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The recent application of proteomics and metabolomics to clinical medicine has demonstrated their potential role in complementing genomics for a better understanding of diseases' patho-physiology. These technologies offer the clear opportunity to identify risk factors, disease-specific or stage-specific biomarkers and to predict therapeutic response. This article is an overview of the recent insights obtained by metabolomic and proteomic studies in inherited kidney disorders. Proteomics studies have allowed the definition of a detailed picture of protein composition, post-translational modifications and interactions in kidney-derived samples, improving our understanding of renal physiology, especially of tubular transport and primary cilium-related functions. Studies on patients' urine samples and experimental models of inherited kidney diseases have provided clues suggesting novel potential pathological mechanisms and biomarkers of disease, for example in polycystic kidney disease. Metabolomic-based studies have been recently applied to assess biological system disturbances caused by specific genetic mutations resulting in inherited kidney disorders. These studies have been mainly carried out on mouse and rat models of cystic and metabolic disorders (such as Fabry disease), and on patients' urine samples. They have provided a significant contribution in understanding disease pathophysiology, promoting the discovery of aberrant biochemical pathways and contributing to the development of targeted therapies.

Proteomics is the study of the "proteome", that is the entire protein complement of a genome. However, it is well recognized that the proteome is far more complex than previously suggested by the "one-gene, oneprotein" central dogma of biology. The proteome encompasses all proteins of a cell or organism at a given time, including not only those translated directly from genetic information but also the array of modified proteins arising from alternative splicing of transcripts and post-translational processing, resulting in modifications that have the potential to alter protein structure or biological function. As proteins are involved in virtually every cellular function, control every regulatory mechanism, and are modified in disease states, the proteome dictates the phenotype of the cell and, consequently, the tissue or organ that the cells comprise. This results in a dynamic, ongoing process of protein expression and modifications. The proteome thus consists of information from protein expression, post-translational modifications, processing and turnover, localization and time. Proteomics is aimed at identifying and characterizing these protein changes and, if applied to the field of cardiovascular sciences, it has the potential to reveal those proteins that are associated with pathogenesis and could be potentially used as predictive or prognostic markers. Cardioproteomic is still in its infancy and relatively few cardiovascular diseases have been investigated. However, it has enormously increased our knowledge of the complexity of the myocardium in terms of protein composition at cellular and organelle levels. The cardiac proteome is further complicated by protein post-translational modifications, which may regulate organelle function in physiological and pathological conditions. Therefore, the incorporation of proteomics into cardiovascular research will provide a means of exploring the mechanisms of disease onset and progression. This will in turn ultimately lead to increased efficiency of diagnosis and/or monitoring of treatment, which could dramatically increase the ability of the clinician to recognize cardiovascular disease states at a relatively early stage, and to improve the therapeutic approach.

II frumento è una specie largamente coltivata nel mondo e rappresenta una delle materie prime più importanti per l’alimentazione umana. Una più approfondita conoscenza delle vie biosintetiche ha aperto la strada a possibili interventi di miglioramento genetico della qualità dell’amido. Nel nostro laboratorio sono state prodotte linee transgeniche di frumento duro ad alto contenuto di amilosio in cui i geni che codificano per gli enzimi di ramificazione IIa (SBEIIa), fondamentali per la sintesi dell’amilopectina, sono stati silenziati. In questo lavoro di Dottorato è stato effettuato uno studio comparativo tra il proteoma della linea wild-type di Svevo e Ofanto e le rispettive linee transgeniche silenziate per il gene SBEIIa, a diversi stadi di sviluppo della cariosside, al fine confrontare gli effetti prodotti da due differenti metodi di trasformazione genetica sul proteoma delle cariossidi di frumento duro. Dalle analisi delle proteine estratte dai granuli di amido e della frazione metabolica sono stati identificati 32 spot differenziamenti espressi tra la linea transgenica MJ16-112 (ottenuta mediante metodo biolistico) e la cultivar di Svevo e 37 spot differenzialmente espressi sulla linea transgenica A431_4p1a (ottenuta mediante trasformazione mediata dall’Agrobatterio) e sulla cultivar Ofanto. Le proteine osservate come differenzialmente espresse sono state: proteine coinvolte nel metabolismo dei carboidrati, nei meccanismi di difesa e nei processi biosintetici della cariosside di frumento. Cambiamenti nel metabolismo dei carboidrati possono essere considerati “attesi”, dato che è stata manipolata la via biosintetica dell’amido nelle linee GM, mentre non sono state rilevate grosse differenze per quanto riguarda la presenza di allergeni o sostanze pericolose all’interno della cariossidi transgeniche. In conclusione i due metodi di trasformazione hanno avuto effetti secondari simili in entrambe le frazioni proteiche, e che tali effetti non sembrano, quindi, influenzati dalle diverse metodiche di trasformazione. Wheat is widely cultivated in the world and represents one of the cereals most important for the human diet. The parameters that mainly influence semolina and flour quality are the proteins and the starch. Starch is of remarkable interest because it can be used for various applications in food and non food industry. It is composed by amylose and amylopectine, whose relative amounts affect its chemical-physical properties and final uses, along with the structure of starch granules and lipids. In the last years various studies have been performed to clarify the mechanisms that regulate starch biosynthesis, in order to produce starches with specific properties, such as a higher amylose content, that has beneficial effects on human health. In our laboratory, high amylose transgenic lines of durum wheat have been produced through the silencing of the Starch Branching Enzyme IIa (SBEIIa) genes. In this work, a 2D electrophoretic comparison between the kernel proteome of a transgenic line of the durum wheat cultivar Svevo with silenced SBEIIa genes and the corresponding untransformed line have been performed. In particular, two developing stages have been considered: the dough (15 dpa) and ripening (physiological maturity) stages. As for the mature stage, the differentially expressed proteins have been identified by the software SameSpots Progenesis (Nonlinear Dynamics, UK) and characterized by MS/MS. In order to compare the effects produced by two different methods of genetic transformation on the proteome of kernels of durum wheat. From the analysis of proteins extracted from starch granules and metabolic fraction, 32 spots were identified differentially expressed between by transgenic line MJ16-112 (obtained by biolistic method) and cultivars Svevo and 37 spots differentially expressed on the transgenic line A431_4p1a (obtained by mediated transformation dall'Agrobatterio) and on the cultivar Ofanto. The proteins were observed as differentially expressed: proteins involved in carbohydrate metabolism, defense mechanisms and biosynthetic processes in the caryopsis of wheat. Changes in carbohydrate metabolism may be considered "expected", since it has been manipulated the biosynthetic pathway of starch in the GM lines, while there were no major differences regarding the presence of hazardous substances or allergens in the transgenic kernels . In conclusion, the two processing methods have similar effects in both protein fractions, and that these effects do not seem, therefore, influenced by the different methods of transformation. Dottorato di ricerca in Biotecnologie vegetali 24. ciclo