Identification of Drosophila heart-specific Cis-Regulatory Modules under Hox control

Cardiac morphogenesis is a complex process governed by evolutionarily conserved transcription factors and signaling molecules. The Drosophila cardiac tube is linear, made of 52 pairs of cardiomyocytes (CMs), which express specific transcription factor genes that have human homologues implicated in Congenital Heart Diseases (CHDs) (NKX2-5, GATA4 and TBX5). The Drosophila cardiac tube is linear and composed of a rostral portion named aorta and a caudal one called heart, distinguished by morphological and functional differences controlled by Hox genes, key regulators of axial patterning. Overexpression and inactivation of the Hox gene abdominal-A (abd-A), which is expressed exclusively in the heart, revealed that abd-A controls heart identity. The aim of our work is to isolate the heart-specific cisregulatory sequences of abd-A direct target genes, the realizator genes granting heart identity. In each segment of the heart, four pairs of cardiomyocytes (CMs) express tinman (tin), homologous to NKX2-5, and acquire strong contractile and automatic rhythmic activities. By tyramide amplified FISH, we found that seven genes, encoding ion channels, pumps or transporters, are specifically expressed in the Tin-CMs of the heart. We initially used online available tools to identify their heart-specific cisregutatory modules by looking for Conserved Non-coding Sequences containing clusters of binding sites for various cardiac transcription factors, including Hox proteins. Based on these data we generated several reporter gene constructs and transgenic embryos, but none of them showed reporter gene expression in the heart. In order to identify additional abd-A target genes, we performed microarray experiments comparing the transcriptomes of aorta versus heart and identified 144 genes overexpressed in the heart. In order to find the heart-specific cis-regulatory regions of these target genes we developed a new bioinformatic approach where prediction is based on pattern matching and ordered statistics. We first retrieved Conserved Noncoding Sequences from the alignment between the D.melanogaster and D.pseudobscura genomes. We scored for combinations of conserved occurrences of ABD-A, ABD-B, TIN, PNR, dMEF2, MADS box, T-box and E-box sites and we ranked these results based on two independent strategies. On one hand we ranked the putative cis-regulatory sequences according to best scored ABD-A biding sites, on the other hand we scored according to conservation of binding sites. We integrated and ranked again the two lists obtained independently to produce a final rank. We generated nGFP reporter construct flies for in vivo validation. We identified three 1kblong heart-specific enhancers. By in vivo and in vitro experiments we are determining whether they are direct abd-A targets, demonstrating the role of a Hox gene in the realization of heart identity. The identified abd-A direct target genes may be targets also of the NKX2-5, GATA4 and/or TBX5 homologues tin, pannier and Doc genes, respectively. The identification of sequences coregulated by a Hox protein and the homologues of transcription factors causing CHDs, will provide a mean to test whether these factors function as Hox cofactors granting cardiac specificity to Hox proteins, increasing our knowledge on the molecular mechanisms underlying CHDs. Finally, it may be investigated whether these Hox targets are involved in CHDs.

RNA Interference and cyclooxygenase-2 (COX-2) regulation in colon cancer cells

Despite new methods and combined strategies, conventional cancer chemotherapy still lacks specificity and induces drug resistance. Gene therapy can offer the potential to obtain the success in the clinical treatment of cancer and this can be achieved by replacing mutated tumour suppressor genes, inhibiting gene transcription, introducing new genes encoding for therapeutic products, or specifically silencing any given target gene. Concerning gene silencing, attention has recently shifted onto the RNA interference (RNAi) phenomenon. Gene silencing mediated by RNAi machinery is based on short RNA molecules, small interfering RNAs (siRNAs) and microRNAs (miRNAs), that are fully o partially homologous to the mRNA of the genes being silenced, respectively. On one hand, synthetic siRNAs appear as an important research tool to understand the function of a gene and the prospect of using siRNAs as potent and specific inhibitors of any target gene provides a new therapeutical approach for many untreatable diseases, particularly cancer. On the other hand, the discovery of the gene regulatory pathways mediated by miRNAs, offered to the research community new important perspectives for the comprehension of the physiological and, above all, the pathological mechanisms underlying the gene regulation. Indeed, changes in miRNAs expression have been identified in several types of neoplasia and it has also been proposed that the overexpression of genes in cancer cells may be due to the disruption of a control network in which relevant miRNA are implicated. For these reasons, I focused my research on a possible link between RNAi and the enzyme cyclooxygenase-2 (COX-2) in the field of colorectal cancer (CRC), since it has been established that the transition adenoma-adenocarcinoma and the progression of CRC depend on aberrant constitutive expression of COX-2 gene. In fact, overexpressed COX-2 is involved in the block of apoptosis, the stimulation of tumor-angiogenesis and promotes cell invasion, tumour growth and metastatization. On the basis of data reported in the literature, the first aim of my research was to develop an innovative and effective tool, based on the RNAi mechanism, able to silence strongly and specifically COX-2 expression in human colorectal cancer cell lines. In this study, I firstly show that an siRNA sequence directed against COX-2 mRNA (siCOX-2), potently downregulated COX-2 gene expression in human umbilical vein endothelial cells (HUVEC) and inhibited PMA-induced angiogenesis in vitro in a specific, non-toxic manner. Moreover, I found that the insertion of a specific cassette carrying anti-COX-2 shRNA sequence (shCOX-2, the precursor of siCOX-2 previously tested) into a viral vector (pSUPER.retro) greatly increased silencing potency in a colon cancer cell line (HT-29) without activating any interferon response. Phenotypically, COX-2 deficient HT-29 cells showed a significant impairment of their in vitro malignant behaviour. Thus, results reported here indicate an easy-to-use, powerful and high selective virus-based method to knockdown COX-2 gene in a stable and long-lasting manner, in colon cancer cells. Furthermore, they open up the possibility of an in vivo application of this anti-COX-2 retroviral vector, as therapeutic agent for human cancers overexpressing COX-2. In order to improve the tumour selectivity, pSUPER.retro vector was modified for the shCOX-2 expression cassette. The aim was to obtain a strong, specific transcription of shCOX-2 followed by COX-2 silencing mediated by siCOX-2 only in cancer cells. For this reason, H1 promoter in basic pSUPER.retro vector [pS(H1)] was substituted with the human Cox-2 promoter [pS(COX2)] and with a promoter containing repeated copies of the TCF binding element (TBE) [pS(TBE)]. These promoters were choosen because they are partculary activated in colon cancer cells. COX-2 was effectively silenced in HT-29 and HCA-7 colon cancer cells by using enhanced pS(COX2) and pS(TBE) vectors. In particular, an higher siCOX-2 production followed by a stronger inhibition of Cox-2 gene were achieved by using pS(TBE) vector, that represents not only the most effective, but also the most specific system to downregulate COX-2 in colon cancer cells. Because of the many limits that a retroviral therapy could have in a possible in vivo treatment of CRC, the next goal was to render the enhanced RNAi-mediate COX-2 silencing more suitable for this kind of application. Xiang and et al. (2006) demonstrated that it is possible to induce RNAi in mammalian cells after infection with engineered E. Coli strains expressing Inv and HlyA genes, which encode for two bacterial factors needed for successful transfer of shRNA in mammalian cells. This system, called “trans-kingdom” RNAi (tkRNAi) could represent an optimal approach for the treatment of colorectal cancer, since E. Coli in normally resident in human intestinal flora and could easily vehicled to the tumor tissue. For this reason, I tested the improved COX-2 silencing mediated by pS(COX2) and pS(TBE) vectors by using tkRNAi system. Results obtained in HT-29 and HCA-7 cell lines were in high agreement with data previously collected after the transfection of pS(COX2) and pS(TBE) vectors in the same cell lines. These findings suggest that tkRNAi system for COX-2 silencing, in particular mediated by pS(TBE) vector, could represent a promising tool for the treatment of colorectal cancer. Flanking the studies addressed to the setting-up of a RNAi-mediated therapeutical strategy, I proposed to get ahead with the comprehension of new molecular basis of human colorectal cancer. In particular, it is known that components of the miRNA/RNAi pathway may be altered during the progressive development of colorectal cancer (CRC), and it has been already demonstrated that some miRNAs work as tumor suppressors or oncomiRs in colon cancer. Thus, my hypothesis was that overexpressed COX-2 protein in colon cancer could be the result of decreased levels of one or more tumor suppressor miRNAs. In this thesis, I clearly show an inverse correlation between COX-2 expression and the human miR- 101(1) levels in colon cancer cell lines, tissues and metastases. I also demonstrate that the in vitro modulating of miR-101(1) expression in colon cancer cell lines leads to significant variations in COX-2 expression, and this phenomenon is based on a direct interaction between miR-101(1) and COX-2 mRNA. Moreover, I started to investigate miR-101(1) regulation in the hypoxic environment since adaptation to hypoxia is critical for tumor cell growth and survival and it is known that COX-2 can be induced directly by hypoxia-inducible factor 1 (HIF-1). Surprisingly, I observed that COX-2 overexpression induced by hypoxia is always coupled to a significant decrease of miR-101(1) levels in colon cancer cell lines, suggesting that miR-101(1) regulation could be involved in the adaption of cancer cells to the hypoxic environment that strongly characterize CRC tissues.

Progettare l'ospitalità: turismi e turisti della città contemporanea

La ricerca si pone come obbiettivo principale quello di individuare gli strumenti in grado di controllare la qualità di una progettazione specifica che risponde alle forti richieste della domanda turistica di un territorio. Parte dalle più semplici teorie che inquadrano una costante condizione dell’uomo, “il VIAGGIARE”. La ricerca si pone come primo interrogativo quello definire una “dimensione” in cui le persone viaggiano, dove il concetto fisico di spazio dedicato alla vita si è spostato come e quanto si sposta la gente. Esiste una sorta di macroluogo (destinazione) che comprende tutti gli spazi dove la gente arriva e da cui spesso riparte. Pensare all'architettura dell’ospitalità significa indagare e comprendere come la casa non è più il solo luogo dove la gente abita. La ricerca affonda le proprie tesi sull’importanza dei “luoghi” appartenenti ad un territorio e come essi debbano riappropriarsi, attraverso un percorso progettuale, della loro più stretta vocazione attrattiva. Così come si sviluppa un’architettura dello stare, si manifesta un’architettura dello spostarsi e tali architetture si confondono e si integrano ad un territorio che per sua natura è esso stesso attrattivo. L’origine terminologica di nomadismo è passaggio necessario per la comprensione di una nuova dimensione architettonica legata a concetti quali mobilità e abitare. Si indaga pertanto all’interno della letteratura “diasporica”, in cui compaiono le prime configurazioni legate alla provvisorietà e alle costruzioni “erranti”. In sintesi, dopo aver posizionato e classificato il fenomeno turistico come nuova forma dell’abitare, senza il quale non si potrebbe svolgere una completa programmazione territoriale in quanto fenomeno oramai imprescindibile, la ricerca procede con l’individuazione di un ambito inteso come strumento di indagine sulle relazioni tra le diverse categorie e “tipologie” turistiche. La Riviera Romagnola è sicuramente molto famosa per la sua ospitalità e per le imponenti infrastrutture turistiche ma a livello industriale non è meno famosa per il porto di Ravenna che costituisce un punto di riferimento logistico per lo scambio di merci e materie prime via mare, oltre che essere, in tutta la sua estensione, caso di eccellenza. La provincia di Ravenna mette insieme tutti i fattori che servono a soddisfare le Total Leisure Experience, cioè esperienze di totale appagamento durante la vacanza. Quello che emerge dalle considerazioni svolte sul territorio ravennate è che il turista moderno non va più in cerca di una vacanza monotematica, in cui stare solo in spiaggia o occuparsi esclusivamente di monumenti e cultura. La richiesta è quella di un piacere procurato da una molteplicità di elementi. Pensiamo ad un distretto turistico dove l’offerta, oltre alla spiaggia o gli itinerari culturali, è anche occasione per fare sport o fitness, per rilassarsi in luoghi sereni, per gustare o acquistare cibi tipici e, allo stesso tempo, godere degli stessi servizi che una persona può avere a disposizione nella propria casa. Il percorso, finalizzato a definire un metodo di progettazione dell’ospitalità, parte dalla acquisizione delle esperienze nazionali ed internazionali avvenute negli ultimi dieci anni. La suddetta fase di ricerca “tipologica” si è conclusa in una valutazione critica che mette in evidenza punti di forza e punti di debolezza delle esperienze prese in esame. La conclusione di questa esplorazione ha prodotto una prima stesura degli “obbiettivi concettuali” legati alla elaborazione di un modello architettonico. Il progetto di ricerca in oggetto converge sul percorso tracciato dai Fiumi Uniti in Ravenna. Tale scelta consente di prendere in considerazione un parametro che mostri fattori di continuità tra costa e città, tra turismo balneare e turismo culturale, considerato quindi come potenziale strumento di connessione tra realtà spesso omologhe o complementari, in vista di una implementazione turistica che il progetto di ricerca ha come primo tra i suoi obiettivi. Il tema dell’architettura dell’ospitalità, che in questo caso si concretizza nell’idea di sperimentare l’ALBERGO DIFFUSO, è quello che permette di evidenziare al meglio la forma specifica della cultura locale, salvandone la vocazione universale. La proposta progettuale si articola in uno studio consequenziale ed organico in grado di promuovere una riflessione originale sul tema del modulo “abitativo” nei luoghi di prossimità delle emergenze territoriali di specifico interesse, attorno alle quali la crescente affluenza di un’utenza fortemente differenziata evidenzia la necessità di nodi singolari che si prestino a soddisfare una molteplicità di usi in contesti di grande pregio.

Profilo genomico e di espressione dell'Osteosarcoma. Identificazione dei geni con alto grado di correlazione tra numero di copie ed espressione

To identify the regions of recurrent copy number abnormality in osteosarcoma and their effect on gene expression, we performed an integrated genome-wide high-resolution array CGH (aCGH) and gene expression profiling analysis on 40 human OS tissues and 12 OS cell lines. This analysis identified several recurrent chromosome regions that contain genes that show a gene dosage effect on gene expression. A further search, performed on those genes that were over-expressed and localized in the frequently amplified chromosomal regions, greatly reduced the number of candidate genes while their characterization using gene ontology (GO) analysis suggests the importance of the deregulation of the G1-to-S phase in the development of the disease. We also identified frequent deletions on 3q in the vicinity of LSAMP and performed a fine mapping analysis of the breakpoints. We precisely mapped the breakpoints in several instances and demonstrated that the majority do not involve the LSAMP gene itself, and that they appear to form by a process of non-homologous end joining. In addition, aCGH analysis revealed frequent gains of IGF1R that were highly correlated with its protein level. Blockade of IGF1R in OS cell lines with high copy number gain led to growth inhibition suggesting that IGF1R may be a viable drug target in OS, particularly in patients with copy number driven overexpression of this receptor.