Viruses infecting bacteria (phages) are the most abundant and ubiquitous entities on Earth and likely critical to any ecosystem, as they influence nutrient cycling, mortality and evolution. Ultimately, their impact depends on whether phage—host interactions lead to intracellular phage coexistence (temperate phage) or cell death (lytic phage). Temperate phages in the lysogenic cycle replicate their genome (either integrated into the host chromosome or extrachromosomally), until induced to become lytic, when they create and release progeny via cell lysis. While knowledge on lytic versus lysogenic outcomes is vast, it largely derives from few model systems that underrepresent natural diversity. Further, less is known about the efficiency of phage—host interactions and the regulation of optimal versus sub-optimal lytic infections, which are predicted as relevant under environmental (nutrients, temperature) and host (availability, density) conditions that are common in the ocean. In this dissertation I characterize the phage—host interactions in a new marine model system, phage ϕ38:1 and its Cellulophaga baltica bacterial host, member of the ubiquitous Bacteroidetes phylum. First, I show ϕ38:1’s ability to infect numerous, genetically similar strains of the C. baltica species, two of which display contrasting infection outcomes–lytic versus sub-optimally lytic or lysogenic on the original versus alternative hosts, respectively. Second, I collaboratively apply new gene marker-based approaches (phageFISH and geneELISA) to study ϕ38:1’s infection at the single-cell level and show that it is sub-optimal on the alternative host, rather than lysogenic. Third, I collaboratively develop whole-genome transcriptome datasets for ϕ38:1 infecting both, the optimal and sub-optimal hosts, to characterize the cellular response to infection and hypothesize potential transcriptional and post-transcriptional regulation of the sub-optimal infection. Together, these findings advance our knowledge of naturally-occurring phage—host interactions with a focus on nearly-unstudied sub-optimal infections.

Sex differences exist in the progression of heart disease, as premenopausal women are protected from developing severe hypertension, aortic stenosis, myocardial infarction and hypertrophic cardiomyopathies. The susceptibility and progression of cardiovascular disease increases in post-menopausal women. This is at least partially underlined by a pronounced decrease in circulating estrogen levels. Estradiol (E2), the most abundant estrogen in premenopausal women, is known to be cardioprotective. Recently, AMP-activated protein kinase (AMPK) has emerged as a prominent player in the development of cardiac hypertrophy and heart failure. AMPK is central to the energetic metabolism of the cell and is activated in response to energy deprivation. E2 has been shown to activate AMPK, by yet an unknown mechanism. The first part of this dissertation focuses on describing the molecular mechanism behind this AMPK activation. We found that E2 activates AMPK through a non- genomic pathway and involves direct interaction of classical estrogen receptors (ERα and ERβ) with the α-catalytic subunit of AMPK. These receptors also associate with the upstream kinase LKB1, which is required for E2-dependent activation of AMPK. Furthermore, the two estrogen receptors play opposite roles, where ERα increases AMPK activation, and ERβ acts as a repressor, inhibiting AMPK phosphorylation. To translate our findings to heart disease, the next step was to determine the effect of ovarian failure, underlined by E2 loss, on AMPK signaling during the progression of cardiac hypertrophy. We hypothesized that ovarian failure decreases cardiac AMPK signaling, translating in worsening of hypertrophy. We found that the status of cardiac AMPK signaling depends on the nature of the hypertrophic stimulus and the timing of ovarian failure in relation to the onset of hypertrophy. Furthermore, we did not detect any differences in the development of cardiac hypertrophy between wild type mice and mice in ovarian failure, which most likely occur down the line. In summary we described a novel mechanism of AMPK activation by the hormone E2. We also explored the effect of estrogen loss on cardiac AMPK activity, and found that it is dependent on factors such as the pathological state of the heart and timing of the intervention. These findings add to our understanding of the molecular mechanisms behind sex differences in energy handling and in the future could be translated into better therapeutics for the treatment of cardiac pathologies.

A cell's ability to sense and respond to mechanical signals highlights the significance of physical forces in biology; however, to date most biomedical research has focused on genetics and biochemical signaling. We sought to further understand the physical mechanisms that guide the cellular migrations that occur in a number of biological processes, such as tissue development and regeneration, bacterial infections and cancer metastasis. We investigated the migration of single cells and determined whether the biomechanics of these cells could be used to elucidate multi-cellular mechanisms. We first studied Borrelia burgdorferi (Bb), the bacterium that causes Lyme disease. We created a mathematical model based on the mechanical interactions between the flagella and cell body that explained the rotation and undulation of the cell body that occurs as the bacterium swims. This model further predicts how the swimming dynamics could be affected by alterations in flagellar or cell wall stiffnesses. Fitting the model to experimental data allowed us to calculate the flagellar torque and drag for Bb, and showed that Treponema pallidum (Tp), the syphilis pathogen, is biomechanically similar to Bb. Next, we used experimentally-determined parameters of Bb's motility to develop a population-level model that accounts for the morphology and spreading of the "bulls-eye" rash that is typically the first indicator of Lyme disease. This work supported clinical findings on the efficacy of antibiotic treatment regimes. Finally, we investigated the dynamics of epithelial monolayers. We found that intracellular contractile stress is the primary driving force behind collective dynamics in epithelial layers, a result previously predicted from a biophysical model. Taken together, these findings identify the relevance of physics in cellular migration and a role of mechanical signaling in biomedical science.

A fundamental problem in developmental and evolutionary biology is understanding the developmental genetic basis of morphological diversity. The current paradigm holds that a genetic and developmental program, or developmental genetic "toolkit", conserved across hundreds of millions of years patterns development in all metazoans. However, outside of a few well-characterized signal transduction pathways and developmental processes, overly broad strokes have been used to paint this "toolkit" metaphor as a hypothesis. Arthropoda, one of the largest groups of metazoans, represent the most morphologically diverse groups of metazoans, making them of particular interest for studies of morphological diversity and its evolution. Arthropoda is also home to one of the most well-understood model systems for developmental and genetic studies, the fruit fly Drosophila melanogaster. However, Drosophila is highly derived among arthropods with respect to the molecular genetic mechanisms that function during its development. As it is expected that all arthropods have access to the same development "toolkit", some changes are expected based on the observable differences in morphology, making arthropods extremely powerful tools for comparative genomic and molecular genetic studies. In this dissertation I characterize how modifications to the developmental "toolkit" contribute to the evolution of morphological diversity using emerging model arthropod systems. First, as part of a collaboration, I show that several genes expected to be conserved in all arthropods, belonging to the Hox family of transcription factors, have been lost from the genome of a phylogenetically basal arthropod, the two-spotted spider mite Tetranychus urticae. Second, I perform a genomic survey and find an overall reduction in the conservation of Drosophila orthologs from several major signal transduction pathways in the Tetranychus genome in comparison with findings from previous insect surveys. Third, I show that arthropod Hox genes, expected to be found in a tightly linked genomic cluster in most arthropod genomes, are not as tightly clustered as previously thought. Fourth, I show that changes in the genomic arrangement of Tetranychus Hox genes correspond with shifts in their expression and morphological change. Finally, I show the terminal Hox gene Abdominal-B is required for proper axial elongation and segment formation (both segment identity and number) during embryogenesis and metamorphosis in the red-flour beetle Tribolium castaneum. Taken together, these findings advance our knowledge of the evolution of morphological change, with a primary focus on Hox genes and their contribution to axial patterning during development.

The relationship between MUC1 and EGFR has been characterized by our lab to be highly tumorigenic. A peptide therapeutic was developed in our lab to block the cytoplasmic interaction of MUC1 and EGFR by competing with the EGFR-binding domain of MUC1. The peptide, PMIP, reduced invasion and proliferation in vitro and reduced tumor growth and metastasis in vivo. These studies demonstrated the potency of MUC1/EGFR interactions in tumor progression, and we sought to explore this concept further. We wanted to clarify a mechanism by which MUC1 and EGFR together drive breast cancer metastasis, and we identified c-Met as a mediator of MUC1 and EGFR-driven cell motility. In two separate assays, we demonstrated that c-Met activity was necessary for MUC1 and EGFR to promote migration and invasion. In addition, we wanted to identify the role of EGFR membrane localization in membrane identity and tumor initiation. We established several EGFR localization mutants to compare to wild-type basolateral EGFR and we performed proof-of-concept experiments to show that these mutants will be useful in future studies. Finally, we studied the effect of MUC1 and EGF loss on tissue architecture and function in the lactating mammary gland. EGF is the primary ligand for EGFR during lactation, and MUC1 is highly expressed during this period of mammary development. In addition, it has been shown that EGFR and MUC1 interact at the apical cell surface of lactating mammary ducts, yet there is no link between lactation and tumor formation. We hypothesized that MUC1 and EGFR interaction may have a role in maintaining tissue architecture and lactation function in the mouse mammary gland. We found instead that the loss of MUC1 and EGF had no noticeable effect on lactation and did not result in tissue defects. These studies further clarified the relationship between MUC1 and EGFR in several different contexts, showing a role for their interaction in metastatic progression, and showing that their ablation has no effect in the lactating mammary gland. Future studies will elucidate the role of MUC1 and EGFR interaction in tumor initiation, and we have taken several steps in our studies toward that goal.

Pleckstrin homology (PH) domains are structurally conserved domains, which generally bind to phosphatidylinositol phosphate (PtdInsP) lipids. They are present in a variety of proteins, including those that are upregulated in cancer growth and metastasis, and represent a crucial component of intracellular signaling cascades and membrane translocation. Thus, they may be considered as attractive targets for cancer drug therapy. AKT (protein kinase B), a pleckstrin homology lipid binding domain and a serine/threonine kinase-containing protein, is a key component of the phophatidylinositol-3-kinase (PI3K)/AKT cell survival signaling pathway which is activated in a variety of cancers, including prostate, pancreatic, and skin cancers. In this study, I report the finding of a novel inhibitor of AKT; PH-427. I describe its effects on binding to the PH domain of AKT thus preventing its binding to PtdIns3-P at the plasma membrane and subsequent activation. In vivo testing of the drug led to reduction of tumor size and numbers in a mouse pancreatic cancer model. Additional testing of PH-427 on squamous cell carcinomas revealed that the drug is able to reduce tumor burden and multiplicity in vivo when topically applied. Thus, we demonstrate proof-of-principle in targeting PH domains as a viable cancer drug therapy option. The effects of PH-427 raised the intriguing possibility that targeting PH domains may have beneficial effects in other signaling pathways with PH domain-containing proteins. Guanine exchange factors (GEFs) contain a Dbl homology (DH) domain and a PH domain and have been shown to be involved in the process of metastasis. More specifically, RacGEFs activate Rac1 GTPase by facilitating the exchange of GDP to GTP. Over-expression of certain GEFs has been shown to contribute to increased malignancy in a variety of cancers. T-lymphoma invasion and metastasis-inducing protein-1 (Tiam1) is a highly conserved GEF and contains an N-terminal pleckstrin homology domain (nPH) and a DH/C-terminal PH domain (cPH). Tiam1 has been found to be over-expressed in several cancers, including breast, colon and prostate cancers. In this study, I describe the identification, development, experimental testing, and potential mechanism of action of novel small molecule inhibitors targeting the RacGEF Tiam1 to inhibit prostate cancer bone metastasis.

Dysregulation of cellular metabolism is associated with multiple diseases including cancer. Polyamines are organic cations shown to control gene expression at the transcriptional, post-transcriptional, and translational level. The activity of ornithine decarboxylase (ODC), the first enzyme in polyamine synthesis, is associated with normal and neoplastic growth. A single nucleotide polymorphism (SNP, rs2302615, SNP +316 nucleotides 3' of the transcriptional start site) in the ODC1 gene has been found to be both functional and prognostic for risk of colorectal carcinogenesis. A comprehensive investigation of genetic variability in ODC1 gene was performed. We confirmed frequencies of 12 SNPs occurring in participants of a clinical cancer prevention trial. We identified haplotypes accounting for over 90% of the genetic diversity in the ODC1 gene. Mechanistically, we addressed two of them, which account for more than half of the participants in the clinical trial. Two ODC1 intron 1 SNPs, rs2302616 (SNP +263 nucleotides 3' of the transcriptional start site) and rs2302615, were found to be associated with disease processes. Both of them predicted metachronous adenoma and response to agents targeting the polyamine pathway in participants of the clinical trial. The rs2302616 functionally modulate a DNA G-quadruplex structure and predicted the ODC1 rate-limiting product putrescine by genotype. Both SNPs cooperate to modulate ODC1 transcriptional activity involving both a G-quadruplex structure and Sp1 binding site at rs2302616, and rs2302615 flanked MYC-binding E-boxes. Haplotype analysis, using both these SNPs, might provide better discrimination of both disease prognosis and treatment prediction in cancer chemoprevention clinical trials.

Obesity rates have risen steeply in recent decades. This is accompanied with increased prevalence of several obesity-related disorders including type 2 diabetes. Genetic, environmental, and lifestyle factors (increased caloric intake and/or decreased physical activity) predispose individuals to type 2 diabetes by decreasing the body's responsiveness to the pancreatic hormone insulin, a physiological phenomenon commonly referred to as insulin resistance. Insulin resistance occurs due to induction of inflammation characterized by increased secretion of pro-inflammatory cytokines from enlarged adipose tissue, endoplasmic reticulum stress, and oxidative stress associated with excess blood glucose. There is a strong correlation between insulin resistance and decreased circulating levels of adiponectin (APN), a hormone implicated in promoting insulin-like activities. Further, inflammation negatively affects both insulin and adiponectin levels. It is recognized that folding of APN 18mer-subunits (insulin-sensitizing oligomer) is hindered in obese and type 2 diabetic individuals. Likewise, formation of normal hexameric insulin complex is compromised in type 2 diabetes. Insulin biogenesis, packaging, and assembly are impaired and unable to compensate for high blood glucose levels. As insulin and APN are key metabolic hormones essential for proper glucose regulation, maintaining their correct folding and assembly is required for conserving overall metabolic homeostasis. This dissertation centers on investigating proper assembly pathways of APN and insulin isoforms to form the higher order complexes necessary for their function. The interaction between APN oligomers was studied in the presence and absence of zinc, previously shown to inhibit formation of disulfide bonds in APN. We observed that zinc protects APN from collapse under acidic conditions and likely stabilizes oligomers through high affinity histidine coordination. The interaction between oligomers was further assessed by analyzing conformational differences between oligomers through tryptophan fluorescence. Reduced oligomers were observed to have significant structural differences compared to oxidized oligomers indicated by changes in fluorescent intensities. The capacity of APN chaperone DSBA-L to promote assembly was also evaluated although no significant changes were observed. In addition, the interaction between zinc and insulin was assessed where we observed that in the presence of zinc, insulin is significantly protected from reduction and precipitation. Zinc formed large complexes with insulin under reducing environments to induce high structural stability of insulin oligomers. We then utilized the strong conformational stability of insulin to develop a novel insulin analog with properties to slowly release insulin in circulation and more quickly in the presence of high glucose concentrations. Insulin modification is at preliminary stages and requires further experimentation. Together, these results indicate that zinc plays a significant role in multimerizing properties to provide high stability towards APN and insulin structures. Zinc enhances multimerization of oligomers to both promote activity of APN and protect insulin from reduction and premature breakdown to monomers. Through this study we better identified the folding pathway of APN and elucidated the strong intermolecular forces involved in oligomer association. In addition, the multimerization pattern of insulin to large conformation complexes is observed to mediate protection under reducing conditions. This has implications in the development of new therapeutic options to promote insulin-sensitization and insulin activity to regulate plasma glucose levels. In addition, we propose the development of a novel insulin-analog to mimic physiological insulin secretion, currently unavailable in the market.

No description available.

Growing evidence indicates that serine proteases known as kallikreins are associated with malignancy and may have potential diagnostic/prognostic applications in cancer. Kallikreins are the largest group of serine proteases. Kallikrein enzymes are often involved in proteolytic cascades through their function in degradation of extracellular matrix proteins and promotion of angiogenesis. Kallikrein 6 (KLK6) is a member of the family of fifteen highly conserved secreted trypsin- or chemotrypsin-like serine proteases. Over-expression of KLK6 has been observed in different pathophysiological states such as neurodegenerative diseases, inflammation and various cancers, including colorectal cancer. In Chapter 3 we elucidated the miRNA-based mechanism of regulation of invasion in metastatic colorectal cancer over-expressing KLK6. We developed HCT116 colon stable isogenic cell lines with knockdown of KLK6 expression using short-hairpin interference RNA (shKLK6 clones). The shKLK6 clones had decreased expression and secretion of KLK6 protein with a minimal effect on cell growth and viability in cell culture. SCID mice injected with shKLK6-3 clone 3 cells exhibited a statistically significant increase in the survival rates (P=0.005), decrease in the incidence of distant metastases and a shift in the location of the metastatic foci closer to the cell's injection site. Levels of KLK6 protein secreted into the bloodstream were significantly lower in animals injected with shKLK6-3 clone 3 compared to HCT116 control clone 1 (P < 0.04). Through bioinformatics analyses we identified and validated three miRNAs, which are important in post-translational modification of bioactive proteins, proliferation, migration and p38 MAPK signaling pathway. In Chapter 4 we developed Caco-2 colon stable isogenic cell lines with expressing enzymatically active or mutant KLK6 protein (Caco-2 stable clones). We employed these cell lines to investigate the importance of KLK6 enzymatic activity of initiation of cell invasion using in vitro and in vivo models.