Breast cancers with overexpression or amplification of the HER2 tyrosine kinase receptor are more aggressive, resistant to chemotherapy, and associated with a worse prognosis. Currently, these breast cancers are treated with the monoclonal antibody trastuzumab (Herceptin®). Unfortunately, not all patients respond to trastuzumab drug therapy; some patients show de novo resistance, while others acquire resistance during treatment. This thesis describes our RNAi studies to identify novel regulators of the HER2 signaling pathway in breast cancer. Three kinome-wide siRNA screens were performed on five HER2 amplified and seven HER2 non-amplified breast cancer cell lines, two normal breast cell lines, as well as two HER2-positive breast cancer cell lines with acquired trastuzumab resistance and their isogenic trastuzumab-sensitive controls. To understand the main kinase drivers of HER2 signaling, we performed a comprehensive screen that selected against growth inhibitors of the non-HER2 amplified breast cancer cell lines. This screen identified the loss of the HER2/HER3 heterodimer as the most prominent selective inhibitor of HER2-amplified breast cancers. In a trastuzumab sensitization screen on five trastuzumab-treated breast cancer cell lines, we identified several siRNA against the PI3K pathway as well as various other signaling pathways that inhibited proliferation. Finally, in a screen for acquired trastuzumab resistance, PKCη and its downstream targets were identified. Loss of PKCη resulted in a decrease in G1/S transition and upregulation of the cyclin dependent kinase inhibitor p27. Initial data suggest that PKCη promotes p27 ubiquitination and degradation. Taken together, these studies provide novel insight into the complex signaling of HER2-positive breast cancers and the mechanisms of resistance to trastuzumab therapy. This work describes how various kinases can modulate cell proliferation, and points to possible novel drug targets for the treatment of HER2-positive breast cancers.

No description available.

Les rétinoïdes sont utilisés dans le traitement d’une variété de tumeurs malignes et lésions précancéreuses. Leurs effets dans des lignées cellulaires dérivées de tumeurs solides tel que le cancer du sein ont été étudiés extensivement. Cependant, les bénéfices dans le cancer du sein restent à date peu clairs. Ceci est probablement du à l’hétérogénéité des tumeurs mammaires et la réponse très variable aux effets antiprolifératifs de l’acide rétinoïque. Dans les lignées cellulaires cancéreuses mammaires, la réponse l’AR est fortement corrélée au niveau d’expression du récepteur aux estrogènes alpha (ERα), qui régule l’expression du gène qui encode le récepteur à l’acide rétinoïque alpha, RARA. Malgré cela, certaines lignées cellulaires ER-négatives, comme la lignée HER2-positive SK-BR-3, ont été décrites comme étant sensibles à l’AR. Dans le Chapter 2: de cette thèse, nous avons étudié les mécanismes de la signalisation ER-dépendante et ER-indépendante dans les cellules cancéreuses mammaires. Nous avons utilisé des lignées ER-négatives et ER-positives pour démontrer qu’une partie de la réponse à l’AR est indépendante de la signalisation par ER. Nous avons identifié plusieurs gènes cibles primaires de l’AR qui ont des effets similaires à l’AR quand ils sont surexprimés dans des cellules mammaires cancéreuses. Cette étude apporte une meilleure compréhension des mécanismes complexes qui mènent à l’arrêt de croissance induit par l’AR dans les cellules cancéreuses mammaires. Dans le Chapitre 3, nous avons regardé plus en détails la signalisation ER-indépendante par l’AR dans des cellules ayant une amplification des gènes HER2 et RARA et nous avons identifié une synergie entre l’AR et le Herceptin dans ces cellules. Nous proposons que les gènes FOXO jouent une rôle dans cette synergie. Les cellules SK BR 3, ayant une coamplification HER2/RARA, pourraient représenter une classe de tumeurs qui pourraient bénéficier d’un traitement avec des rétinoïdes, en augmentent la réponse au Herceptin et potentiellement en réduisant la résistance au Herceptin. En conclusion, les données présentées dans cette thèse aident à mieux comprendre les mécanismes menant à l’arrêt de croissance induit par l’AR dans les cellules cancéreuses mammaires et fournissent une application potentielle pour l’utilisation de l’AR dans le traitement du cancer du sein. / Retinoids are being used in the treatment of several malignancies and precancerous lesions. Their effects on cell lines derived from solid tumors, such as breast cancer, have also been described extensively. Their benefit in breast cancer, however, remains unclear. This might be because of the high levels of heterogeneity of breast tumors and the very variable response to the antiproliferative effects of retinoic acid. In mammary tumor cell lines, the response to retinoic acid is highly correlated with the expression of the estrogen receptor alpha (ERα), which regulates the expression of the retinoic acid receptor alpha gene RARA. However, some ER-negative cell lines, such as the HER2 positive SK-BR-3 cell line, have been reported to be RA-sensitive. In Chapter 2: of this thesis we have investigated the mechanisms of ER-dependent and ER-independent RA signaling in breast cancer cells. Using ER-positive and ER-negative cell lines, we show that part of the response to RA is independent of ER signaling. Several direct retinoic acid targets were identified that could mimic antiproliferative effects of retinoic acid when overexpressed in breast cancer cells. This study has provided better insight in the complex mechanisms that lead to RA-induced growth arrest in breast cancer cells. In Chapter 3: we looked further into the ER-independent RA signaling in HER2/RARA-amplified cells and identified a synergy between RA and Herceptin in these cells. We propose a role for FOXOs in mediating this synergy. HER2/RARA coamplified breast tumors might represent a subclass of tumors that could benefit from retinoid treatment, both increase antitumor effects of Herceptin, as well as in potentially reducing Herceptin resistance. In conclusion, data presented in this thesis give better insight in the mechanisms of RA induced growth arrest in breast cancer cells and provide a potential application of retinoids in a subset of breast tumors.

HER2overexpression is associated with poor breast cancer prognosis and increased risk of metastasis. Current HER2targeted therapies include monoclonal antibody based strategies which work by reducing HER2 levels at the cell surface (trastuzumab), by preventing HER2 dimerization (pertuzumab), or via targeted delivery of a cytotoxic payload (trastuzumab emtansine). Although these therapies are successful in some cases, acquired and inherent resistance to these therapeutics remain a treatment hurdle. Oncolytic viruses (OVs) specifically target and lyse cancer cells while leaving normal cells unharmed. One such OV, VSVΔ51, replicates in interferon (IFN) defective cells, a characteristic of approximately 70% of tumours. We hypothesized that the combination of HER2 targeting therapies with VSVΔ51 could improve therapeutic efficacy. We found that HER2 overexpression was associated with increased virus sensitivity and that modulation of HER2 signaling through a subset of activating ligands and inhibitory drugs could influence infection. We further established that the HER2 monoclonal antibodies trastuzumab and pertuzumab mediate an anti-viral effect on VSVΔ51 spread. Finally, we demonstrate that conjugation of a microtubule targeting agent to trastuzumab can overcome the induced anti-viral state and enhance VSVΔ51 spread specifically in cancer cells. Overall, this work highlights the importance of HER2 signaling and activation on VSVΔ51 spread and shows that conjugation of microtubule destabilizing agents to monoclonal antibodies can enhance VSVΔ51 efficacy.

Les rétinoïdes sont utilisés dans le traitement d’une variété de tumeurs malignes et lésions précancéreuses. Leurs effets dans des lignées cellulaires dérivées de tumeurs solides tel que le cancer du sein ont été étudiés extensivement. Cependant, les bénéfices dans le cancer du sein restent à date peu clairs. Ceci est probablement du à l’hétérogénéité des tumeurs mammaires et la réponse très variable aux effets antiprolifératifs de l’acide rétinoïque. Dans les lignées cellulaires cancéreuses mammaires, la réponse l’AR est fortement corrélée au niveau d’expression du récepteur aux estrogènes alpha (ERα), qui régule l’expression du gène qui encode le récepteur à l’acide rétinoïque alpha, RARA. Malgré cela, certaines lignées cellulaires ER-négatives, comme la lignée HER2-positive SK-BR-3, ont été décrites comme étant sensibles à l’AR. Dans le Chapter 2: de cette thèse, nous avons étudié les mécanismes de la signalisation ER-dépendante et ER-indépendante dans les cellules cancéreuses mammaires. Nous avons utilisé des lignées ER-négatives et ER-positives pour démontrer qu’une partie de la réponse à l’AR est indépendante de la signalisation par ER. Nous avons identifié plusieurs gènes cibles primaires de l’AR qui ont des effets similaires à l’AR quand ils sont surexprimés dans des cellules mammaires cancéreuses. Cette étude apporte une meilleure compréhension des mécanismes complexes qui mènent à l’arrêt de croissance induit par l’AR dans les cellules cancéreuses mammaires. Dans le Chapitre 3, nous avons regardé plus en détails la signalisation ER-indépendante par l’AR dans des cellules ayant une amplification des gènes HER2 et RARA et nous avons identifié une synergie entre l’AR et le Herceptin dans ces cellules. Nous proposons que les gènes FOXO jouent une rôle dans cette synergie. Les cellules SK BR 3, ayant une coamplification HER2/RARA, pourraient représenter une classe de tumeurs qui pourraient bénéficier d’un traitement avec des rétinoïdes, en augmentent la réponse au Herceptin et potentiellement en réduisant la résistance au Herceptin. En conclusion, les données présentées dans cette thèse aident à mieux comprendre les mécanismes menant à l’arrêt de croissance induit par l’AR dans les cellules cancéreuses mammaires et fournissent une application potentielle pour l’utilisation de l’AR dans le traitement du cancer du sein. / Retinoids are being used in the treatment of several malignancies and precancerous lesions. Their effects on cell lines derived from solid tumors, such as breast cancer, have also been described extensively. Their benefit in breast cancer, however, remains unclear. This might be because of the high levels of heterogeneity of breast tumors and the very variable response to the antiproliferative effects of retinoic acid. In mammary tumor cell lines, the response to retinoic acid is highly correlated with the expression of the estrogen receptor alpha (ERα), which regulates the expression of the retinoic acid receptor alpha gene RARA. However, some ER-negative cell lines, such as the HER2 positive SK-BR-3 cell line, have been reported to be RA-sensitive. In Chapter 2: of this thesis we have investigated the mechanisms of ER-dependent and ER-independent RA signaling in breast cancer cells. Using ER-positive and ER-negative cell lines, we show that part of the response to RA is independent of ER signaling. Several direct retinoic acid targets were identified that could mimic antiproliferative effects of retinoic acid when overexpressed in breast cancer cells. This study has provided better insight in the complex mechanisms that lead to RA-induced growth arrest in breast cancer cells. In Chapter 3: we looked further into the ER-independent RA signaling in HER2/RARA-amplified cells and identified a synergy between RA and Herceptin in these cells. We propose a role for FOXOs in mediating this synergy. HER2/RARA coamplified breast tumors might represent a subclass of tumors that could benefit from retinoid treatment, both increase antitumor effects of Herceptin, as well as in potentially reducing Herceptin resistance. In conclusion, data presented in this thesis give better insight in the mechanisms of RA induced growth arrest in breast cancer cells and provide a potential application of retinoids in a subset of breast tumors.

Mass spectrometry (MS) is a power analytical tool which is capable of analyzing biomolecules in great detail, both structurally and quantitatively. With regards to glycans, special considerations regarding sample preparation are necessary in order to achieve reproducible identification and relative quantification of these analytes. A workflow for isolation at the glycopeptide level and subsequent detection at the glycan level with phenylhydrazine, demonstrated that monoclonal antibodies (mAbs) containing a specific amino acid mutation were able to express approximately an additional 50% of the α2,6 disialylated glycan compared to their non-mutant analogues. In a second experiment using mAbs, an azide modified glycan (Ac4ManAz) was introduced both metabolically and enzymatically during mAb production. This glycan is a precursor in the sialic acid pathway and the azide moiety allows for specific chemistry post-production including the potential for highly specific enrichment. The results of this workflow demonstrated that [100 μM] of Ac4ManAz precursor added to the cell media was necessary for metabolic expression. More complex samples however, may contain multiple sites of glycosylation. To conserve the site of attachment, these molecules are often studied at the glycopeptide level, and require enrichment of glycopeptides to improve the lower signal intensity observed in the presence of co-eluting peptides. Carboxymethyl chitosan (CMCH) as well as amine-functionalized magnetic-nanoparticles (MNP) were developed as novel materials for this purpose. CMCH is naturally occurring, and therefore is cost-effective and readily available. In a 12 protein mixture CMCH demonstrated the bulk enrichment of glycopeptides yielding an approximately 20% higher enrichment of sialylated species as compared to a commercially available glycopeptide kit through the use of tandem mass tags for relative quantification. In the same approach, amine functionalized MNP were produced and used to enrich glycopeptides from tryptic digests. This approach was fast (about 10 mins) and quantitatively demonstrated improved retention for sialylated species. Examples of these techniques and their applications are reported in this work. / October 2015

HER2 breast cancer is an aggressive disease that occurs in 20 - 30% of the breast cancer population. Treatment for HER2 breast cancer includes use of an anti-HER2 monoclonal antibody, trastuzumab. Testing for HER2 is of critical importance due to the adverse side effects and substantial costs associated with this anti-HER2 treatment. Currently, two kinds of tests, Fluorescence In Situ Hybridization (FISH) and Immunohistochemistry (IHC), are FDA approved for determination of HER2 status in breast cancers. Clinical and non clinical factors that affect the choice HER2 test and the use of anti-HER2 therapy in breast cancer were analyzed using a data set containing information from six outpatient oncology clinics in the United States. The analysis showed that geographic location, cancer stage, and diagnosis date (pre- or post-publication of testing guidelines) have significant effects on choice of test. With regard to trastuzumab prescription, geographic location and HER2 status have significant effects on the prescription of trastuzumab. In addition, there was a non-significant trend for certain Medicare patients not to receive trastuzumab therapy. These findings indicate that disparities are present in breast cancer care based on geography and cancer stage, and highlight the importance of testing guidelines. The cost effectiveness of FISH vs. IHC was determined, by considering the financial and health-related costs associated with testing and subsequent treatment as well as the accuracy of each test. The results show that FISH is the optimal choice for HER2 testing and is more cost-effective than IHC.

No description available.

Cell separation based on antibody-targeted magnetic beads has been widely used in a number of applications in immunology, microbiology, oncology and more recently, in the isolation of circulating tumour cells (CTCs) in cancer patients. Although other cell separation techniques such as size based cell filtration and Fluorescence Activated Cell Sorting have also been in popular use, immunomagnetic cell isolation possesses the advantages of high throughput, good specificity and reduced cell stress. However, certain fundamental features of the cell-bead interface are still unknown. In this study, some of the key features of the cell-bead synapse were investigated in an effort to improve the efficiency of immunomagnetic cell isolation and reduce its dependence on high expressing cell surface markers. A clinically relevant antibody fragment (Fab) against tyrosine kinase receptor HER2 was applied to study the immunomagnetic isolation of HER2 expressing cancer cells. First, the minimum number of target proteins required on a cell for it to be isolated was determined. Second, the importance of the primary antibody affinity was investigated, using a series of Fab mutants with known kinetics and it was shown that despite starting with sub-nanomolar affinity, improving Fab affinity increased cell isolation. Third, the influence of the connection between the primary antibody and the bead was studied by comparing Fab bridged to the magnetic bead via a secondary antibody, Protein L or streptavidin; the high affinity biotin-streptavidin linkage increased isolation sensitivity by an order of magnitude. Fourth, the effect of manipulating cytoskeletal polymerization and cell membrane fluidity using small molecules was tested; cholesterol depletion decreased isolation and cholesterol loading increased cell isolation. The insights from these observations were then applied to isolate a panel of cell lines expressing a wide range of surface HER2. While the standard approach isolated less than 10% of low HER2 expressing cancer cells from spiked rabbit and human blood, our enhanced approach with the optimized cholesterol level, antibody affinity and antibody-bead linkage could specifically isolate more than 80% of such cells. The final part of this work focussed on developing an antibody clamp that could physically restrict the antigen within its binding site on the Fab and prevent antigen dissociation, using the HER2-Fab complex and the anti-myc peptide antibody 9E10. Work from this thesis provides useful insights into the molecular and cellular parameters guiding immunomagnetic cell isolation and can be used to extend the range of target receptors and biomarkers for tumour cell isolation and other types of cell separation, thereby enhancing the power and capacity of this approach.