This study investigated genetic predictions for amino acid biosynthesis and catabolism by Lactobacillus helveticus CNRZ 32, a commercial cheese flavor adjunct that reduces bitterness and intensifies flavor notes. Conversion of amino acids into volatile and nonvolatile flavor compounds by L. helveticus and other lactic acid bacteria in cheese is thought to represent the rate-limiting step in the development of mature cheese flavor and aroma. One of the primary mechanisms for amino acid breakdown by these microbes involves the reversible action of enzymes involved in biosynthetic pathways, so our group investigated the genetics of amino acid biosynthesis in L. helveticus CNRZ 32. Most lactic acid bacteria are auxotrophic for several amino acids, and phenotypic characterization of L. helveticus CNRZ 32 has shown this bacterium requires 14 amino acids. Reconstruction of amino acid biosynthetic pathways from a draft-quality (incomplete) genome sequence for L. helveticus CNRZ 32 showed generally good agreement between gene content and phenotypic amino acid requirements. One exception involved the requirement ofCNRZ 32 for Asp (or Asn) for growth, where predictions derived from the genome sequence suggested this strain may be able to synthesize Asp from citrate. This prediction was confirmed as Asp auxotrophy in L. helveticus CNRZ 32 could be alleviated by the addition of citrate to a chemically defined medium that lacked Asp and Asn. Genome analysis also predicted that L. helveticus CNRZ 32 possessed ornithine decarboxylase activity, and would therefore catalyze the conversion of ornithine to putrescine, a volatile biogenic amine. Putrescine production in cheese would be undesirable because this compound may impart a rotting flesh flavor and can also have adverse effects on human health. Experiments to confirm ornithine decarboxylase activity in L. helveticus CNRZ 32 using a special growth medium, thin layer chromatography, high performance liquid chromatograph, or 13C nuclear magnetic resonance were unsuccessful, however, which indicated this bacterium does not contribute to putrescine production in cheese.

TRPM7 (Transient Receptor Potential Melastatin-like 7) is an ion channel necessary for the proper development of many cell types. Insight into the precise role of the channel in different cells has been hampered by the lethality of knocking out the gene in model organisms such as the mouse. Here I examine a zebrafish that has a loss-of-function mutation in the gene encoding Trpm7. First, I show that trpm7 is important for the function of developing dopaminergic neurons in the zebrafish. Second, I examine the interaction between trpm7 and the related gene vmat2 in order to develop a cellular mechanism of trpm7 function in presynaptic dopaminergic neurons. Finally, I investigate the necessity of the kinase and ion channel domains of trpm7 in their ability to promote pigmentation in melanophores as a model cell type. Based on the results from these experiments and observations from other researchers, I form a new hypothesis for Trpm7 function in protein sorting. These studies provide a detailed and novel analysis of the function of an ion channel that is necessary for life.

The regenerative tissues such as hair follicles, intestine and teeth have a particular microenvironment known as “stem cell niche” which houses stem cells and act as a signaling center to control stem cell fate. The precise and timely regulation of stem cell renewal and differentiation is essential for tissue formation, growth and homeostasis over the course of a lifetime. However, the molecular underpinning to control this regulation is poorly understood. To address this issue, we use the continuously growing mouse incisor as a model to study the gene regulatory network which controls dental epithelial stem cell (DESC) maintenance, growth and craniofacial morphogenesis. We found FoxO6, a transcription factor mainly expressed in the brain and craniofacial region, control DESC proliferation by regulating Hippo signaling. FoxO6 loss-of-function mice undergo increases in cell proliferation which finally leads to lengthening of the incisors, expansion of the face and skull and enlargement of the mandible and maxilla. We have screened three human FOXO6 single nucleotide polymorphisms which are associated with facial morphology ranging from retrognathism to prognathism. Our study also reveals that Sox2 and Lef-1, two markers for early craniofacial development, are regulated by Pitx2 to control DESC maintenance, differentiation and craniofacial development. Conditional Sox2 deletion in the oral and dental epithelia results in severe craniofacial defects, including ankyloglossia, cleft palate, arrested incisor development and abnormal molar development. The loss of Sox2 in DESCs leads to impaired stem cell proliferation, migration and subsequent dissolution of the tooth germ. On the other hand, conditional overexpression of Lef-1 in oral and dental epithelial region increases DESC proliferation and creates a new labial cervical loop stem cell compartment in dental epithelial stem cell niche, which produces rapidly growing long “tusk-like” incisors. Interestingly, Lef-1 overexpression rescues the tooth arrest defects but not the ankyloglossia or cleft palate in Sox2 conditional deletion mice. Our data also reveal that miRNA and histone remodeler are involved in regulating DESC proliferation and craniofacial morphogenesis. We describe a miR-23a/b:Hmgn2:Pitx2 signaling pathway in regulating dental epithelial cell growth and differentiation. Pitx2 activates expression of amelogenin which is the major protein component for enamel deposition. This activation can be repressed by the chromatin-associated factor Hmgn2. miR-23a and miR-23b directly target Hmgn2, leading to the release of the Hmgn2 inhibition of Pitx2 transcriptional activity and thus enhance Amelogenin production. Phenotypically, ablation of Hmgn2 in mice results in an overgrowth of incisors with increased Amelogenin expression. The findings in this study increase our current understanding of the molecular regulation of dental epithelial stem cell fate. It not only highlights new gene regulatory network that controls dental stem cell maintenance, growth and craniofacial morphogenesis, but also sheds new light on developing novel stem cell therapy or gene therapy for tooth regeneration and dental diseases.

Cleft lip and/or palate (CL/P) is a group of congenital birth defect caused by the failure of the lip and/or palate to properly fuse during facial development. This defect occurs in approximately 1:700 live births and is the most second most common developmental defect. Twin studies and evaluation of family history reveals that risk for CL/P is influenced by genetics. However, to date less than half of the heritable risk for CL/P has been ascribed to specific genes. To identify new genes involved in CL/P, our colleagues, Dr. Manak and Dr. Murray, screened DNA from CL/P patients for rare copy number variants. A single copy deletion of Isthmin1 (ISM1) was identified in this screen. To test the hypothesis that this deletion contributed to the pathogenesis of CL/P we conducted functional tests of the zebrafish ortholog, isthmin1. The results indicated that Ism1 is necessary for development of the face in zebrafish, supporting the hypothesis. Together with Dr. Bassuk, we applied a similar approach to another structural birth defect, spina bifida. Dr. Manak discovered a de novo single copy deletion encompassing Glypican 5 (GPC5) and part of Glypican 6 (GPC6) in a spina bifida patient. Our functional tests in zebrafish support the notion that mutations in GPC5 cause spina bifida in some patients. To identify additional CL/P loci, we investigated two putative transcriptional targets of Interferon Regulatory Factor 6 (IRF6), a transcription factor encoded by a gene which is mutated in the majority of patients with Van der Woude orofacial clefting syndrome. The Cornell lab found evidence that Irf6 regulates expression of grhl3 and klf4 in zebrafish periderm. Partly in response to our findings, Jeff Murray's group sequenced the coding region GRHL3 gene in Van der Woude patients lacking IRF6 mutations and found 8 different coding mutations in GRHL3. We tested 5 of theses GRHL3 mutations in zebrafish-based functional studies, and found the 5 patient-derived GRHL3 variants had dominant negative effects. We conclude that GRHL3 is indeed a CL/P locus. Because all the patient derived variants were dominant negative (as opposed to null), and because such variants would be expected to block the function of the other copy of GRHL3 as well as other family members (GRHL1 and GRHl2), which are also cleft candidate genes. Multiple KLF4 coding mutations were also detected in patients with CL/P. We tested one of them but did not detect evidence of disruption in protein function. We conclude that this mutation does not seem to affect the function of KLF4, even though it was predicted to be damaging. This enforces the idea that conclusions from in silico studies should be examined in vivo. Finally, the protein structure of Irf6 has been examined to identify important residues within the C-terminus of the protein. Using constructs built by Dr. Mankad, we tested 5 different phosphor-mimetic amino acid substitutions. Of the variety of constructs, only Irf6 S447D in zebrafish Irf6 was able to cause ectopic expression of downstream Irf6 targets. This predicts that phosphorylation at S447 is sufficient to activate Irf6. All of these studies have expanded our understanding of the genetics behind CL/P, either by discovering new loci in human patients and testing them in Danio rerio, or from finding downstream targets of Irf6 in zebrafish, sequencing human patients for mutations in those genes, and then testing the functional changes of those variants. From our work with zebrafish, we can determine additional components of the IRF6 regulatory network.

Tooth development is precisely controlled by epithelium-mesenchyme interactions, coordinated signaling pathways and associated transcription factors. Although the processes involved in tooth development are well established, details of the cellular and molecular mechanisms that control tooth development are not fully understood. One of the primary unknown mechanisms is the regulation of dental epithelial stem cells (DESCs), including DESC specification, proliferation and differentiation. In this dissertation, I have addressed this gap in knowledge by studying the role of Pituitary homeobox 2 (Pitx2) and Iroquois 1 (Irx1) in teeth at the cellular and molecular level in mice. PITX2 contains mutations of which are associated for Axenfeld-Rieger syndrome (ARS) in humans and is also required for early tooth development. All the background knowledge is included in Chapter I. In Chapter II, I describe the conditional ablation of Pitx2 in the dental epithelium using a Krt14Cre driver line (Pitx2cKO mice). Knocking out Pitx2 in teeth led to delayed epithelial invagination at bud stage and disruption of tooth morphogenesis at cap stage. At the cellular level, Pitx2 mediates DESC differentiation, daughter cell proliferation in bud stage tooth and regulates enamel knot formation in cap stage tooth. At the molecular level, Pitx2 acts as an upstream regulator of the sonic hedgehog (Shh) signaling pathway by regulating the expression of Shh in the dental epithelial signaling center during early tooth development. In addition, I demonstrated that Pitx2 directly controls the transcription of Irx1. In Chapter III, I determined the cellular and molecular mechanisms of Irx1 in mice. Irx1 general knockout mice were generated by replacing the entire Irx1 gene body with a LacZ reporter gene. Irx1 null mice are neonatal lethal and this lethality is due to pulmonary immaturity with defective surfactant protein secretion. In teeth, Irx1 is expressed in the outer enamel epithelium (OEE) and stratum reticulum (SR) and mediates DESC to OEE and SR differentiation through regulation of Forkhead box protein J1 (Foxj1) and Sex determining region Y-box9 (Sox9). In summary, I identified a Pitx2-Irx1 regulatory network that controls DESC differentiation in teeth, which provided the field with a better understanding of tooth development and tooth regeneration.

B and T lymphocytes are critical to the adaptive immune response against invading microorganisms. B and T cells develop in the bone marrow and thymus, respectively, and initiate a series of proliferative responses once they encounter their cognate antigen in the peripheral lymphoid organs. These developmental and functional processes are controlled by different networks of transcriptional regulators that repress and activate gene expression. Identifying proteins that activate or repress specific genes and integrating these proteins into their transcriptional networks is critical to understanding lymphocyte development and function. The study of B lymphopoiesis and CD4+ T cell functional responses has greatly increased our understanding of how transcriptional regulators and other proteins cooperate to specify cell fates and responses. While many of the key components of these protein networks have been defined, several factors have yet to be described. Chemically induced random mutagenesis is a powerful tool for identifying genes that have critical biological functions. Justy mutant mice were generated by injecting wild-type mice with of N-Ethyl-N-Nitrosourea (ENU), a mutagen, which generated a unique point mutation in the mouse Gon4-like (Gon4l) gene. This mutation was found to specifically blunt B cell development and impair the functional responses of CD4+ T cells. Given that the Gon4l protein contains domains implicated in transcriptional regulation and B lymphopoiesis and T cell responses are regulated transcriptionally, the aim of this project was to characterize T and B lymphocyte populations from Justy mice and provide insights into the mechanisms underlying the regulation of gene expression during these biological processes. The work presented in this dissertation demonstrates that the protein encoded by Gon4l is essential for B lymphopoiesis, likely through the repression of alternate lineage genes. This work also shows that in CD4+ T cells, decreased Gon4l protein expression results in reduced levels of proliferation in response to exogenous IL-2 or T cell receptor (TCR) engagement. Additionally, Justy mutant CD4+ T cells display a reduced ability to generate IFNγ-producing cells in response to Th1 polarization in vitro. Collectively, these defects correlate with elevated levels of genes known to specifically inhibit the above developmental and functional processes. Thus, this dissertation proposes that Gon4l acts as a transcriptional repressor within the protein networks controlling B lymphopoiesis and CD4+ T cell responses.

Gynecological cancers present a tremendous disease burden worldwide. Endometrial cancer, the most common gynecological malignancy, is predominantly a disease of deranged glandular function. The mechanisms by which known environmental risk factors influence the mutational profile of endometrial cancer are poorly understood. Non-HPV vulvar cancer, on the other hand, is a very rare gynecological malignancy of vulvar squamous cells with little known about its pathogenesis. Surgical resection of vulvar cancer is associated with high post-surgical morbidity. Pivotal to improving treatment and outcomes for patients with gynecological cancers is an understanding of the molecular drivers unique to each tumor type. To inform our understanding of endometrial gland regulation, I began my investigations with an assessment of normal endometrial adenogenesis in vivo and present the first evidence implicating the necessity of Sox17 in endometrial gland development. My data suggest Sox17 mediates adenogenesis via a non-cell autonomous mechanism from within the stromal compartment of the endometrium. I then interrogated the contribution of SOX17 to dysregulated glandular function in Type I endometrial adenocarcinoma in vitro. My findings reveal an oncogenic role of SOX17 in the Ishikawa Type 1 endometrial cancer cell line, with homozygous loss of SOX17 impairing cellular proliferation, blunting the cancer phenotype of these cells. The majority of cancers, including gynecological cancers, develop from the accumulation of genetic mutations that occur sporadically in cells over time. The complexity and heterogeneity of solid tumors, however, renders the identification of mutations responsible for driving tumorigenesis difficult. The Sleeping Beauty (SB) insertional mutagenesis system can be used to streamline sporadic tumor formation and driver mutation identification. I present results from an initial attempt to develop an SB model of endometrial cancer and discuss ways in which the SB system can be harnessed to evaluate tumorigenesis in a variety of tissue types and microenvironmental contexts. Finally, I present an SB model of metastatic vulvar cancer. Primary tumors from this model resulted in the identification of 76 novel candidate drivers of vulvar cancer, with the ubiquitin-specific peptidase, Usp9x, the most commonly disrupted gene in our screen. I show data suggesting that differential expression of Usp9x isoforms may underlie Usp9x-mediated tumorigenesis and preliminary data demonstrating the relevance of USP9X to human vulvar cancer. Taken as a whole, these data contribute to our scientific understanding of gynecological tissue homeostasis and cancers, lay the foundation for the development of an SB model of endometrial cancer, and describe the first reported model system for studying HPV-naive vulvar cancer in vivo.

Neurons are specialized cells that communicate via electrical and chemical signaling. It is well-known that homeostatic mechanisms exist to potentiate neuronal output when activity falls. Likewise, while neurons rely on excitable states to function, these same excitable states must be kept in check for stable function. However, the identity of molecular factors and pathways regulating these pathways remain elusive. Chapter 2 of this thesis reports the findings from an RNA interference- and electrophysiology-based screen to identify factors necessary for the long-term maintenance of homeostatic synaptic potentiation. Data is reported to resolve a long-standing question as to the role of presynaptic Cav2-type channels in homeostatic synaptic potentiation at the Drosophila NMJ. It is shown that reduction in Cav2 channel expression and resultant activity is not sufficient to occlude homeostatic potentiation. Thus, the homeostatic block of a amino-acid substituted Cav2-type calcium channel (cacS) channel is presumed to be due to loss of a specific signaling or binding activity, but not due to overall diminishment in channel function. It is also reported that both Drosophila homologs of phospholipase Cβ (PLCβ) and its putative activator Gαq were found to be necessary for a scaling up of neurotransmitter release upon genetic ablation of glutamate receptors. These factors are canonically involved in the activation of intracellular calcium stores through the inositol trisphosphate receptor (IP3R) and the closely related ryanodine receptor (RyR). Likewise, the Drosophila homolog of Cysteine String Protein (Csp) is identified as important for long-term homeostatic potentiation. CSP has also been reported to be involved in regulation of intracellular calcium. PLCβ, Gαq, and CSP are also known to regulate Cav2-type channels directly, and this possibility, as well as others, are discussed as mechanisms underlying their roles in homeostatic potentiation. Chapter 3 of this thesis reports the extended findings from expression of a gain-of-function Cav2-type channel. The Cav2.1 channel in humans is known to cause a dominant, heritable form of migraine called familial hemiplegic migraine (FHM). Two amino-acid substitutions causative for migraine were cloned into their analogous residues of the Drosophila Cav2 homolog. Expression of these migraine-modeled channels gave rise to several forms of hyperexcitability. Hyperexcitability defects included abnormal evoked waveforms, generation of spontaneous action potential-like events, and multi-quantal release. It is shown that these forms of hyperexcitability can be mitigated through targeted down-regulation of the PLCβ-IP3R-RyR intracellular signaling pathway. Chapter 4 presents an extended discussion as to the roles for presynaptic calcium channels, PLCβ, and CSP in homeostatic synaptic potentiation, and the mechanism underlying hyperexcitability downstream of gain-of-function Cav2-type channels. The proposed model aims to bridge the involvement of the PLCβ pathway in both homeostatic potentiation and neuronal excitability. Last, the implications for these findings on human disease conditions are elucidated.

Patients with Axenfeld-Rieger Syndrome (ARS) present various dental abnormalities. ARS is genetically associated with mutations in the PITX2 gene, which encodes one of the earliest transcription factors to initiate tooth development. Thus, Pitx2 has long been considered as an upstream regulator of the transcriptional hierarchy in tooth development. However, it is unclear how its mutant forms cause ARS dental anomalies. In this report, we outline the transcriptional mechanism that is defective in ARS. We demonstrate that during normal tooth development Pitx2 activates Amelogenin (Amel) expression, whose product is required for enamel formation, and that this regulation is perturbed by missense PITX2 mutations found in ARS patients. We further show that Pitx2-mediated Amel activation is enhanced and controlled by co-factors and target genes of Pitx2. These co-factors include cooperative transcription factors such as Dlx2 and FoxJ1; chromatin-associated remodeler factor Hmgn2; and Wnt signaling components such as Lef-1, β-catenin and Dact2. We also unveil a novel Pitx2 target gene Irx1 that functions in dental epithelium differentiation. Consistent with a physiological significance to these modulations, we show that FoxJ1, Dact2, Irx1 knockout mice and K14-Hmgn2 transgenic mice display various types of amelogenesis defects including enamel hypoplasia - consistent with the human ARS phenotype. Collectively, these findings define transcriptional mechanisms and multi-level regulations involved in normal tooth development and shed light on the molecular underpinnings of the enamel defect observed in ARS patients who carry PITX2 mutations. Moreover, our findings validate the etiology of the enamel defect in novel mouse models of enamel hypoplasia. The impact of this study on current understanding of the dental epithelium development and the translational value lie in the gene network we identified. By manipulating components of the network, pluripotent dental cells can be reprogrammed and serve as new source for tooth regeneration. Our findings brought insights of novel gene therapy approach that can alleviate the dental problems of patients with ARS and other developmental anomalies.

Nox1 is of considerable importance because of its involvement in a wide variety of pathologies. Activation of Nox1 induces generation of reactive oxygen species (ROS) and cell migration, events critical for the pathogenesis of cardiovascular disease, amyotropic lateral sclerosis, gastrointestinal disease, immunological disorders, and multiple forms of cancer [1-8]. In order to best determine how to treat Nox1-mediated disease, we must gain a better understanding of the mechanisms that control Nox1 activation. Within the last decade, many studies have found that protein phosphorylation and protein trafficking are critical regulatory mechanisms that control the activation of multiple Nox proteins. Yet, to date, no studies have characterized Nox1 phosphorylation or trafficking. We hypothesized that the activity of Nox1 is controlled by its phosphorylation at specific residues and by its sub-cellular localization; and that modifying Nox1 phosphorylation or localization will alter Nox1-dependent signaling. To test this hypothesis, we utilized both in vivo and in vitro approaches. We found that phosphorylation of Nox1 is significantly increased under pathological conditions in three in vivo models: (1) in atherosclerotic vs. normal aorta from monkey, (2) in neointimal vascular smooth muscle cells (VSMCs) vs. medial VSMCs from rat following aortic balloon injury, and (3) in ligated vs. normal carotid from mouse. Studies using mass spectroscopy, pharmacological inhibition, siRNA, and in vitro phosphorylation identify PKC-βI as a kinase that mediates Nox1 phosphorylation and subsequent ROS production and VSMC migration. Site-directed mutagenesis of predicted Nox1 phospho-residues revealed that cells expressing mutant Nox1 T429A have a significant decrease in TNF-α-stimulated ROS production, VSMC migration and Nox1 NADPH oxidase complex assembly compared to cells expressing wild-type Nox1. Isothermal calorimetry (ITC) revealed that a peptide containing the Activation Domain of NoxA1 (LEPMDFLGKAKVV) binds to phosphorylated Nox1 peptide (KLK-phos-T(429)- QKIYF) but not non-phosphorylated Nox1 peptide. These findings indicate that phosphorylation of Nox1 residue T429 by PKC-βI promotes TNF-α-induced Nox1 NADPH oxidase complex assembly, ROS production, and VSMC migration. Nox1 localization and trafficking studies reveal that Nox1 endocytosis is necessary for TNF-α-induced Nox1 ROS production; and that mutation of a Nox1 VLV motif inhibits Nox1 endocytosis and ROS production. These studies have provided new evidence that phosphorylation and sub-cellular localization are involved in the regulation of Nox1 ROS production and cell migration and offer new insights as to how Nox1 activity can be targeted for the purpose of treating Nox1-mediated diseases.