<p>Michelle N. Ingle. M.S., Purdue University, December 2019. Computational Modeling of Transforming Growth Factor-β2 Receptor Complex Assembly. Major Professor: David M. Umulis.</p> <p> </p> <p> Transforming growth factor (TGF)-β1, TGF-β2, and TGF-β3 are secreted signaling proteins that play an essential role in tissue development, immune response, and physiological homeostasis. TGF-β ligands signal through a tetrameric complex made up of two type I receptors (TβRI) and two type II receptors (TβRII). Dysregulation of TGF-β signaling has been linked to uncontrolled cell proliferation and cancer metastasis. An accurate understanding of TGF-β’s receptor complex assembly pathway may allow for pharmacological intervention and/or preservation of proper TGF-β signaling.</p> <p> Amongst the ligand types, TGF-β1 and TGF-β3 are efficient signalers, presumably by strong binding to both type I and II receptors. However, TGF-β2 has a very weak affinity for TβRII and requires an additional membrane-bound protein called betaglycan (BG) to achieve similar levels of downstream signaling. While computational modeling has been performed on the signaling pathway of the TGF-β system, to date no computational modeling has aimed to decipher BG’s role in the potentiation of TGF-β2 signal. To determine the role of BG in selectively facilitating signaling by TGF-β2, we developed computational models with different assumptions based on the levels of cooperativity between receptor subtypes and types of BG behavior (No Receptor Recruitment model, Single-stage Receptor Recruitment model, and Two-stage Receptor Recruitment model). </p> <p> With each of the receptor recruitment models we hypothesized that BG uses two domains to successfully enhance TGF-β2 signaling. This model was first proposed in Villarreal et al., 2016 and is further investigated in this work using a two-step computational approach. First, a root mean square error (RMSE) calculation was performed between our computational models with no BG present and published experimental signaling data in cell lines with no BG present. Lower RMSE values indicate the simulated data is more representative of experimental signaling behavior when no BG is present. The second round of model validation was performed by adding BG into the simulations and comparing its behavior to experimentally determined and hypothesized behaviors of BG. </p> <p> In summary, the simulations indicate there may be more cooperative receptor recruitment present in the system then stated in literature. Furthermore, it appears that BG binding to TGF-β2 ligand through two domains provides an effective transfer mechanism that can be tuned to control differential signaling between TGF-β ligand subtypes. Experiments were then suggested in order to support or refute one of the models offered in this thesis. For the purpose of uncovering how BG enhances TGF-β2 signaling, the computational work performed in this thesis highlights the areas where researchers should focus their experimental efforts and provides a baseline model for further computational work in the TGF-β system.</p>

O crescimento gengival induzido por ciclosporina-A (CG) é caracterizado por uma variedade de sinalizações que envolvem fatores de crescimento e proteoglicanos, porém pouco compreendidas. Investigamos a expressão gênica dos proteoheparans sulfato de superfície celular sindecam-2 (SDC-2), -4 (SDC-4) e betaglicam nesse CG. A quantidade total e relativa de glicosaminoglicanos sulfatados (GAGs) e a distribuição de SDC-2 e SDC-4 no tecido gengival também foram analisadas. Métodos: A expressão de mRNA dos proteoglicanos SDC-2, SDC-4 e betaglicam foi analisada pela reação de polimerase em cadeia e transcrição reversa (RT-PCR) em amostras gengivais de 9 indivíduos com CG (grupo CsA) e 6 com gengiva normal (grupo controle). Os GAGs foram extraídos e purificados dos tecidos gengivais e analisados tanto por eletroforese em gel de agarose quanto por espectrofotometria. Foi realizada uma avaliação imunohistoquímica dos tecidos com anticorpos para SDC-2 e SDC-4, para sua localização nos tecidos. Os grupos foram comparados pelo teste t de Student. Resultados: Todos os proteoglicanos estudados mostraramse aumentados no grupo CsA (165% para SDC-2, 308% para SDC-4 e 42% para betaglicam), comparativamente ao grupo controle (P < 0.0001). Não foram observadas diferenças significativas na quantidade total e relativa de GAGs. A imunohistoquímica mostrou uma distribuição marcante de SDC-2 e SDC-4 no componentes epitelial, conjuntivo, vascular, nervoso e inflamatório, incluindo os compartimentos celulares e matriciais de toda a casuística. Nossos resultados revelam expressão aumentada de mRNA de SDC-2, SDC-4 e betaglicam no crescimento gengival induzido pela ciclosporina-A, porém não se observaram diferenças na quantidade de glicosaminoglicanos sulfatados em relação ao tecido gengival não exposto ao fármaco. / Cyclosporin-induced gingival overgrowth (CIGO) comprises a variety of signaling pathways including growth factors and proteoglycans that remains not fully understood. We investigated the gene expression of the cell-surface heparan sulfate proteoglycans syndecan-2 (SDC-2), -4 (SDC-4) and betaglycan in CIGO. Total and relative amounts of sulfated glycosaminoglycans (GAGs) and the distribution of SDC-2 and SDC-4 in the gingival tissue were also analyzed. Methods: mRNA expression of the proteoglycans SDC-2, -4 and betaglycan was analyzed by reverse transcription polymerase chain reaction (RT-PCR) in gingival samples obtained from 9 individuals with CIGO and 6 with a normal gingiva (control group). GAGs were extracted and purified from gingival tissues and analyzed by agarose gel electrophoresis and spectrophotometry. An immunohistochemical evaluation using panels of antibodies for SDC-2 and -4 was performed for localization in the tissues. Groups were compared by the Student's t test. Results: All proteoglycans expressions revealed increase in the CIGO group (165% for SDC-2, 308% for SDC-4 and 42% for betaglycan) compared to the control group (P < 0.0001). No significant differences were observed for the total and relative amounts of GAGs. Immunohistochemistry showed a marked distribution of SDC-2 and SDC-4 in gingival epithelial, connective, vascular, neural and inflammatory components comprising cellular and matrix environments in both groups. Our results reveal increased mRNA expression of SDC-2, SDC-4 and betaglycan in CIGO, but no significant differences in the sulfated glycosaminoglycans component in situ.

O crescimento gengival induzido por ciclosporina-A (CG) é caracterizado por uma variedade de sinalizações que envolvem fatores de crescimento e proteoglicanos, porém pouco compreendidas. Investigamos a expressão gênica dos proteoheparans sulfato de superfície celular sindecam-2 (SDC-2), -4 (SDC-4) e betaglicam nesse CG. A quantidade total e relativa de glicosaminoglicanos sulfatados (GAGs) e a distribuição de SDC-2 e SDC-4 no tecido gengival também foram analisadas. Métodos: A expressão de mRNA dos proteoglicanos SDC-2, SDC-4 e betaglicam foi analisada pela reação de polimerase em cadeia e transcrição reversa (RT-PCR) em amostras gengivais de 9 indivíduos com CG (grupo CsA) e 6 com gengiva normal (grupo controle). Os GAGs foram extraídos e purificados dos tecidos gengivais e analisados tanto por eletroforese em gel de agarose quanto por espectrofotometria. Foi realizada uma avaliação imunohistoquímica dos tecidos com anticorpos para SDC-2 e SDC-4, para sua localização nos tecidos. Os grupos foram comparados pelo teste t de Student. Resultados: Todos os proteoglicanos estudados mostraramse aumentados no grupo CsA (165% para SDC-2, 308% para SDC-4 e 42% para betaglicam), comparativamente ao grupo controle (P < 0.0001). Não foram observadas diferenças significativas na quantidade total e relativa de GAGs. A imunohistoquímica mostrou uma distribuição marcante de SDC-2 e SDC-4 no componentes epitelial, conjuntivo, vascular, nervoso e inflamatório, incluindo os compartimentos celulares e matriciais de toda a casuística. Nossos resultados revelam expressão aumentada de mRNA de SDC-2, SDC-4 e betaglicam no crescimento gengival induzido pela ciclosporina-A, porém não se observaram diferenças na quantidade de glicosaminoglicanos sulfatados em relação ao tecido gengival não exposto ao fármaco. / Cyclosporin-induced gingival overgrowth (CIGO) comprises a variety of signaling pathways including growth factors and proteoglycans that remains not fully understood. We investigated the gene expression of the cell-surface heparan sulfate proteoglycans syndecan-2 (SDC-2), -4 (SDC-4) and betaglycan in CIGO. Total and relative amounts of sulfated glycosaminoglycans (GAGs) and the distribution of SDC-2 and SDC-4 in the gingival tissue were also analyzed. Methods: mRNA expression of the proteoglycans SDC-2, -4 and betaglycan was analyzed by reverse transcription polymerase chain reaction (RT-PCR) in gingival samples obtained from 9 individuals with CIGO and 6 with a normal gingiva (control group). GAGs were extracted and purified from gingival tissues and analyzed by agarose gel electrophoresis and spectrophotometry. An immunohistochemical evaluation using panels of antibodies for SDC-2 and -4 was performed for localization in the tissues. Groups were compared by the Student's t test. Results: All proteoglycans expressions revealed increase in the CIGO group (165% for SDC-2, 308% for SDC-4 and 42% for betaglycan) compared to the control group (P < 0.0001). No significant differences were observed for the total and relative amounts of GAGs. Immunohistochemistry showed a marked distribution of SDC-2 and SDC-4 in gingival epithelial, connective, vascular, neural and inflammatory components comprising cellular and matrix environments in both groups. Our results reveal increased mRNA expression of SDC-2, SDC-4 and betaglycan in CIGO, but no significant differences in the sulfated glycosaminoglycans component in situ.

La Bone Morphogenetic Protein-1 (BMP-1) est une métalloprotéase impliquée dans la maturation et l'activation de nombreuses molécules extracellulaires. Parmi celles-ci, on trouve notamment les collagènes fibrillaires, les protéines les plus abondante chez l'Homme, ainsi que les facteurs de croissance de la superfamille du TGF-ß, des protéines pléiotropes. Au travers de ses fonctions, BMP-1 joue un rôle crucial au cours du développement embryonnaire mais également durant les processus physiologiques et pathologiques de remodelage tissulaire (cicatrisation, fibroses, croissance osseuse, cancers...).Le projet présenté dans ce manuscrit a consisté à étudier plusieurs fonctions importantes de BMP-1 au niveau moléculaire et à caractériser les conséquences de ces activités au niveau de plusieurs types cellulaires.Dans un premier temps, un test quantitatif a été mis au point afin de pouvoir étudier en temps réel l'effet de BMP-1 sur les collagènes fibrillaires ainsi que les mécanismes de sa régulation. Par la suite, de nouveaux substrats de BMP-1 ont été mis en évidence, parmi lesquels des co-récepteurs du TGF-ß (Bétaglycan, CD109) ainsi qu'une protéine matricellulaire (TSP-1). L'étude de ces activités a permis de caractériser les multiples voies par lesquelles BMP-1 est capable de réguler l'activité du facteur de croissance TGF-ß.De plus, nous avons mis en évidence que le clivage de ces différents substrats entraine une modulation importante du phénotype de plusieurs lignées cellulaires (HT1080, HEK-293T) avec des effets au niveau de l'adhésion, la prolifération et la migration cellulaire. En conclusion, ce travail révèle que les activités de BMP-1 s'étendent bien au-delà de ce qui est actuellement décrit / Bone Morphogenetic Protein (BMP-1) is a metalloprotease known to be involved in the maturation and activation of several important extracellular proteins, including fibrillar collagens and growth factors of the TGF-beta superfamily. As a consequence, it is essential for embryonic development and tissue remodeling and has been clearly involved in lethal diseases such as fibrosis and cancer.This thesis project focused on the major molecular functions of BMP-1 and their implications for the phenotype of several cell types. First, a quantitative and real-time assay was developed to study the effect of BMP-1 and associated regulatory proteins on fibrillar collagens. Then, new BMP-1 substrates, such as TGF-ß co-receptors (Betaglycan and CD109) and matricellular proteins (TSP-1) were characterized in detail. Especially, we evidenced that these activities played a major role in the regulation of the TGF-ß pathway.Furthermore, we shown that these BMP-1 activities induce major phenotype changes (adhesion, proliferation, migration) in several cell lines including HT1080 and HEK-293T. Altogether, this work reveals that BMP-1 substrates extend far beyond what is presently described and open several perspectives for future studies