Mass spectrometry-based protein profiling strategies for biomarker discovery in liver and inflammatory bowel diseases

The study of protein expression profiles for biomarker discovery in serum and in mammalian cell populations needs the continuous improvement and combination of proteins/peptides separation techniques, mass spectrometry, statistical and bioinformatic approaches. In this thesis work two different mass spectrometry-based protein profiling strategies have been developed and applied to liver and inflammatory bowel diseases (IBDs) for the discovery of new biomarkers. The first of them, based on bulk solid-phase extraction combined with matrix-assisted laser desorption/ionization - Time of Flight mass spectrometry (MALDI-TOF MS) and chemometric analysis of serum samples, was applied to the study of serum protein expression profiles both in IBDs (Crohn’s disease and ulcerative colitis) and in liver diseases (cirrhosis, hepatocellular carcinoma, viral hepatitis). The approach allowed the enrichment of serum proteins/peptides due to the high interaction surface between analytes and solid phase and the high recovery due to the elution step performed directly on the MALDI-target plate. Furthermore the use of chemometric algorithm for the selection of the variables with higher discriminant power permitted to evaluate patterns of 20-30 proteins involved in the differentiation and classification of serum samples from healthy donors and diseased patients. These proteins profiles permit to discriminate among the pathologies with an optimum classification and prediction abilities. In particular in the study of inflammatory bowel diseases, after the analysis using C18 of 129 serum samples from healthy donors and Crohn’s disease, ulcerative colitis and inflammatory controls patients, a 90.7% of classification ability and a 72.9% prediction ability were obtained. In the study of liver diseases (hepatocellular carcinoma, viral hepatitis and cirrhosis) a 80.6% of prediction ability was achieved using IDA-Cu(II) as extraction procedure. The identification of the selected proteins by MALDITOF/ TOF MS analysis or by their selective enrichment followed by enzymatic digestion and MS/MS analysis may give useful information in order to identify new biomarkers involved in the diseases. The second mass spectrometry-based protein profiling strategy developed was based on a label-free liquid chromatography electrospray ionization quadrupole - time of flight differential analysis approach (LC ESI-QTOF MS), combined with targeted MS/MS analysis of only identified differences. The strategy was used for biomarker discovery in IBDs, and in particular of Crohn’s disease. The enriched serum peptidome and the subcellular fractions of intestinal epithelial cells (IECs) from healthy donors and Crohn’s disease patients were analysed. The combining of the low molecular weight serum proteins enrichment step and the LCMS approach allowed to evaluate a pattern of peptides derived from specific exoprotease activity in the coagulation and complement activation pathways. Among these peptides, particularly interesting was the discovery of clusters of peptides from fibrinopeptide A, Apolipoprotein E and A4, and complement C3 and C4. Further studies need to be performed to evaluate the specificity of these clusters and validate the results, in order to develop a rapid serum diagnostic test. The analysis by label-free LC ESI-QTOF MS differential analysis of the subcellular fractions of IECs from Crohn’s disease patients and healthy donors permitted to find many proteins that could be involved in the inflammation process. Among them heat shock protein 70, tryptase alpha-1 precursor and proteins whose upregulation can be explained by the increased activity of IECs in Crohn’s disease were identified. Follow-up studies for the validation of the results and the in-depth investigation of the inflammation pathways involved in the disease will be performed. Both the developed mass spectrometry-based protein profiling strategies have been proved to be useful tools for the discovery of disease biomarkers that need to be validated in further studies.

Development of muliplexed analytical methods based on bioluminescent whole-cell biosensors

The subject of this Ph.D. research thesis is the development and application of multiplexed analytical methods based on bioluminescent whole-cell biosensors. One of the main goals of analytical chemistry is multianalyte testing in which two or more analytes are measured simultaneously in a single assay. The advantages of multianalyte testing are work simplification, high throughput, and reduction in the overall cost per test. The availability of multiplexed portable analytical systems is of particular interest for on-field analysis of clinical, environmental or food samples as well as for the drug discovery process. To allow highly sensitive and selective analysis, these devices should combine biospecific molecular recognition with ultrasensitive detection systems. To address the current need for rapid, highly sensitive and inexpensive devices for obtaining more data from each sample,genetically engineered whole-cell biosensors as biospecific recognition element were combined with ultrasensitive bioluminescence detection techniques. Genetically engineered cell-based sensing systems were obtained by introducing into bacterial, yeast or mammalian cells a vector expressing a reporter protein whose expression is controlled by regulatory proteins and promoter sequences. The regulatory protein is able to recognize the presence of the analyte (e.g., compounds with hormone-like activity, heavy metals…) and to consequently activate the expression of the reporter protein that can be readily measured and directly related to the analyte bioavailable concentration in the sample. Bioluminescence represents the ideal detection principle for miniaturized analytical devices and multiplexed assays thanks to high detectability in small sample volumes allowing an accurate signal localization and quantification. In the first chapter of this dissertation is discussed the obtainment of improved bioluminescent proteins emitting at different wavelenghts, in term of increased thermostability, enhanced emission decay kinetic and spectral resolution. The second chapter is mainly focused on the use of these proteins in the development of whole-cell based assay with improved analytical performance. In particular since the main drawback of whole-cell biosensors is the high variability of their analyte specific response mainly caused by variations in cell viability due to aspecific effects of the sample’s matrix, an additional bioluminescent reporter has been introduced to correct the analytical response thus increasing the robustness of the bioassays. The feasibility of using a combination of two or more bioluminescent proteins for obtaining biosensors with internal signal correction or for the simultaneous detection of multiple analytes has been demonstrated by developing a dual reporter yeast based biosensor for androgenic activity measurement and a triple reporter mammalian cell-based biosensor for the simultaneous monitoring of two CYP450 enzymes activation, involved in cholesterol degradation, with the use of two spectrally resolved intracellular luciferases and a secreted luciferase as a control for cells viability. In the third chapter is presented the development of a portable multianalyte detection system. In order to develop a portable system that can be used also outside the laboratory environment even by non skilled personnel, cells have been immobilized into a new biocompatible and transparent polymeric matrix within a modified clear bottom black 384 -well microtiter plate to obtain a bioluminescent cell array. The cell array was placed in contact with a portable charge-coupled device (CCD) light sensor able to localize and quantify the luminescent signal produced by different bioluminescent whole-cell biosensors. This multiplexed biosensing platform containing whole-cell biosensors was successfully used to measure the overall toxicity of a given sample as well as to obtain dose response curves for heavy metals and to detect hormonal activity in clinical samples (PCT/IB2010/050625: “Portable device based on immobilized cells for the detection of analytes.” Michelini E, Roda A, Dolci LS, Mezzanotte L, Cevenini L , 2010). At the end of the dissertation some future development steps are also discussed in order to develop a point of care (POCT) device that combine portability, minimum sample pre-treatment and highly sensitive multiplexed assays in a short assay time. In this POCT perspective, field-flow fractionation (FFF) techniques, in particular gravitational variant (GrFFF) that exploit the earth gravitational field to structure the separation, have been investigated for cells fractionation, characterization and isolation. Thanks to the simplicity of its equipment, amenable to miniaturization, the GrFFF techniques appears to be particularly suited for its implementation in POCT devices and may be used as pre-analytical integrated module to be applied directly to drive target analytes of raw samples to the modules where biospecifc recognition reactions based on ultrasensitive bioluminescence detection occurs, providing an increase in overall analytical output.

Bioanalytical applications of multicolour bioluminescence imaging: new tools for drug discovery and development

The subject of this thesis is multicolour bioluminescence analysis and how it can provide new tools for drug discovery and development.The mechanism of color tuning in bioluminescent reactions is not fully understood yet but it is object of intense research and several hypothesis have been generated. In the past decade key residues of the active site of the enzyme or in the surface surrounding the active site have been identified as responsible of different color emission. Anyway since bioluminescence reaction is strictly dependent from the interaction between the enzyme and its substrate D-luciferin, modification of the substrate can lead to a different emission spectrum too. In the recent years firefly luciferase and other luciferases underwent mutagenesis in order to obtain mutants with different emission characteristics. Thanks to these new discoveries in the bioluminescence field multicolour luciferases can be nowadays employed in bioanalysis for assay developments and imaging purposes. The use of multicolor bioluminescent enzymes expanded the potential of a range of application in vitro and in vivo. Multiple analysis and more information can be obtained from the same analytical session saving cost and time. This thesis focuses on several application of multicolour bioluminescence for high-throughput screening and in vivo imaging. Multicolor luciferases can be employed as new tools for drug discovery and developments and some examples are provided in the different chapters. New red codon optimized luciferase have been demonstrated to be improved tools for bioluminescence imaging in small animal and the possibility to combine red and green luciferases for BLI has been achieved even if some aspects of the methodology remain challenging and need further improvement. In vivo Bioluminescence imaging has known a rapid progress since its first application no more than 15 years ago. It is becoming an indispensable tool in pharmacological research. At the same time the development of more sensitive and implemented microscopes and low-light imager for a better visualization and quantification of multicolor signals would boost the research and the discoveries in life sciences in general and in drug discovery and development in particular.

Il Fantastico e gli Oggetti del primo Novecento

La ricerca si propone di inquisire il modo in cui il fantastico del primo Novecento utilizza la rappresentazione finzionale degli oggetti ai fini della propria emersione. Si ipotizza che certi schemi rappresentativi elaborati da autori fantastici come Hoffmann, Poe o Maupassant siano riscontrabili anche nella letteratura del XX secolo, e vengano reimpiegati per rispondere a una mutata situazione socioculturale. La tesi è bipartita: la prima parte, che è a sua volta suddivisa in due capitoli, funziona da cornice teorica e storica alle analisi testuali. Vi si discute del concetto di immagine; e da tale discussione viene derivata una precisa idea di spazio e di oggetto letterari. In seguito si procede a una ricostruzione della storia del fantastico ottocentesco (dalla quale non sono assenti riflessioni teoriche e in particolare genologiche), che da un lato è volta a storicizzare l’idea di “genere fantastico”; dall’altro ha come obiettivo l’identificazione di una tipologia di oggetti strutturalmente legata a quel genere narrativo. Due sono le classi di oggetti così individuate, e altrettanti i capitoli che compongono la seconda parte del lavoro. Entrambi i tipi di oggetto, che per semplicità si possono chiamare oggetti-feticcio e oggetti spettrali, stanno a metà strada tra immaginario e reale; ma mentre l’oggetto-feticcio ha qualcosa in più rispetto a un oggetto descritto realisticamente, l’oggetto spettrale ha un che di deficitario, e non giunge al risultato di una completa materializzazione. Tra gli autori affrontati compaiono Papini, Pirandello, Bontempelli, Savinio, Landolfi; né mancano riferimenti ad autori di altre nazioni da Kafka a Sartre, da James a Virginia Woolf, in ottemperanza all’idea di considerare il fantastico italiano all’interno di una più ampia geografia letteraria.

L’iconografia dell’imperatore alato nel contesto della teologia politica bizantina

La presente ricerca di dottorato si propone di esaminare l’evoluzione della teologia politica bizantina e dei suoi riflessi nella propaganda imperiale nel periodo compreso tra il XIII e il XIV secolo, attraverso lo studio delle manifestazioni dell'ideologia nell'iconografia e nella numismatica del periodo in esame. L'intreccio interdisciplinare di questi ambiti di ricerca, iconografia e numismatica - con una metodologia innovativa, i cui risultati si profilano estremamente proficui - permette di comprendere i caratteri concreti, ma forse più reconditi, del realizzarsi dell'ideologia politica e della propaganda imperiale nell'impero bizantino ormai ridotto ad una costellazione di potentati particolari di estensione limitata. Il tema specifico di questo studio ha come oggetto alcune iconografie ritenute inedite, o meno tradizionali, nel panorama numismatico bizantino, emesse, in particolare, dalla zecca di Tessalonica tra XIII e XIV secolo, che vengono qui esaminate in funzione dell’evoluzione della rappresentazione imperiale. Tra di esse emerge l’inedita iconografia dell’imperatore pteroforo per la sua valenza di interscambiabilità semantica con l’immagine arcangelica. Lo studio si è proposto l’obiettivo principale di rintracciare elementi iconologici quanto più possibile comuni tra tutti i soggetti iconografici presi in esame, vagliando il substrato ideologico e propagandistico sotteso alla valenza iconologica per ogni tipologia numismatica.

Development of new therapeutic approaches in the treatments of Inflammatory Bowel Diseases: functional food and nutraceuticals vs synthetic peptides based vaccines

Inflammatory Bowel Diseases (IBD) are intestinal chronic relapsing diseases which ethiopathogenesis remains uncertain. Several group have attempted to study the role of factors involved such as genetic susceptibility, environmental factors such as smoke, diet, sex, immunological factors as well as the microbioma. None of the treatments available satisfy several criteria at the same time such as safety, long-term remission, histopatological healing, and specificity. We used two different approaches for the development of new therapeutic treatment for Inflammatory Bowel Disease. The first is focused on the understanding of the potential role of functional food and nutraceuticals nutrients in the treatment of IBD. To do so, we investigated the role of Curcuma longa in the treatment of chemical induced colitis in mice model. Since Curcma Longa has been investigated for its antinflammatory role related to the TNFα pathway as well investigators have reported few cases of patients with ulcerative colites treated with this herbs, we harbored the hypothesis of a role of Curcuma Longa in the treatment f IBD as well as we decided to assess its role in intestinal motility. The second part is based on an immunological approach to develop new drugs to induce suppression in Crohn’s disease or to induce mucosa immunity such as in colonrectal tumor. The main idea behind this approach is that we could manipulate relevant cell-cell interactions using synthetic peptides. We demonstrated the role of the unique interaction between molecules expressed on intestinal epithelial cells such as CD1d and CEACAM5 and on CD8+ T cells. In normal condition this interaction has a role for the expansion of the suppressor CD8+ T cells. Here, we characterized this interaction, we defined which are the epitope involved in the binding and we attempted to develop synthetic peptides from the N domain of CEACAM5 in order to manipulate it.

New synthetic bile acid analogue agonists of FXR and TGR5 receptors: Analytical methodologies for the study of their physico-chemical properties, pharmacokinetic activity and metabolism.

This thesis reports an integrated analytical approach for the study of physicochemical and biological properties of new synthetic bile acid (BA) analogues agonists of FXR and TGR5 receptors. Structure-activity data were compared with those previous obtained using the same experimental protocols on synthetic and natural occurring BA. The new synthetic BA analogues are classified in different groups according also to their potency as a FXR and TGR5 agonists: unconjugated and steroid modified BA and side chain modified BA including taurine or glycine conjugates and pseudo-conjugates (sulphonate and sulphate analogues). In order to investigate the relationship between structure and activity the synthetic analogues where admitted to a physicochemical characterization and to a preliminary screening for their pharmacokinetic and metabolism using a bile fistula rat model. Sensitive and accurate analytical methods have been developed for the quali-quantitative analysis of BA in biological fluids and sample used for physicochemical studies. Combined High Performance Liquid Chromatography Electrospray tandem mass spectrometry with efficient chromatographic separation of all studied BA and their metabolites have been optimized and validated. Analytical strategies for the identification of the BA and their minor metabolites have been developed. Taurine and glycine conjugates were identified in MS/MS by monitoring the specific ion transitions in multiple reaction monitoring (MRM) mode while all other metabolites (sulphate, glucuronic acid, dehydroxylated, decarboxylated or oxo) were monitored in a selected-ion reaction (SIR) mode with a negative ESI interface by the following ions. Accurate and precise data where achieved regarding the main physicochemical properties including solubility, detergency, lipophilicity and albumin binding . These studies have shown that minor structural modification greatly affect the pharmacokinetics and metabolism of the new analogues in respect to the natural BA and on turn their site of action, particularly where their receptor are located in the enterohepatic circulation.

La documentazione monetale come fonte per la storia di Classe (Ravenna) Gli scavi condotti nell’area portuale (anni 2001-2005) e nell’area della basilica di San Severo (anni 2006-2010)

Gli scavi effettuati a Classe, a sud di Ravenna, presso i siti archeologici dell'area portuale e della Basilica di San Severo, hanno portato alla luce un numero abbondante di moneta, 2564 dall'area portuale e 224 dalla basilica, un totale di 2788 reperti monetali, di cui solo 863 sono leggibili e databili. La datazione dei materiali dell’area portuale, fondata agli inizi del V secolo, parte dal II secolo a.C. fino all’VIII secolo d.C.. La maggior parte dei reperti è relativa al periodo tra il IV e il VII secolo, il momento di massima importanza del porto commerciale, con testimonianza di scambi con altri porti del bacino mediterraneo, in particolare con l’Africa del Nord e il Vicino Oriente. La documentazione proveniente dalla Basilica di San Severo, fondata alla fine del VI secolo per la custodia delle reliquie del santo, mostra un trend diverso dal precedente, con monetazione che copre un arco cronologico dal I secolo a.C. fino al XIV secolo d.C.. La continuità dell’insediamento è dimostrato dall’evidenza numismatica, seppur scarsa, fino alla costruzione del monastero a sud della basilica, l’area dalla quale provengono la maggior parte delle monete. I quantitativi importanti di monetazione tardoantica, ostrogota e bizantina, in particolare di tipi specifici come il Felix Ravenna, ipoteticamente coniato a Roma, oppure il ½ e il 1/4 di follis di produzione saloniana emesso da Giustiniano I, hanno concesso uno studio dettagliato per quello che riguarda il peso, le dimensioni e lo stile di produzione di queste emissioni. Questi dati e la loro distribuizione sul territorio ha suggerito nuove ipotesi per quello che riguarda la produzione di questi due tipi presso la zecca di Ravenna. Un altro dato importante è il rinvenimento di emissioni di Costantino VIII, alcune rare e altre sconosciute, rinvenute solo nel territorio limitrofo a Classe e Ravenna.

Giosuè Carducci nella cultura primonovecentesca

La tesi indaga la ricezione di Carducci nella cultura italiana ed europea dei primi decenni del XX secolo attraverso lo studio delle commemorazioni, delle memorie, degli articoli e dei saggi dedicati al poeta maremmano, al fine di mettere in luce il complesso ruolo ricoperto dallo scrittore e le strumentalizzazioni di cui è stato vittima.

Semi-synthetic bile acids as novel drug candidate in liver diseases: physico-chemical characterization and HPLC-ES-MS/MS methods for their quali-quantitative analysis in different experimental animal models

The physico-chemical characterization, structure-pharmacokinetic and metabolism studies of new semi synthetic analogues of natural bile acids (BAs) drug candidates have been performed. Recent studies discovered a role of BAs as agonists of FXR and TGR5 receptor, thus opening new therapeutic target for the treatment of liver diseases or metabolic disorders. Up to twenty new semisynthetic analogues have been synthesized and studied in order to find promising novel drugs candidates. In order to define the BAs structure-activity relationship, their main physico-chemical properties (solubility, detergency, lipophilicity and affinity with serum albumin) have been measured with validated analytical methodologies. Their metabolism and biodistribution has been studied in “bile fistula rat”, model where each BA is acutely administered through duodenal and femoral infusion and bile collected at different time interval allowing to define the relationship between structure and intestinal absorption and hepatic uptake ,metabolism and systemic spill-over. One of the studied analogues, 6α-ethyl-3α7α-dihydroxy-5β-cholanic acid, analogue of CDCA (INT 747, Obeticholic Acid (OCA)), recently under approval for the treatment of cholestatic liver diseases, requires additional studies to ensure its safety and lack of toxicity when administered to patients with a strong liver impairment. For this purpose, CCl4 inhalation to rat causing hepatic decompensation (cirrhosis) animal model has been developed and used to define the difference of OCA biodistribution in respect to control animals trying to define whether peripheral tissues might be also exposed as a result of toxic plasma levels of OCA, evaluating also the endogenous BAs biodistribution. An accurate and sensitive HPLC-ES-MS/MS method is developed to identify and quantify all BAs in biological matrices (bile, plasma, urine, liver, kidney, intestinal content and tissue) for which a sample pretreatment have been optimized.

New analytical LC-mass spectrometry methodologies for the quali-quantitative determination of natural substances and drugs in complex matrices

This thesis reports an integrated analytical and physicochemical approach for the study of natural substances and new drugs based on mass spectrometry techniques combined with liquid chromatography. In particular, Chapter 1 concerns the study of Berberine a natural substance with pharmacological activity for the treatment of hepatobiliary and intestinal diseases. The first part focused on the relationships between physicochemical properties, pharmacokinetics and metabolism of Berberine and its metabolites. For this purpose a sensitive HPLC-ES-MS/MS method have been developed, validated and used to determine these compounds during their physicochemical properties studies and plasma levels of berberine and its metabolites including berberrubine(M1), demethylenberberine(M3), and jatrorrhizine(M4) in humans. Data show that M1, could have an efficient intestinal absorption by passive diffusion due to a keto-enol tautomerism confirmed by NMR studies and its higher plasma concentration. In the second part of Chapter 1, a comparison between M1 and BBR in vivo biodistribution in rat has been studied. In Chapter 2 a new HPLC-ES-MS/MS method for the simultaneous determination and quantification of glucosinolates, as glucoraphanin, glucoerucin and sinigrin, and isothiocyanates, as sulforaphane and erucin, has developed and validated. This method has been used for the analysis of functional foods enriched with vegetable extracts. Chapter 3 focused on a physicochemical study of the interaction between the bile acid sequestrants used in the treatment of hypercholesterolemia including colesevelam and cholestyramine with obeticolic acid (OCA), potent agonist of nuclear receptor farnesoid X (FXR). In particular, a new experimental model for the determination of equilibrium binding isotherm was developed. Chapter 4 focused on methodological aspects of new hard ionization coupled with liquid chromatography (Direct-EI-UHPLC-MS) not yet commercially available and potentially useful for qualitative analysis and for “transparent” molecules to soft ionization techniques. This method was applied to the analysis of several steroid derivatives.

Processi integrati per l’intensificazione di processo: reazione di fotocatalisi accoppiata alla pervaporazione, la dialisi e all’ozonizzazione

L’accoppiamento di diverse operazioni unitarie può in certi casi portare ad una cosiddetta “intensificazione di processo”, cioè ad un aumento sostanziale delle rese, dell’efficienza e della sostenibilità. Nel presente lavoro sono state pertanto analizzate le potenzialità di accoppiamento della fotocatalisi, il più studiato tra i “processi di ossidazione avanzata”, sia con alcuni processi a membrana per la sintesi verde di aromi sia con l’ozonizzazione per la depurazione di acque. È stato dimostrato che in entrambi i casi l’ottenimento di una significativa intensificazione di processo dipende in gran parte dai parametri operativi, in particolare dal rapporto, delta, tra la velocità caratteristica di fotocatalisi e quella del processo accoppiato. Nel caso della sintesi di aromi, in cui la fotocatalisi viene accoppiata con la pervaporazione o con la dialisi ricircolando al reattore il retentato dalla cella con la membrana. Il parametro delta dipende dalla velocità di reazione, dalle proprietà di trasporto delle membrane e naturalmente dal volume del rettore e dall’area della membrana. La reazione fotocatalitica produce l’aroma, ad esempio vanillina da acido ferulico, per ossidazione parziale e grazie al recupero del prodotto se ne evita l’ulteriore ossidazione aumentandone pertanto la resa. L’operare in apparati separati offre diversi vantaggi come la possibilità di variare senza vincoli il rapporto tra area della membrana e volume del reattore, ma impone di considerare anche il grado effettivo di accoppiamento dei processi. In questo caso, come evidenziato dal modello matematico, un sufficientemente elevato rapporto di ricircolo consente comunque di integrare efficacemente i processi. Nell’ozonizzazione fotocatalitica si hanno due importanti vantaggi: l’aumento della velocità di degradazione grazie alla sinergia tra i processi e la capacità di controllare la formazione di prodotti pericolosi. La sinergia viene massimizzata ad un valore ottimale di delta, mentre la formazione dei prodotti indesiderati viene controllata operando secondo le procedure che sono state individuate.

Development of effect-based bio-chemiluminescent cell bioassays for nutraceutical and biomedical applications

The final goal of the bioassay developed during the first two years of my Ph.D. was its application for the screening of antioxidant activity of nutraceuticals and for monitoring the intracellular H2O2 production in peripheral blood mononuclear cells (PBMCs) from hypercholesterolemic subjects before and after two months treatment with Evolocumab, a new generation LDL-cholesterol lowering drug. Moreover, a recombinant bioluminescent protein was developed during the last year using the Baculovirus expression system in insect cells. In particular, the protein combines the extracellular domain (ECD) of the Notch high affinity mutated form of one of the selective Notch ligands defined as Jagged 1 (Jag1) with a red emitting firefly luciferase since a pivotal role of “aberrant” Notch signaling activation in colorectal cancer (CRC) was reported. The probe was validated and characterized in terms of analytical performance and through imaging experiments, in order to understand if Jagged1-FLuc binding correlates with a Notch signaling overexpression and activation in CRC progression.