratuito. Il contenuto dinamico dell’applicazione web deve essere generato da un linguaggio di programmazione tipo “scripting” che automatizzi operazioni di inserimento, modifica, cancellazione, visualizzazione di larghe quantità di dati. E’ stato scelto il PHP, linguaggio open-source sviluppato appositamente per la realizzazione di pagine web dinamiche, perfettamente utilizzabile con il database MySQL. E’ stata definita l’architettura del database creando le tabelle contenenti i dati e le relazioni tra di esse: le anagrafiche, i dati relativi ai campioni, microrganismi isolati e agli antibiogrammi con le categorie interpretative relative al dato antibiotico. Definite tabelle e relazioni del database è stato scritto il codice associato alle funzioni principali: inserimento manuale di antibiogrammi, importazione di antibiogrammi multipli provenienti da file esportati da strumenti automatizzati, modifica/eliminazione degli antibiogrammi precedenti inseriti nel sistema, analisi dei dati presenti nel database con tendenze e andamenti relativi alla prevalenza di specie microbiche e alla chemioresistenza degli stessi, corredate da grafici. Lo sviluppo ha incluso continui test delle funzioni via via implementate usando reali dati clinici e sono stati introdotti appositi controlli e l’introduzione di una semplice e pulita veste grafica. / Drug resistance is a huge problem for healthcare and to face it a monitoring system based on collection and analysis of laboratory epidemiological data is required. The PHD project was focused on the development of a web application, which we called ResMon2, for management of such type of data (drug resistance of bacteria present in clinical isolates) useable in a hospital. A web platform associated with a relational database was created in order to have an application easy to update inserting new data without directly editing the HTML pages of the application. The open-source MySQL database was chosen since it has many assets: extremely stable, high performance, supported by a huge online community and it is free. The dynamic content of the web application is generated using a scripting-type programming language: PHP. It is an open-source language precisely developed for construction of dynamic-content web pages perfect for automation of inserting, editing, deleting and displaying functions of data. Besides, it integrates easily with MySQL database thanks to many integrated functions for dynamic data manipulation. A new database was designed creating tables and relations among them: registries, samples, isolated microorganisms and antibiogram data (sensitive, resistant, intermediate). Once defined the database the PHP and HTML code composing the main functions of the application was written. Such functions are: manual insert of single antibiogram, multiple antibiograms importing from specific instruments data files, edit/delete of previously inserted antibiograms, data analysis for trends detection of specific microorganisms species prevalence and of their drug resistance, with attached cake-type graphics and histograms. All functions were tested with real sample clinical data and were provided with specific controls, and simple and clean graphics were added to the application.

The Reverse Vaccinology (RV) approach allows using genomic information for the delineation of new protein-based vaccines starting from an in silico analysis. The first powerful example of the application of the RV approach is given by the development of a protein-based vaccine against serogroup B Meningococcus. A similar approach was also used to identify new Staphylococcus aureus vaccine candidates, including the ferric hydroxamate-binding lipoprotein FhuD2. S. aureus is a widespread human pathogen, which employs various different strategies for iron uptake, including: (i) siderophore-mediated iron acquisition using the endogenous siderophores staphyloferrin A and B, (ii) siderophore-mediated iron acquisition using xeno-siderophores (the pathway exploited by FhuD2) and (iii) heme-mediated iron acquisition. In this work the high resolution crystal structure of FhuD2 in the iron (III)-siderophore-bound form was determined. FhuD2 belongs to the Periplasmic Binding Protein family (PBP ) class III, and is principally formed by two globular domains, at the N- and C-termini of the protein, that make up a cleft where ferrichrome-iron (III) is bound. The N- and C-terminal domains, connected by a single long α-helix, present Rossmann-like folds, showing a β-stranded core and an α-helical periphery, which do not undergo extensive structural rearrangement when they interact with the ligand, typical of class III PBP members. The structure shows that ferrichrome-bound iron does not come directly into contact with the protein; rather, the metal ion is fully coordinated by six oxygen donors of the hydroxamate groups of three ornithine residues, which, with the three glycine residues, make up the peptide backbone of ferrichrome. Furthermore, it was found that iron-free ferrichrome is able to subtract iron from transferrin. This study shows for the first time the structure of FhuD2, which was found to bind to siderophores ,and that the protein plays an important role in S. aureus colonization and infection phases.

Background: Neisseria meningitides represents a major cause of meningitis and sepsis. The meningococcal regulator NadR was previously shown to repress the expression of the Neisserial Adhesin A (NadA) and play a major role in its phase-variation. NadA is a surface exposed protein involved in epithelial cell adhesion and colonization and a major component of 4CMenB, a novel vaccine to prevent meningococcus serogroup B infection. The NadR mediated repression of NadA is attenuated by 4-HPA, a natural molecule released in human saliva. Results: In this thesis we investigated the global role of NadR during meningogoccal infection, identifying through microarray analysis the NadR regulon. Two distinct types of NadR targets were identified, differing in their promoter architectures and 4HPA responsive activities: type I are induced, while type II are co-repressed in response to the same 4HPA signal. We then investigate the mechanism of regulation of NadR by 4-HPA, generating NadR mutants and identifying classes or residues involved in either NadR DNA binding or 4HPA responsive activities. Finally, we studied the impact of NadR mediated repression of NadA on the vaccine coverage of 4CMenB. A selected MenB strains is not killed by sera from immunized infants when the strain is grown in vitro, however, in an in vivo passive protection model, the same sera protected infant rats from bacteremia. Finally, using bioluminescent reporters, nadA expression in the infant rat model was induced in vivo at 3 h post-infection. Conclusions: Our results suggest that NadR coordinates a broad transcriptional response to signals present in the human host, enabling the meningococcus to adapt to the relevant host niche. During infectious disease the effect of the same signal on NadR changes between different targets. In particular NadA expression is induced in vivo, leading to efficient killing of meningococcus by anti-NadA antibodies elicited by the 4CMenB vaccine.

An increased incidence of Clostridium difficile infection (CDI) is associated with the emergence of epidemic strains characterised by high genetic diversity. Among the factors that may have a role in CDI there is a family of 29 paralogs, the cell wall proteins (CWPs), which compose the outer layer of the bacterial cell and are likely to be involved in colonisation. Previous studies have shown that 12 of the29 cwp genes are clustered in the same region, named after slpA (cwp1) the slpA locus, whereas the remaining 17 paralogs are distributed throughout the genome. The variability of 14 of these 17 cwp paralogs was determined in 40 C. difficile clinical isolates belonging to six of the currently prevailing PCR ribotypes. Based on sequence conservation, these cwp genes were divided into two groups, one comprising cwp loci having highly conserved sequences in all isolates, and the other 5 loci showing low genetic conservation between isolates of the same PCR ribotype as well as between different PCR ribotypes. Three conserved CWPs, Cwp16, Cwp18 and Cwp25, and two variable ones, Cwp26 and Cwp27, were characterised further by Western blot analysis of total cell extracts or S-layer preparations of the C. difficile clinical isolates. Expression of genetically invariable CWPs is well conserved in all isolates, while genetically variable CWPs are not always expressed at comparable levels even in strains containing identical sequences but belonging to different PCR ribotypes. In addition, we chose to analyse the immune response obtained in a protection experiment, carried out in hamsters, using a protein microarray approach to study the in vivo expression and the immunoreactivity of several surface proteins, including 18 Cwps.

The next generation of vaccine adjuvant are represented by a wide ranging set of molecules called Toll like agonists (TLR’s). Although many of these molecules are complex structures extracted from microorganisms, small molecule TLR agonists have also been identified. However, delivery systems have not been optimized to allow their effective delivery in conjunction with antigens. Here we describe a novel approach in which a small molecule TLR agonist has been conjugated directly to antigens to ensure effective co delivery. We describe the conjugation of a relevant protein, a recombinant protective antigen from S.pneumoniae (RrgB), which is linked to a TLR7 agonist. Following thorough characterization to ensure there was no aggregation, the conjugate was evaluated in a murine infection model. Results showed that the conjugate extended animals’ survival after lethal challenge with S.pneumoniae. Comparable results were obtained with a 10 fold lower dose than that of the native unconjugated antigen. Notably, the animals immunized with the same dose of unconjugated TLR7 agonist and antigen showed no adjuvant effect. The increased immunogenicity was likely a consequence of the co-localization of TLR7 agonist and antigen by chemical binding and is was more effective than simple co-administration. Likely, this approach can be adopted to reduce the dose of antigen required to induce protective immunity, and potentially increase the safety of a broad variety of vaccine candidates

Staphylococcus aureus is a Gram positive pathogen that causes various human infections and represents one of the most common causes of bacteremia. S. aureus is able to invade a variety of non-professional phagocytes and that can survive engulfment by neutrophils, producing both secreted and surface components that compromise innate immune responses. In the contest of our study we evaluated the functional activity of vaccine specific antibodies by opsonophagocytosis killing assay (OPKA). Interestingly a low level of killing of the staphylococcal cells has been observed. In the meanwhile intracellular survival studies showed that S. aureus persisted inside phagocytes for several hours until a burst of growth after 5 hours in the supernatant. These data suggest that the strong ability of S. aureus to survive in the phagocytes could be the cause of the low killing measured by OPKA. Moreover parallel studies on HL-60 cells infected with S. aureus done by using transmission electron microscopy (TEM) interestingly showed that staphylococcal cells have an intracellular localization (endosomal vacuoles) and that they are able not only to maintain the integrity of their membrane but also to replicate inside vacuolar compartments. Finally in order to generate 3D volume of whole bacteria when present inside neutrophilic vacuoles, we collected a series of tomographic two-dimensional (2D) images by using a transmission electron microscope, generating 5 different tomograms. The three-dimensional reconstruction reveals the presence of intact bacteria within neutrophil vacuoles. The S. aureus membrane appears completely undamaged and integral in contrast with the physiological process of phagosytosis through vacuoles progression. S. aureus bacteria show a homogenous distribution of the density in all the three dimensions (X, Y, Z). All these evidences definitely explain the ability of the pathogen to survive inside the endosomal vacuoles and should be the cause of the low killing level.

Enterobacteriaceae genomes evolve through mutations, rearrangements and horizontal gene transfer (HGT). The latter evolutionary pathway works through the acquisition DNA (GEI) modules of foreign origin that enhances fitness of the host to a given environment. The genome of E. coli IHE3034, a strain isolated from a case of neonatal meningitis, has recently been sequenced and its subsequent sequence analysis has predicted 18 possible GEIs, of which: 8 have not been previously described, 5 fully meet the pathogenic island definition and at least 10 that seem to be of prophagic origin. In order to study the GEI distribution of our reference strain, we screened for the presence 18 GEIs a panel of 132 strains, representative of E. coli diversity. Also, using an inverse nested PCR approach we identified 9 GEI that can form an extrachromosomal circular intermediate (CI) and their respective attachment sites (att). Further, we set up a qPCR approach that allowed us to determine the excision rates of 5 genomic islands in different growth conditions. Four islands, specific for strains appertaining to the sequence type complex 95 (STC95), have been deleted in order to assess their function in a Dictyostelium discoideum grazing assays. Overall, the distribution data presented here indicate that 16 IHE3034 GEIs are more associated to the STC95 strains. Also the functional and genetic characterization has uncovered that GEI 13, 17 and 19 are involved in the resistance to phagocitation by Dictyostelium d thus suggesting a possible role in the adaptation of the pathogen during certain stages of infection. / I genomi degli organismi della famiglia delle Enterobacteriaceae evolvono attraverso mutazioni, riarrangiamenti, e attraverso il meccanismo del trasferimento orizzontale di geni (HGT). Quest'ultima via evolutiva si esplica attraverso l'acquisizione, da parte del batterio ricevente, di moduli di materiale genetico di provenienti da altri microorganismi. Questi moduli donerebbero un vantaggio evolutivo ripsetto a determinate condizioni ambientali in cui si viene a trovare il batterio. L'analisi bioinformatica del genoma del ceppo di E. coli IHE3034 (isolato da un caso di meningite neonatale) ha ipotizzato la presenza di 18 isole genomiche (GEI) di cui: 8 mai descritte in precedenza e di cui 10 di origine profagica. Nel presente lavoro abbiamo effettuato uno studio della distribuzione di queste isole su 132 ceppi di E. coli rappresentativi di tutti i patotipi. Utilizzando un approccio basato sulla PCR abbiamo scoperto che 9 GEI sono ancora capaci di formare intermedi circolari (CI) e a sequenziare i rispettivi siti di ricombinazione. Inoltre utilizzando la PCR Real Time siamo riusciti a studiare le variazioni nella frequenza di excisione di 5 isole crescendo i batteri in diverse condizioni di crescita. Inoltre sono stati generati mutanti per delezione di 4 Isole specifiche di ceppi appartenenti al gruppo clonale 95 (STC95). I suddetti mutanti sono poi stati testati per la loro abilità di sopravvivenza alla fagocitosi da parte dell'amoeba Dictyostelium discoideum.

ABSTRACT Human cytomegalovirus (HCMV) employs many different mechanisms to escape and subvert the host immune system surveillance. Among these different mechanisms the role of human IgG Fc receptors (FcγR) in HCMV pathogenesis is still unclear. In mammalians, FcγRs are expressed on the surface of all haematopoietic cells and have a multifaceted role in regulating the activity of antibodies to generate a well-balanced immune response. Viral proteins with Fcγ binding ability are highly diffuse among herpesviruses. They interfere with the host receptors functions in order to counteract immune system recognition. So far, two human HCMV Fcγ binding proteins have been described: UL119 and RL11. This work was aimed to the identification and characterization of HCMV Fcγ binding proteins. The study is divided in two parts: first the characterization of UL119 and RL11; second the identification and characterization of novel HCMV Fcγ binding proteins. Regarding the first part, we demonstrated that both UL119 and RL11 internalize Fcγ fragments from transfected cells surface through a clathrin dependent pathway. In infected cells both proteins were found in the viral assembly complex and on virions surface as envelope associated glycoproteins. Moreover, internalized Fcγ in infected cells do not undergo lysosomal degradation but rather traffic in early endosomes up to the viral assembly complex. Regarding the second part, we were able to identify two novels Fcγ binding protein coded by CMV: RL12 and RL13. The latter was also further characterized as recombinant protein in terms of cellular localization, Fc binding site and IgG internalization ability. Finally binding specificity of both RL12 and RL13 seems to be confined to human IgG1 and IgG2. Taken together, these data show that HCMV codes for up to 4 FcγR and that they could have a double role both on virus and on infected cells.

Cellular response to γ-rays is mediated by ATM-p53 axis. When p53 is phosphorylated, it can transactivate several genes to induce permanent cell cycle arrest (senescence) or apoptosis. Epithelial and mesenchymal cells are more resistant to radiation-induced apoptosis and respond mainly by activating senescence. Hence, tumor cells in a senescent state might remain as “dormant” malignant in fact through disruption of p53 function, cells may overcome growth arrest. Oncocytic features were acquired in the recurring neoplasia after radiation therapy in patient with colonrectal cancer. Oncocytic tumors are characterized by aberrant biogenesis and are mainly non-aggressive neoplasms. Their low proliferation degree can be explained by chronic destabilization of HIF1α, which presides to adaptation to hypoxia and also plays a pivotal role in hypoxia-related radio-resistance. The aim of the present thesis was to verify whether mitochondrial biogenesis can be induced following radiation treatment, in relation of HIF1α status and whether is predictive of a senescence response. In this study was demonstrate that mitochondrial biogenesis parameters like mitochondrial DNA copy number could be used for the prediction of hypoxic status of tissue after radiation treatment. γ-rays induce an increase of mitochondrial mass and function, in response to a genotoxic stress that pushes cells into senescence. Mitochondrial biogenesis is only indirectly regulated by p53, whose activation triggers a MDM2-mediated HIF1α degradation, leading to the release of PGC-1β inhibition by HIF1α. On the other hand, this protein blunts the mitochondrial response to γ-rays as well as the induction of p21-mediated cell senescence, indicating prevalence of the hypoxic over the genotoxic response. Finally in vivo, post-radiotherapy mtDNA copy number increase well correlates with lack of HIF1α increase in the tissue, concluding this may be a useful molecular tool to infer the trigger of a hypoxic response during radiotherapy, which may lead to failure of activation of senescence.