Thymic stromal lymphopoietin (TSLP) is a pleotropic cytokine highly implicated in the pathophysiology of asthma and allergic diseases. Although there are robust data regarding the associations of TSLP polymorphisms with the development of allergy and asthma, there is very little information on how these TSLP variants functionally affect downstream effector pathways and disease phenotype. The overall objective of this thesis was to investigate how TSLP polymorphisms are linked to alterations in TSLP secretion and subsequent downstream cellular events. Initially, we investigated the influence of innate and adaptive stimuli on epithelial-derived TSLP expression and secretion, including effects on dendritic cells (DC). We show that polyinosinic:polycytidylic acid (polyI:C) and allergen-specific T cells induced enhanced TSLP secretion from asthmatic bronchial epithelial cells (BEC) compared to non-asthmatic BEC. Furthermore, activated-BEC culture supernatants induced TSLP-dependent CCL17 production from monocyte-derived DC in relation to clinical asthmatic status (Chapter 2). Next, we examined effects of TSLP on hemopoietic progenitor eosinophil-basophil (Eo/B) differentiation, demonstrating enhanced TSLP-mediated hemopoiesis ex vivo in relation to clinical atopic status. We further demonstrated p38MAPK-dependent autocrine signaling by TNFα in TSLP-mediated human Eo/B differentiation ex vivo (Chapter 3). Lastly, to explore the potential functional consequences of a key variant of the TSLP gene, we investigated associations between the rs1837253 TSLP variant and ex vivo production of TSLP in nasal epithelial cells (NEC). We showed that NEC derived from individuals with the “protective” minor allele have diminished TSLP secretion, which suggests that this rs1837253 polymorphism may be directly involved in the regulation of TSLP secretion (Chapter 4). The novel work presented herein provides further evidence for TSLP regulation of distinct immunological pathways in allergic immune inflammatory airway responses initiated at the epithelial surface, and thus (by implication) of allergic disease. These observations support the concept that TSLP is potentially an important biomarker and therapeutic target for allergic diseases characterized by increased Th2 and/or eosinophilic-basophilic inflammation. Continued investigations into the functional mechanisms linking TSLP variants to allergic disease phenotype are of critical importance. / Dissertation / Doctor of Science (PhD)

Some of life’s most important behaviors are guided by the sense of smell. Detecting and interpreting odor information influences food-seeking, predator avoidance, sociality, competition, mating rituals, and more, shaping how organisms interact with their environment. In vertebrates, odors are detected by olfactory sensory neurons (OSNs) of the main olfactory epithelium (MOE). OSNs rely on olfactory receptors (ORs) to recognize odorants and trigger neural activation. The OR gene pool is typically vast, containing between 200-4000 olfactory receptor genes across mammals, yet mature OSNs stably express only one gene from one allele. Data from mice show that ORs are anatomically restricted to designated sections of the MOE, but within these zones, OR expression appears mosaic and random. Since the discovery of the OR gene pool 30 years ago, deciphering how OSNs choose which OR they are going to express remains a central question. While multiple differentiation-dependent alterations to the OSN nucleus are required for OR expression, the most notable contribution comes from the organization of OR-gene specific enhancers, called Greek Islands (GIs), around the chosen allele. GIs use the transcription factors Lhx2 and Ebf1, as well as the coactivator Ldb1, to form a nucleoprotein complex known as the Greek Island Hub (GIH) to associate with the active OR gene and support its transcription. Bulk Hi-C data show that GIs form strong, specific, and singular associations with the active OR gene, suggesting a possible role for the GIH in singular OR choice. However, single-cell Hi-C analysis shows that multiple GIHs exist in every OSN with no clear differences between them, complicating the contribution of the GIH. Furthermore, ectopic OR gene activation is sufficient to drive association of an OR locus with a GIH and bias choice, suggesting a role for OR transcription itself in supporting its own stable expression. To clarify the genomic transformations that result in the formation of multiple GIHs, I performed combined scRNA-seq and scATAC-seq in the MOE. I determined that a selective inactivation event was taking place during the INP3-to-iOSN transition, where OSNs would silence a large fraction of the GI pool. GI inactivation takes place during a phase preceding OR choice, where OR expression is polygenic but skewed towards one OR. My single-cell Hi-C analysis verifies the presence of multiple GIHs per cell, with similar GI-GI interaction properties, but I also observe that the single active GIH contains much more specific GI-OR gene interactions than those in inactive GIHs. These architectural differences are supported by Liquid Hi-C and H3K27ac HiChIP analysis where I observe that the active GIH is more highly acetylated than inactive GIHs and possesses more euchromatic physical properties. Taken together these data show that while most GIs were initially euchromatic during the polygenic phase of OR expression, once choice has taken place, GIHs possess distinct OR interaction properties, chromatin marks, and physical features that are determined by their association with the active OR gene. I believe that these data are best explained by a winner-takes-all event, where GIHs containing transcribed OR genes during the polygenic phase are in competition for choice. Once one OR begins to win, it recruits resources to maintain its expression which consequently results in the silencing of other GIHs. Ectopic induction of OR gene transcription is sufficient to bias choice and silence other ORs by impeding their specific association with a GIH. I find that this does not depend on the coding properties of OR protein, as the transcription of non-coding OR mRNAs still results in OR gene silencing. I describe this competition as a symmetry breaking process, where asymmetrical reorganization of transcriptional resources to a single GIH is mediated by non-coding properties of a single highly expressed OR mRNA, culminating in the stable expression of that allele alone for the remainder of a cell’s lifetime.

No description available.

No description available.

No description available.

No description available.

No description available.

Yes-associated protein (Yap) transcriptional co-activator, a major downstream effector of Hippo signaling pathway, controls organ size by modulating cell proliferation and apoptosis. The Hippo signaling cascade phosphorylates Yap, and this phosphorylation inhibits the nuclear retention of Yap, which is essential for cell proliferation. Thus, the loss of Hippo pathway components leads to enlarged organs through increased Yap activity in the nucleus. Our initial study showed that Yap was expressed in the developing retina and retinal pigment epithelium (RPE), suggesting Yap's tissue-specific roles during the eye development. Intriguingly, Yap proteins were localized at the apical junctions in addition to the nucleus and cytosol of the retinal progenitor cells, adding another level of regulation. To uncover the tissue- and localization-specific functions of Yap, we generated a Yap conditional knockout mouse with Rx-Cre for the ablation of the Yap gene in the developing retina and RPE. Upon deletion of Yap, the retina showed severe lamination defects with numerous folding, which is reminiscent of the polarity and adhesion loss. The RPE, a single pigmented cell layer overlying the retina, lost pigmentation and changed into a multi-layered epithelium. The marker analysis revealed that 1) in the retina, the localization of the polarity complex proteins such as Pals1, Crb1 and atypical PKC were disrupted, suggesting Yap's indispensable role in junctional stability, and 2) the level of Otx2 in RPE decreased while those of Chx10 and beta-tubulin increased, suggesting transdifferentiation of RPE into the retina. In addition, the deletion of Yap induced a decrease in proliferation and an increase in apoptosis, ultimately resulting in microphthalmia. In conclusion, our results are consistent with the model that Yap functions in the stabilization of apical proteins for maintenance of the laminar organization, determination of RPE territory, and regulation of proliferation and apoptosis during the eye development. / Cell Biology

Ruminant livestock maintain an important role in meeting the nutrient requirements of the global population through their unique ability to convert plant fiber into human-edible meat and milk products. Volatile fatty acids (VFA) produced by rumen microbial fermentation of feed substrates represent around 70% of the ruminant animal's metabolic energy supply. Rumen fermentation profiles may directly impact productivity because the types of VFA produced are utilized at differing efficiencies by the animal. Improving our understanding of factors that control these fermentative outcomes would therefore aid in optimizing the productive efficiency of ruminant livestock. Improvements in animal efficiency are now more important than ever as the livestock industry must adapt to continue meeting the nutritional needs of a growing global population in the context of increased resource restrictions and requirements to lower the environmental impact of production. The relationship between diet and VFA ultimately supplied to the animal is complex and poorly understood due to the influence of numerous nutritional, biochemical, and microbial variables. The central aim of this body of work was therefore to explore and characterize how fermentation dynamics, rumen environmental characteristics, and the rumen microbiome behave in response to variations in the supply of fermentative substrate. The objective of our first experiment was to describe a novel in vitro laboratory technique to rank livestock feeds based on their starch degradability. This experiment also compared the starch degradation rates estimated by the in vitro method to the rates estimated by a traditional in situ method using sheep. A relationship between the degradation rates determined by these two procedures was observed, but only when feed nutrient content was accounted for. While this in vitro approach may not be able to reflect actual ruminal starch degradation rates, it holds potential as a useful laboratory technique for assessing relative differences in starch degradability between various feeds. Our second experiment aimed to measure changes in VFA dynamics, rumen environmental characteristics, and rumen epithelial gene expression levels in response to dietary sources of fiber and protein designed to differ in their rumen availabilities. Conducted in sheep, this study utilized beet pulp and timothy hay as the more and less available fiber source treatments, respectively, and soybean meal and heat-treated soybean meal as the more and less available protein source treatments, respectively. Results indicated that rumen environmental parameters and epithelial gene expression levels were not significantly altered by treatment. However, numerous shifts in response to both protein and fiber treatments were observed in fermentation dynamics, especially in interconversions of VFA. The objective of the third investigation was to assess whether the rumen microbiome can serve as an accurate predictor of beef and dairy cattle performance measurements and compare its predictive ability to that of diet explanatory variables. The available literature was assembled into a meta-analysis and models predicting dry matter intake, feed efficiency, average daily gain, and milk yield were derived using microbial and diet explanatory variables. Comparison of model quality revealed that the microbiome-based predictions may have comparable accuracy to diet-based predictions and that microbial variables may be used in combination with diet to improve predictions. In our fourth experiment, the objective was to investigate rumen microbial responses to the fiber and protein diet treatments detailed in Experiment 2. Responses of interest included relative abundances of bacterial populations at three taxonomic levels (phylum, family, and genus) in addition to estimations of community richness and diversity. Numerous population shifts were observed in response to fiber treatment. Prominent fibrolytic population abundances as well as richness and diversity estimations were found to be greater with timothy hay treatment and lower with beet pulp whereas pectin degraders increased in abundance on beet pulp. Microbial responses associated with protein treatment were not as numerous but appeared to reflect taxa with roles in protein metabolism. These four investigations revealed that significant changes can occur in VFA fermentation and rumen microbial populations when sources of nutrient substrates provided in a ruminant animal's diet are altered and that a new approach may be useful in investigating degradation of another important substrate for fermentation (starch) in a laboratory setting. Our findings also determined that animal performance can be predicted to a certain extent by rumen microbial characteristics. Collectively, these investigations offer an improved understanding of factors that influence the process of converting feed to energy sources in the ruminant animal. / Doctor of Philosophy / Ruminant animals, such as beef cattle, dairy cattle, and sheep, play a major role in delivering essential nutrients to the human population through their provision of meat and dairy products. The current growth projections of the global population, in addition to increased concerns surrounding greenhouse gas emissions and restrictions on resources such as land and water make it important for us to consider ways of optimizing the productivity of these animals. A unique feature of ruminants is their ability to conduct microbial fermentation of large amounts of plant matter in their rumens to produce energetically valuable compounds called volatile fatty acids (VFA), which are the primary source of energy that the animals use for growth, reproduction, and milk production. One promising way of improving animal productivity is to increase the amount of energy from the diet that becomes available to fuel the animal's body processes; however, the process of converting feed to VFA is complicated and currently not well understood. The overall aim of this body of work was therefore to explore various nutritional, ruminal, and microbial factors that are known to impact fermentation in order to 1) increase our understanding of how these factors interconnect and 2) put us in a better position to manipulate these factors for optimal animal performance. The goal of our first experiment was to devise and use a novel laboratory technique to rank livestock feeds based on the degradability of their starch content, which is an important substrate for VFA fermentation. Our observations indicate that this technique may be a useful tool to help us determine relative differences between feeds based on their starch degradabilities in a laboratory setting. Our second experiment investigated the effects of feeding varying sources of fiber (beet pulp and timothy hay) and protein (heat-treated and untreated soybean meals) to sheep in terms of their VFA fermentation, rumen conditions, and the expression of certain key genes in the epithelial tissue of the rumen wall. While rumen environmental characteristics and epithelial gene expression remained largely unchanged, numerous key aspects of VFA fermentation, predominantly carbon exchanges between different VFA, were altered in response to nutrient source. The third investigation described in this work examined the ability of the microbial populations responsible for rumen fermentation to explain variation in beef and dairy cow productivity compared with the ability of diet characteristics to explain this variation. Using statistical methods to analyze the reports currently available in scientific literature, our findings indicate that the rumen microbiome and diet may exert independent effects on productivity levels and that the microbiome may be used to enhance diet-based predictions of animal performance. Finally, we explored variations in the sheep rumen microbiome in response to the diet treatments utilized in Experiment 2. We observed minimal impact of protein source on the microbiome, but numerous microbial responses were evident when fiber source was varied. These responses included decreases of fiber-degrading bacterial populations and increases in pectin-degrading populations when beet pulp was fed compared to timothy hay. Taken together, these experiments help to provide us with a more comprehensive picture of the numerous factors involved in the process of converting feed to a usable form of energy for ruminant livestock.

No / Here, we studied how epithelial energy metabolism impacts overall skin development by selectively deleting intraepithelial mtDNA in mice by ablating a key maintenance factor (TfamEKO), which induces loss of function of the electron transport chain (ETC). Quantitative (immuno)histomorphometry demonstrated that TfamEKO mice showed significantly reduced hair follicle (HF) density and morphogenesis, fewer intrafollicular keratin15+ epithelial progenitor cells, increased apoptosis, and reduced proliferation. TfamEKO mice also displayed premature entry into (aborted) HF cycling by apoptosis-driven HF regression (catagen). Ultrastructurally, TfamEKO mice exhibited severe HF dystrophy, pigmentary abnormalities, and telogen-like condensed dermal papillae. Epithelial HF progenitor cell differentiation (Plet1, Lrig1 Lef1, and β-catenin), sebaceous gland development (adipophilin, Scd1, and oil red), and key mediators/markers of epithelial–mesenchymal interactions during skin morphogenesis (NCAM, versican, and alkaline phosphatase) were all severely altered in TfamEKO mice. Moreover, the number of mast cells, major histocompatibility complex class II+, or CD11b+ immunocytes in the skin mesenchyme was increased, and essentially no subcutis developed. Therefore, in contrast to their epidermal counterparts, pilosebaceous unit stem cells depend on a functional ETC. Most importantly, our findings point toward a frontier in skin biology: the coupling of HF keratinocyte mitochondrial function with the epithelial–mesenchymal interactions that drive overall development of the skin and its appendages.