Gardner's syndrome is an autosomal dominant disease presenting multiple colonic polyps with a predisposition for malignant change. In addition to colonic polyp formation by early adolescence, extracolonic lesions appear often prior to polyp formation. One theoretical mechanism for the origin of polyps and malignancies in Gardner's syndrome is a genetic defect in the natural killer cell activity of patients with this disease. Natural killer cells are a of lymphocytes that spontaneously lyse tumor cells subpopulation and virally transformed cells. A study was undertaken to determine the natural killer activity of patients with Gardner's syndrome .

Individuals with Down syndrome (US) suffer from increased incidence of respiratory infections and lymphoblastic leukemia, and a death rate that is particularly high in the first 5 years of life. Relatively few studies have probed immune parameters in young US children. Primary immune defects in DS may be masked by a degree of immune maturity in adults, and hygienic factors may have an effect on immune capability throughout the years. A study of young children can give clearer evidence of the actual primary immune defects in DS. Blood samples were drawn from 20 DS children under 6 years old and from age-matched controls. Packed blood cell volume was measured, various blood cell subpopulations were enumerated and differential counts were performed. Several tests of cellular immune function were performed and plasma zinc levels were determined using atomic adsorption spectrophotometry. Elevated hematocrit levels were observed in the US group. White blood cell counts and proportions of rosette-forming cells were normal in blood from DS children. Altered neutrophil and lymphocyte proportions in DS samples resulted from a depressed number of circulating lymphocytes in the these subjects. This indicated that T cell numbers are low in DS. DS individuals had a low number of circulating OKT4+ T cells which resulted in significantly depressed T4:T8 ratios. Cells from DS subjects exhibited a reduced proliferative response to phytohemagglutinin; a low response to the optimal concentration of concanavalin A was seen with DS samples, but at suboptimal doses the response was normal; suboptimal concentrations of pokeweed mitogen elicited normal responses by cells from DS children. Preliminary results suggest that interleukin-2 (IL-2) production in young children may correlate positively with age and that DS subjects may produce normal or elevated amounts of IL-2. This suggests that IL-2 receptor function may be defective in T cells from DS children. DS children had normal natural killer cell activity and cells from those children were no more sensitive to the augmenting effects of interferon-alpha than cells from control children. Plasma zinc levels in DS appeared to be normal. These findings not only provide evidence that the primary immune defect in DS involves low levels of T cells, but they show depressed number and function of helper T cells and suggest defective IL-2 receptor expression in DS.

Multiple Sclerosis (MS) is an inflammatory autoimmune disease of the central nervous system, characterized by axonal demyelination and multifocal inflammation. Like many autoimmune diseases, it is a sexually dimorphic disease, being 3-4 times more common in females than in males. p38α MAP kinase (MAPK) has an integral role in modulating inflammatory processes in autoimmunity. Conditionally ablating p38α MAPK in myeloid cells in B6 mice shows a sex difference in the animal model of MS, experimental autoimmune encephalomyelitis (EAE). In the absence of sex hormones, this sex difference was reversed, suggesting a role for sex hormones in modulating p38α MAPK signaling in EAE. Based on these findings, we hypothesized that pro-inflammatory functions in EAE is p38-indepdendent in the presence of androgens and p38-dependent in the presence of estrogens. For the purposes of this project, the role of androgens was evaluated. Both in vivo and in vitro techniques were used to assess how androgen receptor (AR) signaling: 1) impacts EAE pathogenesis, and 2) impacts the role of p38α in EAE pathogenesis and macrophage function. To this end, using Cre-Lox technology, we generated mice deficient in: 1) AR globally or conditionally in macrophages, as well as 2) mice doubly deficient in AR and p38α. In vivo results from p38α-sufficient global AR knockout mice show no effect of global AR deletion on EAE pathogenesis. Surprisingly, results from p38α-sufficient conditional AR knockout mice showed significant worsening in disease compared to WT counterparts, suggesting that AR signaling in myeloid cells has a protective role in EAE pathogenesis. These findings implicate a protective role for AR signaling in EAE. Studies with mice doubly deficient in p38α and AR to determine whether AR regulates the role of p38α in EAE are ongoing, but so far show no effect on AR deletion on the role of p38α MAPK. Further studies with larger cohorts of mice are needed elucidate the relationship between AR and p38α MAPK signaling in myeloid cells in EAE pathogenesis. In vitro studies using the immortalized macrophage cell line RAW 264.7 showed that pharmacologic inhibition of p38 MAPK after stimulation with LPS reduced the production of classic pro-inflammatory cytokines IL-6 and TNFα, and effect that was not affected by treatment with 5-dihydrotestosterone, suggesting that the AR does not modulate the role of p38α in cytokine production. These findings implicate no direct role of AR signaling on the functional role of p38α MAPK in the myeloid cell lineage in inflammatory and autoimmune responses.

Our understanding of genetic predisposition to inflammatory and autoimmune diseases has been enhanced by large scale quantitative trait loci (QTL) linkage mapping and genome-wide association studies (GWAS). However, the resolution and interpretation of QTL linkage mapping or GWAS findings are limited. In this work, we complement genetic predictions for several human diseases including multiple sclerosis (MS) and systemic capillary leakage syndrome (SCLS) with genetic and functional data in model organisms to associate genes with phenotypes and diseases. Focusing on MS, an autoimmune inflammatory disease of the central nervous system (CNS), we experimentally tested the effect of three of the GWAS candidate genes (SLAMF1, SLAMF2 and SLAMF7) in the experimental autoimmune encephalomyelitis (EAE) mouse model and found a male-specific locus distal to these loci regulating CNS autoimmune disease. Functional data in mouse suggests this male-specific locus modulates the frequency of immune cells including CD11b+, TCRαβ+CD4+Foxp3+, and TCRαβ+CD8+IL-17+ cells during EAE disease. Orchiectomy experiments demonstrate that this male specific phenotype is dependent on testis but not testosterone (T) or 5α-dihydrotestosterone (DHT). Using a bioinformatic approach, we identified SLAMF8 and SLAMF9 along with other differentially expressed genes in linkage with MS-GWAS predictions whose expression is testis-dependent, but not directly regulated by T or DHT, as potential positional candidates regulating CNS autoimmune disease. Further refinement of this locus is required to identify the causal gene(s) that may be targeted for prevention and/or treatment of MS in men. Using SCLS, an extremely rare disorder of unknown etiology characterized by recurrent episodes of vascular leakage, we identified and modeled this disease in an inbred mouse strain, SJL, using susceptibility to histamine- and infection-triggered vascular leak as the major phenotypic readout. This trait “Histamine hypersensitivity” (Histh/Histh) was mapped to a region on Chr 6. Remarkably, Histh is syntenic to the genomic locus most strongly associated with SCLS in humans (3p25.3). Subsequent studies found that the Histh locus is not unique to SJL but additional mouse strains also exhibit Histh phenotype. Considering GWAS studies in SCLS are limited by the small number of patients, we utilized interval-specific SNP-based association testing among Histh phenotyped mouse strains to predict Histh candidates. Furthermore, to dissect the complexity of Histh QTL, we developed network-based functional prediction methods to rank genes in this locus by predicting functional association with multiple Histh-related processes. The top-ranked genes include Cxcl12, Ret, Cacna1c, and Cntn3, all of which have strong functional associations and are proximal to SNPs segregating with Histh. Lastly, we utilized the power of integrating genetic and functional approaches to understand susceptibility to Bordetella pertussis and pertussis toxin (PTX) induced histamine sensitization (Bphs/Bphs), a sub-phenotype with an established role in autoimmunity. Congenic mapping in mice had earlier linked Bphs to histamine H1 receptor gene (Hrh1/H1R) and demonstrated that H1R differs at three amino acid residues in Bphs-susceptible and -resistant mice. Our subsequent studies identified eight inbred mouse strains that were susceptible to Bphs despite carrying a resistant H1R allele. Genetic analyses mapped the locus complementing Bphs to mouse Chr 6, in linkage disequilibrium with Hrh1; we have designated this Bphs-enhancer (Bphse). Similar to the approaches used for Histh, we utilized interval-specific SNP based association testing and network-based functional enrichment to predict nine candidate loci for Bphse including Atp2b2, Atg7, Pparg, Syn2, Ift122, Raf1, Mkrn2, Timp4 and Gt(ROSA)26Sor. Overall, these studies demonstrate the power of integrating genetic and functional methods in humans and animal models to predict highly plausible loci underlying QTL/GWAS data.

The purpose of this investigation was to observe changes induced by types 1 and 2 herpes simplex viruses (HSY 1 and HSY 2) when these viruses were cultivated in fish 2 cells. The possibility of attempting to use human strains of herpesviruses in order to transform normal fish tissue culture preparations was considered. Three different fish cell cultures were tested: CHSE-214 cell lines were derived from embryonic chinook salmon (Oncorhynohus tshawytscha), and STE-137 cell lines were obtained from embryonic steelhead trout (Salmo gairdneri). Cells isolated from immature ovaries of rainbow trout (Salmo gairdneri) were propagated by the investigator in these studies. Both HSV 1 and HSV 2 demonstrated cytopathic effects on the 3 different cell types described above when these cells were observed during the exponential growth phase. If virus was added before cells were dividing actively, or when the cells were maintained in a stationary phase of growth, no effect was observed. Several methods were employed in an attempt to trans- form fish cells grown in tissue culture. Different quantities of live virus, preparations of ultraviolet light in- activated virus and purified viral DNA were used in these studies but malignant conversion by known viral components was not achieved. In these experiments, the 2B strain of cells obtained originally from immature ovaries of rainbow trout appeared to undergo spontaneous transformation thereby becoming established as a permanent cell line. To date tissue cultures designated 2B have undergone 25 transfers in this laboratory.

Endemic Burkitt lymphoma (eBL) is the leading pediatric cancer in sub-Saharan Africa and is associated with Epstein-Barr virus (EBV) and Plasmodium falciparum malaria co-infections. Current treatment options in Africa are combination chemotherapy with a survival rate hovering around 50%. Relapsed or refractory eBL patients have failed to receive any targeted treatments in the clinic. Our focus was to delineate immune responses in eBL, interrogate the tumor variation in responses to targeted treatments and develop mouse models that can be used to target essential mediators of tumor pathogenesis. Immune-based treatments including immune checkpoint inhibition have recently become an effective therapeutic modality in oncology. However, some B cell lymphomas such as Hodgkin Lymphoma (HL), are more receptive to checkpoint inhibition than others suggesting a need to understand the efficacy of checkpoint inhibition on different lymphoma subtypes. Checkpoint inhibitors act by blocking inhibitory receptors on T cells and improving anti-tumor responses. One of the goals of this thesis was to characterize checkpoint inhibitors on Tumor-infiltrating lymphocytes (TILs) in eBL tumors and to identify T cell subsets that exhibit increased expression of inhibitory receptors, poor cytokine production, poor proliferation and express transcription factors associated with exhaustion. Using scRNA seq, we identified T cell clusters that co-expressed inhibitory receptors, poor proliferative markers but also sustained costimulatory signals, as well as cytokine expression suggesting a pre dysfunctional state and not terminally exhausted state. Furthermore, we quantified the dominant co-inhibitory receptors PD1 and TIGIT that are upregulated in the tumor microenvironment via immunohistochemistry (IHC) and in peripheral blood of eBL patients via flow cytometry. We compared eBL patients with healthy pediatric cohorts with a history of persistent malaria exposure to those who had little to no malaria infections, to understand uniquely T cell mediated responses in BL children. Tumors had high co-expression of PD1 and TIGIT but fewer PD1 only populations, suggesting that both ligands may play a role in restraining immune activation via IHC. Next, we investigated if PD1 ligands or TIGIT ligands were overexpressed in eBL tumors. Nectin-2, TIGIT ligand was highly expressed in eBL tumors but was not highly correlated with TIGIT expression. These studies provide insights for PD1/ TIGIT blockade in Burkitt lymphoma patients. Additionally, we established new patient-derived cell lines from eBL tumors to study tumor variation and to study targeted treatments. We established five new patient-derived eBL lines BL717, BL 719, BL720, BL725, and BL740 that were interrogated for their inter-patient variation by studying their gene expression profiles. Further, we developed a patient cell-line derived xenograft (CDX) mouse model by injecting newly patient-derived BL cell lines in immunodeficient mice (NSG BL) and studying BL tumorigenesis. Having successfully established NSG BL tumors, we observed differences in tumor growth sensitivity and survival. We tested rituximab efficacy, one of the most established treatments for B cell lymphomas in our mouse model. We also identified pathways associated with unfolded protein response (UPR) and the mammalian target of rapamycin (mTOR) signaling, as well as apoptosis in one of the cell line xenografts, BL740, in response to rituximab. BL717, BL720 cell line xenograft failed to control tumor growth and was enriched in IFN-ɑ signature genes. This mouse model will prove to be useful to study combination therapy against eBL tumors as well as mechanisms of resistance to drug targets. Collectively, these studies provide insights into intratumoral variation including subtypes during tumor progression and expression profiles of TILs in eBL tumors. This will be important in designing new therapeutic strategies as well as help pose novel therapeutic targets.

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No description available.

Emerging infectious diseases of wildlife are among the greatest threats to biodiversity. Indeed, when pathogens are introduced into naïve host populations, they can impose novel selective pressures that may cause severe host declines or even extinction. However, disease impacts may vary both within and among host species. Thus, one of the key goals for management is to identify factors that drive variation in host susceptibility to infection, as they may improve our understanding of hosts' potential to develop disease resistance and/or tolerance and inform conservation strategies aimed at facilitating host persistence. For instance, Pseudogymnoascus destructans (Pd) - an invasive pathogenic fungus that causes white-nose syndrome (WNS) in hibernating bats - is highly virulent, has killed millions of bats in North America, and continues to spread at an alarming rate. Yet, the continued persistence of bat colonies in contaminated areas despite initial mass mortality events suggests variation in survival among infected individuals. I thus aimed to better understand intraspecific drivers of variation in bat susceptibility to WNS and their implications for population persistence and management in affected areas. Specifically, my objectives were to: 1) evaluate the extent to which variation in hibernaculum microclimate temperature and humidity affects Pd infection severity and disease progression in affected bats during hibernation, 2) compare how bats from colonies that vary in duration of exposure to Pd and from different age classes behaviorally respond to the infection, and examine how these behavioral changes affect host fitness and 3) model the population dynamics of remnant bat populations to assess the likeliness of persistence and the potential effectiveness of management interventions in affected colonies. I addressed these objectives through field research, experimental infection studies, and demographic modeling of the little brown myotis (Myotis lucifugus). In my dissertation, I first provide causal evidence of environmentally-driven variation in pathogen growth and infection severity on bats in the field. Both warmer and more humid microclimates contribute to the severity of the infection by promoting the production of conidia, the erosion of wing tissues, and, therefore, the transmission potential and virulence of Pd. I then document potential mechanistic links between Pd-induced behavioral change and host fitness. Higher infection levels, independent of bats' past exposure to Pd or age class, may cause individuals to groom longer, prolong euthermic arousals, accelerate the depletion of fat reserves, and ultimately increase mortality risk. Finally, I predict that populations will face a high risk of extirpation in the next decade or two if no management action is taken, but that interventions such as environmental control of Pd and hibernaculum microclimate manipulation can prevent short-term population collapse in remnant bat populations. Together, these studies provide key, mechanistic insight into the pathology of WNS and the probability of persistence of affected bat colonies, while highlighting the importance of prioritizing winter habitat preservation and enhancement for the conservation of hibernating bats. / Biology

As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a pre-antibiotic era urgently requires the discovery of novel antibiotics. Actinomycetes, a family of bacteria commonly isolated from soil, are a proven source of clinically useful antibiotics. However, easily identifiable metabolites have been exhausted and the rediscovery of common antibiotics thwarts searches for rarer molecules. Sequencing of actinomycete genomes reveals that they contain far more biosynthetic gene clusters with the potential to encode antibiotics than whose products can be readily observed in the laboratory. The work presented in this thesis revolves around developing approaches to mine these previously inaccessible metabolites as a source of new antibiotics. First, I describe how inactivation of biosynthetic gene clusters for common antibiotics can uncover rare antibiotics otherwise masked in these strains. By applying CRISPR-Cas9 to knockout genes encoding nuisance antibiotics, I develop a simple strategy to reveal the hidden biosynthetic potential of actinomycete strains that can be used to discover rare or novel antibiotics. Second, I describe the use of the evolutionary history of biosynthetic gene clusters to prioritize divergent members of an antibiotic family, the glycopeptide antibiotics, that are likely to possess new biological activities. Using these predictions, I uncover a novel functional class of glycopeptide antibiotics that blocks the action of autolysins, essential peptidoglycan hydrolases required for remodelling the cell wall during growth. Finally, I apply target-directed genome mining, which makes use of target duplication as a predicted resistance mechanism within an antibiotic’s biosynthetic gene cluster. Using this approach, I discover the association of a family of gene clusters with the housekeeping protease ClpP and characterize the produced metabolite’s effect on ClpP function. These three research projects mine previously inaccessible chemical matter from a proven source of antibiotics, actinomycetes. The techniques and antibiotics described are required now more than ever to develop life-saving antibiotics capable of combatting multidrug-resistant pathogens. / Dissertation / Doctor of Philosophy (PhD) / Antibiotics are essential for treating life-threatening infections, but the rise of antibiotic resistance renders them ineffective. To treat these drug-resistant infections, new antibiotics that work in new ways are required. A family of bacteria commonly isolated from soil called Actinomycetes produce most antibiotics we use today, but it has become increasingly difficult to find new antibiotics from this source. My work describes three techniques that can be applied to actinomycetes to help overcome the challenges associated with antibiotic discovery. Specifically, these techniques guide discovery efforts by making use of regions in actinomycete genomes called biosynthetic gene clusters that often encode antibiotics. In doing so, I describe ways to uncover rare antibiotics from actinomycete strains that produce common and uninteresting antibiotics, use antibiotic family trees to discover antibiotics that work in new ways, and apply antibiotic resistance to identify biosynthetic gene clusters likely to act on a certain bacterial target.