A Thesis submitted to The University of Arizona College of Medicine - Phoenix in partial fulfillment of the requirements for the Degree of Doctor of Medicine. / Recent advances in cancer immunology, highlighted by immune checkpoint inhibitors, have demonstrated that immunotherapy is a viable option in the oncologist’s armamentarium. Despite these advances, many patients are nonresponders. Preliminary studies have suggested that non-responders lack a de-novo anti-tumor antigen immune response that can be unmasked by checkpoint blockade; thus, strategies to induce anti-tumor immune responses are needed. We hypothesized that many tumor associated antigens (Ag) are readily susceptible to immune attack, but only in the context of identifying the tumor antigen epitopes that can reliably initiate an immune response, regardless of individual patient human leukocyte antigen (HLA) haplotype restrictions. We further hypothesized that epitope prediction strategies which seek to identify pan- or highly promiscuous-HLA binding epitopes would reduce the number of potential candidates and be more likely to accurately identify high-priority tumor Ag epitopes. Utilizing known HLA-serotype frequencies and setting a threshold of ninety percent of population coverage, regardless of race or ethnicity, twenty-nine different HLA-DRB1 haplotypes were chosen for antigen prediction utilizing the open source epitope prediction algorithm netMHCIIpan. Predictions were also performed for HLA-A serotypes utilizing the open source algorithm netMHCpan. Predicted epitopes were synthesized in the form of synthetic long peptides and tested in immune system sensitization assays involving unfractionated peripheral blood mononuclear cells (PBMC). Briefly, PBMC were subjected to a two-step culture, first synchronizing their exposure to the long peptides with aggressive surrogate activation of innate immunity, followed by IL-7-modulated T-cell hyperexpansion. Predictions resulted in identification of highly promiscuous-HLA binding epitopes. Unexpectedly, these epitopes clustered together forming high priority regions: unique “hot spots” with high densities of promiscuous HLA-binding epitopes from the widely expressed oncoproteins MUC1, HER2/neu and CMV-pp65 (p<0.0001, for predicted HLA-DRB1 binding affinities, compared to non-hot spot regions). Added synthetic long peptides (>20aa) derived from “hot spot” regions of MUC1, HER2/neu, and CMVpp65 reliably produced selective and sustained expansion of both CD4+ and CD8+ peptide-specific, interferon-γ (IFNγ)-producing Tcells when synchronized with step 2 exposure to exogenous IL-7 (p<0.0001 and p=0.0048, for CD4+ and CD8+ Ag-specific T-cells, respectively, compared to T-cells directed against peptides from non-hot spot regions). “Hot spot” peptide Ag-specific T-cells preferentially recognized endogenous tumor derived MUC1, either in MUC1 expressing tumor cell killing assays (p=0.038, compared to non-peptide Ag-specific T-cells) or as MUC1 tumor lysate when pulsed onto restimulatory PBMC (p=0.022 and 0.025, for CD4+ and CD8+ T-cells, respectively, compared to T-cells directed against peptides from non-hot spot regions). This mechanistically rational antigen selection sequence, effective even for unvaccinated donors, regardless of HLA-haplotype, enables rapid identification of tumor protein regions relevant for cancer immunology, including adoptive immunotherapy, vaccines, and even identification of tumor neo-antigens unique to each patient.

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MUC1, a protein of epithelial and carcinoma cells, has recently been shown on activated T cells where it inhibits CD3-stimulated proliferation. Two immunoregulatory domains similar to ITAM and ITIMs are present on its cytoplasmic tail, suggesting that MUC1 can act as both a costimulatory and coinhibitory molecule of T cells. In my work, I have examined immunoregulatory function of MUC1 on human T cells. We first showed that MUC1, when ligated in a population of unpurified T cells with an anti-CD3 and a crosslinking antibody, enhances proliferative and cytokine responses in a NF-AT-dependent manner by recruiting the AP-1 transcription factor and translocating it into the nucleus. With purified CD3+ T cells, we instead observed inhibition after MUC1/CD3 coligation and crosslinking. Reconstituting with irradiated CD3- cells, we discovered that MUC1 costimulation is dependent on the amount of accessory cells. These data imply a novel role for MUC1 in T cell immunoregulation. / Experimental Surgery

MUC1 est une mucine membranaire dont l'expression est augmentée et altérée dans le cancer et l'ischémie rénale. La transition épithélium-mésenchyme (TEM) est un processus dynamique de plasticité cellulaire impliqué dans la progression métastatique et la réparation tissulaire. Nos travaux montraient l'implication de MUC1 dans la plasticité épithéliale rénale à travers l'action de MUC1 dans des lignées cancéreuses rénales et dans des modèles murin et humain de régénération rénale. Dans le carcinome rénal, nous démontrions que (i) MUC1 et SNAIL, facteur de transcription de la TEM, étaient surexprimés dans une série de carcinomes sarcomatoïdes, (ii) SNAIL augmentait indirectement l'expression MUC1, (iii) la surexpression de MUC1 induisait la TEM, (iv) le domaine C-terminal de MUC1 (MUC1-C) augmentait l'interaction de la beta-caténine avec le promoteur de SNAIL favorisant l'activité transcriptionnelle de SNAIL, et (v) le blocage de la localisation nucléaire de MUC1-C diminuait l'activation de la voie Wnt /beta caténine et celle de SNAIL. Au total, nos résultats démontraient que MUC1 est un acteur de la TEM rénale associé au cancer et apparaît comme une nouvelle cible thérapeutique.Dans la régénération rénale, nous montrions que (i) la régénération rénale s'accompagnait d'une plasticité épithéliale transitoire compatible avec une TEM dans un modèle murin et sur des biopsies de greffon humain, (ii) MUC1 était induite au cours de la TEM associée à la régénération, (iii) l'absence de MUC1 (souris Ko Muc1)s'associait à des lésions tubulaires rénales plus sévères, et (iv) l'induction de MUC1 était inversement corrélée au degré de fibrose rénale. Au total, nos résultats suggèrent un rôle de néphroprotection conféré par MUC1 aux cellules épithéliales rénales au cours de la régénération. / MUC1 is overexpressed in renal carcinoma and ischemia. The epithelial-mesenchymal transition (EMT) is a dynamic process consisted of cellular plasticity involved in tumoral progression and tissue repair. Our work showed the involvement of MUC1 in renal epithelial plasticity through the action of MUC1 in renal cancer cell lines and in mouse and human kidney regeneration models.MUC1 is overexpressed in human carcinomas. The transcription factor SNAIL can activate epithelial-mesenchymal transition (EMT) in cancer cells. In this study, in renal carcinoma, we demonstrate that (i) MUC1 and SNAIL were overexpressed in human sarcomatoid carcinomas, (ii) SNAIL increased indirectly MUC1 expression, (iii) MUC1 overexpression induced EMT, (iv) MUC1 C-terminal domain (MUC1-C) and beta-catenin increased SNAIL transcriptional activity by interaction with its promoter and (v) blocking MUC1-C nuclear localization decreased Wnt/beta-catenin signaling pathway activation and SNAIL expression. Altogether, our findings demonstrate that MUC1 is an actor in EMT and appears as a new therapeutic target.In renal regeneration, we demonstrated that (i) regeneration was characterized by a transient EMT in mouse model and human biopsies allograft, (ii) MUC1 was induced during EMT-regeneration associated, (iii) the lack of MUC1 (Muc1 KO mouse) was associated with more severe renal tubular damage, and (iv) MUC1 induction was inversely correlated with renal fibrosis. Altogether, our results suggest MUC1 mitigates renal ischemic damage through EMT activation during regeneration.

Transcription factor AP2C (TFAP2C) is believed to be involved in breast cancer carcinogenesis. However, the molecular mechanisms of regulating its trans-activation activity are not well understood. One of the potential mechanisms is through p53-mediated regulation. Using ChIP-seq analysis to map the TFAP2C occupancy across the genome, we found that the introduction of p53 to HCT 116 p53 -/- colon cancer cell line significantly augments TFAP2C occupancy on the promoter regions of a group of genes. Of these, six genes were further investigated. First, TFAP2C binding sites were identified in the center of ChIP-seq peaks on the promoters of the six genes and these were verified by gel shift assays. One of these genes, MUC1, was then determined to be activated by TFAP2C in MCF-7 breast cancer cell line. Subsequently, MUC1 was selected as the model target gene to elucidate the mechanism for p53-mediated enhancement of TFAP2C occupancy. We hypothesized that DNA methylation of the MUC1 promoter is altered by p53, leading to the increased TFAP2C occupancy to its TFBS on MUC1 promoter. To examine this, CpG methylation assay was performed. The result showed the DNA methylation of MUC1 promoter region remains identical with or without over-expression of p53 in HCT 116 p53 -/- cell line. From these studies, I conclude that 1) introduction of p53 augments TFAP2C binding on specific gene targets; 2) MUC1 gene is activated by TFAP2C and two TFAP2C binding sites were verified; 3) promoter DNA methylation does not explain the increased occupancy of TFAP2C on MUC1 promoter.

Adenocarcinomas e distroglicanopatias são doenças graves que estão associadas a quadros de hipoglicosilação de mucinas tumorais, como a MUC1 (transmembrane glycoprotein Mucin 1) e de mucinas de ?-distroglicana (?-DG). Um dos mais importantes desafios associados à terapia anti-câncer refere-se ao desenvolvimento de estratégias terapêuticas que permitam o direcionamento da ação de drogas anti-tumorais para a célula cancerosa com o objetivo de evitar o acometimento de células saudáveis. Nessa linha, é crucial a construção de sistemas de liberação de medicamentos sítio específicos por meio de marcadores tumorais. Quanto ao diagnóstico das distroglicanopatias, atualmente este se baseia principalmente na observação de manifestações clínicas, biópsias musculares e medidas enzimáticas, sendo que os anticorpos monoclonais disponíveis no mercado não são específicos para a condição do músculo distrófico. Dessa forma, mucinas tumorais e mucinas de ?-DG modificadas tem sido consideradas potenciais alvos para o desenvolvimento de novas estratégias diagnósticas e/ou terapêuticas aplicáveis a estas doenças. Para este trabalho, foram sintetizados, em fase sólida, glicopeptídeos miméticos de MUC1 e ?-DG hipoglicosilados, os quais foram utilizados como ferramenta de busca por novos anticorpos recombinantes. Estes antígenos foram imobilizados em uma placa e sobre eles foi aplicada uma biblioteca de fragmentos de anticorpos (Fabs) humanos recombinantes para o desenvolvimento do processo de seleção pela tecnologia de Phage Display. Após quatro rounds consecutivos de seleção, os genes codificadores dos Fabs da biblioteca não selecionada e selecionada foram sequenciados e analisados in silico na plataforma ATTILA. Esta análise permitiu rastrear o enriquecimento dos domínios VH e VL durante a seleção, além de possibilitar a escolha de inúmeros clones para produção. Para este trabalho, quatro fragmentos de anticorpos scFvs recombinantes inéditos para a mucina tumoral MUC1 e ?-DG hipoglicosilados foram desenhados e clonados em vetor de expressão pET29(a) contendo um marcador de identificação (peptídeo FLAG) e outro de purificação (cauda de histidina). A expressão de um scFv recombinante anti-MUC1 foi realizada em E. coli BL21-DE3 pela adição de 0,5mM de IPTG com indução a 20ºC por 16 horas. A purificação foi realizada por cromatografia de afinidade em resina de níquel, seguida de gel filtração, sendo estas etapas monitoradas por SDS-PAGE. A identificação imunoquímica da proteína recombinante foi confirmada por Western Blot, utilizando o anticorpo anti-FLAG. Entende-se que este trabalho, por meio da produção de novas ferramentas biotecnológicas, poderá cooperar para o desenvolvimento de novas formas abordagens diagnósticas e/ou terapêuticas para tumores e distroglicanopatias. / Adenocarcinomas and dystroglycanopathies are serious diseases associated with hypoglycosylation of tumoral mucins, such as MUC1 (transmembrane glycoprotein Mucin 1) and ?-dystroglican mucins (?-DG). One of the most important challenges associated with anti-cancer therapy is the development of therapeutic strategies that allow the targeting of anti-tumor drugs to the cancer cell in order to avoid the involvement of healthy cells. In this regard, the construction of site-specific drug delivery systems by tumor markers is crucial. The diagnosis of dystroglicanopathies are currently based on the observation of clinical manifestations, muscle biopsies and enzymatic measures, and the available monoclonal antibodies are not specific for the dystrophic muscle condition. Thus, tumoral mucins and modified ?-DG mucins have been considered potential targets for the development of new diagnostic and/or therapeutic strategies applicable to these diseases. For this work, glycoproteins MUC1 and ?-DG hypoglycosylated mimetics were synthesized by solid phase reaction, and were used as a search tool for new recombinant antibodies. These antigens were immobilized in a plate and a library of recombinant human antibody (Fabs) fragments was applied thereon for the development of the screening process by Phage Display technology. After four consecutive rounds of selection, the Fabs coding genes from the unselected and selected library were sequenced and analyzed in silico on ATTILA platform. This analysis allowed us to track the enrichment of the VH and VL domains during selection process, and also presented several option of clones to choose for production. For this work, four novel fragments of recombinant scFvs antibodies specific for tumoral mucin MUC1 and ?-DG hypoglycosylated were designed and cloned into pET29 (a) expression vector containing an identification marker (FLAG peptide) and a purification tag (histidine tail). Expression of a recombinant anti-MUC1 scFv was performed on E. coli BL21-DE3 by the addition of 0.5 mM of IPTG with induction at 20°C for 16 hours. Purification was performed by affinity chromatography on nickel resin, followed by gel filtration, these steps being monitored by SDS-PAGE. Immunochemical identification of the recombinant protein was confirmed by Western Blot, using the anti-FLAG antibody. It is understood that this work, through the production of new biotechnological tools, could cooperate for the development of new forms of diagnostic and/or therapeutic approaches for tumors and dystroglicanopathies.

Le cancer du sein triple négatif (TN) est un cancer présentant des résistances aux agents de chimiothérapie. Malgré la forte expression de l’EGFR, il est aussi résistant aux anti-EGFR. Ces mécanismes de résistance ne sont pas connus.MUC1 est une protéine transmembranaire largement glycosylée. Sa fonction extracellulaire est impliquée dans la régulation des récepteurs membranaires dont l’EGFR. Comme les autres glycoprotéines membranaires, son unité extracellulaire (MUC1-N) peut moduler la réponse cellulaire immune par hypersialylation. Son unité intracellulaire (MUC1-C) possède des sites de phosphorylation impliqués dans plusieurs voies de signalisation telles que PI3K/AKT/mTOR ou RAS/RAF/MEK/ERK. Ces dernières régulent l’autophagie qui est un mécanisme de survie cellulaire associé à la résistance aux agents de chimiothérapie.Nous avons démontré que les TN présentaient des modifications quantitatives et qualitatives de l’expression de MUC1, altérant probablement les régulations des voies associées à MUC1/EGFR dont l’autophagie. L’activation de l’autophagie explique la résistance aux traitements des agents de chimiothérapie. L’IL17 est un facteur pro-inflammatoire secrété par du microenvironnement tumoral et associé également à la résistance des agents de chimiothérapie des TN, par activation de la voie MEK/ERK, suggérant son implication à activer l’autophagie.En conclusion, nos travaux permettent d’émettre l’hypothèse que l’inhibition de l’autophagie et/ou MUC1 et/ou IL17 pourrait augmenter la sensibilité aux traitements de chimiothérapie ou des thérapies ciblées dirigées contre les TN. / Triple negative breast cancer (TN) is often associated to chemioresistance. Moreover, despite an EGRF over-expression, TN is also resistant to anti-EGFR drugs. These resistance mechanisms are not known yet.MUC1 is a transmembrane broadly glycosylated protein. Its extracellular unit (MUC-N) is involved to membrane receptor regulations, as EGFR. As other membrane glycoproteins, MUC1 could modulate, by over-sialylation, the immune cellular response. Its intracellular unit (MUC-C) presents phosphorylation sites involved in numerous signal pathways such as PI3K/AKT/mTOR or RAS/RAF/MEK/ERK. Both pathways regulate autophagy which is a survival cellular mechanism associated to resistance of chemiotherapy drugs.We showed that TN presents quantitative and qualitative MUC1 alterations, likely associated with dys-regulation of autophagy/MUC1/EGFR pathways. The activation of autophagy explains the chemiotherapy resistance. IL17 is a proinflammatory interleukin secreted by the tumor microenvironment. In TN, IL17 is also associated to chemiorestistance throughout the MEK/ERK pathways, suggesting its involving activating autophagy.In conclusion, our work allows us to hypothesize that inhibition of autophagy and/or MUC1 and/or IL17 could be increase the sensibility to chemiotherapy or targeted therapies against TN.

Le carcinome rénal représente 5% des tumeurs de l’adulte et se développe au niveau des tubules rénaux. Le sous-type histologique majeur des cancers du rein est le carcinome rénal à cellules claires (cRCC). 90% des cRCC présentent une inactivation biallélique du gène suppresseur de tumeur de Von Hippel Lindau (VHL) induisant une activation constitutive de la voie de l’hypoxie via le facteur de transcription HIF1-α (Hypoxia Inducible Factor) qui contribue à la physiologie des tumeurs. Les cRCC sont des tumeurs à la fois radio- et chimiorésistantes, rendant la prise en charge thérapeutique des patients très difficile.Nos recherches consistaient en l’étude des rôles de la mucine membranaire MUC1, dont la queue cytoplasmique (MUC1 CT) peut interagir avec différentes voies de signalisation et agir en tant que co-activateur transcriptionnel de nombreux gènes impliqués dans la progression tumorale et la diffusion métastatique. Des travaux antérieurs réalisés au laboratoire montraient que la surexpression de MUC1 observée dans les cRCC était associée au statut métastatique des patients et marquait un mauvais pronostic. Cette surexpression de MUC1 est également impliquée dans la voie de l’hypoxie, voie majeure de la carcinogenèse rénale. Le premier objectif de l’étude était donc de déterminer les effets de la surexpression de MUC1 sur les propriétés des cellules de cRCC. Nous montrons ainsi que le domaine extracellulaire de MUC1 ainsi que sa partie cytoplasmique sont impliqués dans l’augmentation des capacités migratoires et de la viabilité des cellules cancéreuses rénales et qu’elle leur confère une résistance à l’anoïkis, programme de mort cellulaire déclenché lorsque la cellule perd ses contacts avec les cellules voisines ou avec la matrice extra-cellulaire et diminuent les propriétés d’agrégation des cellules tumorales. Nous montrons également que MUC1 est impliquée dans la chimiorésistance des cRCC en induisant l’expression de genes de chimiorésistance comme ABCG2 et GSTO2. Nous montrons par ailleurs que les propriétés invasives des cellules de cRCC sont exclusivement liées à MUC1 CT. Le deuxième objectif de l’étude était d’identifier les mécanismes moléculaires à l’origine du clivage de MUC1 CT. En utilisant différentes stratégies (siARN, inhibiteurs pharmacologiques et peptides), nous montrons pour la première fois que deux sheddases, ADAM10 et ADAM17 et la gamma secrétase sont nécessaires au clivage de MUC1 C, permettant ainsi sa délocalisation nucléaire et l’augmentation des propriétés invasives des cellules de cRCC. Enfin, nous montrons que la surexpression de MUC1 augmente l’expression protéique d’ADAM10/17, suggérant une boucle de régulation positive existant en conditions pathologiques.En conclusion, notre étude souligne le rôle de MUC1 dans la progression tumorale rénale et montre que la localisation nucléaire de MUC1-C est à l’origine de l’acquisition d’un phénotype invasif et chimiorésistant via l’action des sheddases ADAM10/17 et de la gamma secrétase. MUC1 apparait alors comme une cible thérapeutique potentielle intéressante dans la prise en charge des cRCC. / Renal cell carcinoma corresponds to 5% of all adult malignancies and originates from renal tubules. The main histologic subtype is represented by clear renal cell carcinoma. Ninety percent of cRCC present a biallelic inactivation of the von Hippel Lindau (VHL) tumor suppressor gene resulting in constitutive activation of hypoxia signaling pathway via the Hypoxia Inducible Factor (HIF) -1 transcription factor that contributes to the physiology of tumours. cRCC is typically highly resistant to conventional systemic therapies. MUC1 is a membrane-anchored mucin and its cytoplasmic tail (CT) can interact with many signaling pathways and act as a co-transcription factor to activate genes involved in tumor progression and metastasis. Previous studies have shown that MUC1 is diffusely overexpressed in cRCC and MUC1 overexpression has been found to be associated with metastatic disease and a worse prognosis.MUC1 is overexpressed in renal cell carcinoma with correlation to prognosis and has been implicated in the hypoxic pathway, the main renal carcinogenetic pathway. In this context, we assessed the effects of MUC1 overexpression on renal cancer cells properties. Using shRNA strategy and/or different MUC1 constructs, we found that MUC1-extracellular domain and MUC1 CT are both involved in increase of migration, cell viability, resistance to anoikis and to decrease of cell aggregation in cancer cells. We also showed that MUC1 is involved in cRCC chemoresistance by inducing chemoresistance genes expression like ABCG2 and GSTO2. Invasiveness depends only on MUC1 CT. Then, by using siRNA strategy and/or pharmacological inhibitors or peptides, we showed that sheddases ADAM10, ADAM17 and gamma-secretase are necessary for MUC1 C-terminal subunit (MUC1-C) nuclear location and in increase of invasion property. Finally, MUC1 overexpression increases ADAM10/17 protein expression suggesting a positive regulatory loop. In conclusion, we report that MUC1 acts in renal cancer progression and MUC1-C nuclear localization is driving invasiveness of renal cancer cells through a sheddase/gamma secretase dependent pathway. MUC1 appears as a therapeutic target by blocking MUC1 cleavage or nuclear translocation by using pharmacological approach and peptide strategies.

The epidermal growth factor family of receptors is important in the development and progression of many types of cancers including, breast, lung, and glioblastoma. The family consists of 4 members (EGFR/erbB1, Her2/erbB2, erbB3, and erbB4). In all breast cancer cases, EGFR expression is deregulated 20 to 30% of the time; however in the most aggressive form of breast cancer (basal-like) EGFR expression is upregulated in 60% of cases. EGFR's expression and activity can be altered in transformed cells through a variety of mechanisms, such as novel protein-protein interactions, gene amplification, mutations, and loss of regulatory proteins. In this work we have examined the role of cancer specific protein interactions of EGFR with MUC1 and beta-catenin in the progression of breast cancer.Herein I report that the interaction of MUC1 and EGFR in breast cancer cells alters EGFR localization by promoting EGFR nuclear translocation. Importantly, I discovered that the presence of MUC1 mediates EGFR's interaction with chromatin. More specifically, I found that EGFR interacts with the cyclin D1 promoter region in a MUC1-dependent fashion which resulted in a significant increase in cyclin D1 protein expression. Nuclear EGFR localization has been shown to correlate with resistance to anti-EGFR therapies, which indicates that MUC1's interaction with EGFR could be a mechanism of resistance.MUC1's interaction with both EGFR and beta-catenin can promote transformation therefore a peptide therapy was developed, PMIP, which mimics the hypothesized interaction domains of MUC1's cytoplasmic tail. PMIP was designed to inhibit the interaction of MUC1/EGFR and MUC1/beta-catenin thereby regulating EGFR expression and promoting beta-catenin localization to adherens junctions. PMIP effectively enters the cytosol of cells and inhibits the target interactions. Importantly, PMIP inhibited invasion and proliferation of breast cancer cells and in mice significantly reduced the growth rate of breast cancer xenograft and genetically-driven tumors. This study demonstrated that the use of peptides to inhibit intracellular protein interactions is a viable option that would have limited toxic side-effects. Overall, this work reveals a new regulatory role of EGFR localization and activity by MUC1 and that this mechanism is viable therapeutic breast cancer target.Lastly, in a mouse model of breast cancer I examined the role of EGFR tyrosine kinase activity in beta-catenin dependent tumorigenesis. A transgenic mouse model of breast cancer, MMTV-Wnt-1, was bred onto an EGFR kinase deficient background. I discovered that the loss of EGFR kinase activity in this model resulted in a significant delay in tumor onset and inhibited tumor growth. These findings indicate a cooperation of EGFR and beta-catenin dependent signaling pathways, which promote transformation of glandular epithelial cells.