Oxylipins biosynthesis in Lactobacillus helveticus in the presence of oxidative stress

This PhD thesis is aimed at studying the possible pathways and the mechanisms that can trigger oxylipins biosynthesis, and particularly that of short chain aldehydes and alcohols, in Lactobacillus helveticus, also in the presence of oxidative stress, using a totally labelled linoleic acid as precursor. In plants and fungi these molecules, involved in defence mechanisms against pathogens and in communication systems, derive from the oxidation of cellular unsaturated fatty acids (UFAs) and their accumulation is associated with stress exposure. Since some oxylipins are produced also by lactobacilli, it is possible to hypothesize that a metabolic pathway from UFAs to oxylipins, similar to what happens in plants and fungi, is present also in lactic acid bacteria. The results obtained pointed out that some volatile molecules are the result of UFAs catabolism, since they appear only when cells are incubated in their presence. Labelled linoleic acid is integrated in the membrane and subsequently transformed into aldehydes and alcohols, whose extent and carbon atoms number depend on stress exposure. The enzymes responsible for this metabolic pathway in plants and fungi (e.g. lipoxygenase, dioxygenase) seem to be absent in Lactobacillus helveticus and in other lactobacilli. Proteomic analyses show the over expression of many proteins, including thioredoxin reductase (part of the bacterial oxidative defence system), mainly in cells grown with linoleic acid without oxidative stress exposure, confirming that linoleic acid itself induces oxidative stress. 6 general oxidoreductases (class including dioxygenases and peroxidase) were found and therefore a deeper investigation on them could be productive in elucidating all steps involved in oxylipins biosynthesis in bacteria. Due to the multiple role of oxylipins (flavouring agents, antimicrobial compounds and interspecific signalling molecules) the identification of genes involved and regulating factors should have an important biotechnological impact, also allowing the overproduction of selected bioactive molecules.

Phenotypic and molecular characterization of ethylene biosynthesis in apples

Ethylene plays an important role in apple fruit development. Its biosynthesis is catalyzed by two enzymes ACS and ACO. The first is considered to catalyzes the rate-limiting step of ethylene production and in apple two different alleles (MdACS1-1 and MdACS1-2) of this gene have been identified. The presence in the promoter region of MdACS1-2 allele of a SINE insertion is considered to be responsible for a low transcription level and a pronounced reduction in ethylene production in apple cultivar homozygous for this allele. However, the specific expression of each MdACS1 allele has never been reported as well as any in vivo analysis of its 5’-flanking region. With the present study we addressed these issues by developing a set of qPCR allele specific primers for MdACS1 and by a functional characterization of the MdACS1 promoters by transient expression analysis. qPCR analysis on different apple tissues and stages of development demonstrated that MdACS1-2 allele is never express and that MdACS1-1 allele is ripening-related and expresses predominantly but not exclusively in apple fruit. To test MdACS1 promoter in fruit the only protocol available in literature for transient transformation of apple fruit was evaluated and optimized. Twenty chimeric promoter::reporter constructs were generated and analyzed by Agrobacterium-transient transformation. The in vivo analysis allowed to identify an enhancer-like region of 261 bp in MdACS1 promoter and a region of 57 bp in MdACS1-2 responsible, also if not alone, in the inactivation of the MdACS1-2 allele. Through the assessment of ethylene production in a segregating progeny derived from the cross between Fuji and Mondial Gala (homozygous for MdACS1-2 allele) we demonstrated that at least two other genes may be involved in apple ethylene production. An hypothesis that could explain the difference between Fuji and Mondial Gala have been proposed.

ABC transporters of the A subfamily: potential prognostic markers and candidates for antibody selection from phage-display libraries for therapeutic use in Ewing sarcoma

The prognostic value of ABC transporters in Ewing sarcoma is still poorly explored and controversial. We described for the first time the impact of various ABCs on Ewing sarcoma prognosis by assessment of their gene expression in two independent cohorts of patients. Unexpected associations with favourable outcomes were observed for two ABCs of the A-subfamily, ABCA6 and ABCA7, whereas no associations with the canonical multidrug ABC transporters were identified. The ABCs of the A-subfamily are involved in cholesterol/phospholipids transportation and efflux from cells. Our clinical data support the drug-efflux independent contribution to cancer progression of the ABCAs, which has been confirmed in PDX-derived cell lines. The impact of these ABCA transporters on tumor progression seems to be mediated by lowering intracellular cholesterol, supporting the role of these proteins in lipid transport. In addition, the gene expression of ABCA6 and ABCA7 is regulated by transcription factors which control lipid metabolism: ABCA6 was induced by the binding of FoxO1/FoxO3a to its promoter and repressed by IGF1R/Akt signaling, whereas the expression of ABCA7 was regulated by p53. The data point to ABCA6 and ABCA7 as potential prognostic markers in Ewing sarcoma and suggest the IGF1/ABCA/lipid axis as an intriguing therapeutic target. Agonist monoclonal antibodies towards ABCA6/7 or inhibitors of cholesterol biosynthesis, such as statins or aminobiphoshonates, may be investigated as therapeutic options in combination with chemotherapy. Considering that no monoclonal antibodies selectively targeting extracellular domains of ABCA6/7 are available, the second part of the project has been dedicated to the generation of human antibody phage-display libraries as tools for selecting monoclonal antibodies. A novel synthetic human antibody phage-display library has been designed, cloned and characterized. The library takes advantages of the high variability of a designed naïve repertoire to be a useful tool for isolating antibodies towards all potential antigens, including the ABCAs.

Analysis of extracellular vesicles from patients with advanced pancreatic cancer identifies miRNAs with predictive value for treatment with gemcitabine + nab-paclitaxel

Pancreatic cancer (PC) is the seventh leading cause of cancer death. Despite recent therapy advancements, 5-year survival is 11%. Resistance to therapy is common, and no predictive factors, except for BRCA1/2 and PALB2 mutations, can drive treatment selection. Based on the easy isolation of extracellular vesicles (EVs) from blood and the role of EV-borne miRNAs in chemoresistance, we analyzed EVs and their miRNA content in order to identify predictive factors. First, we analyzed samples from 28 PC patients and 7 healthy subjects, in order to establish methods for isolation and analysis of EVs and their miRNA content. We observed a significantly different expression of 28 miRNAs, including oncogenic or tumor suppressor miRNAs, showing the ability of our approach to detect candidate biomarkers. Then, we analyzed samples of 21 advanced PC patients, collected before first-line treatment with gemcitabine + nab-paclitaxel, and compared findings in responders and non-responders. EVs have been analyzed with Nanoparticle tracking analysis, flow cytometry and RNA-Seq; then, laboratory results have been matched with clinical data. Nanoparticle tracking analysis did not show any significant difference. Flow cytometry showed a lower expression of SSE4 and CD81 in responders. Finally, miRNA analysis showed 25 upregulated and 19 downregulated miRNAs in responders. In particular, in responders we observed upregulation of miR-141-3p, miR-141-5p, miR-200a-3p, miR-200b-3p, miR-200c-3p, miR-375-3p, miR-429, miR-545-5p. These miRNAs have targets with a previously reported role in PC. In conclusion, we show the feasibility of the proposed approach to identify EV-derived biomarkers with predictive value for therapy with gemcitabine + nab-paclitaxel in PC. Our findings highlight the possibility to exploit liquid biopsy for personalized treatment in PC, in order to maximize chances of response and patients’ outcome. These findings are worthy of further investigation: in the same setting, with different chemotherapy schedules, and in different disease settings such as preoperative therapy.

Understanding the role of microglial extracellular vesicles (EVs) in neuroinflammation spreading: an in vitro study

Neuroinflammation is a crucial pathogenic mechanism that commonly underlies most neurodegenerative diseases. Microglia, the immune cells of the brain, play a critical role that changes depending on the stage of neuropathology: at early phases of brain diseases microglia display the neuroprotective phenotype which is switched to the classically activated pro-inflammatory subtype at later stages, contributing to neurodegeneration. The microglial phenotypic shift is characterized by a change in the release of bioactive molecules both soluble and through extracellular vesicles. Our in vitro studies aim to understand whether different types of activation could determine change in vesicles content, in particular miRNAs, and whether this could influence the activation state of control microglial cells. Microglial polarization has been induced in two different in vitro models: N9, microglial murine cell line, have been treated by using LPS towards a proinflammatory/neurotoxic phenotype or ATP towards antinflammatory/neuroprotective status; HMC3, human microglial cell line, have been activated using IFN-+ATP. We demonstrated that conditioned media/exosomes obtained from donor microglia were able to promote a pro-inflammatory phenotype in control cells, leading us to prove the existence of a neuroinflammation spreading process mediated by extracellular vesicles of microglia with a crucial role of miRNAs. Increased expression of miRNA-34a observed in N9 model underlines a possible contribution in the diffusion of proinflammatory activation of microglia. Thus, we tried to downregulate miR-34a expression using cleaving sequences of anti-mir-34a DNAzyme delivered by DNA nanostructures aimed to confirm the involvement of miR-34a in microglia polarization towards the neurotoxic phenotype. In conclusion, this thesis work reveal a new inflammation spreading mechanism that involves release of vesicles containing specific cargos by donor polarized microglia, particularly miRNAs, able to influence the phenotypic shift in unpolarized microglia: this process deserves to be deeply investigated as potential therapeutic target to counteract neurodegenerative diseases.

Radical chemistry of the catechol/quinone system and its role in the control of lipid peroxidation and melanin biosynthesis

The catechol (1,2-dihydroxybenzene) is a privileged structural motif among natural antioxidants like flavonoids, owing to its reactivity with alkylperoxyl radicals due to the stability of the semiquinone radical. The exploration of the relevance and mechanism of this non-conventional antioxidant chemistry in heterogenous biomimetic systems (aqueous micelles and unilamellar liposomes) is explored for the first time in Chapter 1. Results show antioxidant behaviour that surpasses that of nature’s premiere antioxidant α-tocopherol and relies on the cross-dismutation of alkylperoxyl and hydroperoxyl radicals at the water-lipid interface with regeneration of the catechol function from the oxidized quinone. The design and synthesis of new biomimetic catechol-type antioxidants by conjugation of thiols (e.g. cysteine) with quinones highlighted an unusual 1,6-type regioselectivity, which had been previously reported but never fully rationalized. Owing to its importance both in nature and in the development of new antioxidants, we investigated it in detail in Chapter 2. We could prove the onsetting of a radical-chain mechanism intermediated by thiyl and thiosemiquinone radicals at the basis of the “anomalous nucleophilic addition” of thiols to ortho-quinones, which paves the way to better understanding of the chemistry of such systems. The oxidation of catechols to the corresponding quinones is also a key reaction in the biosynthesis of melanins, mediated by enzyme Tyrosinase.