The human genome is characterized by an extent of functions that act further than its genetic role. Indeed, the genome can also affect cellular processes by nongenetic means through its physical and structural properties, specifically by exerting mechanical forces that shape nuclear morphology and architecture. The balancing between two chromatin compartments with antagonist functions, namely Transcriptional and Polycomb condensates, is required for preserving nuclear mechanical properties and its perturbation is causative of the pathogenic condition Kabuki syndrome (KS) (Fasciani et al., 2020). KS is a rare monogenic disease caused by the haploinsufficiency in the KMT2D gene encoding for MLL4, a H3K4-specific methyltransferase important for the regulation of gene expression. By interrogating the effect of KMT2D haploinsufficiency in Mesenchymal Stem Cells (MSCs) we discovered that MLL4 loss of function (LoF) impaired Polycomb-dependent chromatin compartmentalization, altering the nuclear architecture and the cell mechanoresponsiveness during differentiation (Fasciani et al., 2020). These results suggest that altered nuclear mechanics rely on chromatin architecture and could potentially lead to changes in cell responses to external mechanical stimuli. In the present work, we investigated the role of Transcriptional and Polycomb condensates in tuning nuclear responses to different external mechano-physical conditions. To affect nuclear mechanics, we employed the use of several mechanical devices (e. g. substrate stiffness, microchannels with constrictions, and cell confinement). We found that Polycomb and Transcriptional condensates are modulated by changes in substrate rigidity in healthy conditions and that MLL4 LoF impairs the MSCs nuclear condensates-driven mechanical response. Furthermore, we observed that MLL4 LoF impacts nuclear adaptation to confined spaces by incrementing susceptibility to nuclear envelope rupture. We also showed that the increased nuclear fragility in MLL4 LoF is accompanied by an alteration of cell migratory capacity and survival rate. Altogether these findings suggest that MLL4 LoF impairs cell responses to external mechanical stimuli, shedding light on the pathological connection between the altered cell mechanoresponsiveness during differentiation and KS phenotype in terms of skeletal and cartilage anomalies.

Retinoids are a class of compounds derived from the metabolism of vitamin A and β-carotene. Retinoid signaling has vital functions in both vertebrate and invertebrate embryogenesis such as the formation of body axes and the control of organogenesis. Genetic evidence suggests a role of retinoids in cell fate decision, maturation and homeostasis of the prostate epithelium. Knockout (KO) of the retinoic acid receptor gamma (RARG) gene in mice leads to growth deficits and male sterility due to squamous metaplasia and keratinization of the seminal vesicles and prostate. Noteworthy, synergistic antitumor effects of retinoids and vitamin D have been described in prostate cancer cell lines, although a mechanistic link between retinoic acid (RA) signaling and prostate epithelium differentiation and tumorigenesis has not yet been elucidated. Here, taking advantage of mouse prostate organoids (mPrOs), we report an essential role for RA in the differentiation and integrity of the periurethral and proximal luminal compartments of the prostate epithelium. Mechanistically, RA, through the activation of RARγ, promotes the expression of Foxa1, a pioneer transcription factor that cooperates with androgen receptor (AR) in directing progenitor cells towards the luminal lineage. Reduced RA signaling in organoids leads to downregulation of key structural and polarity proteins along with a loss of luminal identity, a phenotype that is fully rescued by constitutive expression of exogenous Foxa1. Overall, our study demonstrates the importance of RA signaling in prostate epithelium differentiation and homeostasis. In addition to the tumorigenic role of Foxa1 mutations recently described in several human cancers, alteration in RA pathway due to altered uptake/absorption/metabolism of vitamin A and β-carotene, or depending on specific molecular dysfunctions (e.g., epigenetic RARB silencing), could represent a critical rheostat for prostate tumorigenesis.

Cell-free transcription and translation reactions lie at the heart of the rising field known as in vitro synthetic biology and their existence is fundamental for the reconstitution of artificial cells. While researchers are exploring different ways to create such reactions, the common feature that they share is the use of a template DNA to carry the information for the specific function that the reaction is required to perform. The scope of this thesis is to elucidate the relationship between the genotype and the phenotype in such reactions, investigating both transcription and translation using state of the art fluorescence spectroscopy.

Although the understanding of genetic predisposition to prostate cancer (PCa) has been improved through genome-wide association studies (GWAS), little is known about the biological implication of germline variants residing in coding or non-coding regions in cancer development and progression. Our hypothesis is that inherited variants may predispose to specific early recurrent genomic events observed in PCa adenocarcinomas, possibly in the context of variable androgen receptor (AR) signaling that changes during a man’s lifetime. Recent in silico analysis by our group on potential association between germline variants and PCa specific somatic lesions identified a non-coding polymorphic regulatory element at the 7p14.3 locus associated with DNA repair and hormone regulated transcript levels and with an early recurrent prostate cancer specific somatic mutation in the Speckle-Type POZ protein (SPOP) gene (OR=5.54, P=1.22e-08) in human prostate tissue data. In order to functionally characterize the polymorphic 7p14.3 locus (rs1376350, single nucleotide polymorphism, G>A), we set up to establish isogenic cell lines harboring the minor allele by using the CRISPR/Cas9 system. In parallel, CRISPR/Cas9 system was used to knock out different portion of the region encompassing the 7p14.3 variant and to eliminate transcription factors (TFs) binding sites that were identified from previous in silico analysis (i.e. AR and CCAAT/Enhancer Binding Protein (C/EBP) beta (CEBPβ)). The transcriptomes of edited pools and edited single clones from macrodeletion (731 bp), microdeletion (50 bp) and alterations of TFs binding sites were analyzed and compared to the transcriptomes of isogenic cells heterozygous (A/G) and homozygous (A/A) for the minor allele A of the risk variant rs1376350 (with or without AR overexpression). These data identified a set of genes scattered throughout the genome with the same pattern of deregulation suggesting the implication of the variant on the regulation of genes residing in different chromosomes. Additionally, ChIP-qPCR experiments for histone modification supported the identification of the 7p14.3 locus with enhancer activity. Furthermore, ChIP-qPCR of histone mark associated with transcriptional activation or repression in isogenic cells harboring the minor allele A upon AR overexpression showed that the activity of the locus is higher for the minor allele A compared to G, independently from AR activation. Despite the limitations of our model and the current lack of validation in other cells, we confirmed that some of the differentially expressed genes that emerged from the comparative analysis of edited cells are deregulated in human normal and tumor prostate samples as well. This work is a proof of concept of germline predisposition to molecularly distinct cancer subclasses and has the potential to nominate new mechanisms of cancer development. Future work aims to elucidate the mechanisms implicated in the deregulation of the transcriptome by combining the information obtained until now with potential new players that we expect to identify by Mass Spectrometry experiments. To clarify the link between the 7p14.3 variant and the somatic mutations in SPOP, we plan to express mutant SPOP in isogenic cells harboring the minor allele and to asses DNA damage response upon overexpression or silencing of TFs binding at and around the rs1376350 variant. My work is an example of how the CRISPR/Cas9 system can be used to develop a technical framework with convergent approaches to functionally characterize polymorphic regulatory regions including but not limited to the establishment of isogenic cells upon single nucleotide editing.

Neuroblastoma (NB) is a very heterogeneous tumour derived from undifferentiated cells of the neural crest. It is the most common extracranial solid tumour in children, characterised by a large variability of the clinical outcome. The clinically aggressive form of the disease, the high-risk neuroblastoma, affects about 50% of patients, which, unfortunately, despite the intensity of therapies, have a survival rate of less than 50%. Although the introduction of two new therapeutic solutions based on the use of 13-cis-retinoic acid and the immunotherapy with a chimeric monoclonal antibody against the GD2 ganglioside, 20% of patients affected by the high-risk disease are still entirely refractory to treatments, and 60% will relapse. In this panorama, identifying new strategies specific for critical NB targets is endowed with great potential to improve the survival rate and long-term quality of life and reduce the elevated toxicity of current treatments. LIN28B is an RNA binding protein extensively overexpressed in NB. Its exogenous expression in mouse sympatho-adrenergic lineage is able to reproduce the human disease, underlying the importance of LIN28B in NB pathogenesis. LIN28B prevents the maturation of let-7 miRNA family members, an important group of tumour suppressors that induce differentiation and, at the same time, decrease cell proliferation. We hypothesised that interfering with the LIN28B/let-7 miRNA interaction could lead to an increase in let-7 miRNA levels and, consequently, to a decrease in cell proliferation and an induction of cell differentiation, ultimately reducing NB aggressiveness. First, we created NB cell lines with stable LIN28B down-regulation, and we observed an expected increase in let-7 miRNA levels. We then verified if the rise in the let-7 miRNAs could induce the cells' differentiation by analysing a panel of stemness and differentiation markers such as SOX2, SOX9 and β-III-tubulin, detecting a decrease in the stemness markers and an increase in the differentiation-related markers. Following a high-throughput screening, performed and validated with two orthogonal biochemical techniques, the Alpha screen and the REMSA, we identified molecule A as the molecule with the best inhibitory activity on the LIN28B/let-7 miRNA interaction. After the biochemical validation, we proceeded to assess molecule A activity in vitro on NB cell lines. Molecule A resulted to be very unstable in cell culture conditions, therefore we decided to include the molecule in PLGA-PEG nanoparticles to preserve its stability in solution and improve its activity. Upon encapsulation, we observed a substantial increase in molecule A effects, leading to a strong increment in mature let-7 miRNAs and a consequent inhibition of cellular growth. Finally, we tested if the let-7 miRNAs increment caused by molecule A treatment was sufficient to induce NB cells differentiation, as observed with stable LIN28B-downregulation. We detected an increase in differentiation marker levels suggesting that the treatment with Molecule A nanoparticles is able to lead to the induction of neuronal differentiation processes in NB cells. Although these last results need to be confirmed with further experiments, they clearly show that the LIN28B/let-7 miRNA axis represents a good therapeutic target and that molecule A and/or other molecules able to interfere with this interaction deserve further preclinical and clinical evaluation.

High-risk neuroblastoma (NB) is an aggressive childhood tumor that originates from progenitor neural crest cells. Even if the therapeutic protocol for NB is articulate and aggressive, the outcome remains dismal, with the 5-year disease-free overall survival below rating 50%. A novel drug combination strategy can possibly provide a new solution to this unmet therapeutic need. 13-cis retinoic acid (13-cis-RA, isotretinoin) is an anti-proliferative and pro-differentiative agent currently used in the post-consolidation phase of NB therapy. To identify molecules able to potentiate the anti-proliferative activity of 13-cis-RA, NB cells were treated with a library of 169 naturally occurring polyphenols in combination with the retinoid. This in vitro screen led to the identification of isorhamnetin as a synergistic partner of 13-cis-RA, producing an 80% reduction in cell viability. At the molecular level, this synergistic effect is followed by a marked increase in the expression of a member of the catecholamine receptor superfamily: the adrenergic receptor alpha-1B (ADRA1B) suggesting that this receptor might represent a key mediator of the synergistic effect of 13-cis-RA and isorhamnetin observed in vitro. This finding redirected our attention to the class of adrenergic receptors (ARs) as novel targets in NB. To investigate the role of ADRA1B in the synergism, we generated CHP134 NB cell lines knocked-out (KO) for the receptor and observed that exposure of CHP134 KO cell to 13-cis-RA leads to a reduction of cell viability and neural differentiation. We, therefore, substituted the genetic KO strategy with the alpha-1B adrenergic antagonist, L765,314, obtaining the same results. Subsequently, we extended the analysis on the role of adrenergic receptors (AR) performing a biased screen using two libraries of AR-ligands. The screen results confirm that the molecules working as alpha-1-ARs antagonists are those that greatly increase cell sensitivity to 13-cis-RA with reduction of cell viability and increase in differentiation. We confirmed our observation in NB xenograft mice models in vivo, treating mice with a combination of 13-cis-RA and the FDA approved alpha-1 AR antagonist doxazosin. The proposed pharmacological treatment was effective in slowing tumor growth, leading to tumors of smaller size. From our results, we can conclude that the deletion or inhibition of alpha-1-AR sensitizes NB cells to 13-Cis-RA, both in terms of induction of apoptosis and neural differentiation. Since NB is a catecholamine-rich tumor, we propose that antagonization of alpha-1-AR disrupts the established autocrine pro-survival circuit generated by catecholamines in NB and restores the ability of the cells to follow the pro-differentiative and pro-apoptotic programs endorsed by 13-cis-RA. Considering the druggable nature of the alpha-1-AR receptors, we indicate this class of receptors as a novel pharmacological target for the treatment of neuroblastoma.

The sequence-specific transcription factor p53 is considered a master gene of cellular responses to homeostasis changes. It is also a prominent tumor suppressor gene with the title of “guardian of the genome”. The increasing number of transcriptome analyses in cell lines treated with different agents activating p53, continues to add complexity to the vast transcriptional networks p53 regulates. To investigate mRNA translational control as an additional dimension of p53-directed gene expression responses, we performed translatome analyses upon its activation either by different agents or cellular contexts. Considered as a proxy for the proteome, the translatome allows us to characterize the translational status of each mRNA, independently from transcriptional modulations, and to evaluate the implications or correlations of changes in relative mRNA translation efficiencies with the phenotypic outcome. We first performed treatment-specific translatome profiling in MCF7 cells upon Doxorubicin and Nutlin-3a treatments. Among translated genes, we detected the presence of translationally enhanced mRNAs with a virtually absent transcriptional modulation; those genes were enriched for apoptotic functions, suggesting that the apoptotic phenotype might be controlled not only at the transcriptional, but also at the translational level. Seeking mechanisms underlying the mRNAs translational rate upon p53 activation, we identified the modulation of six RNA-binding proteins, where hnRNPD (AUF1) and CPEB4 are direct p53 targets, whereas SRSF1, DDX17, YBX1 and TARDBP are indirect targets, modulated at the translational level in a p53-dependent manner. In detail, we demonstrated the contribution of at least two p53-dependent translational mechanisms related to YBX1 translational repression, suggesting the presence of a controlled regulon at the crossroad of YBX1 mRNA translation. Given our finding that apoptotic genes appear to be controlled by p53 also at the translational level, we decided to explore whether mRNAs translational control mechanisms are indeed an additional checkpoint to the phenotype. To this aim, we performed a cell-type specific translatome study upon Nutlin-3a treatment, a drug with evident therapeutic prospective. SJSA1, HCT116 and MCF7 cells were chosen as they exhibit different cellular responses to Nutlin-3A (cell cycle arrest, apoptosis, or both, respectively). Our preliminary data suggests that translational modulation can affect the complex process of cell fate choice upon p53 activation. Indeed, a lack of overlap among genes differentially modulated at the translational level was evident. Motif search analysis at the 5’- and 3’-UTR of those genes highlighted the presence of different motifs in the three cell lines and the specific correlation of a C-rich motif with the apoptotic phenotype. Preliminary data on this motif will be presented and discussed. Two independent projects will be presented as appendixes, both of them related to the general idea that more than one factor may determine the p53 response. Starting from the analysis of possible p53 interactions with other transcriptional co-factors, we investigated the cooperative interaction between p53 and NFκB. For the second project, combining data previously obtained by means of yeast-based p53 transactivation assays, we developed an algorithm, p53retriever, to scan DNA sequences and thus identify p53 response elements and classify them based on their transactivation potential.

Surface porous silicon based ceramics are a class of materials with excellent mechanical, physical and chemical properties and for this reason they are widely used in different fields of application. The resultant properties of these material are due principally to the combination of the chemical composition (coordination with the Si atom) and the specific geometry of the pattern. These parameters are able to influence phenomena such as the biological activity, the exposed surface area and the thermal, mechanical and chemical resistance. Techniques used nowadays to synthesize these ceramics with a specific patter are usually really complicated, expensive and time-consuming with limitations for the large-scale industrial application. The Breath Figure method is a new fast and highly controllable technique that allows to decorate the surface of polymer films with different porous patterns. A large variety of starting materials can be used to perform this process, obtaining porous films with different characteristics and with a specific control on the entire process. In this work we used a UV cross-linkable polysiloxane as precursor for the Breath Figure process in order to combine the pattern procedure with the polymer derived ceramic method. Initially, the effects of the process variables on the final surface porosity was evaluated, identifying the parameters which most influence the final material. After the patterning, materials with different characteristics were pyrolyzed under different atmospheres in order to induce simultaneously the ceramic conversion and the chemical modification of the silicone structure. Three different porous silicon-based ceramics were obtained using flowing air, nitrogen and ammonia during the heat treatments, respectively: silicon dioxide, silicon oxycarbide and silicon oxynitride. All these material have been proposed as implant coating for different body districts, but recent studies demonstrated the potential application of silicon oxynitrides as bone implant coatings due to the enhanced bioactivity and osteoinductivity of the ceramic. For this reason in the second part of this work we evaluated the potential bioactivity of surface porous silicon oxynitrides in terms of bioactive silicon ions release capability and effects of different porosity degrees on cells behavior. Four different surface pattern were applied on titanium alloy disks and used for an in vitro characterization using human Mesenchymal Stem Cells and compared with uncoated titanium. The results indicated that the silicon ions release from the coating surface leads to an increase of the cellular activity with the porous pattern influencing the hMSC initial adhesion and proliferation.

The human gut microbiota plays a crucial role in the functioning of the gastrointestinal tract and its alteration can lead to gastrointestinal abnormalities and inflammation. Additionally, the gut microbiota modulates central nervous system (CNS) activities affecting several aspect of host physiology. Motivated by the increasing evidences of the role of the gut microbiota in the complex set of interactions connecting the gut and the CNS, known as gut-brain axis, in this Ph.D. thesis we asked whether the gastrointestinal abnormalities and inflammation commonly associated with neurological disorders such as Rett syndrome (RTT) and Autism could be related to alterations of the bacterial and fungal intestinal microbiota. First, since only few reports have explored the fungal component of the gut microbiota in health and disease, we characterized the gut mycobiota in a cohort of healthy individuals, in order to reduce the gap of knowledge concerning factors influencing the intestinal microbial communities. Next, we compared the gut microbiota of three cohorts of healthy, RTT and autistic subjects to investigate if these neurological disorders harbour alterations of the gut microbiota. Culture-based and metataxonomics analysis of the faecal fungal populations of healthy volunteers revealed that the gut mycobiota differs in function of individuals’ life stage in a gender-related fashion. Different fungal species were isolated showing phenotypic adaptation to the intestinal environment. High frequency of azoles resistance was also found, with potential clinical significance. It was further observed that autistic subjects are characterized by a reduced incidence of Bacteroidetes and that Collinsella, Corynebacterium, Dorea and Lactobacillus were the taxa predominating in the gut microbiota of autistic subjects. Constipation has been associated with different bacterial patterns in autistic and neurotypical subjects, with constipated autistic individuals characterized by higher levels of Escherichia/Shigella and Clostridium cluster XVIII than constipated neurotypical subjects. RTT is a neurological disorder caused by loss-of-function mutations of MeCP2 and it is commonly associated with gastrointestinal dysfunctions and constipation. We showed that RTT subjects harbour bacterial and fungal microbiota altered from those of healthy controls, with a reduced microbial richness and dominated by Bifidobacterium, different Clostridia and Candida. The alterations of the gut microbiota observed did not depend on the constipation status of RTT subjects while this microbiota produced altered SCFAs profiles potentially contributing to the constipation itself. Phenotypical and immunological characterizations of faecal fungal isolates from RTT subjects showed Candida parapsilosis as the most abundant species isolated in RTT, genetically unrelated to healthy controls’ isolates and with elevated resistance to azoles. Furthermore these isolates induced high levels of IL-10 suggesting increased tolerance and persistence within the host. Finally, the importance of multiple sequence alignment (MSA) accuracy in microbiome research was investigated comparing three implementations of the widely used NAST algorithm. By now, different implementations of NAST have been developed but no one tested the performances and the accuracy of the MSAs generated with these implementations. We showed that micca, a new bioinformatics pipeline for metataxonomics data improves the quality of NAST alignments by using a fast and memory efficient reimplementation of the NAST algorithm.

Background. Infections caused by Pseudomonas aeruginosa are the main cause of morbidity and mortality in Cystic Fibrosis (CF) patients and occur via primary colonisation of the airway followed by the accumulation of pathoadaptive mutations in the bacterial genome which increase fitness in the lung environment and result in chronicization. A better understanding of i) the evolutionary dynamics occurring during chronic airway infections in CF patients and ii) the genetic adaptation of strains to the CF lung environment, might give further clues for preventive measures or novel therapies to control CF infections in the future. In this work, we obtained genomic sequences of 40 P. aeruginosa isolates from a single CF patient collected over an eight-year period (2007-2014) and analysed the population in terms of clonality of the isolates, phylogenetic relationships, and presence of polymorphisms and variants between the strains. Population structure and microevolution. In silico Multilocus Sequence Typing (MLST) analysis revealed a characteristic single clonal population dominated by a previously characterized sequence type (ST390) and a small number of new, closely related ST variants (ST1863, ST1864, ST1923). EBURST analysis of the sequence types revealed that all members of this population belong to the same clonal lineage and likely evolved from a single ancestral colonizing strain. Furthermore, the phylogenetic analysis based on SNPs also divided the population into two subpopulations derived from the evolution of the first infecting strain. The annotation of SNPs allowed us to identify mutations with moderate or high impact. Genes with high impact variants encoded respiratory nitrate reductase subunit gamma nail, polyprotein signal peptidase lspA, the ABC transporter-binding protein aaltP, the copper resistance protein A precursor pcoAin, and four hypothetical proteins. The evolution of strains in the CF airway is characterized by the loss of many virulence traits, including motility and protease secretion, along with the acquisition of multidrug resistance. Functional phenotypic assays of the collection, including motility and secretion of proteases, showed a decrease over time in the persistent isolates. We also determined the antibiotic susceptibility profile of the collection; while early isolates were found to be susceptible to almost all these antibiotics, resistant phenotypes dramatically increased over time in the population. Functional studies on specific strains. To identify additional functional variations related to pathoadaptive mutations occurring in the course of chronic infection in CF, we then selected three isolates for further characterization: one early CF isolate (TNCF_23 isolated in 2007); one clonal late CF isolate (TNCF_175 isolated in 2014); one clinical isolate (VrPa97) from a non-CF patient belonging to the same sequence type (ST390) as the former isolates. With this approach, we aimed to identify additional phenotypic and functional variations between isolates with a very homogeneous genomic background, in an attempt to find out new pathoadaptive mutations occurring in the course of chronic infection in CF. Specifically, the following traits were investigated: killing of C. elegans and G. mellonella (in vivo virulence); immunomodulatory properties (IL-8 ELISA assay); competitive growth in Artificial Sputum Medium (ASM); functionality of Type Six Secretion System (T6SS). Despite their close genetic relatedness, considerable variations were observed between the three isolates, among which the late isolate TNCF_175 showed several alterations 7 putatively resulting from the adaptation process to the CF lung. TNCF_175 presented a mutation in tssK3, part of H3-T6SS; this mutation (C958T) was therefore introduced in the reference strains PAO1 and PA14, and mutated strains were subsequently complemented; killing rate on C. elegans and growth rate in ASM in mutant and complemented strains were evaluated. Conclusions. A rare feature of this strain collection is the consistent number of clonal isolates obtained from a single patient over a rather long period of 8 eight years, thus providing a model to look at microevolutionary trends within a highly homogenous bacterial population, and avoiding potential biases due to the host genetic background and clinical history. In spite of the close genomic relatedness of all isolates, a surprisingly high diversity was observed for the majority of tested phenotypes. Investigating the competitive ability of early versus late strains we propose a role for T6SS in the adaptation process to the CF lung environment. Our data suggest that once persistence has been established, a strain no longer requires its T6SS, allowing loss of function mutations to occur. Conversely, acute and early CF strains still carry a number of virulence factors, including T6SS that potentially provide an advantage in outcompeting other microorganisms in the initial stage of CF infection.