Academic literature on the topic 'Approcci proteomici'
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Journal articles on the topic "Approcci proteomici"
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Jain, K. K. "Oncoproteomics: State-of-the-Art." Technology in Cancer Research & Treatment 1, no. 4 (August 2002): 219–20. http://dx.doi.org/10.1177/153303460200100401.
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Proteomics is a promising approach in the identification of proteins and biochemical pathways involved in carcinogenesis. Proteomic technologies are now being incorporated in oncology in the post-genomic era. Cancer involves alterations in protein expression and provides a good model not only for detection of biomarkers but also their use in drug discovery. Proteomics has an impact on diagnostics as well as drug discovery. Genomics still remains an important approach but the value of proteomics lies in the fact that most of the diagnostics and drugs target proteins. The importance of application of proteomics in oncology is recognized by the publication of this special issue of TRCT.
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Sharma, Vipin Kumar, and Ravi Kumar. "Current applications of proteomics: a key and novel approach." International Journal of Advances in Medicine 6, no. 6 (November 25, 2019): 1953. http://dx.doi.org/10.18203/2349-3933.ijam20195259.
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Proteomics represented vital applications of technologies in the identification and quantification of high to moderate proteins (cellular signalling networks) found in biological matrix such as tissues, cells and fluids. Proteomics based technical knowledge is applied and verified in several preclinical research settings such as invention of diagnostic markers for specific disease and have shown to be increased in clinical applications. Extensive studies on proteomics resulted in detection of biomarkers that have been highly advanced in using diseases for cancer, lungs, cardiovascular, renal and neuro-regenerative and Parkinson's disease by introducing human origins for biocompatibility such as urine and serum. Advancement in the proteomic methods is conferring candidate right direction for clinical usage. In this review, recent developments and widely used proteomics approaches such as Mass Spectrometry (MS), Microarray chips are elaborately addressed and also focused merits and demerits of commonly used advanced approaches such as Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and Data Independent Acquisition (DIA) and other used proteomics and that roles, in order to aid clinicians, were also discussed in the light of biomedical applications.
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Kline, Rachel A., Lena Lößlein, Dominic Kurian, Judit Aguilar Martí, Samantha L. Eaton, Felipe A. Court, Thomas H. Gillingwater, and Thomas M. Wishart. "An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research." Cells 11, no. 17 (August 26, 2022): 2653. http://dx.doi.org/10.3390/cells11172653.
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Recent advances in proteomic technologies now allow unparalleled assessment of the molecular composition of a wide range of sample types. However, the application of such technologies and techniques should not be undertaken lightly. Here, we describe why the design of a proteomics experiment itself is only the first step in yielding high-quality, translatable results. Indeed, the effectiveness and/or impact of the majority of contemporary proteomics screens are hindered not by commonly considered technical limitations such as low proteome coverage but rather by insufficient analyses. Proteomic experimentation requires a careful methodological selection to account for variables from sample collection, through to database searches for peptide identification to standardised post-mass spectrometry options directed analysis workflow, which should be adjusted for each study, from determining when and how to filter proteomic data to choosing holistic versus trend-wise analyses for biologically relevant patterns. Finally, we highlight and discuss the difficulties inherent in the modelling and study of the majority of progressive neurodegenerative conditions. We provide evidence (in the context of neurodegenerative research) for the benefit of undertaking a comparative approach through the application of the above considerations in the alignment of publicly available pre-existing data sets to identify potential novel regulators of neuronal stability.
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Gajahin Gamage, Nadeeka Thushari, Rina Miyashita, Kazutaka Takahashi, Shuichi Asakawa, and Jayan Duminda Mahesh Senevirathna. "Proteomic Applications in Aquatic Environment Studies." Proteomes 10, no. 3 (September 1, 2022): 32. http://dx.doi.org/10.3390/proteomes10030032.
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Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.
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Glazyrin, Yury E., Dmitry V. Veprintsev, Irina A. Ler, Maria L. Rossovskaya, Svetlana A. Varygina, Sofia L. Glizer, Tatiana N. Zamay, et al. "Proteomics-Based Machine Learning Approach as an Alternative to Conventional Biomarkers for Differential Diagnosis of Chronic Kidney Diseases." International Journal of Molecular Sciences 21, no. 13 (July 7, 2020): 4802. http://dx.doi.org/10.3390/ijms21134802.
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Diabetic nephropathy, hypertension, and glomerulonephritis are the most common causes of chronic kidney diseases (CKD). Since CKD of various origins may not become apparent until kidney function is significantly impaired, a differential diagnosis and an appropriate treatment are needed at the very early stages. Conventional biomarkers may not have sufficient separation capabilities, while a full-proteomic approach may be used for these purposes. In the current study, several machine learning algorithms were examined for the differential diagnosis of CKD of three origins. The tested dataset was based on whole proteomic data obtained after the mass spectrometric analysis of plasma and urine samples of 34 CKD patients and the use of label-free quantification approach. The k-nearest-neighbors algorithm showed the possibility of separation of a healthy group from renal patients in general by proteomics data of plasma with high confidence (97.8%). This algorithm has also be proven to be the best of the three tested for distinguishing the groups of patients with diabetic nephropathy and glomerulonephritis according to proteomics data of plasma (96.3% of correct decisions). The group of hypertensive nephropathy could not be reliably separated according to plasma data, whereas analysis of entire proteomics data of urine did not allow differentiating the three diseases. Nevertheless, the group of hypertensive nephropathy was reliably separated from all other renal patients using the k-nearest-neighbors classifier “one against all” with 100% of accuracy by urine proteome data. The tested algorithms show good abilities to differentiate the various groups across proteomic data sets, which may help to avoid invasive intervention for the verification of the glomerulonephritis subtypes, as well as to differentiate hypertensive and diabetic nephropathy in the early stages based not on individual biomarkers, but on the whole proteomic composition of urine and blood.
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Bouamrani, Ali, Jessica Ternier, David Ratel, Alim-Louis Benabid, Jean-Paul Issartel, Elisabeth Brambilla, and François Berger. "Direct-Tissue SELDI-TOF Mass Spectrometry Analysis: A New Application for Clinical Proteomics." Clinical Chemistry 52, no. 11 (November 1, 2006): 2103–6. http://dx.doi.org/10.1373/clinchem.2006.070979.
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Abstract Background: New molecular profiling technologies can aid in analysis of small pathologic samples obtained by minimally invasive biopsy and may enable the discovery of key biomarkers synergistic with anatomopathologic analysis related to prognosis, therapeutic response, and innovative target validation. Thus proteomic analysis at the histologic level in healthy and pathologic settings is a major issue in the field of clinical proteomics. Methods: We used surface-enhanced laser desorption ionization-time-of-flight mass spectrometry (SELDI-TOF MS) technology with surface chromatographic subproteome enrichment and preservation of the spatial distribution of proteomic patterns to detect discrete modifications of protein expression. We performed in situ proteomic profiling of mouse tissue and samples of human cancer tissue, including brain and lung cancer. Results: This approach permitted the discrimination of glioblastomas from oligodendrogliomas and led to the identification of 3 potential markers. Conclusion: Direct tissue proteomic analysis is an original application of SELDI-TOF MS technology that can expand the use of clinical proteomics as a complement to the anatomopathological diagnosis.
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Laronga, Christine, and Richard R. Drake. "Proteomic Approach to Breast Cancer." Cancer Control 14, no. 4 (October 2007): 360–68. http://dx.doi.org/10.1177/107327480701400406.
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Background Breast cancer is the most common cancer affecting women worldwide. Despite tremendous advances in screening, diagnosis, and treatment, the causes of this disease remain elusive and complex. Proteomics is a rapidly developing field that can explore the heterogeneity of breast cancer and supplement the wealth of information gained from genomics. Methods This article serves as an overview of the application of matrix-assisted laser desorption/ionization source with a time-of-flight (MALDI-TOF) proteomic techniques as applied to breast cancer. Examples of the clinical applicability of MALDI-TOF mass spectrometry are provided but represent only a fraction of the potential uses yet to be discovered. In addition, a brief summary of the bioinformatics issues that surround proteomics is included. Results Mass spectrometry has provided new proteomic approaches to unravel the complexities of clinical specimens relevant to breast cancer diagnostics. In particular, MALDI-TOF mass spectrometry analysis has been used to differentiate cancer profiles from benign profiles in samples from sera, plasma, tissue, nipple fluid, and ductal lavage. Some discriminating proteins have subsequently been identified. Conclusions Mass spectrometry applications to breast cancer diagnostics continue to be developed but are evolving faster than bioinformatics/statistical analysis can adapt. The future of these techniques in terms of clinical investigation is limitless, but in terms of general applicability, these applications are currently cost-prohibitive.
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Giannopoulou, Eugenia G., Spiros D. Garbis, Antonia Vlahou, Sofia Kossida, George Lepouras, and Elias S. Manolakos. "Proteomic Feature Maps: A new visualization approach in proteomics analysis." Journal of Biomedical Informatics 42, no. 4 (August 2009): 644–53. http://dx.doi.org/10.1016/j.jbi.2009.01.007.
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Canetti, Diana, Francesca Brambilla, Nigel B. Rendell, Paola Nocerino, Janet A. Gilbertson, Dario Di Silvestre, Andrea Bergamaschi, et al. "Clinical Amyloid Typing by Proteomics: Performance Evaluation and Data Sharing between Two Centres." Molecules 26, no. 7 (March 29, 2021): 1913. http://dx.doi.org/10.3390/molecules26071913.
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Amyloidosis is a relatively rare human disease caused by the deposition of abnormal protein fibres in the extracellular space of various tissues, impairing their normal function. Proteomic analysis of patients’ biopsies, developed by Dogan and colleagues at the Mayo Clinic, has become crucial for clinical diagnosis and for identifying the amyloid type. Currently, the proteomic approach is routinely used at National Amyloidosis Centre (NAC, London, UK) and Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche (ITB-CNR, Milan, Italy). Both centres are members of the European Proteomics Amyloid Network (EPAN), which was established with the aim of sharing and discussing best practice in the application of amyloid proteomics. One of the EPAN’s activities was to evaluate the quality and the confidence of the results achieved using different software and algorithms for protein identification. In this paper, we report the comparison of proteomics results obtained by sharing NAC proteomics data with the ITB-CNR centre. Mass spectrometric raw data were analysed using different software platforms including Mascot, Scaffold, Proteome Discoverer, Sequest and bespoke algorithms developed for an accurate and immediate amyloid protein identification. Our study showed a high concordance of the obtained results, suggesting a good accuracy of the different bioinformatics tools used in the respective centres. In conclusion, inter-centre data exchange is a worthwhile approach for testing and validating the performance of software platforms and the accuracy of results, and is particularly important where the proteomics data contribute to a clinical diagnosis.
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Chang, Chiz-Tzung, Chao-Yuh Yang, Fuu-Jen Tsai, Shih-Yi Lin, and Chao-Jung Chen. "Mass Spectrometry-Based Proteomic Study Makes High-Density Lipoprotein a Biomarker for Atherosclerotic Vascular Disease." BioMed Research International 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/164846.
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High-density lipoprotein (HDL) is a lipid and protein complex that consists of apolipoproteins and lower level HDL-associated enzymes. HDL dysfunction is a factor in atherosclerosis and decreases patient survival. Mass spectrometry- (MS-) based proteomics provides a high throughput approach for analyzing the composition and modifications of complex HDL proteins in diseases. HDL can be separated according to size, surface charge, electronegativity, or apoprotein composition. MS-based proteomics on subfractionated HDL then allows investigation of lipoprotein roles in diseases. Herein, we review recent developments in MS-based quantitative proteomic techniques, HDL proteomics and lipoprotein modifications in diseases, and HDL subfractionation studies. We also discuss future directions and perspectives in MS-based proteomics on HDL.
Dissertations / Theses on the topic "Approcci proteomici"
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MAFFICINI, Andrea. "Nuovi approcci proteomici per l'identificazione di potenziali marcatori di neoplasie pancreatiche." Doctoral thesis, Università degli Studi di Verona, 2007. http://hdl.handle.net/11562/337987.
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Lo sviluppo di approcci rapidi ed automatizzati come la tecnologia multidimensionale di
identificazione proteica (MudPIT) sta rendendo la proteomica uno strumento sempre più
efficiente per l’analisi delle proteine in miscele complesse, permettendo l’identificazione di
nuovi marcatori biologici che sono di importanza critica per una migliore comprensione
della biologia dei tumori e per rendere la sua rilevazione più precoce e meno invasiva. Lo
scopo del presente studio era quello di identificare nuove proteine rilasciate dalle cellule di
adenocarcinoma duttale del pancreas, usando piccole quantità di campione ed un sistema
automatizzato; le evidenze sperimentali così ottenute sarebbero state utilizzate per
verificare in vitro ed in vivo, con metodiche più tradizionali quali western blot, RT-PCR ed
immunoistochimica, la presenza delle proteine selezionate come possibili marcatori. È stata
dunque applicata la tecnologia MudPIT, che incorpora la cromatografia capillare
bidimensionale e la spettrometria di massa in tandem, per l’analisi di piccole quantità di
surnatanti privi di siero derivanti dalla coltura di cellule Suit-2 non trattate oppure attivate
con esteri del forbolo e ionoforo. I potenziali marcatori prescelti sono stati valutati in altre
linee cellulari di cancro del pancreas, adenocarcinomi primitivi e xenotrapiantati in topi
nu/nu. L’analisi MudPIT effettuata su campioni di 10 μl di surnatanti ha permesso
l’identificazione complessiva di 46 proteine tra cellule attivate e non trattate. Di queste
proteine, 21 sono classificate come secrete sui database pubblicamente disponibili e 10
non erano state precedentemente associate al carcinoma duttale del pancreas. Questo
gruppo comprende le proteine CSPG2/versican, Mac25/angiomodulina, IGFBP-1,
HSPG2/perlecan, syndecan 4, FAM3C, APLP2, ciclofilina B, K2 microglobulina, ed ICA69. Le
evidenze sperimentali che queste proteine siano rilasciate dalle cellule tumorali in vivo
sono state ottenute, per CSPG2/versican e Mac25/angiomodulina, mediante
immunoistochimica. L’analisi è stata eseguita tanto su tumori primitivi quanto su di un
modello, consistente in cellule della linea Suit-2 incluse in una matrice amorfa (Matrigel®)
e trapiantate per una settimana in topi atimici. Si è inoltre dimostrato, mediante il
confronto tra cellule non trattate ed attivate con esteri del forbolo, che l’analisi MudPIT
può fornire dati semiquantitativi correlati con la quantità relativa di proteina presente nel
campione analizzato; anche quest’osservazione è stata convalidata mediante misurazione
del diverso livello di espressione di tre proteine rispettivamente inibite
(Mac25/angiomodulina), non modificate (CSPG2/versican) ed indotte (MMP-1). Si è poi
indagata, su una casistica di 100 pazienti con varie patologie pancreatiche, l’espressione di
forme solubili di uPAR (suPAR), il cui ligando uPA era tra le proteine maggiormente indotte
in seguito all’attivazione delle cellule in vitro. L’analisi è stata fatta utilizzando una
metodica immunoenzimatica (saggio ELISA) su sieri ed urine dei casi disponibili presso la
biobanca della clinica chirurgica dell’Università di Verona. E’ stato riscontrato un
significativo incremento dei valori di suPAR nei sieri di pazienti affetti da adenocarcinoma
duttale del pancreas rispetto alle altre patologie infiammatorie o neoplastiche del
pancreas; i dati delle urine, pur se meno netti, indicano comunque una tendenza simile ed
incoraggiano ad un incremento del numero di campioni sui quali effettuare ulteriori analisi.
Confrontato con altre metodiche, dunque, MudPIT è stato in grado di fornire in modo
rapido e riproducibile dati su di una serie di molecole rilasciate da cellule neoplastiche, che
hanno quindi caratteristiche di sicuro interesse quali potenziali marcatori di malattia
potenzialmente rilevabili nei liquidi biologici. Gli sviluppi futuri di tale approccio
comprendono, oltre all’ampliamento dell’analisi MudPIT su un numero maggiore di linee
cellulari, lo sviluppo di nuovi reagenti per l’identificazione quelle molecole per le quali essi
non sono attualmente disponibili.Non disponibile
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Vitorino, Rui Miguel Pinheiro. "Dental caries: a proteomic approach." Doctoral thesis, Universidade de Aveiro, 2004. http://hdl.handle.net/10773/17671.
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Doutoramento em BioQuímicaA cárie dentária é uma doença complexa que afecta uma grande parte da população mundial independentemente do sexo, idade ou etnia. Este processo é dependente de factores biológicos que se encontram presentes na saliva e placa dentária. Em seguimento do referido, amostras de saliva foram colectadas de indivíduos caracterizados em função dos índices DMFT e DMFS. A avaliação dos convencionais parâmetros clínicos como por exemplo fluxo salivar, capacidade tampão, pH usados na avaliação do risco para a cárie dentária em combinação com dieta, hábitos de higiene e tabagismo foram realizados para todos os indivíduos participantes do qual se observou a ausência de uma positiva correlação com o índice DMFT. Uma vez que os factores biológicos presentes na saliva influenciam o processo da cárie dentária, o objectivo deste trabalho consistiu na investigação de uma possível correlação entre as proteínas e peptídeos da saliva e o processo da cárie dentária. A caracterização das proteínas e peptídeos da saliva foi alcançada utilizando electroforese bidimensional (2-DE), cromatografia líquida de alta resolução (HPLC) combinada com a espectrometria de massa (MS), do qual resultou a identificação de 38 proteínas das quais 12 foram identificadas pela primeira vez por 2-DE e 22 peptídeos por HPLC-MS também identificados pela primeira vez. Ensaios realizados para o estudo da composição da película dentária seguiram a mesma metodologia descrita para a caracterização das proteínas e peptídeos da saliva sendo realizados inicialmente in vitro e confi rmados posteriormente por ensaios in vivo. A adsorção dos componentes salivares à hidroxiapatite é um processo selectivo com predominância de componentes salivares de baixo peso molecular. Contudo, amilase, lactoferrina, IgA salivar e anidrase carbónica VI foram também identificadas. A extracção sequencial usando guanidina e ácido trifluoroacético das proteínas/peptídeos adsorvidas à hidroxiapatite permitiu uma avaliação da força das ligações estabelecidas. Destes ensaios verificou-se que proteínas ricas em prolina (PRP-1/3), cistatina S, statherina e histatina 1 estabeleciam interacções fortes com a hidroxiapatite permanecendo adsorvidas após extracção com guanidina. As proteínas caracterizadas da saliva e da película dentária foram correlacionadas com o índice DMFT apresentando uma predominância de elevadas quantidades de cistatinas, PRP -1/3, statherina e histatina 1 no grupo de indivíduos sem cárie. O reduzido número de fragmentos em associação com as elevadas quantidades de cistatinas podem sugerir um controle mais eficiente da actividade proteólitica evitando desta maneira a degradação de importantes proteínas salivares no grupo de indivíduos sem cárie. A composição da película dentária é afectada pela composição proteica da saliva encontrando-se as referidas proteínas em maior quantidade. Os dados obtidos sugerem uma eficiente protecção por parte das proteínas da saliva contra a cárie dentária em particular a PRP-1/3, statherina e histatina 1, provavelmente devido à sua participação nos processos de remineralização na superfície do dente, e das cistatinas na diminuição da actividade proteólitica.
Dental caries is a complex disease process that affects a large proportion of the world population, regardless of gender, age and ethnicity. This process is dependent upon biological factors that are present within saliva and dental plaque. Following this, whole saliva was collected from selected individuals characterised according its DMFT and DMFS scores. Evaluation of the conventional clinical parameters such as flow rate, buffering capacity, pH used for caries risk assessment in combination with diet, hygiene and smoke habits was performed for all participating subjects showing absence of a statistic positive correlation with DMFT index. Since biological factors present on saliva influence dental caries process, the aim of this study was to investigate how salivary proteins and peptides are correlated with this pathology. Characterisation of salivary proteins and peptides was achieved using twodimensional gel electrophoresis (2-DE) and high performance liquid chromatography (HPLC) in combination with mass spectrometry (MS) resulting in the identification of 38 proteins, being 12 proteins identified by 2-DE and 22 peptides by HPLC-MS were identified for the first time. Experiments to study enamel pellicle composition were performed following the same methodology described for salivary proteins and peptides, initially in vitro being supported with in vivo assays. Adsorption of salivary components to hydroxyapatite showed to be a selective process with a predominance of low molecular weight salivary components. However, amylase, lactoferrin, S-IgA, carbonic anhydrase VI were also identified. A sequential extraction, using of guanidine and trifluoroacetic acid, of the adsorbed proteins/peptides to hydroxyapatite allowed to evaluate the strength of the establish interactions. From this experiments, proline-rich proteins (PRP -1/3), cystatin S, statherin, histatin 1 exhibited a strong interaction with hydroxyapatite remaining adsorbed after guanidine extraction. Characterised salivary proteins from whole saliva and enamel pellicle were correlated with DMFT index showing a predominance of higher amounts of cystatins, PRP-1/3, statherin and histatin 1 in caries free group. Decreased number of fragments in association with higher amounts of cystatins may suggest a more effective control in proteolytic activity which avoid the degradation of important salivary proteins from caries free group. Acquired pellicle composition is affected by whole saliva protein composition being the above referred proteins present in higher amounts. Obtained data suggest an effective protective role of several salivary proteins to dental caries in particular of PRP-1/3, statherin and histatin 1, possibly due to their participation on remineralization processes at the tooth surface, and of cystatins probably by decreasing proteolytic activity.
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SEMERARO, SABRINA. "APPROCCI DI PROTEOMICA E GLICOMICA NELL'EPATOCITA NORMALE E PATOLOGICO." Doctoral thesis, Università degli studi di Trieste, 2006. http://thesis2.sba.units.it/store/handle/item/13218.
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2004/2005In questo lavoro si è cercato di fornire gli strumenti per l'analisi del proteoma della membrana plasmatica con particolare interesse nei confronti delle glicoproteine e delle eventuali modificazioni della loro componente oligosaccaridica, nell'ambito deii'HCC, con lo scopo di individuare nuovi marker glicoproteici da utilizzare in diagnostica e terapia. La componente oligosaccaridica delle glicoproteine di membrana viene coinvolta e continuamente rimaneggiata in diversi processi biologici, che vanno dalla regolazione del sistema immunitario alla comunicazione cellulare, dallo sviluppo embrionale alla capacità patogenetica degli agenti infettivi, dal ripiegamento della catena lineare dei polipeptidi fino allo sviluppo dei tumori e di altre importanti patologie[1J. La limitata disponibilità di dati sperimentali di riferimento per quanto riguarda un approccio di proteomica della membrana plasmatica, ha reso ardua l'interpretazione di molti dei risultati ottenuti riportati in questo lavoro di Tesi. In via preliminare si è reso necessario mettere a punto la maggior parte dei protocolli sperimentali atti ad ottenere il maggior grado di informazioni possibile in merito all'espressione differenziale delle glicoproteine di membrana. Questa fase propedeutica ma indispensabile ha impegnato gran parte del tempo richiesto per lo sviluppo di questo progetto di ricerca. L'approccio sperimentale ha previsto l'utilizzo di due modelli di linea epatocitaria. La linea CHANG, derivante da tessuto di fegato normale, mostra una notevole somiglianza con le cellule normali di fegato ed è citata spesso in letteratura come modello di epatocita in condizione fisiologica[2J. Le cellule HepG2 sono una linea cellulare stabilizzata in coltura derivata da cellule di un epatocarcinoma umano. In primo luogo è stato necessario mettere a punto un metodo di estrazione, confrontando e modificando alcune delle metodofogie già esistenti, al fine di sviluppare una strategia che permettesse di ottenere i risultati migliori in termini di purezza e arricchimento del campione proteico4 Più precisamente, tra queUe disponibili, due sono state messe a confronto e svituppate a seconda detre nostre esigenze . Analizzando i campioni di proteine estratte secondo la strategia differenziate proposta da MoUoyf31 dopo separazione etettroforeticai si è osservato un potenziale arricchimento in proteine dl membrana,. ma la contaminazione da parte della componente dtopfasmatica o proveniente dalle membrane degli organe Ui è. risultata essere ancora troppo a.fta .. Al metodo appena lndicato si è prefertto· queflo che prevede fa marcatura con un derivato della biotina e Ja successiva purificazione su colonna funzionalizzata con avidina[4l: si .è dimostrato, infatti, che attraverso questo metodo estrattivo si possono ottenere proteine che presentano un peso molecolare elevato e che per la maggior parte appartengono alla classe deHe glicoproteine, essendoci una buona corrispondenza tra n profiJo proteico rivelato in colorazione argentica e quello rivelato con un metodo di colorazione specifico per le glicoproteine (ProQ Emerald 300). Inoltre, tramite analisi di immunocitochimica, in fase pre-estrattiva, e di western blot si è verificato che tutte le proteine estratte sono biotinilate; infine, dai gel bidimensionali ottenuti sono evidenziabili le caratteristiche tipiche delle glicoproteine, che si presentano come trenini di spot costituiti delle diverse glicoforme esistenti, differenti tra loro sia per pi che per massa relativa. l'osservazione di questi risultati ci ha fatto ragionevolmente supporre che il metodo di estrazione e purificazione prescelto portasse, effettivamente, ad un arricchimento in proteine di membrana. Successivamente l'analisi comparativa eseguita sulle mappe prote;che relative alta linea· cellulare· CHANG ed HepG2 ha messo in luce numerose differenze, dì tipo proteìco, esistenti a livello della membrana cellulare, ma ha evidenziato anche aJcune somigJianze degne di nota. s; è sceJto dì cominciare l'identificazione delle proteine da quelle che risultavano comuni ad entrambe le linee cellulari e che, ad una prima osservazione dei gel, si presentavano come treni di spot associabili a diverse glicoforme di una glicoproteina. Le analisi di spettrometria di massa hanno fornito risultati interessanti·; anche se inaspettati.. Di particolare importanza è il ritrovamento di segnali attribuibili a proteine con funzioni di Chaperoninei4J .. Tra queste sono state identificate, costantemente:: GR.P78/Bip, HSP60, MTHSP75, HSP90, gp96/GRP94 per entrambe le linee cellulari., mentre POI è stata identificata nelle HepG2. Ed è stata proprio " l' inusualità " di .questo dato che ci ha stimolato a proseguire su una nuova linea interpretativa e a verificare fa possibilità che effettivamente queste proteine fossero presenti su una membrana plasmatica dei modelli cellulari studiati1 da un lato per vatidare le metodologie sviluppate, dall'altro per sfruttare il potenziale informativo fornito da un dato che, seppure anomalo, rimane comunque estremamente interessante. La particolarità di questo risultato risiede nella "anomala" localizzazione topografica di questa dasse di proteine che, normalmente, hanno una tipica.. ma non esclusiva.. localizzazione citoplasmatica o collocazione a livello di reticolo endoplasmatico. Per molte di queste chaperonine si è cercato di dare un interpretazione all'inconsueta localizzazione. In questo lavoro sono state analizzate in maniera più dettagllatate proteine che, tra quelle identificate, presentavano aspetti interessanti sia da.t punto di v.ista funzionale (HSP90 e GRP78) che glicobiologico (gp96). Caratteristica di· tutte- le- proteine- con localizzazione· a llveflo· def- RE, come- GRP94 e GRP78, è la presenza, nella porzione C-terminale, di una particolare sequenza amminoacidica KDEL {lys-Asp-Giu-Leu) che ne garantirebbe la· permanenza a- livello- del· REr51.. Nonostante questa peculiarità, esistono diversi riscontri sperimentali che dimostrano la localizzazione dì GRP78 e gp96 anche a livello della membrana plasmatìca dove sì. assocerebbero con altre proteine in alcuni casi non ancora identificate, per formare complessi di diverse dimensioni.. I meccanismi molecolari chiamati in causa per spiegare la "fuga" di proteine KDEL dal RE alla superficie della membrana plasmatica sono diversi. Ad esempio alcuni dati sembrerebbero attribuire questo evento ad una saturazione dei recettori per KDEL con conseguente perdita di alcune proteine che sarebbero in grado di migrare verso la membrana plasmatica. In altri casi il difetto nel sistema di ritenzione potrebbe essere dovuto alla presenza di .forme tronche delle proteine o difettive del dominio di riconoscimento. Un'altra ipotesi prevede che l'associazione delle proteine KDEL con proteine che sono destinate ad essere esportate verso la membrana plasmatica possa bloccare stericamente H dominio KDEL, impedendone l'interazione con il· rispettivo recettore e comportando la comigrazione verso la membrana plasmatica. Queste ossetvazioni, per quanto interessanti, rappresentano comunque solo interpretazioni finalistiche di un comportamento- che, alla fuce dei risultati riportati in questo favoro e di· quelli in letteratura, potrebbe essere molto più importante e di maggior significato biologico: non è un caso che tutti i dati più significativi e, al momento,. più. c.ompJeti. riguardano forme ceJJuJari associate a. trasformazioni neoplastiche .. Su HSP90, in letteratura, sono state fatte le considerazioni più interessanti. Dati recenti attestano la sua localizzazione sulla superficie cellulare in particolare sulla -membrana -dei -neuroni nelle fasi .precoci delt.o sviluppo de.l sistema nervoso: si ipotizza che questa chaperonina sia coinvolta nella migrazione cellulare[6J. Inoltre, è stato proposto che, sulla superficie cellulare, .HSP90 svolgesse un .ruolo attivo, in questo caso ln senso migratorio, partecipando a qualche meccanismo che· porta la cellula a· staccarsi dalla matrice extracellulare e dalle cellule vicine. Questo dipenderebbe dalla stretta relazione che esiste tra HSP90 e MMP2, enzima. coinvolto nel rimodellamento-della-matrice extracellulare[7l. Dal punto dì vista dì un approccio glicomico alla trasformazione neoplastìca e facendo salvo il concetto ormai accettato e dimostrato della stretta associazione tra. Ja trasformazione neo.pJastica e la: modificazione dei. pattem di glicosilazione appare piuttosto interessante l'osservazione secondo la quale alcune di queste proteine vengano attivate ad alti livelli in presenza di inibitori della glicosilazione. Le alterazioni della glicosilazione potrebbero essere, entro certi limiti, assimilate agli effetti prodotti dal trattamento con inibitori della glicosilazione. Non bisogna dimenticare, inoltre, che questi chaperone molecolari sono deputati al controllo e alla successiva eliminazione di proteine non correttamente ripiegate e/o glicosilate: una loro alterata funzionalità potrebbe risolversi in una mancata eliminazione o sequestramento detta proteina non funzionale con conseguente trasporto della stessa al compartimento di competenza. La presenza, quindi, di proteine non correttamente gticosilate sulla membrana plasmatica potrebbe essere· dovuta a meccanismi di· eliminazione alterati a livello del RE- e del· Golgi. Certamente questa è semplice considerazione ipotetica che, in ogni caso, potrebbe costituire una buona base di partenza per ulteriori e più a-pprofonditi. studi. In questo lavoro si è cercato non solo di ottenere gli strumenti per facilitare la comprensione del proteoma di membrana ma anche. porre. te basi per lo studio e ·la caratterizzazione degli N-glicani associati a questo compartimento. Quest'ultimo aspetto sperimentale è piuttosto rilevante: la possibilità di sviluppare una gUcoproteomica in senso stretto- si è sempre scontrata con .ta sostanziale incompatibilità dei metodi disponibili in letteratura, che comportavano o la perdita della componente saccaridica o n· sacrificio di quella proteicarsJ. Fintanto che l'approccio glicoproteomico era rivolto esclusivamente all'identi.ficazione de.l complessQ delle proteine espresse da una cellula; ciò· non· ha mai costituito un problema; quando· invece si rende necessaria un'analisi di un compartimento esclusivo come quello della membrana plasmatica, dove la componente glicoproteica è poco rappresentata, il discorso è diverso. In taf senso, f'ottimìzzazìone degfi approcci sperimentali di 2-DE che consentono la simultanea caratterizzazione della porzione oligosaccaridica e di quella proteica è auspicabile se non indispensabile... Proprio in quest'ottica risiede l'importanza dei risultati ottenuti in questo ·lavoro, ossia nell'aver messo a punto un efficiente metodo di degli cosilazione in gelr9J in associazione alla separazione 20-E, che permettesse di mantenere integra ed analizzabile sia la componente oligosaccaridica che quella proteica, per lo sviluppo di una completa glicomica della membrana plasmatica.
XVIII Ciclo
1974
Versione digitalizzata della tesi di dottorato cartacea.
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Franco, Catarina de Matos Ferraz. "Proteomics based approach to understand tissue regeneration." Doctoral thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica, 2011. http://hdl.handle.net/10362/14118.
Full textAbstract:
Dissertation presented to obtain the PhD degree in BiochemistryMost echinoderm species share an outstanding capacity for regeneration that is maintained throughout the adult animal lifespan. Regeneration allows these deuterostomes to recover from predation injuries or selfinduced arm autotomy, which are known to occur frequently in nature. Although echinoderms are extremely interesting in terms of their phylogenetic proximity to chordates, most areas of echinoderm research have been neglected in recent years. These wonderful animals quickly shifted from being the preferred animal models in the 19th-20th centuries of the pioneer regenerationists to scientific oblivion. Other species, for which the possibility of conducting genetic studies became available, are now favored. After the sequencing of an echinoderm species genome, the sea urchin Strongylocentrotus purpuratus in 2006, several scientific reports of interesting molecular studies were published.(...)
Fundação para a Ciência e a Tecnologia
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Chan, C. W. "A proteomic approach to studying oligodendrocyte signalling." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.597430.
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In this study, my aim was to investigate oligodendrocyte signalling using a non-candidate, unbiased, proteomic approach. First, in collaboration with my industrial sponsors Merck Sharpe and Dohme, the potential of using 2-dimensional differential in gel electrophoresis (2D DIGE) to study oligodendrocyte signalling was evaluated. Although differentially expressed proteins between the 2 proteomes under analysis could be identified, it was concluded that 2D DIGE would be an unsuitable method to study oligodendrocyte biology. An alternative approach was therefore pursued in which a specific subset of the proteome was analysed. Previously, α6β1 integrin has been shown to be involved in oligodendrocyte survival and morphological differentiation. A protocol was developed whereby protein complexes co-immunoprecipitated with α6β1 integrin could be identified by mass spectroscopy analysis. Multiple proteins were identified including β1 integrin, contactin, plectin and heterogeneous ribonuclear protein K (hnRNP K). Characterisation and function of contactin in oligodendrocyte α6β1 integrin signalling was then investigated. Contactin expression throughout oligodendrocyte in vitro differentiation was confirmed by both Western blotting and Immunocytochemistry. The interaction of contactin and α6β1 was also verified by traditional co-immunoprecipitation. siRNA knockdown of contactin had no effect on in vitro oligodendrocyte morphological differentiation. However, contactin siRNA knockdown did block oligodendrocyte enhanced survival of the α6β1 integrin substrate, laminin-2, in response to platelet derived growth factor (PDGF). Therefore, by taking a proteomic approach, I have identified a novel interaction between α6β1 integrin and contactin, and a potential role of contactin in α6β1 integrin mediated survival signalling.
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Paton, Louise Nancy. "Intermediate filament protein assembly : a proteomic approach." Thesis, University of Canterbury. Biological Science, 2005. http://hdl.handle.net/10092/7989.
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Intermediate filament proteins (IFPs) form the main structural elements of a wool fibre. The IFPs of wool are comprised of two families; the acidic type I family and the neutral-basic type II family. During follicle development, one type I and one type II IFP develop into an obligate heteropolymer, which, through a series of associations with other heteropolymers, forms an intermediate filament.
Two-dimensional polyacrylamide gel electrophoresis (20-PAGE) methods have been used to provide high-resolution separation of wool IFPs. Improvements in the method for maintaining reducing conditions and chaotrope constitution, combined with low % T polyacrylamide gels, allowed the high-resolution separation of the two keratin IFP families and their individual family members. The IFPs were separated to produce a clearly defined spot pattern, with numerous discrete minor spots not previously observed.
Genomic studies have reported that there are eight genes which produce eight abundant IFPs in wool. It was hypothesised that the large number of additional spots seen on a 20-PAGE gel was due to post-translational modification (PTM) of the protein. Several common PTMs of proteins produce charge heterogeneity, including phosphorylation and glycosylation. However, analysis of wool IFPs by 20- PAGE techniques and mass spectrometry revealed no evidence of phosphorylation or glycosylation modifications.
Conformational equilibria as a cause of protein charge heterogeneity has recently been reported. Investigations with both the type I and type II IFPs have shown that when single protein spots from a 20-PAGE separation are eluted, re-focused and re-electrophoresed, several spots are formed on both the acidic and basic side of the original spot. The cause of this heterogeneity is thought to be a conformational equilibrium between several different forms of the same protein in the rehydration solution used for the first dimension. This technique allowed the accurate assignment of IFPs resolved by 20-PAGE to protein families.
Fractionation methods to separate the IFPs and intermediate filament associated proteins (IFAPs) were successfully developed. Further fractionation into the type I and type II IFPs was achieved along with partial success at isolating individual spots. In vitro assembly experiments with the different IFP families gives important information about the strength of different protein pairings. To date there are no reproducible, efficient, in vitro assembly conditions for keratinised wool IFPs. A comprehensive study to investigate assembly conditions for keratinised wool IFPs was undertaken.
Assembly of filaments from IFPs was achieved after a partial digestion with chymotrypsin. Filaments were formed that varied in diameter from 10 to 40 nm, showing that higher ordered structures were being formed. This demonstrates that IFPs can be successfully assembled in vitro to form filamentous structures that may be able to be manipulated for biomaterial uses.
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Martins, Telma Patrícia Cova. "Study of PAH using a proteomic approach." Master's thesis, Universidade de Aveiro, 2013. http://hdl.handle.net/10773/11567.
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Mestrado em Bioquímica - Bioquímica ClínicaA hipertensão arterial pulmonar é uma doença com mau prognóstico que coloca em risco a vida dos pacientes, e cuja severidade e sintomas estão fortemente relacionados com a função do ventrículo direito. A caquexia cardíaca é uma complicação da insuficiência cardíaca crónica que resulta de um desequilíbrio entre as vias catabólica e anabólica. Este desequilíbrio é consequência de uma série de processos imunológicos, metabólicos e neurohormonais. Apesar de vários biomarcadores terem sido propostos no contexto da insuficiência cardíaca, a maioria é usada apenas para indicação de prognóstico. A aplicação da proteómica à análise de fluidos biológicos para estudo da insuficiência cardíaca e caquexia associada poderá ser útil na identificação de um painel complementar de biomarcadores com melhor desempenho e poder de diagnóstico. De modo a caracterizar o efeito da hipertensão arterial pulmonar nos perfis proteico e proteolítico da urina dos pacientes, recorreu-se a tecnologias como SDS-PAGE nanoLC-MS/MS e zimografia. Os dados da análise por nanoLC-MS/MS foram submetidos à base de dados UniProt, sendo depois analisados com base em ferramentas bioinformáticas. Foi identificado um total de 277 proteínas, sendo que 51 delas eram comuns a todos os indivíduos. Várias proteínas exclusivas foram identificadas tanto nos pacientes com hipertensão arterial pulmonar, como nos indivíduos saudáveis. A WNK4 foi a única proteína comum aos 2 pacientes. Em suma, os resultados evidenciam uma elevada actividade proteolítica na urina de pacientes com hipertensão arterial pulmonar, enfatizando a inflamação e caquexia associadas à doença, e permitiram também sugerir a WNK4 como um novo potencial biomarcador para o diagnóstico da hipertensão arterial pulmonar.
Pulmonary arterial hypertension is a life-threatening disease associated with poor prognosis, whose severity of symptoms and survival are strongly related with right ventricular function. Cardiac cachexia is a serious complication of chronic heart failure that results from an imbalance of catabolic and anabolic pathways. This imbalance is caused by a series of immunological, metabolic and neurohormonal processes. Although several biomarkers have been proposed in the context of heart failure, most of them present only potential prognostic value. The application of biofluids’ proteomics to the study of heart failure and related cachexia may help to identify a panel of complementary biomarkers with better performance and diagnostic power. In order to characterize the effect of pulmonary arterial hypertension on the urinary protein and proteolytic profiles, SDS-PAGE nanoLC-MS/MS and zymography were performed. Data from nanoLC-MS/MS was submitted to UniProt database and then were analyzed using bioinformatics tools. A total of 277 proteins were identified and 51 of them are common between all the individuals. Several exclusive proteins were identified in both pulmonary arterial hypertension patients and healthy subjects and WNK4 was the only common protein between pulmonary arterial hypertension patients. Taken together, data highlight a high proteolytic activity in the urine of pulmonary arterial hypertension patients, emphasizing the disease-related inflammation and cachexia and also allow to suggest WNK4 as a new potential biomarker for the diagnosis of pulmonary arterial hypertension.
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IALICICCO, Manuela. "Autochton landraces characterization: proteomic and genomic approach." Doctoral thesis, Università degli studi del Molise, 2012. http://hdl.handle.net/11695/66284.
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I risultati riportati nella tesi riguardano lo studio di caratterizzazione di due ecotipi autoctoni molisani di lenticchia (Lens culinaris M.) e l'utilizzo di un nuovo approccio per la genotipizzazione delle varietà locali.
In particolare il lavoro si è concentrato su tre argomenti principali: 1) l'uso della proteomica per studiare la variabilità genetica esistente tra diverse popolazioni di lenticchia, 2) la risposta di varietà autoctone di lenticchia allo stress salino e 3) l'uso del loop-mediated isothermal DNA amplification (LAMP) per l'amplificazione dei microsatelliti (SSR).
Per raggiungere il primo obiettivo, lo studio si è concentrato sull'analisi proteomica del seme maturo di lenticchia. L'utilizzo dell'elettroforesi bidimensionale ha permesso l'individuazione di 135 spot ben risolti, che rappresentano la prima mappa del proteoma del seme maturo di lenticchia. Inoltre l'analisi statistica multivariata, effettuata utilizzando i dati quantitativi degli spot risultati differenzialmente espressi, ha portato all'individuazione delle proteine che risultano indispensabili per la differenziazione delle diverse popolazioni di lenticchia analizzate, come riportato in Scippa et al., 2010. La diversità delle due varietà locali di lenticchia (Capracotta e Conca Casale) del Molise è stata studiata utilizzando un approccio integrato costituito da analisi a livello morfologico, genetico e proteomico, come dimostrano i risultati pubblicati in Viscosi et al., 2010. Inoltre, un ulteriore studio è stato eseguito al fine di approfondire le informazioni sulla caratterizzazione proteomica delle lenticchie di Capracotta e Conca Casale. I dati ottenuti sono stati elaborati mediante un'analisi statistica uni- e multivariata mediante cui sono state individuate le proteine, risultanti principalmente coinvolte nella risposta agli stress abiotici e biotici, che caratterizzano i due ecotipi autoctoni.
Successivamente, il lavoro ha studiato a livello fisiologico e biochimico, la risposta delle due varietà molisane di lenticchia e di cinque varietà commerciali allo stress salino. In particolare è stato analizzato come lo stress salino influenza la germinazione e causa modificazioni nell'espressione di alcune proteine. Inoltre, l'analisi statistica multivariata è stata effettuata per identificare le proteine importanti coinvolte nella risposta a questo tipo di stress.
Infine la tesi di dottorato si è focalizzata sull'individuazione di un nuovo approccio molecolare da utilizzare ai fini della genotipizzazione delle varietà locali. Il lavoro è stato svolto incorporando un microsatellite (SSR) del riso all'interno di un LAMP assay e ha dimostrato che i risultati sono coerenti con l'analisi eseguita mediate amplificazione del microsatellite attraverso la tradizionale PCR. Inoltre, il LAMP assay è caratterizzato da un' elevata sensibilità, dato che risulta in grado di amplificare il DNA target anche quando questo è presente in poche copie.
Il lavoro riportato nella tesi di dottorato rappresenta una novità nel campo del proteoma del seme di lenticchia e dimostra che la proteomica è un potente strumento per l'analisi della biodiversità in ecotipi appartenenti ad una stessa specie. Inoltre, il lavoro conferma che gli studi di proteomica possono notevolmente contribuire a comprendere i complessi meccanismi coinvolti nella risposta della pianta allo stress salino. L'originalità della tesi di dottorato è rappresentata anche dal nuovo uso del metodo LAMP per amplificare SSR.The results reported in the thesis are related with the study of characterization of two autochthonous lentil (Lens culinaris M.) landraces of Molise region and of a new approach for genotyping of local varieties. In particular the work has been focused on three major issues: 1)use of proteomics to investigate natural variation within and between lentil populations, 2) response of lentil to salt stress and 3) use of the loop-mediated isothermal DNA amplification (LAMP) method to amplify SSR. To accomplish the first objective investigations have been focused on the proteomic analysis of mature seed of lentil. The use of 2DE couple to the MS/MS allowed the identification of 135 well resolved spots which represent the first lentil seed proteome reference map. In addition the multivariate statistical analyses carried out on spots, resulted differentially expressed between different lentil populations, led to detection of the proteins which were essential for population discrimination, as shown in the paper Scippa et al., 2010. The diversity of two lentil landraces (Capracotta and Conca Casale) from Molise was studied using a combination of morphological, genetic and proteomic analyses, as shown by results published in the paper by Viscosi et al., 2010.Moreover, a further study has been carried out to deepen the knowledge about proteomic characterization of Capracotta and Conca Casale. The data obtained were elaborated by uni-and multivariate statistical analysis to identify the proteins that characterize the lentil ecotypes, mainly involved in abiotic and biotic stress responses. On the base of aforementioned results, the PhD project proceeded in analyzing the physiological and proteomic response of two lentil landraces from Molise and five commercial varieties to salt stress. In particular it has been investigated how salt stress affected seed germination and caused changes in expression of proteins. Furthermore, the multivariate statistical analysis was performed using quantitative data of spots in order to identify important proteins involved in saline stress response. The third aim of the PhD thesis was the detection of a new molecular approach for genotyping of local varieties. Work has been carried out by incorporation rice simple sequence repeat (SSR) motif within a LAMP assay. It has been demonstrated that results were consistent with analysis performed by PCR. In addition, LAMP assay was characterized by high sensitive being able to amplify from near single copy of target. The work reported in the PhD thesis represents a novelty in the field of proteome of lentil seed and it surely shows that proteomics is a powerful tool for analysis of biodiversity in ecotypes of a single plant species. Furthermore, the work confirms that proteomics studies can significantly contribute to understand the complex mechanisms involved in the plant response to salt stress. The originality of the PhD thesis is also represented by novel use of the loop-mediated isothermal DNA amplification method to amplify SSR.
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Prokopi, Marianna. "Redefining endothelial progenitor cells using a proteomics approach." Thesis, King's College London (University of London), 2012. https://kclpure.kcl.ac.uk/portal/en/theses/redefining-endothelial-progenitor-cells-using-a-proteomics-approach(abf89161-9cc5-4363-8fb2-9ed175648313).html.
Full textAbstract:
The concept of endothelial progenitor cells (EPCs) has attracted considerable interest in cardiovascular research, but despite a decade of research there are still no specific markers for EPCs and results from clinical trials remain controversial. To identify membrane proteins, which could serve as potential markers for EPCs, an alternative proteomic method was adopted to obtain sufficient membrane material for proteomic analysis. Microparticles (MPs), the intact vesicles formed from the plasma membrane, were harvested from the conditioned medium of EPC cultures and their protein composition was analysed by liquid chromatography-tandem mass spectrometry. Surprisingly, the platelet-specific integrin alpha lib emerged as the most abundant integrin in EPC cultures. Subsequent experiments confirmed that the conventional methods for isolating peripheral blood-derived mononuclear cells (PBMNCs) lead to a substantial contamination with platelets. Notably, platelets readily disintegrate into platelet MPs when activated during PBMNCs isolation conditions. These platelet MPs are taken up by the PBMNCs, which acquire "endothelial" characteristics (CD31, von Willebrand factor [VWF], lectin-binding), and angiogenic properties. In a large population-based study (n =526), platelets emerged as a positive predictor for the number of colony-forming units and early outgrowth EPCs. This study provides the first evidence that the cell type consistent with current definitions of an EPC phenotype may arise from an uptake of platelet MPs by mononuclear cells resulting in a gross misinterpretation of their cellular progeny. In addition, the release of platelet MPs at sites of vascular injury may play a role in orchestrating tissue repair and contribute to the activation of an angiogenic programme in monocytes by inducing the expression of non-coding regulatory RNA, known as microRNAs, which act as translational repressers. The uptake of platelet MPs by mononuclear cells induced the release of the CXCL7 chemokine which in turn guided a de novo induction of miR-885-5p in mononuclear cells. The increased expression of miR-885-5p resulted in the targeted reduction of the actin-bundling protein LCP-1, facilitating the adhesive and migratory ability of mononuclear cells. These findings demonstrate the advantage of using an unbiased proteomic approach to assess cellular phenotypes and advise caution in attributing the benefits inclinical trials using unselected bone marrow mononuclear cells (BMCs) to stem cell-mediated repair.
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SERRAO, SIMONE. "Potential Salivary Biomarkers In Mastocytosis: A Proteomics Approach." Doctoral thesis, Università degli Studi di Cagliari, 2020. http://hdl.handle.net/11584/284376.
Full textAbstract:
Mastocytosis is a myeloproliferative neoplasm characterized by infiltration of clonally derived mast cells in different tissues. According to mast cells localization, it is possible to discriminate cutaneous mastocytosis (CM) from systemic mastocytosis (SM), the latter involving at least an extracutaneous organ, like bone marrow, liver, spleen and gastrointestinal tract. Some of the SM patient can develop also cutaneous lesions (SM+C). Oral cavity is commonly involved in the symptomatology. Disease classification is often tricky. In the first part of this thesis, in order to highlight possible qualitative/quantitative modifications of the salivary proteome associated to the different forms of the disease, we investigated salivary samples collected from 6 CM, 35 SM patients, among which 8 with only systemic symptoms (SM-C) and 27 with both systemic and cutaneous symptoms (SM+C), and 48 healthy controls by a top-down proteomic approach. Low-resolution HPLC-ESI-MS analysis of the acid soluble fractions of saliva highlighted different proteomic profiles in the three patients’ groups, showing that the salivary samples of the patients were characterized by a down-regulation of peptides and proteins involved in the homeostasis and defense of the oral cavity, and in the innate immunity and in inflammation not only in the oral cavity but at systemic level, such as aPRPs, statherin, histatins and cystatins. Only two proteins with regulatory roles in the innate immunity and inflammation, S100A8 and antileukoproteinase, resulted up-regulated in patients differently to all the other salivary proteins analyzed, suggesting the establishment of a response by the organism to the injuries caused by the disease. Interestingly, some differences have been found among the patients in the concentration of α-defensins 1, thymosin β-4, and the truncated forms of cystatin D-R26 variant, and some truncated forms of P-B and statherin. Correlation between the protein/peptide levels and tryptase concentration evidenced that acidic PRPs, statherin and P-B fragments, and cystatin D-R26 des1-5 correlated positively just in SM-C group, while thymosin β-4 correlated negatively.
Since the interesting data on cystatin D, in the second part of the thesis I focused on the characterization of the salivary protein complex aggregating to the cystatin D-C26 variant (named by us SIC-D). Indeed, the C-26 variant is usually undetectable in acid soluble fraction of saliva but measurable in whole saliva. Pools of whole saliva from 4 CM, 3 SM-C, 14 SM+C, and 20 sex/age matched healthy controls, were submitted to immunoprecipitation with cystatin D-C26 antibody followed by SDS-PAGE/western-blot under reducing and non-reducing conditions. Since the low volume of CM samples, the tryptic digestion, and the nano-HPLC-high-resolution-MS/MS analysis were performed only in SM-C, SM+C and control samples. The quantitative comparison was performed with Proteome Discoverer 2.2 software. SIC-D included 44 proteins, among which IgA, IgG, PIgR, annexins, α-defensin 1/2, S100A8, carbonic anhydrase 6, prolactin-inducible protein, lysozyme C and dermicidin. Several qualitative/quantitative differences were highlighted with respect to controls and between the two patient groups. The most relevant were: all the patients exhibited lower levels of IgA, PIgR, DMBT-1 and S100A8 than controls, but higher levels of IgG, α-defensins 1/2 and carbonic anhydrase 6. The highest level of cystatin D-C26 was found in SM+C patients, which were different from SM-C for annexin A2. Both SM-C and SM+C showed the presence of antileukoproteinase and S100A14.
The results on the acid-soluble fraction of saliva and the preliminary results on the SIC-D complex are promising in order to find candidate markers able to discriminate the different forms of mastocytosis.
Books on the topic "Approcci proteomici"
1
Mauro, Fasano, ed. The proteomic approach in neurodegenerative disease research. Trivandrum, Kerala, India: Research Signpost, 2007.
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2
Mauro, Fasano, ed. The proteomic approach in neurodegenerative disease research. Trivandrum, Kerala, India: Research Signpost, 2007.
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3
Gil, Alterovitz, Benson Roseann, and Ramoni Marco F, eds. Automation in proteomics and genomics: An engineering case-based approach. Chichester, West Sussex, U.K: John Wiley, 2008.
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4
Ye, Shui Qing. Bioinformatics: A practical approach. Boca Raton: Chapman & Hall/CRC, 2008.
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5
Majid, Sabhiya, Muneeb U. Rehman, and Shafat Ali. Proteomics: A Promising Approach for Cancer Research. Elsevier Science & Technology Books, 2023.
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Majid, Sabhiya, Muneeb U. Rehman, and Shafat Ali. Proteomics: A Promising Approach for Cancer Research. Elsevier Science & Technology, 2023.
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Infrared Proteomics, Pathology and Guided Surgery: A Practical Approach. Wiley & Sons, Limited, John, 2004.
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Ramoni, Marco, Gil Alterovitz, and RoseAnn Benson. Automation in Proteomics and Genomics: An Engineering Case-Based Approach. Wiley & Sons, Limited, John, 2009.
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Ramoni, Marco, Gil Alterovitz, and Roseann M. Benson. Automation in Proteomics and Genomics: An Engineering Case-Based Approach. Wiley & Sons, Incorporated, John, 2009.
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(Editor), Gil Alterovitz, and Marco F. Ramoni (Editor), eds. Systems Bioinformatics: An Engineering Case-Based Approach. Artech House Publishers, 2007.
Find full textBook chapters on the topic "Approcci proteomici"
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Francois, Patrice, Alexander Scherl, Denis Hochstrasser, and Jacques Schrenzel. "Proteomic Approach to Investigate MRSA." In Methods in Molecular Biology, 179–99. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-468-1_14.
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Zingde, Surekha M. "Proteomics for Cancer: Approaches and Challenges." In Unravelling Cancer Signaling Pathways: A Multidisciplinary Approach, 343–68. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-32-9816-3_14.
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Kaur, Amanpreet, Anil Kumar, and M. Sudhakara Reddy. "Plant–Pathogen Interactions: A Proteomic Approach." In Understanding Host-Microbiome Interactions - An Omics Approach, 207–25. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-5050-3_13.
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Bhardwaj, Swati, Venkateshwarlu Yellaswamy Gudur, and Amit Acharyya. "An Accelerated Computational Approach in Proteomics." In Series in BioEngineering, 389–432. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-9097-5_16.
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Wienkoop, Stefanie, and Christiana Staudinger. "Proteomics, Quantification-Unbiased and Target Approach." In Encyclopedia of Systems Biology, 1799–800. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_1151.
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Rao, P. S. Srinivasa, Yuen Peng Tan, Jun Zheng, and Ka Yin Leung. "UnravelingEdwardsiella tardaPathogenesis Using the Proteomics Approach." In Methods of Biochemical Analysis, 237–44. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2005. http://dx.doi.org/10.1002/0471973165.ch14.
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Kommu, Sashi S., and Emanuel Petricoin. "The Proteomic Approach to Prostate Cancer." In Prostate Cancer: A Comprehensive Perspective, 157–67. London: Springer London, 2012. http://dx.doi.org/10.1007/978-1-4471-2864-9_13.
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Bespyatykh, Julia, Georgij Arapidi, and Egor Shitikov. "Proteogenomic Approach for Mycobacterium tuberculosis Investigation." In Shotgun Proteomics, 191–201. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1178-4_12.
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Leszczynski, Dariusz. "Proteomics Approach in Mobile Phone Radiation Research." In Cancer Risk Evaluation, 265–73. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2011. http://dx.doi.org/10.1002/9783527634613.ch17.
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Rout, Gyana Ranjan, and Sunil Kumar Senapati. "Stress Tolerance in Plants: A Proteomics Approach." In Molecular Stress Physiology of Plants, 359–86. India: Springer India, 2013. http://dx.doi.org/10.1007/978-81-322-0807-5_15.
Full textConference papers on the topic "Approcci proteomici"
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Selvam, Anjan Panneer, and Shalini Prasad. "Single Molecule Analysis Tool (SMAT) for Multiplexed Label-Free Assessment of Rare Cell Populations." In ASME 2014 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/imece2014-40225.
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A nanowell sensor for single molecular proteomic analysis of lung cancer has been designed. The nanowell sensor is an electrochemical immunoassay and comprises of a heterogenous nanoporous arrays integrated on to a gold microelectronic platform. The sensor operates on the principle of electrochemical impedance spectroscopy (EIS). Our approach to classification of lung cancer is based on screening for levels of expression of specific proteomic biomarkers associated with lung cancer stem cells. Proteomic activity for two lung cancer cell lines for two specific markers (ALDH1A1 and ALDH1A3) was quantified. Test samples prepared by synthetically spiking human pooled serum were tested and quantified for cancer stem cell marker activity. The lowest proteomic activity measured with (a) ALDH1A3 was 0.01 ng/mL and (b) ALDH1A1 was 1 ng/mL correlating to the detection of unit stem cell count.
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Hashim, O. "Proteomics Approach To Cancer Studies." In 2nd International University of Malaya Research Imaging Symposium (UMRIS) 2005: Fundamentals of Molecular Imaging. Kuala Lumpur, Malaysia: Department of Biomedical Imaging, University of Malaya, 2005. http://dx.doi.org/10.2349/biij.1.1.e7-41.
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Baroni, D., P. P. Cardo, and P. Arrigo. "Backward proteomic approach for microrna's target recognition." In 2011 6th International Symposium on Health Informatics and Bioinformatics (HIBIT). IEEE, 2011. http://dx.doi.org/10.1109/hibit.2011.6450803.
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Nolasco Jauregui, Oralia. "A Machine Learning approach to Neural Information Decoding of Spike Train Distances in the Peripheral Nervous System." In LatinX in AI at Neural Information Processing Systems Conference 2019. Journal of LatinX in AI Research, 2019. http://dx.doi.org/10.52591/lxai2019120817.
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Decoding the neural signal has proved to be an elusive goal. We explore the use of sequence analysis algorithms to identify repeating patterns of spike train distances and found that they could be associated to the stimulus in the rat peripheral system with good results. The use of these algorithms is very common in genomics and proteomics for genetic sequence analysis but rarely applied to neural systems analysis. We are convinced that with proper tuning they could yield useful results.
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Bekker, Niek, Alienke Van Pijkeren, Justina Clarinda Wolters, Alejandro Sánchez Brotons, Victor Guryev, Rainer Bischoff, Wynand Alkema, et al. "Proteomics approach to identify COPD-related changes in pulmonary fibroblasts." In ERS International Congress 2021 abstracts. European Respiratory Society, 2021. http://dx.doi.org/10.1183/13993003.congress-2021.oa1215.
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Frolov, A. A., T. E. Bilova, K. Ealing, A. Kim, A. A. Tsarev, T. V. Mamontova, E. M. Lukasheva, et al. "Age-related changes in legume root nodules: proteomic an approach." In IX Congress of society physiologists of plants of Russia "Plant physiology is the basis for creating plants of the future". Kazan University Press, 2019. http://dx.doi.org/10.26907/978-5-00130-204-9-2019-453.
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Katam, Ramesh, Hemanth KN Vasanthaiah, and Sheikh M. Basha. "Proteomic Approach to Screen Peanut Genotypes with Enhanced Nutritional Qualities." In 2007 Frontiers in the Convergence of Bioscience and Information Technologies. IEEE, 2007. http://dx.doi.org/10.1109/fbit.2007.94.
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Bocu, Razvan, and Sabin Tabirca. "Proteomic Data Analysis Optimization Using a Parallel MPI C Approach." In 2010 International Conference on Biosciences. IEEE, 2010. http://dx.doi.org/10.1109/biosciencesworld.2010.11.
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Wende, K., A. Kramer, K. D. Weltmann, and K. Masur. "Deciphering non thermal plasma - human cell interaction using the proteomics approach." In 2012 IEEE 39th International Conference on Plasma Sciences (ICOPS). IEEE, 2012. http://dx.doi.org/10.1109/plasma.2012.6383861.
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Grossi, Gerarda. "Integrated transcriptomic and proteomic approach to identify the majorToxoneuron nigricepsvenom proteins." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.112623.
Full textReports on the topic "Approcci proteomici"
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Hayes, Ronald L. Biochemical Markers of Brain Injury: An Integrated Proteomics-Based Approach. Fort Belvoir, VA: Defense Technical Information Center, February 2005. http://dx.doi.org/10.21236/ada437666.
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Hayes, Ronald L. Biochemical Markers of Brain Injury: An Integrated Proteomics Based Approach. Fort Belvoir, VA: Defense Technical Information Center, February 2004. http://dx.doi.org/10.21236/ada425658.
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Hayes, Ronald L. Biochemical Markers of Brain Injury: An Integrated Proteomics-Based Approach. Fort Belvoir, VA: Defense Technical Information Center, December 2011. http://dx.doi.org/10.21236/ada561092.
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Hayes, Ronald L. Biochemical Markers of Brain Injury: An Integrated Proteomics-Based Approach. Fort Belvoir, VA: Defense Technical Information Center, February 2007. http://dx.doi.org/10.21236/ada474912.
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Songyang, Zhou. A Proteomic Approach to Identify Phosphorylation-Dependent Targets of BRCT Domains. Fort Belvoir, VA: Defense Technical Information Center, March 2008. http://dx.doi.org/10.21236/ada487327.
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Songyang, Zhou. A Proteomic Approach to Identify Phosphorylation-Dependent Targets of BRCT Domains. Fort Belvoir, VA: Defense Technical Information Center, March 2006. http://dx.doi.org/10.21236/ada458980.
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Tyner, Angela L. A Small Scale Proteomics Approach for Identifying Proteins Regulated by the Breast Tumor Kinase BRK Signal Transduction Pathway. Fort Belvoir, VA: Defense Technical Information Center, June 2002. http://dx.doi.org/10.21236/ada406106.
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Avni, Adi, and Gitta L. Coaker. Proteomic investigation of a tomato receptor like protein recognizing fungal pathogens. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600030.bard.
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Maximizing food production with minimal negative effects on the environment remains a long-term challenge for sustainable food production. Microbial pathogens cause devastating diseases, minimizing crop losses by controlling plant diseases can contribute significantly to this goal. All plants possess an innate immune system that is activated after recognition of microbial-derived molecules. The fungal protein Eix induces defense responses in tomato and tobacco. Plants recognize Eix through a leucine-rich-repeat receptor- like-protein (LRR-RLP) termed LeEix. Despite the knowledge obtained from studies on tomato, relatively little is known about signaling initiated by RLP-type immune receptors. The focus of this grant proposal is to generate a foundational understanding of how the tomato xylanase receptor LeEix2 signals to confer defense responses. LeEix2 recognition results in pattern triggered immunity (PTI). The grant has two main aims: (1) Isolate the LeEix2 protein complex in an active and resting state; (2) Examine the biological function of the identified proteins in relation to LeEix2 signaling upon perception of the xylanase elicitor Eix. We used two separate approaches to isolate receptor interacting proteins. Transgenic tomato plants expressing LeEix2 fused to the GFP tag were used to identify complex components at a resting and activated state. LeEix2 complexes were purified by mass spectrometry and associated proteins identified by mass spectrometry. We identified novel proteins that interact with LeEix receptor by proteomics analysis. We identified two dynamin related proteins (DRPs), a coiled coil – nucleotide binding site leucine rich repeat (SlNRC4a) protein. In the second approach we used the split ubiquitin yeast two hybrid (Y2H) screen system to identified receptor-like protein kinase At5g24010-like (SlRLK-like) (Solyc01g094920.2.1) as an interactor of LeEIX2. We examined the role of SlNRC4a in plant immunity. Co-immunoprecipitation demonstrates that SlNRC4a is able to associate with different PRRs. Physiological assays with specific elicitors revealed that SlNRC4a generally alters PRR-mediated responses. SlNRC4a overexpression enhances defense responses while silencing SlNRC4 reduces plant immunity. We propose that SlNRC4a acts as a non-canonical positive regulator of immunity mediated by diverse PRRs. Thus, SlNRC4a could link both intracellular and extracellular immune perception. SlDRP2A localizes at the plasma membrane. Overexpression of SlDRP2A increases the sub-population of LeEIX2 inVHAa1 endosomes, and enhances LeEIX2- and FLS2-mediated defense. The effect of SlDRP2A on induction of plant immunity highlights the importance of endomembrane components and endocytosis in signal propagation during plant immune . The interaction of LeEIX2 with SlRLK-like was verified using co- immunoprecipitation and a bimolecular fluorescence complementation assay. The defence responses induced by EIX were markedly reduced when SlRLK-like was over-expressed, and mutation of slrlk-likeusing CRISPR/Cas9 increased EIX- induced ethylene production and SlACSgene expression in tomato. Co-expression of SlRLK-like with different RLPs and RLKs led to their degradation, apparently through an endoplasmic reticulum-associated degradation process. We provided new knowledge and expertise relevant to expression of specific be exploited to enhance immunity in crops enabling the development of novel environmentally friendly disease control strategies.
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Ghanim, Murad, Joe Cicero, Judith K. Brown, and Henryk Czosnek. Dissection of Whitefly-geminivirus Interactions at the Transcriptomic, Proteomic and Cellular Levels. United States Department of Agriculture, February 2010. http://dx.doi.org/10.32747/2010.7592654.bard.
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Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that interfere with whitefly-mediated begomovirus transmission. The project objectives were to: 1) Perform gene expression analyses using microarrays to study the response of whiteflies (B, Q and A biotypes) to the acquisition of begomoviruses (Tomato yellow leaf curl (TYLCV) and Squash leaf curl (SLCV). 2) Construct a whitefly proteome from whole whiteflies and dissected organs after begomovirus acquisition. 3) Validate gene expression by q-RTPCR and sub-cellular localization of candidate ESTs identified in microarray and proteomic analyses. 4) Verify functionality of candidate ESTs using an RNAi approach, and to link these datasets to overall functional whitefly anatomical studies. During the first and second years biological experiments with TYLCV and SLCV acquisition and transmission were completed to verify the suitable parameters for sample collection for microarray experiments. The parameters were generally found to be similar to previously published results by our groups and others. Samples from whole whiteflies and midguts of the B, A and Q biotypes that acquired TYLCV and SLCV were collected in both the US and Israel and hybridized to B. tabaci microarray. The data we analyzed, candidate genes that respond to both viruses in the three tested biotypes were identified and their expression that included quantitative real-time PCR and co-localization was verified for HSP70 by the Israeli group. In addition, experiments were undertaken to employ in situ hybridization to localize several candidate genes (in progress) using an oligonucleotide probe to the primary endosymbiont as a positive control. A proteome and corresponding transcriptome to enable more effective protein identification of adult whiteflies was constructed by the US group. Further validation of the transmission route of begomoviruses, mainly SLCV and the involvement of the digestive and salivary systems was investigated (Cicero and Brown). Due to time and budget constraints the RNAi-mediated silencing objective to verify gene function was not accomplished as anticipated. HSP70, a strong candidate protein that showed over-expression after TYLCV and SLCV acquisition and retention by B. tabaci, and co-localization with TYLCV in the midgut, was further studies. Besides this protein, our joint research resulted in the identification of many intriguing candidate genes and proteins that will be followed up by additional experiments during our future research. To identify these proteins it was necessary to increase the number and breadth of whitefly ESTs substantially and so whitefly cDNAs from various libraries made during the project were sequenced (Sanger, 454). As a result, the proteome annotation (ID) was far more successful than in the initial attempt to identify proteins using Uniprot or translated insect ESTs from public databases. The extent of homology shared by insects in different orders was surprisingly low, underscoring the imperative need for genome and transcriptome sequencing of homopteran insects. Having increased the number of EST from the original usable 5500 generated several years ago to >600,000 (this project+NCBI data mining), we have identified about one fifth of the whitefly proteome using these new resources. Also we have created a database that links all identified whitefly proteins to the PAVEdb-ESTs in the database, resulting in a useful dataset to which additional ESTS will be added. We are optimistic about the prospect of linking the proteome ID results to the transcriptome database to enable our own and other labs the opportunity to functionally annotate not only genes and proteins involved in our area of interest (whitefly mediated transmission) but for the plethora of other functionalities that will emerge from mining and functionally annotating other key genes and gene families in whitefly metabolism, development, among others. This joint grant has resulted in the identification of numerous candidate proteins involved in begomovirus transmission by B. tabaci. A next major step will be to capitalize on validated genes/proteins to develop approaches to interfere with the virus transmission.
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Chen, Xiaole, Peng Wang, Yunquan Luo, Yi-Yu Lu, Wenjun Zhou, Mengdie Yang, Jian Chen, Zhi-Qiang Meng, and Shi-Bing Su. Therapeutic Efficacy Evaluation and Underlying Mechanisms Prediction of Jianpi Liqi Decoction for Hepatocellular Carcinoma. Science Repository, September 2021. http://dx.doi.org/10.31487/j.jso.2021.02.04.sup.
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Objective: The aim of this study was to assess the therapeutic effects of Jianpi Liqi decoction (JPLQD) in hepatocellular carcinoma (HCC) and explore its underlying mechanisms. Methods: The characteristics and outcomes of HCC patients with intermediate stage B who underwent sequential conventional transcatheter arterial chemoembolization (cTACE) and radiofrequency ablation (RFA) only or in conjunction with JPLQD were analysed retrospectively. The plasma proteins were screened using label-free quantitative proteomics analysis. The effective mechanisms of JPLQD were predicted through network pharmacology approach and partially verified by ELISA. Results: Clinical research demonstrated that the Karnofsky Performance Status (KPS), traditional Chinese medicine (TCM) syndrome scores, neutropenia and bilirubin, median progression-free survival (PFS), and median overall survival (OS) in HCC patients treated with JPLQD were superior to those in patients not treated with JPLQD (all P<0.05). The analysis of network pharmacology, combined with proteomics, suggested that 52 compounds targeted 80 potential targets, which were involved in the regulation of multiple signaling pathways, especially affecting the apoptosis-related pathways including TNF, p53, PI3K-AKT, and MAPK. Plasma IGFBP3 and CA2 were significantly up-regulated in HCC patients with sequential cTACE and RFA therapy treated with JPLQD than those in patients not treated with JPLQD (P<0.001). The AUC of the IGFBP3 and CA2 panel, estimated using ROC analysis for JPLQD efficacy evaluation, was 0.867. Conclusion: These data suggested that JPLQD improves the quality of life, prolongs the overall survival, protects liver function in HCC patients, and exhibits an anticancer activity against HCC. IGFBP3 and CA2 panels may be potential therapeutic targets and indicators in the efficacy evaluation for JPLQD treatment, and the effective mechanisms involved in the regulation of multiple signaling pathways, possibly affected the regulation of apoptosis.