Cancers display heterogeneity in genetic profiles of the individual cancer cells and in the composition of different malignant and non-malignant cell populations. Such intra-tumor heterogeneity plays a role in treatment response and the emergence of resistance to cancer therapies. Approaches that address this complexity and improve stratification of patients for treatment are therefore highly warranted. Thus, the aims of this thesis were to further develop and apply in situ technologies for expression and mutation analyses of candidate cancer genes to gain a deeper understanding of cancer biology and to study intra-tumor heterogeneity. In paper I, we established and validated a procedure for scalable in situ hybridization of large gene sets in human formalin-fixed paraffin-embedded tissues for analysis of gene expression. This method was used in paper II for large-scale expression analysis of the tyrosine kinome and phosphatome, two gene families whose members are frequently mutated in many forms of cancers. Systematic, compartment-specific expression mapping at cell type resolution enabled us to identify several novel vascular markers that have gone unnoticed in bulk transcriptomic analyses. In papers III and IV, we used padlock probes for in situ mutation detection in single cells for studies of genetic intra-tumor heterogeneity. In paper III, multiplex detection and genotyping of oncogenic point mutations was demonstrated in routinely processed tissue materials, whereas in paper IV we further the application by demonstrating multiplex detection of fusion gene transcripts. Collectively, the work presented in this thesis employs in situ-based methods to obtain spatial resolution of gene expression and mutation patterns in normal and cancer tissues, thereby broadening our understanding of the cancer genome.

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 108-119).

Thèse de doctorat : Pharmacologie moléculaire et cellulaire : Strasbourg 1 : 2008. / Titre provenant de l'écran-titre. Bibliogr. p. 197-221.

Thesis (Ph. D.)--West Virginia University, 2001. / Title from document title page. Document formatted into pages; contains vi, 195 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 182-190).

Thesis (Ph.D.)--University of Alabama at Birmingham, 2008. / Title from PDF title page (viewed on Feb. 18, 2010). Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 180-209).

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 102-112).

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 147-158).

<p>The vasculature has a crucial function in normal physiology, enabling the transport of oxygen and nutrients to cells throughout the body. In turn, endothelial cells, which form the inner-most lining of blood vessels, are key regulators of vascular function. In addition to forming a barrier which separates the circulation from underlying tissues, endothelial cells respond to diverse extracellular cues and produce a variety of biologically-active mediators in order to maintain vascular homeostasis. Disruption of normal vascular function is a prominent feature of a variety of pathological conditions. Thus, elucidating the signaling pathways regulating endothelial function is critical for understanding the role of endothelial cells in both normal physiology and pathology, as well as for potential development of therapeutic interventions.</p><p>In this dissertation, we use a combination of pharmacological inhibition and knockdown studies, along with generation of endothelial conditional knockout mice, to demonstrate an important role of the Abelson (Abl) family of non-receptor tyrosine kinases (Abl and Arg) in vascular function. Specifically, loss of endothelial expression of the Abl kinases leads to late-stage embryonic and perinatal lethality in conditional knockout mice, indicating a crucial requirement for Abl/Arg kinases in normal vascular development and function. Endothelial <italic>Abl</italic>/<italic>Arg</italic>-null embryos display focal regions of vascular loss and tissue damage, as well as increased endothelial cell apoptosis. An important pro-survival function for the Abl kinases is further supported by our finding that either microRNA-mediated <italic>Abl</italic>/<italic>Arg</italic> depletion or pharmacological inhibition of the Abl kinases increases endothelial cell susceptibility to stress-induced apoptosis <italic>in vitro</italic>. The Abl kinases are activated in response to treatment with the pro-angiogenic growth factors vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF). We show that both VEGF- and bFGF-mediated endothelial cell survival is impaired following Abl kinase inhibition.</p><p>These studies have uncovered a previously unappreciated role for the Abl kinases in the regulation of the angiopoietin/Tie2 signaling pathway, which functions to support endothelial cell survival and vascular stability. Loss of Abl/Arg expression leads to reduced mRNA and protein levels of the Tie2 receptor, resulting in impaired activation of intracellular signaling pathways by the Tie2 ligand angiopoietin-1 (Angpt1), as well as decreased Angpt1-mediated endothelial cell survival following serum-deprivation stress. Notably, we found that the Abl kinases are activated following Angpt1 stimulation, suggesting a unique dual role for Abl and Arg in Angpt/Tie2 signaling, potentially modulating Tie2 downstream signaling responses, as well as regulating Tie2 receptor expression.</p><p>Further, we show an important contribution of the Abl family kinases to the regulation of endothelial permeability responses both <italic>in vitro</italic> and <italic>in vivo</italic>. The Abl kinases are activated in response to a diverse group of permeability-inducing factors, including VEGF and the inflammatory mediators thrombin and histamine. We show that inhibition of Abl kinase activity, using either the ATP-competitive inhibitor imatinib or the allosteric inhibitor GNF-2, protects against disruption of endothelial barrier function by the permeability-inducing factors <italic>in vitro</italic>. VEGF-induced vascular permeability similarly is decreased in conditional knockout mice lacking endothelial Abl expression, as well as following treatment with Abl kinase inhibitors <italic>in vivo</italic>. Mechanistically, we show that loss of Abl kinase activity is accompanied by activation of the barrier-stabilizing GTPases (guanosine triphosphatases) Rac1 and Rap1, as well as inhibition of agonist-induced Ca<super>2+</super> mobilization and generation of acto-myosin contractility.</p><p>Taken together, these results demonstrate involvement of the Abl family kinases in the regulation of endothelial cell responses to a broad range of pro-angiogenic and permeability-inducing factors, as well as a critical requirement for the endothelial Abl kinases in normal vascular development and function <italic>in vivo</italic>. These findings have implications for the clinical use of Abl kinase inhibitors.</p> / Dissertation

Focal adhesion kinase (FAK), a non-receptor kinase, is a key regulator of integrin and focal adhesion signaling required for cancer cell survival, cell migration, and cell invasion. Amplification/Overexpression of FAK occurs in a wide variety of human cancers, supporting a role in carcinogenesis. Moreover, preclinical studies using cancer models where FAK is genetically inhibited indicate that this kinase is a potential therapeutic target to interfere with cancer progression. However, very little progress has been made in the identification of chemical inhibitors for potential therapeutic applications, in contrast to other kinases. Herein, I report optimization of the high-throughput in vitro Glo kinase assay for screening inhibitors of FAK kinase activity. Screening a large library of small molecule chemicals using these assays identified at least twenty FAK inhibitors, including a new FAK inhibitor developed by Pfizer and undergoing human clinical trials, and the non-specific kinase inhibitor staurosporine. Molecular studies of selective FAK inhibitors are undergoing in my host laboratory. In addition to this in vitro assay, I established similar assays to examine FAK kinase and adapter function in intact cells. The latter consists of ErbB-transformed cells deficient in FAK, and their matched cells where wild-type or kinase-dead FAK was restored. Biological characterization of these models revealed that both FAK kinase and adaptor activities cooperate for the regulation of cell migration, cell invasion, and tumor formation.