Biological analysis of the in-vitro effects of homologous recombination inhibition and its use in cancer treatment through synthetic lethality

Synthetic lethality represents an anticancer strategy that targets tumor specific gene defects. One of the most studied application is the use of PARP inhibitors (e.g. olaparib) in BRCA1/2-less cancer cells. In BRCA2-defective tumors, olaparib (OLA) inhibits DNA single-strand break repair, while BRCA2 mutations hamper homologous recombination (HR) repair. The simultaneous impairment of those pathways leads BRCA-less cells to death by synthetic lethality. The projects described in this thesis were aimed at extending the use of OLA in cancer cells that do not carry a mutation in BRCA2 by combining this drug with compounds that could mimic a BRCA-less environment via HR inhibition. We demonstrated the effectiveness of our “fully small-molecule induced synthetic lethality” by using two different approaches. In the direct approach (Project A), we identified a series of neo-synthesized compounds (named RAD51-BRCA2 disruptors) that mimic BRCA2 mutations by disrupting the RAD51-BRCA2 interaction and thus the HR pathway. Compound ARN 24089 inhibited HR in human pancreatic adenocarcinoma cell line and triggered synthetic lethality by synergizing with OLA. Interestingly, the observed synthetic lethality was triggered by tackling two biochemically different mechanisms: enzyme inhibition (PARP) and protein-protein disruption (RAD51-BRCA2). In the indirect approach (Project B), we inhibited HR by interfering with the cellular metabolism through inhibition of LDH activity. The obtained data suggest an LDH-mediated control on HR that can be exerted by regulating either the energy supply needed to this repair mechanism or the expression level of genes involved in DNA repair. LDH inhibition also succeeded in increasing the efficiency of OLA in BRCA-proficient cell lines. Although preliminary, these results highlight a complex relationship between metabolic reactions and the control of DNA integrity. Both the described projects proved that our “fully small-molecule-induced synthetic lethality” approach could be an innovative approach to unmet oncological needs.

Characterisation of RNase Y in H. pylori: a non-essential enzyme involved in the processing of cag-PAI non coding RNA 1 (CncR1) sRNA

The importance of Helicobacter pylori as a human pathogen is underlined by the plethora of diseases it is responsible for. The capacity of H. pylori to adapt to the restricted host-associated environment andto evade the host immune response largely depends on a streamlined signalling network. The peculiar H. pylori small genome size combined with its paucity of transcriptional regulators highlights the relevance of post-transcriptional regulatory mechanisms as small non-coding RNAs (sRNAs). However, among the 8 RNases represented in H. pylori genome, a regulator guiding sRNAs metabolism is still not well studied. We investigated for the first time the physiological role in H. pylori G27 strain of the RNase Y enzyme. In the first line of research we provide a comprehensive characterization of the RNase Y activity by analysing its genomic organization and the factors that orchestrate its expression. Then, based on bioinformatic prediction models, we depict the most relevant determinants of RNase Y function, demonstrating a correlation of both structure and domain organization with orthologues represented in Gram-positive bacteria. To unveil the post-transcriptional regulatory effect exerted by the RNase Y, we compared the transcriptome of an RNase Y knock-out mutant to the parental wild type strain by RNA-seq approach. In the second line of research we characterized the activity of this single strand specific endoribonuclease on cag-PAI non coding RNA 1 (CncR1) sRNA. We found that deletion or inactivation of RNase Y led to the accumulation of a 3’-extended CncR1 (CncR1-L) transcript over time. Moreover, beneath its increased half-life, CncR1-L resembled a CncR1 inactive phenotype. Finally, we focused on the characterization of the in vivo interactome of CncR1. We set up a preliminary MS2-affinity purification coupled with RNA-sequencing (MAPS) approach and we evaluated the enrichment of specific targets, demonstrating the suitability of the technique in the H. pylori G27 strain.

Max Bill in Italia . Lo spazio logico dell'architettura

I Max Bill is an intense giornata of a big fresco. An analysis of the main social, artistic and cultural events throughout the twentieth century is needed in order to trace his career through his masterpieces and architectures. Some of the faces of this hypothetical mural painting are, among others, Le Corbusier, Walter Gropius, Ernesto Nathan Rogers, Kandinskij, Klee, Mondrian, Vatongerloo, Ignazio Silone, while the backcloth is given by artistic avant-gardes, Bauhaus, International Exhibitions, CIAM, war events, reconstruction, Milan Triennali, Venice Biennali, the School of Ulm. Architect, even though more known as painter, sculptor, designer and graphic artist, Max Bill attends the Bauhaus as a student in the years 1927-1929, and from this experience derives the main features of a rational, objective, constructive and non figurative art. His research is devoted to give his art a scientific methodology: each work proceeds from the analysis of a problem to the logical and always verifiable solution of the same problem. By means of composition elements (such as rhythm, seriality, theme and its variation, harmony and dissonance), he faces, with consistent results, themes apparently very distant from each other as the project for the H.f.G. or the design for a font. Mathematics are a constant reference frame as field of certainties, order, objectivity: ‘for Bill mathematics are never confined to a simple function: they represent a climate of spiritual certainties, and also the theme of non attempted in its purest state, objectivity of the sign and of the geometrical place, and at the same time restlessness of the infinity: Limited and Unlimited ’. In almost sixty years of activity, experiencing all artistic fields, Max Bill works, projects, designs, holds conferences and exhibitions in Europe, Asia and Americas, confronting himself with the most influencing personalities of the twentieth century. In such a vast scenery, the need to limit the investigation field combined with the necessity to address and analyse the unpublished and original aspect of Bill’s relations with Italy. The original contribution of the present research regards this particular ‘geographic delimitation’; in particular, beyond the deep cultural exchanges between Bill and a series of Milanese architects, most of all with Rogers, two main projects have been addressed: the realtà nuova at Milan Triennale in 1947, and the Contemporary Art Museum in Florence in 1980. It is important to note that these projects have not been previously investigated, and the former never appears in the sources either. These works, together with the most well-known ones, such as the projects for the VI and IX Triennale, and the Swiss pavilion for the Biennale, add important details to the reference frame of the relations which took place between Zurich and Milan. Most of the occasions for exchanges took part in between the Thirties and the Fifties, years during which Bill underwent a significant period of artistic growth. He meets the Swiss progressive architects and the Paris artists from the Abstraction-Création movement, enters the CIAM, collaborates with Le Corbusier to the third volume of his Complete Works, and in Milan he works and gets confronted with the events related to post-war reconstruction. In these years Bill defines his own working methodology, attaining an artistic maturity in his work. The present research investigates the mentioned time period, despite some necessary exceptions. II The official Max Bill bibliography is naturally wide, including spreading works along with ones more devoted to analytical investigation, mainly written in German and often translated into French and English (Max Bill himself published his works in three languages). Few works have been published in Italian and, excluding the catalogue of the Parma exhibition from 1977, they cannot be considered comprehensive. Many publications are exhibition catalogues, some of which include essays written by Max Bill himself, some others bring Bill’s comments in a educational-pedagogical approach, to accompany the observer towards a full understanding of the composition processes of his art works. Bill also left a great amount of theoretical speculations to encourage a critical reading of his works in the form of books edited or written by him, and essays published in ‘Werk’, magazine of the Swiss Werkbund, and other international reviews, among which Domus and Casabella. These three reviews have been important tools of analysis, since they include tracks of some of Max Bill’s architectural works. The architectural aspect is less investigated than the plastic and pictorial ones in all the main reference manuals on the subject: Benevolo, Tafuri and Dal Co, Frampton, Allenspach consider Max Bill as an artist proceeding in his work from Bauhaus in the Ulm experience . A first filing of his works was published in 2004 in the monographic issue of the Spanish magazine 2G, together with critical essays by Karin Gimmi, Stanislaus von Moos, Arthur Rüegg and Hans Frei, and in ‘Konkrete Architektur?’, again by Hans Frei. Moreover, the monographic essay on the Atelier Haus building by Arthur Rüegg from 1997, and the DPA 17 issue of the Catalonia Polytechnic with contributions of Carlos Martì, Bruno Reichlin and Ton Salvadò, the latter publication concentrating on a few Bill’s themes and architectures. An urge to studying and going in depth in Max Bill’s works was marked in 2008 by the centenary of his birth and by a recent rediscovery of Bill as initiator of the ‘minimalist’ tradition in Swiss architecture. Bill’s heirs are both very active in promoting exhibitions, researching and publishing. Jakob Bill, Max Bill’s son and painter himself, recently published a work on Bill’s experience in Bauhaus, and earlier on he had published an in-depth study on ‘Endless Ribbons’ sculptures. Angela Thomas Schmid, Bill’s wife and art historian, published in end 2008 the first volume of a biography on Max Bill and, together with the film maker Eric Schmid, produced a documentary film which was also presented at the last Locarno Film Festival. Both biography and documentary concentrate on Max Bill’s political involvement, from antifascism and 1968 protest movements to Bill experiences as Zurich Municipality councilman and member of the Swiss Confederation Parliament. In the present research, the bibliography includes also direct sources, such as interviews and original materials in the form of letters correspondence and graphic works together with related essays, kept in the max+binia+jakob bill stiftung archive in Zurich. III The results of the present research are organized into four main chapters, each of them subdivided into four parts. The first chapter concentrates on the research field, reasons, tools and methodologies employed, whereas the second one consists of a short biographical note organized by topics, introducing the subject of the research. The third chapter, which includes unpublished events, traces the historical and cultural frame with particular reference to the relations between Max Bill and the Italian scene, especially Milan and the architects Rogers and Baldessari around the Fifties, searching the themes and the keys for interpretation of Bill’s architectures and investigating the critical debate on the reviews and the plastic survey through sculpture. The fourth and last chapter examines four main architectures chosen on a geographical basis, all devoted to exhibition spaces, investigating Max Bill’s composition process related to the pictorial field. Paintings has surely been easier and faster to investigate and verify than the building field. A doctoral thesis discussed in Lausanne in 1977 investigating Max Bill’s plastic and pictorial works, provided a series of devices which were corrected and adapted for the definition of the interpretation grid for the composition structures of Bill’s main architectures. Four different tools are employed in the investigation of each work: a context analysis related to chapter three results; a specific theoretical essay by Max Bill briefly explaining his main theses, even though not directly linked to the very same work of art considered; the interpretation grid for the composition themes derived from a related pictorial work; the architecture drawing and digital three-dimensional model. The double analysis of the architectural and pictorial fields is functional to underlining the relation among the different elements of the composition process; the two fields, however, cannot be compared and they stay, in Max Bill’s works as in the present research, interdependent though self-sufficient. IV An important aspect of Max Bill production is self-referentiality: talking of Max Bill, also through Max Bill, as a need for coherence instead of a method limitation. Ernesto Nathan Rogers describes Bill as the last humanist, and his horizon is the known world but, as the ‘Concrete Art’ of which he is one of the main representatives, his production justifies itself: Max Bill not only found a method, but he autonomously re-wrote the ‘rules of the game’, derived timeless theoretical principles and verified them through a rich and interdisciplinary artistic production. The most recurrent words in the present research work are synthesis, unity, space and logic. These terms are part of Max Bill’s vocabulary and can be referred to his works. Similarly, graphic settings or analytical schemes in this research text referring to or commenting Bill’s architectural projects were drawn up keeping in mind the concise precision of his architectural design. As for Mies van der Rohe, it has been written that Max Bill took art to ‘zero degree’ reaching in this way a high complexity. His works are a synthesis of art: they conceptually encompass all previous and –considered their developments- most of contemporary pictures. Contents and message are generally explicitly declared in the title or in Bill’s essays on his artistic works and architectural projects: the beneficiary is invited to go through and re-build the process of synthesis generating the shape. In the course of the interview with the Milan artist Getulio Alviani, he tells how he would not write more than a page for an essay on Josef Albers: everything was already evident ‘on the surface’ and any additional sentence would be redundant. Two years after that interview, these pages attempt to decompose and single out the elements and processes connected with some of Max Bill’s works which, for their own origin, already contain all possible explanations and interpretations. The formal reduction in favour of contents maximization is, perhaps, Max Bill’s main lesson.

Manipolazione del metabolismo degli xenobiotici da frutta convenzionale ed attività chemiopreventiva

A reduced cancer risk associated with fruit and vegetable phytochemicals initially dictated chemopreventive approaches focused on specific green variety consumption or even single nutrient supplementations. However, these strategies not only failed to provide any health benefits but gave rise to detrimental effects. In parallel, public-health chemoprevention programmes were developed in the USA and Europe to increase whole vegetable consumption. Among these, the National Cancer Institute (NCI) sponsored plan “5 to 9 a day for a better health” was one of the most popular. This campaign promoted wide food choice through the consumption of at least 5 to 9 servings a day of colourful fruits and vegetables. In this study the effects of the diet suggested by NCI on transcription, translation and catalytic activity of both xenobiotic metabolizing (XME) and antioxidant enzymes were studied in the animal model. In fact, the boost of both antioxidant defences and “good” phase-II together with down-regulation of “bad” phase-I XMEs is still considered one of the most widely-used strategies of cancer control. Six male Sprague Dawley rats for each treatment group were used. According to the Italian Society of Human Nutrition, a serving of fruit, vegetables and leafy greens corresponds to 150, 250 and 50 g, respectively, in a 70 kg man. Proportionally, rats received one or five servings of lyophilized onion, tomato, peach, black grape or lettuce – for white, red, yellow, violet or green diet, respectively - or five servings of each green (“5 a day” diet) by oral gavage daily for 10 consecutive days. Liver subcellular fractions were tested for various cytochrome P450 (CYP) linked-monooxygenases, phase-II supported XMEs such as glutathione S-transferase (GST) and UDP-glucuronosyl transferase (UDPGT) as well as for some antioxidant enzymes. Hepatic transcriptional and translational effects were evaluated by reverse transcription-polymerase chain reaction (RT-PCR) and Western blot analysis, respectively. dROMs test was used to measure plasmatic oxidative stress. Routine haematochemical parameters were also monitored. While the five servings administration didn’t significantly vary XME catalytic activity, the lower dose caused a complex pattern of CYP inactivation with lettuce exerting particularly strong effects (a loss of up to 43% and 45% for CYP content and CYP2B1/2-linked XME, respectively; P<0.01). “5 a day” supplementation produced the most pronounced modulations (a loss of up to 60% for CYP2E1-linked XME and a reduction of CYP content of 54%; P<0.01). Testosterone hydroxylase activity confirmed these results. RT-PCR and Western blot analysis revealed that the “5 a day” diet XMEs inactivations were a result of both a transcriptional and a translational effect while lettuce didn’t exert such effects. All administrations brought out none or fewer modulation of phase-II supported XMEs. Apart from “5 a day” supplementation and the single serving of lettuce, which strongly induced DT- diaphorase (an increase of up to 141 and 171%, respectively; P<0.01), antioxidant enzymes were not significantly changed. RT-PCR analysis confirmed DT-diaphorase induction brought about by the administration of both “5 a day” diet and a single serving of lettuce. Furthermore, it unmasked a similar result for heme-oxygenase. dROMs test provided insight into a condition of high systemic oxidative stress as a consequence of animal diet supplementation with “5 a day” diet and a single serving of lettuce (an increase of up to 600% and 900%, respectively; P<0.01). Haematochemical parameters were mildly affected by such dietary manipulations. According to the classical chemopreventive theory, these results could be of particular relevance. In fact, even if antioxidant enzymes were only mildly affected, the phase-I inactivating ability of these vegetables would be a worthy strategy to cancer control. However, the recorded systemic considerable amount of reactive oxygen species and the complexity of these enzymes and their functions suggest caution in the widespread use of vegan/vegetarian diets as human chemopreventive strategies. In fact, recent literature rather suggests that only diets rich in fruits and vegetables and poor in certain types of fat, together with moderate caloric intake, could be associated with reduced cancer risk.

Transcriptional functions of DNA Topoisomerases at a genome-wide scale and a single gene levels

The DNA topology is an important modifier of DNA functions. Torsional stress is generated when right handed DNA is either over- or underwound, producing structural deformations which drive or are driven by processes such as replication, transcription, recombination and repair. DNA topoisomerases are molecular machines that regulate the topological state of the DNA in the cell. These enzymes accomplish this task by either passing one strand of the DNA through a break in the opposing strand or by passing a region of the duplex from the same or a different molecule through a double-stranded cut generated in the DNA. Because of their ability to cut one or two strands of DNA they are also target for some of the most successful anticancer drugs used in standard combination therapies of human cancers. An effective anticancer drug is Camptothecin (CPT) that specifically targets DNA topoisomerase 1 (TOP 1). The research project of the present thesis has been focused on the role of human TOP 1 during transcription and on the transcriptional consequences associated with TOP 1 inhibition by CPT in human cell lines. Previous findings demonstrate that TOP 1 inhibition by CPT perturbs RNA polymerase (RNAP II) density at promoters and along transcribed genes suggesting an involvement of TOP 1 in RNAP II promoter proximal pausing site. Within the transcription cycle, promoter pausing is a fundamental step the importance of which has been well established as a means of coupling elongation to RNA maturation. By measuring nascent RNA transcripts bound to chromatin, we demonstrated that TOP 1 inhibition by CPT can enhance RNAP II escape from promoter proximal pausing site of the human Hypoxia Inducible Factor 1 (HIF-1) and c-MYC genes in a dose dependent manner. This effect is dependent from Cdk7/Cdk9 activities since it can be reversed by the kinases inhibitor DRB. Since CPT affects RNAP II by promoting the hyperphosphorylation of its Rpb1 subunit the findings suggest that TOP 1inhibition by CPT may increase the activity of Cdks which in turn phosphorylate the Rpb1 subunit of RNAP II enhancing its escape from pausing. Interestingly, the transcriptional consequences of CPT induced topological stress are wider than expected. CPT increased co-transcriptional splicing of exon1 and 2 and markedly affected alternative splicing at exon 11. Surprisingly despite its well-established transcription inhibitory activity, CPT can trigger the production of a novel long RNA (5’aHIF-1) antisense to the human HIF-1 mRNA and a known antisense RNA at the 3’ end of the gene, while decreasing mRNA levels. The effects require TOP 1 and are independent from CPT induced DNA damage. Thus, when the supercoiling imbalance promoted by CPT occurs at promoter, it may trigger deregulation of the RNAP II pausing, increased chromatin accessibility and activation/derepression of antisense transcripts in a Cdks dependent manner. A changed balance of antisense transcripts and mRNAs may regulate the activity of HIF-1 and contribute to the control of tumor progression After focusing our TOP 1 investigations at a single gene level, we have extended the study to the whole genome by developing the “Topo-Seq” approach which generates a map of genome-wide distribution of sites of TOP 1 activity sites in human cells. The preliminary data revealed that TOP 1 preferentially localizes at intragenic regions and in particular at 5’ and 3’ ends of genes. Surprisingly upon TOP 1 downregulation, which impairs protein expression by 80%, TOP 1 molecules are mostly localized around 3’ ends of genes, thus suggesting that its activity is essential at these regions and can be compensate at 5’ ends. The developed procedure is a pioneer tool for the detection of TOP 1 cleavage sites across the genome and can open the way to further investigations of the enzyme roles in different nuclear processes.

The effect of osmolytes on protein fold stability at the single-molecule level

By pulling and releasing the tension on protein homomers with the Atomic Force Miscroscope (AFM) at different pulling speeds, dwell times and dwell distances, the observed force-response of the protein can be fitted with suitable theoretical models. In this respect we developed mathematical procedures and open-source computer codes for driving such experiments and fitting Bell’s model to experimental protein unfolding forces and protein folding frequencies. We applied the above techniques to the study of proteins GB1 (the B1 IgG-binding domain of protein G from Streptococcus) and I27 (a module of human cardiac titin) in aqueous solutions of protecting osmolytes such as dimethyl sulfoxide (DMSO), glycerol and trimethylamine N-oxide (TMAO). In order to get a molecular understanding of the experimental results we developed an Ising-like model for proteins that incorporates the osmophobic nature of their backbone. The model benefits from analytical thermodynamics and kinetics amenable to Monte-Carlo simulation. The prevailing view used to be that small protecting osmolytes bridge the separating beta-strands of proteins with mechanical resistance, presumably shifting the transition state to significantly higher distances that correlate with the molecular size of the osmolyte molecules. Our experiments showed instead that protecting osmolytes slow down protein unfolding and speed-up protein folding at physiological pH without shifting the protein transition state on the mechanical reaction coordinate. Together with the theoretical results of the Ising-model, our results lend support to the osmophobic theory according to which osmolyte stabilisation is a result of the preferential exclusion of the osmolyte molecules from the protein backbone. The results obtained during this thesis work have markedly improved our understanding of the strategy selected by Nature to strengthen protein stability in hostile environments, shifting the focus from hypothetical protein-osmolyte interactions to the more general mechanism based on the osmophobicity of the protein backbone.

Design and Synthesis of Naphthalene Diimides Based Small Molecules as Anticancer Agents: Targeting the Polyamine Transporter, G-quadruplex Structures and HDAC

Cancer is a multifactorial disease characterized by a very complex etiology. Basing on its complex nature, a promising therapeutic strategy could be based by the “Multi-Target-Directed Ligand” (MTDL) approach, based on the assumption that a single molecule could hit several targets responsible for the pathology. Several agents acting on DNA are clinically used, but the severe deriving side effects limit their therapeutic application. G-quadruplex structures are DNA secondary structures located in key zones of human genome; targeting quadruplex structures could allow obtaining an anticancer therapy more free from side effects. In the last years it has been proved that epigenetic modulation can control the expression of human genes, playing a crucial role in carcinogenesis and, in particular, an abnormal expression of histone deacetylase enzymes are related to tumor onset and progression. This thesis deals with the design and synthesis of new naphthalene diimide (NDI) derivatives endowed with anticancer activity, interacting with DNA together with other targets implicated in cancer development, such as HDACs. NDI-polyamine and NDI-polyamine-hydroxamic acid conjugates have been designed with the aim to provide potential MTDLs, in order to create molecules able simultaneously to interact with different targets involved in this pathology, specifically the G-quadruplex structures and HDAC, and to exploit the polyamine transport system to get selectively into cancer cells. Macrocyclic NDIs have been designed with the aim to improve the quadruplex targeting profile of the disubstituted NDIs. These compounds proved the ability to induce a high and selective stabilization of the quadruplex structures, together with cytotoxic activities in the micromolar range. Finally, trisubstituted NDIs have been developed as G-quadruplex-binders, potentially effective against pancreatic adenocarcinoma. In conclusion, all these studies may represent a promising starting point for the development of new interesting molecules useful for the treatment of cancer, underlining the versatility of the NDI scaffold.