Made available in DSpace on 2015-07-22T20:50:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-05-27 / Objetivo: Investigar a imuno-expressão do c-kit e sua correlação com o prognóstico em pacientes portadores de Osteossarcoma e o efeito do Mesilato de Imatinibe (STI571) na proliferação e invasão de linhagens de células humanas de osteossarcoma. Material e Método Estudo retrospectivo com realização de imunohistoquímica dos blocos de parafina de 52 pacientes com osteossarcoma de extremidades de alto grau, tratados no Instituto de Oncologia Pediátrica e diagnosticados no Departamento de Patologia da UNIFESP. Somente espécimes pré-quimioterapia foram analisados. Imunoexpressão forte e citoplasmática foram considerados como positivos. A linhagem cellular MG 63 foi incubada e o efeito inibitório do STI571 na proliferação e invasão dessas células tumorais in vitro foi estudada. Resultados: 24 casos (46,15%) expressaram o c-kit, sendo que esses tumores positivos tiveram pior resposta à qumioterapia pré-operatória. Não foi encontrada correlação entre os casos c-kit positivos e sobrevida global e livre de doença. STI571 inibiu a proliferação de células de osteossarcoma in vitro, em baixas doses e a invasão dessas células, em altas doses. Conclusões: Osteossarcomas expressam c-kit e esses tumores c-kit positivos são maus respondedores (têm menos necrose) à quimioterapia pré-operatória. O Mesilato de Imatinibe inibe a proliferação de células de osteossarcomas que expressam o c-kit, mas não inibem a invasão. Esses achados permitem sugerir que o STI571 pode ser uma nova estratégia no tratamento dos pacientes portadores de osteossarcomas. / Purpose: To investigate the immunoexpression and its prognostic relevance of KIT in patients with osteosarcomas and the effect of Imatinib mesylate (STI571) on proliferation and invasion of human cell osteosarcoma line. Material and Methods: A retrospective immunohistochemical study was performed on archival formalin fixed paraffin-embedded tissue obtained from Department of Pathology of Federal University of São Paulo of 52 high-grade patients with primary osteosarcomas of extremities treated at the Instituto de Oncologia Pediátrica. Only pre-chemotherapy specimens were analysed. Strong cytoplasmic and membranous staining cases were taken as positive. The human cell line MG 63 was incubated and inhibitory effect of STI571 on cell proliferation and invasion was studied. Results: Twenty four cases (46,15%) expressed c-kit and tumours ckit positive had lower necrosis pos chemotherapy. No correlation was found between ckit expression and overall and disease free survival. STI571 inhibited the rates of cell growth of osteosaroma cells in low doses and invasion in high doses Conclusions: Tumours c-kit positives had worse response to chemotherapy and STI571 plays a role in blocking or slowing the rate of growth of osteosarcoma cells expressing ckit, but not the invasive capacity of these neoplastic cells. These data suggested that Imatinib Mesylate could be a therapeutic target of strategies against Osteosarcoma that express c-kit. / TEDE / BV UNIFESP: Teses e dissertações

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Histotripsy is a non-thermal, non-invasive focused ultrasound therapy using controlled acoustic cavitation to mechanically disintegrate tissue into an acellular homogenate. Histotripsy applies microsecond-length, high pressure (> 10 MPa) pulses to initiate the rapid expansion and collapse of nuclei in a millimeter-scale focal region, applying large stresses and strains to targeted tissues. The cavitation "bubble cloud" generated during histotripsy treatment can be visualized in real time on ultrasound imaging, assisting with treatment guidance and monitoring. Past studies have demonstrated histotripsy's potential for a variety of applications, but histotripsy has not yet been investigated for superficial musculoskeletal tumor ablation. Additionally, preliminary investigations using histotripsy to ablate brain tumors are underway, but require advanced histotripsy devices capable of overcoming attenuation of the therapeutic ultrasound signal by the skull and rely on MRI for real-time guidance. As a result, open questions remain regarding ultrasound-guided histotripsy for brain tumors. Early evidence also suggests that histotripsy ablation may induce immunogenic changes in the tumor microenvironment. Continued research is needed to explain and corroborate these findings under conditions more immunologically representative of human cancers, such as in large animal models with spontaneous tumors. This dissertation investigates the safety and feasibility of using ultrasound-guided histotripsy to ablate superficial soft tissue sarcomas (STS), osteosarcomas (OS), and brain tumors and considers the immunological impacts of histotripsy treatment for STS and OS. The research described herein (1) investigates the ability of histotripsy to treat superficial STS tumors in companion animals with spontaneous tumors, (2) investigates the feasibility of treating bone tumors with histotripsy through a series of ex vivo and in vivo studies, and (3) applies histotripsy for the minimally invasive treatment of superficial brain tumors. The completion of this dissertation will provide significant insight into the ability of ultrasound-guided histotripsy to treat novel tumor types (i.e., STS, OS, and brain tumors) and the potential role of histotripsy in veterinary medicine. Future work will build upon the studies detailed in this dissertation to optimize ultrasound-guided histotripsy for the treatment of complete STS, OS, and brain tumors in veterinary and human patients. / Doctor of Philosophy / Histotripsy is a non-invasive focused ultrasound therapy that mechanically breaks down targeted tissues through acoustic cavitation. Histotripsy is currently being developed for a number of clinical applications, including tumor ablation, but its potential for treating many cancer types remains unknown. Histotripsy uses very short, high pressure ultrasound pulses to initiate the nucleation of bubbles in the target region. These bubbles then expand and rapidly collapse to impart large stresses and strains on surrounding tissues, leaving behind only acellular debris. The cavitation "bubble cloud" generated during histotripsy treatment can be visualized on ultrasound imaging, offering real-time treatment guidance and monitoring. Histotripsy has not yet been investigated for superficial musculoskeletal tumor ablation, and preliminary studies using histotripsy to ablate brain tumors are underway, but require advanced histotripsy devices still under development. As a result, open questions remain regarding histotripsy ablation as a treatment for musculoskeletal and brain tumors. Additionally, early evidence suggests that histotripsy ablation may be able to stimulate an immune response, treating not only the targeted tumor but also multifocal or metastatic disease. Continued research is needed to explain and corroborate these findings under conditions more similar to human cancers, such as in large animal models with naturally-occurring tumors. This dissertation investigates the safety and feasibility of using ultrasound-guided histotripsy to ablate superficial soft tissue sarcomas (STS), osteosarcomas (OS), and brain tumors and considers the immunological impacts of histotripsy treatment for STS and OS. This research (1) investigates the ability of histotripsy to treat superficial STS tumors in companion animals with spontaneous tumors, (2) investigates the feasibility of treating bone tumors with histotripsy through a series of ex vivo and in vivo studies, and (3) applies histotripsy for the minimally invasive treatment of superficial brain tumors. The completion of this dissertation will provide significant insight into the ability of ultrasound-guided histotripsy to treat novel tumor types (i.e., STS, OS, and brain tumors) and the potential role of histotripsy in veterinary medicine. Future work will build upon the studies detailed in this dissertation to optimize ultrasound-guided histotripsy for the treatment of complete STS, OS, and brain tumors in veterinary and human patients.

Les sarcomes sont des tumeurs malignes des tissus conjonctifs, représentant moins de 1%des tumeurs malignes de l’adulte, mais près de 8% de l’ensemble des cancers pédiatriques. Enraison de leur rareté, de leur grande variété histologique et de leur potentiel évolutifhétérogène, les sarcomes sont des pathologies difficiles à traiter, tant sur le plan diagnostique,pronostique que thérapeutique. Ces dernières années, l’avènement de techniques d’analyse pangénomiques par biologie moléculaire a permis d’améliorer la prise en charge clinique des sarcomes, mais les microARN sont des biomarqueurs émergents encore peu utilisés. au cours de c e travail de thèse, nous avons cjhoisi d'étudier la valeur des profils d'expression des micrfoARN dans les rhabdomyosarcomes et les ostéosarcomes. Les données brutes des profils d'expression ont été obtenues à l'aidre d'une technologie à moyen débit basée sur des réactions de PCR quantitative. Nous avons tout d'abord développé une méthodologie d'ananlyse permettant d'obtenir des données d'expression précises, reproductibles et à forte valeur ajoutée, à partir de matériel biologique hétérogène.. Dans un second temps, nous avons montré que les profils d'expression de microARN permettent d'améliorer la prise en charge clinique des deuc types de sarcomes étudiés : il est possible d'affiner la classification nosologique des rhabdomyosarcomes, et de prédire la réponse des ostéosarcomes à la chimiothérapie néo-adjuvante. La recherche de nouvelles applications cliniques liées aux profils d'expression des micorARN doit donc être poursuivie, et peut désormais l'être grâce à l'outil robuste que nous avons développé au cours de cette thèse. / Sarcomas are malignant soft tissue tumors, accounting for 1% of adult tumors and 8% of all pediatric malignancies. Sarcomas are rare, and display a variety of histological subtypes and clinical characteristics. Therefore, everyday management is difficult in terms of diagnosis,prognosis and treatment. Recently, the development of pangenomic molecular techniquesimproved the clinical management of sarcomas, but the use of microRNAs as biomarkers is still being investigated.In the present work, we studied the value of microRNA expression profiles inrhabdomyosarcomas and osteosarcomas. Raw data of expression profiles were obtained using amedium throughput technology based on quantitative PCR. We first developed an analysismethodology to gain accurate, reproducible and relevant expression data, starting fromheterogeneous samples. Furthermore, we showed that microRNA expression profiles canimprove the clinical management of both sarcoma entities: they are helpful to upgrade the fine nosological classification of rhabdomyosarcomas, and they are able to predict the response of osteosarcomas to neoadjuvant chemotherapy. Searching for new clinical applications tomicroRNA expression profiles must be pursued.

Τα πεπτίδια, είτε ως πρωτεϊνικά θραύσματα είτε ως φυσικές οντότητες, χαρακτηρίζονται από την ακολουθία τους και από τα λειτουργικά τους χαρακτηριστικά. Ο σκοπός αυτής της Διδακτορικής Διατριβής είναι η ανάπτυξη μιας μεθοδολογίας εξόρυξης δεδομένων για μοναδικά tags και πεπτιδικά/πρωτεϊνικά χαρακτηριστικά του ανθρώπινου πρωτεώματος καθώς επίσης η ανάλυση και η εφαρμογή αυτών των βιολογικών δεδομένων σε πρωτεϊνες που σχετίζονται με τον καρκίνο. Δημιουργήθηκε μια αποθήκη αρχείων η οποία περιέχει μοριακά βάρη με ακρίβεια 0.01 Da που συνδέονται με τις αντίστοιχες πεπτιδικές ακολουθίες ανθρώπινων πρωτεϊνών της Swiss-Prot βάσης. Αυτές οι πρωτεϊνες διασπάστηκαν εξαντλητικά παρέχοντας ανεξαρτησία στις πεπτιδικές ακολουθίες από άλλες μεθόδους που βασίζονται στην ενζυματική διάσπαση. Από αυτήν την αποθήκη δεδομένων, διαχωρίστηκαν τα μοριακά βάρη που είναι μοναδικά και φτάνουν μέχρι τα 10 kDa καθώς και οι μοναδικές πεπτιδικές ακολουθίες (μέχρι 10 kDa). Στα πλαίσια της αξιοποίησης των δεδομένων εξόρυξης για την ταυτοποίηση των πρωτεϊνών, αναπτύχθηκε μια ευρέως διαθέσιμη διαδικτυακή εφαρμογή όπου γίνεται η αντιστοίχιση των μοριακών βαρών υψηλής ανάλυσης με πεπτίδια και πρωτεϊνες. Μια ακόμη διαδικτυακή εφαρμογή αναπτύχθηκε για να προσφέρει την πληροφορία της μοναδικότητας των μοριακών βαρών και των πεπτιδικών ακολουθιών στο ανθρώπινο πρωτέωμα. Η εφαρμογή μπορεί να αναζητήσει μοναδικά πρωτεϊνικά θραύσματα που προκύπτουν από την εζυματική διάσπαση πρωτεϊνών και να προσφέρει την πληροφορία για όλα τα μοναδικά μοριακά βάρη και τις μοναδικές πεπτιδικές ακολουθίες που περιέχονται σε μια πρωτεϊνη. Πολλές φορές χρειάζεται η μαζική διαχείριση των πεπτιδίων από λίστες. Για το σκοπό αυτό, αναπτύχθηκε ένας web server ο οποίος διαχειρίζεται τις πεπτιδικές λίστες, αναλύοντας τα χαρακτηριστικά των πεπτιδίων και ομαδοποιώντας τα πεπτίδια σύμφωνα μα αυτά τα χαρακτηριστικά, ενώ οπτικοποιείται η ομαδοποίηση με την χρήση ενός java applet. Το PepServe είναι ένα χρήσιμο εργαλείο για την κατανόηση της κατανομής των πεπτιδικών χαρακτηριστικών για ένα σύνολο πεπτιδίων. Τέλος, αναλύθηκαν σύνολα πρωτεϊνών που σχετίζονται με διάφορες περιπτώσεις καρκίνων, για πεπτιδικά χαρακτηριστικά. Αυτή η ανάλυση έχει σκοπό την εύρεση πιθανών προτιμήσεων σε χαρακτηριστικά και την εύρεση μοναδικών tags των πρωτεϊνών που σχετίζονται με καρκίνους. Τα μοναδικά tags μπορούν να χρησιμοποιηθούν στην ανακάλυψη βιοδεικτών και την ανάπτυξη νεων φαρμάκων για την πιο αποτελεσματική διάγνωση και θεραπεία. / Peptides, either as protein fragments or as naturally occurring entities are characterized by their sequence and function features. The purpose of the present Ph.D. thesis is to develop a datamining method for unique tags and peptide/protein characteristics in the human proteome and to analyze and apply the derived biological data in cancer-related proteins. A file repository has been created, containing indexed information that relates molecular masses with an accuracy of 0.01 Da to the corresponding peptides existing in human proteins. These proteins have been deposited in a completely digested protein database (Swiss-Prot) providing independence from any specific enzyme/digestion method. From this repository, the unique molecular masses, ranging from 1 to 10 kDa, and the unique peptide sequences from all the possible sequence fragments (up to 10 kDa) have been mined. A publicly available web application has been developed which facilitates a high resolution mapping of measured molecular masses to peptides and proteins, irrespectively of the enzyme/digestion method used. Μulti-filtering may be applied in terms of measured mass tolerance, molecular mass and isoelectric point range as well as pattern matching to refine the results In addition, another publicly available web application has been developed that offers information concerning the uniqueness of molecular masses and peptide sequences in the human proteome. The application is able to search for unique protein fragments derived computationally from enzymatic digestion driven by certain enzymes. Furthermore, the application can list all the unique masses and peptides of a given protein. Through this application, researchers are able to find unique tags, either on a molecular mass level or on a sequence level. A web server has beed developed that manages peptide lists in terms of feature analysis as well as interactive clustering and visualization of the given peptides. PepServe is a useful tool towards understanding peptide feature distribution among a group of peptides. Finally, cancer-related proteins have been analyzed producing peptide features and peptide feature’s sequence uniqueness resulting in some feature preferences and peptide unique tags. These unique tags can be used in biomarker discovery, and novel drug development for an efficient diagnosis and treatment.