Regulatory T cells (Tregs) suppress adaptive immunity and inflammation. In cancer, Tregs hinder therapeutic responses due to suppression of anti-tumor activity in the tumor microenvironment. Although these cells play a role in suppressing anti-tumor responses, development of therapeutics that target Tregs is limited by their low abundance, heterogeneity, and lack of specific cell surface markers. To study Treg mechanisms of suppression, a human T cell line, MoT, was identified and characterized as a model of human Foxp3+ Tregs. MoT cells express surface markers consistent with PBMC-derived Tregs and inhibit proliferation of CD4+ responder PBMCs in a ratio-dependent manner. Transwell membrane separation prevented suppression of stimulated CD4+ PBMC proliferation by MoT cells, suggesting cell-cell contact is required for suppressive activity. Suppression was found to be independent of soluble cytokines and known immune checkpoint pathways, providing evidence that a Foxp3+ Treg population suppresses immune responses by an unknown cell contact-dependent mechanism. To investigate potential cell surface molecules that mediate suppression, monoclonal antibodies (mAbs) were generated to a known immunosuppressive protein, Galectin-1, and to MoT cell surface proteins. MAbs were identified that bind and functionally block suppressive activity. Another mechanism of immune suppression involves the PD-1/PD-L1 pathway, which is exploited by tumor cells to resist T cell killing and escape immune clearance. Since PD-L1 has emerged as an effective therapeutic target, anti-PD-L1 CAR T cells were generated and demonstrated to kill PD-L1-positive tumor cells. These results expand upon the current knowledge of Treg function and CAR T cell therapy and may lead to enhanced anti-tumor immunity to improve patient responses.

Coccidioidomycosis, or Valley fever, is an endemic pneumonia of the arid and semi-arid regions of North and South America and is responsible for up to 30% of community-acquired pneumonias in endemic and highly populated areas of the United States southwest. The causative agents of Valley fever are the dimorphic fungi Coccidioides immitis and Coccidioides posadasii, which grow as mycelia in the environment and spherules within the lungs of vulnerable hosts. The current diagnostics for Valley fever are severely lacking due to poor sensitivity and invasiveness, strongly contributing to a 23-day median time-to-diagnosis. There is a critical need for sensitive and non-invasive diagnostics for identifying Valley fever lung infections. The long-term goal of my work is to substantially shorten the time-to-diagnosis for Valley fever through the development of sensitive and specific breath-based diagnostics for coccidioidomycosis lung infections. Herein, I characterized the volatile organic compounds (VOCs) produced by C. immitis and C. posadasii in vitro and evaluated the relationship of the volatile metabolomes to lifecycle. I explored the VOC profiles of bronchoalveolar lavage fluid (BALF) samples from mouse model lung infections of Valley fever. Finally, I investigated the VOC profiles of BALF from persons with community-acquired pneumonia. All VOCs were analyzed by headspace solid-phase microextraction and comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (HS-SPME-GC×GC-TOFMS). The volatile metabolomes were compared using a variety of statistical analyses. For the in vitro samples, I detected a total of 353 VOCs that were at least two-fold more abundant in a Coccidioides culture versus medium controls and found the volatile metabolome of Coccidioides is more dependent on lifecycle than species. The mouse BALF samples indicate that lung infection VOCs are correlated to cytokine production and classify mice based on their individual level of infection. From the human BALF samples, I identified VOCs that were able to differentiate between Coccidioides and bacterial pneumonia. Combined, these studies suggest that Coccidioides spp. and the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test.

Coccidioidomycosis, or valley fever (VF), is a fungal infection caused by Coccidioides that is highly endemic in southern Arizona and central California. The antibody response to infection in combination with clinical presentation and radiographic findings are often used to diagnose disease, as a highly sensitive and specific antigen-based assay has yet to be developed and commercialized. In this dissertation, a panel of monoclonal antibodies (mAbs) was generated in an attempt to identify circulating antigen in VF-positive patients. Despite utilizing a mixture of antigens, almost all mAbs obtained were against chitinase 1 (CTS1), a protein previously identified as a main component in serodiagnostic reagents. While CTS1 was undoubtedly a dominant seroreactive antigen, it was not successfully detected in circulation in patient samples prompting a shift toward further understanding the importance of CTS1 in antibody-based diagnostic assays. Interestingly, depletion of this antigen from diagnostic antigen preparations resulted in complete loss of patient IgG reactivity by immunodiffusion. This finding encouraged the development of a rapid, 10-minute point-of-care test in lateral flow assay (LFA) format to exclusively detect anti-CTS1 antibodies from human and non-human animal patients with coccidioidal infection. A CTS1 LFA was developed that demonstrated 92.9% sensitivity and 97.7% specificity when compared to current quantitative serologic assays (complement fixation and immunodiffusion). A commercially available LFA that utilizes a proprietary mixture of antigens was shown to be less sensitive (64.3%) and less specific (79.1%). This result provides evidence that a single antigen can be used to detect antibodies consistently and accurately from patients with VF. The LFA presented here shows promise as a helpful tool to rule-in or rule-out a diagnosis of VF such that patients may avoid unnecessary antibacterial treatments, improving healthcare efficiency.

Metabolomics focuses on the study of metabolic changes occurring in varioussystems and utilizes quantitative and semi-quantitative measurements of multiple metabolites in parallel. Mass spectrometry (MS) is the most ubiquitous platform in this field, as it provides superior sensitivity regarding measurements of complex metabolic profiles in biological systems. When combined with MS, multivariate statistics and advanced machine learning algorithms provide myriad opportunities for bioinformatics insights beyond simple univariate data comparisons. In this dissertation, the application of MS-based metabolomics is introduced with an emphasis on biomarker discovery for human disease detection. To advance disease diagnosis using MS-based metabolomics, numerous statistical techniques have been implemented in this research including principal component analysis, factor analysis, partial least squares-discriminant analysis (PLS-DA), orthogonal PLS-DA, random forest, receiver operating characteristic analysis, as well as functional pathway/enzyme enrichment analyses. These approaches are highly useful for improving classification sensitivity and specificity related to disease-induced biological variation and can help identify useful biomarkers and potential therapeutic targets. It is also shown that MS-based metabolomics can distinguish between clinical and prodromal disease as well as similar diseases with related symptoms, which may assist in clinical staging and differential diagnosis, respectively. Additionally, MS-based metabolomics is shown to be promising for the early and accurate detection of diseases, thereby improving patient outcomes, and advancing clinical care. Herein, the application of MS methods and chemometric statistics to the diagnosis of breast cancer, coccidioidomycosis (Valley fever), and senile dementia (Alzheimer's disease) are presented and discussed. In addition to presenting original research, previous efforts in biomarker discovery will be synthesized and appraised. A Comment will be offered regarding the state of the science, specifically addressing the inefficient model of repetitive biomarker discovery and the need for increased translational efforts necessary to consolidate metabolomics findings and formalize purported metabolic markers as laboratory developed tests. Various factors impeding the translational throughput of metabolomics findings will be carefully considered with respect to study design, statistical analysis, and regulation of biomedical diagnostics. Importantly, this dissertation will offer critical insights to advance metabolomics from a scientific field to a practical one including targeted detection, enhanced quantitation, and direct-to-consumer considerations.

For untargeted volatile metabolomics analyses, comprehensive two-dimensional gas chromatography (GC×GC) is a powerful tool for separating complex mixtures and can provide highly specific information about the chemical composition of a variety of samples. With respect to human disease, the application of GC×GC in untargeted metabolomics is contributing to the development of diagnostics for a range of diseases, most notably bacterial infections. Pseudomonas aeruginosa, in particular, is an important human pathogen, and for individuals with cystic fibrosis (CF), chronic P. aeruginosa lung infections significantly increase morbidity and mortality. Developing non-invasive tools that detect these infections earlier is critical for improving patient outcomes, and untargeted profiling of P. aeruginosa volatile metabolites could be leveraged to meet this challenge. The work presented in this dissertation serves as a case study of the application of GC×GC in this area.Using headspace solid-phase microextraction and time-of-flight mass spectrometry coupled with GC×GC (HS-SPME GC×GC-TOFMS), the volatile metabolomes of P. aeruginosa isolates from early and late chronic CF lung infections were characterized. Through this study, the size of the P. aeruginosa pan-volatilome was increased by almost 40%, and differences in the relative abundances of the volatile metabolites between early- and late-infection isolates were identified. These differences were also strongly associated with isolate phenotype. Subsequent analyses sought to connect these metabolome-phenome trends to the genome by profiling the volatile metabolomes of P. aeruginosa strains harboring mutations in genes that are important for regulating chronic infection phenotypes. Subsets of volatile metabolites that accurately distinguish between wild-type and mutant strains were identified. Together, these results highlight the utility of GC×GC in the search for prognostic volatile biomarkers for P. aeruginosa CF lung infections. Finally, the complex data sets acquired from untargeted GC×GC studies pose major challenges in downstream statistical analysis. Missing data, in particular, severely limits even the most robust statistical tools and must be remediated, commonly through imputation. A comparison of imputation strategies showed that algorithmic approaches such as Random Forest have superior performance over simpler methods, and imputing within replicate samples reinforces volatile metabolite reproducibility.

An estimated 267 million women worldwide are HSV-2 seropositive, including roughly 20% of reproductive-aged American women. HSV-2 is a neurotropic virus that establishes a persistent, life-long infection that increases risk for STI acquisition in individuals. The vaginal epithelium represents a critical first line of defense against infection, and during acute infection, underlying immune mechanisms in the epithelium may be critical to protect against disease pathogenesis. The recently identified pro-inflammatory cytokine IL-36gamma has been shown to be expressed at mucosal epithelia, including the female reproductive tract (FRT) and may be an important factor in host defense. Although IL-36gamma has been shown to be induced in the FRT after exposure to microbial products, the contributions of IL-36gamma to host defense mechanisms in response to this clinically relevant STI pathogen are not well understood. This dissertation describes the regulation of IL-36gamma in the FRT and explores its contribution to the host response against genital HSV-2 infection.

To test the hypothesis that IL-36gamma is a key regulator of mucosal inflammation and immunity in the FRT, hormonal regulation of IL-36gamma in the FRT was investigated using estrogen- and progesterone-conditioned mice. From this preliminary study, it was shown that progesterone dampens IL36G expression relative to estrogen and may potentially increase susceptibility to infection. Next, the impact of IL-36gamma treatment on HSV-2 infection and replication in human 3-D vaginal epithelial cells was explored. In parallel, the impact of intravaginal IL-36gamma delivery on HSV-2 disease pathogenesis was evaluated using a lethal murine challenge model. IL-36gamma pre-treatment significantly limited HSV-2 replication in vitro and in vivo and was associated with transient neutrophil infiltration that corresponded with decreased disease severity and increased survival in mice. Last, the requirement for IL-36gamma in host defense was investigated utilizing IL-36gamma-/- mice in a lethal HSV-2 murine challenge model. Following infection, IL-36gamma-/- mice exhibited significantly impaired neutrophil recruitment, decreased overall survival time, and significantly increased viral neuroinvasion relative to wild type mice. Collectively, these data indicate that IL-36gamma is a crucial regulator of HSV-2-induced neutrophil infiltration and appears to function in a previously uncharacterized manner to limit viral neuroinvasion in genital HSV-2 disease pathogenesis.

Valley Fever (VF), is a potentially lethal fungal pneumonia caused by Coccidioides spp., which is estimated to cause ~15-30% of all community-acquired pneumonias in the highly endemic Greater Phoenix and Tucson areas of Arizona. However, an accurate antigen-based diagnostic is still lacking. In order to identify protein and glycan antigen biomarkers of infection, I used a combination of genomics, proteomics and glycomics analyses to provide evidence of genus-specific proteins and glycosylations. The next goal was to determine if Coccidioides-specific glycans were present in biological samples from VF patients. Urine collected from 77 humans and 63 dogs were enriched for glycans and evaluated by mass spectrometry for Coccidioides-specific glycans and evaluated against a panel of normal donor urines, urines from patients infected with other fungi, and fungal cultures from closely related pneumonia-causing fungi. A combination of 6 glycan biomarkers was 100% sensitive and 100% specific in the diagnosis of human VF subjects, while only 3 glycan biomarkers were needed for 100% sensitivity and 100 specificity in the diagnosis of dog VF subject. Additionally, a blinded trial of 23 human urine samples was correctly able to classify urine samples with 93.3% sensitivity and 100% specificity. The results of this research provides evidence that Coccidioides genus-specific glycosylations have potential as antigens in diagnostic assays.

Biomarkers find a wide variety of applications in oncology from risk assessment to diagnosis and predicting and monitoring recurrence and response to therapy. Developing clinically useful biomarkers for cancer is faced with several challenges, including cancer heterogeneity and factors related to assay development and biomarker performance. Circulating biomarkers offer a rapid, cost-effective, and minimally-invasive window to disease and are ideal for population-based screening. Circulating immune biomarkers are stable, measurable, and can betray the underlying antigen when present below detection levels or even no longer present. This dissertation aims to investigate potential circulating immune biomarkers with applications in cancer detection and novel therapies. Over 600,000 cancers each year are attributed to the human papillomavirus (HPV), including cervical, anogenital and oropharyngeal cancers. A key challenge in understanding HPV immunobiology and developing immune biomarkers is the diversity of HPV types and the need for multiplexed display of HPV antigens. In Project 1, nucleic acid programmable protein arrays displaying the proteomes of 12 HPV types were developed and used for serum immunoprofiling of women with cervical lesions or invasive cervical cancer. These arrays provide a valuable high-throughput tool for measuring the breadth, specificity, heterogeneity, and cross-reactivity of the serologic response to HPV. Project 2 investigates potential biomarkers of immunity to the bacterial CRISPR/Cas9 system that is currently in clinical trials for cancer. Pre-existing B cell and T cell immune responses to Cas9 were detected in humans and Cas9 was modified to eliminate immunodominant epitopes while preserving its function and specificity. This dissertation broadens our understanding of the immunobiology of cervical cancer and provides insights into the immune profiles that could serve as biomarkers of various applications in cancer.

CD8+ T-lymphocytes (CTLs) are central to the immunologic control of infections and are currently at the forefront of strategies that enhance immune based treatment of a variety of tumors. Effective T-cell based vaccines and immunotherapies fundamentally rely on the interaction of CTLs with peptide-human leukocyte antigen class I (HLA-I) complexes on the infected/malignant cell surface. However, how CTLs are able to respond to antigenic peptides with high specificity is largely unknown. Also unknown, are the different mechanisms underlying tumor immune evasion from CTL-mediated cytotoxicity. In this dissertation, I investigate the immunogenicity and dysfunction of CTLs for the development of novel T-cell therapies. Project 1 explores the biochemical hallmarks associated with HLA-I binding peptides that result in a CTL-immune response. The results reveal amino acid hydrophobicity of T-cell receptor (TCR) contact residues within immunogenic CTL-epitopes as a critical parameter for CTL-self
onself discrimination. Project 2 develops a bioinformatic and experimental methodology for the identification of CTL-epitopes from low frequency T-cells against tumor antigens and chronic viruses. This methodology is employed in Project 3 to identify novel immunogenic CTL-epitopes from human papillomavirus (HPV)-associated head and neck cancer patients. In Project 3, I further study the mechanisms of HPV-specific T-cell dysfunction, and I demonstrate that combination inhibition of Indoleamine 2, 3-dioxygenase (IDO-1) and programmed cell death protein (PD-1) can be a potential immunotherapy against HPV+ head and neck cancers. Lastly, in Project 4, I develop a single-cell assay for high-throughput identification of antigens targeted by CTLs from whole pathogenome libraries. Thus, this dissertation contributes to fundamental T-cell immunobiology by identifying rules of T-cell immunogenicity and dysfunction, as well as to translational immunology by identifying novel CTL-epitopes, and therapeutic targets for T-cell immunotherapy.

Thrombus (blood clot) formation is at the roots of hemostasis and pathological thrombosis. Although many studies have successfully elucidated the cellular and molecular mechanisms underlying thrombus formation, there is still a void in understanding the processes limiting thrombus growth beyond that needed for stabilization. As a hemostatic thrombus grows, its surface consisting primarily of platelets changes to that composed of fibrin, which mechanically stabilizes the thrombus. Formation of fibrin ceases after some time; however, it is unclear why this fibrin is non-thrombogenic. This is puzzling since fibrin is known to support strong integrin-mediated adhesion of both platelets and leukocytes in vitro. Therefore, it would be expected that the fibrin surface of hemostatic thrombi in the circulation also support accumulation of these cells and thus continuous thrombus growth or degradation. Nevertheless, many in vivo studies did not detect any accumulation of blood cells including platelets at the fibrin surfaces of thrombi. This finding suggests the existence of natural processes that modulate the adhesive properties of fibrin to ensure proper regulation of thrombus growth, stability and degradation. In this dissertation, I document and discuss the findings supporting the existence of anti-adhesive mechanisms and their physiological relevance in surface-mediated control of thrombus growth and stability. The studies discussed in my dissertation have the potential to establish a novel aspect of hemostasis. Furthermore, it may provide new insights into the intricate and dynamic interplay between the mechanisms underlying hemostatic balance, which is essential to understanding the dysfunction of this process during pathological conditions.