Matching Items (19)
Description
Immunosignature is a technology that retrieves information from the immune system. The technology is based on microarrays with peptides chosen from random sequence space. My thesis focuses on improving the Immunosignature platform and using Immunosignatures to improve diagnosis for diseases. I first contributed to the optimization of the immunosignature platform by introducing scoring metrics to select optimal parameters, considering performance as well as practicality. Next, I primarily worked on identifying a signature shared across various pathogens that can distinguish them from the healthy population. I further retrieved consensus epitopes from the disease common signature and proposed that most pathogens could share the signature by studying the enrichment of the common signature in the pathogen proteomes. Following this, I worked on studying cancer samples from different stages and correlated the immune response with whether the epitope presented by tumor is similar to the pathogen proteome. An effective immune response is defined as an antibody titer increasing followed by decrease, suggesting elimination of the epitope. I found that an effective immune response usually correlates with epitopes that are more similar to pathogens. This suggests that the immune system might occupy a limited space and can be effective against only certain epitopes that have similarity with pathogens. I then participated in the attempt to solve the antibiotic resistance problem by developing a classification algorithm that can distinguish bacterial versus viral infection. This algorithm outperforms other currently available classification methods. Finally, I worked on the concept of deriving a single number to represent all the data on the immunosignature platform. This is in resemblance to the concept of temperature, which is an approximate measurement of whether an individual is healthy. The measure of Immune Entropy was found to work best as a single measurement to describe the immune system information derived from the immunosignature. Entropy is relatively invariant in healthy population, but shows significant differences when comparing healthy donors with patients either infected with a pathogen or have cancer.
ContributorsWang, Lu (Author) / Johnston, Stephen (Thesis advisor) / Stafford, Phillip (Committee member) / Buetow, Kenneth (Committee member) / McFadden, Grant (Committee member) / Arizona State University (Publisher)
Created2018
Description
Vaccinia virus is a cytoplasmic, double-stranded DNA orthopoxvirus. Unlike mammalian cells, vaccinia virus produces double-stranded RNA (dsRNA) during its viral life cycle. The protein kinase R, PKR, is one of the principal host defense mechanisms against orthopoxvirus infection. PKR can bind double-stranded RNA and phosphorylate eukaryotic translation initiation factor, eIF2α, shutting down protein synthesis and halting the viral life cycle. To combat host defenses, vaccinia virus encodes E3, a potent inhibitor of the cellular anti-viral eIF2α kinase, PKR. The E3 protein contains a C-terminal dsRNA-binding motif that sequesters dsRNA and inhibits PKR activation. We demonstrate that E3 also interacts with PKR by co-immunoprecipitation. This interaction is independent of the presence of dsRNA and dsRNA-binding by E3, indicating that the interaction is not due to dsRNA-bridging.
PKR interaction mapped to a region within the dsRNA-binding domain of E3 and overlapped with sequences in the C-terminus of this domain that are necessary for binding to dsRNA. Point mutants of E3 were generated and screened for PKR inhibition and direct interaction. Analysis of these mutants demonstrates that dsRNA-binding but not PKR interaction plays a critical role in the broad host range of VACV. Nonetheless, full inhibition of PKR in cells in culture requires both dsRNA-binding and PKR interaction. Because E3 is highly conserved among orthopoxviruses, understanding the mechanisms that E3 uses to inhibit PKR can give insight into host range pathogenesis of dsRNA producing viruses.
PKR interaction mapped to a region within the dsRNA-binding domain of E3 and overlapped with sequences in the C-terminus of this domain that are necessary for binding to dsRNA. Point mutants of E3 were generated and screened for PKR inhibition and direct interaction. Analysis of these mutants demonstrates that dsRNA-binding but not PKR interaction plays a critical role in the broad host range of VACV. Nonetheless, full inhibition of PKR in cells in culture requires both dsRNA-binding and PKR interaction. Because E3 is highly conserved among orthopoxviruses, understanding the mechanisms that E3 uses to inhibit PKR can give insight into host range pathogenesis of dsRNA producing viruses.
ContributorsFoster, Clayton (Co-author) / Alattar, Hamed (Co-author) / Jacobs, Bertram (Thesis director) / Blattman, Joseph (Committee member) / McFadden, Grant (Committee member) / School of Life Sciences (Contributor) / W. P. Carey School of Business (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Blood donations today undergo extensive screening for transfusion transmitted infections (TTI) since the discovery of the first infectious agent in the early 1900s. Nucleic Acid Testing (NAT) is a serological test used widely in disease detection. NAT is known to rapidly and effectively detect pathogenic genomic material in blood by reducing the "window period" of infection. However, NAT produces false negative results for disease positive samples posing a risk of disease transmission. Therefore, NAT is used in conjunction with the Enzyme-Linked Immunosorbent Assay (ELISA) to mitigate these risks. However, the ELISA assay also poses the same risk as NAT. This study proposes immunosignaturing as an alternative serological test that may combat this risk and investigates whether it would be more effective than other standardized serological tests in disease detection. Immunosignaturing detects antibodies by utilizing a microarray of randomized peptide sequences. Immunosignaturing provides information about an individual's immune health from the pattern of reactivity of antibody-peptide binding. Unlike ELISA and NAT, immunosignaturing can be programmed to detect any disease and detect multiple diseases simultaneously. Using ELISA, NAT, and immunosignaturing, immune profiles of asymptomatic patients were constructed for 10 different classes of blood borne diseases. A pattern of infection was identified for each disease and the sensitivity and specificity of these assays were assessed relative to each other. Results indicate that immunosignaturing can be a viable diagnostic tool in blood testing. Immunosignatures demonstrated increased sensitivity and specificity compared to ELISA and NAT in discerning disease positive and negative samples within and across different classes of disease.
ContributorsSharma, Megumi (Author) / McFadden, Grant (Thesis director) / Nickerson, Cheryl (Committee member) / Green, Alex (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
In this study, we investigated the inactivation of wild-type vMyx-GFP (MYXV) using different methods. Assays were performed in vitro to test the following inactivation methods: heat, longwave UV only, longwave UV with psoralen (P + LWUV), and psoralen (P) only. In vitro assays demonstrated that the psoralen alone treatment did not cause any inactivation. These results showed that effective inactivation using psoralen was likely reliant on subsequent UV irradiation, creating a synergistic effect. Additionally, the UV and P + LWUV treatment demonstrated inactivation of MYXV, although by different mechanisms, as the UV-only treated virus demonstrated background infection, while P + LWUV treated virus did not. In mice, P + LWUV and UV treatment of MYXV demonstrated to be effective inactivation methods and likely preserved the antigenic epitopes of MYXV, allowing for the production of neutralizing antibodies in mice. More research is recommended on the heat treatment of MYXV as neutralizing antibodies were not observed, possibly due to the treatment denaturing antigenic epitopes or needing more booster injections to reach the threshold antibody concentration for protection. Furthermore, we demonstrated that the intraperitoneal (IP) injection of inactivated MYXV was superior to the subcutaneous injection in eliciting a strong immune response. The increased neutralizing antibodies observed after IP injection could be due to the advantage that the IP route has of reaching lymphoid tissue faster.
ContributorsSprout, Jamie (Co-author) / Davoudi, Sahar (Co-author) / McFadden, Grant (Thesis director) / Rahman, Masmudur (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
In this study, we investigated the inactivation of wild-type vMyx-GFP (MYXV) using different methods. Assays were performed in vitro to test the following inactivation methods: heat, longwave UV only, longwave UV with psoralen (P + LWUV), and psoralen (P) only. In vitro assays demonstrated that the psoralen alone treatment did not cause any inactivation. These results showed that effective inactivation using psoralen was likely reliant on subsequent UV irradiation, creating a synergistic effect. Additionally, the UV and P + LWUV treatments demonstrated inactivation of MYXV, although by different mechanisms, as the UV-only treated virus demonstrated background infection, while P + LWUV treated virus did not. In mice, P + LWUV and UV treatment of MYXV demonstrated effective inactivation methods and likely preserved the antigenic epitopes of MYXV, allowing for the production of neutralizing antibodies in mice. More research may need to be conducted on the heat treatment of MYXV as neutralizing antibodies were not observed, possibly due to the treatment denaturing antigenic epitopes or needing more booster injections to reach the threshold antibody concentration for protection. Furthermore, we demonstrated that the intraperitoneal (IP) injection of inactivated MYXV was superior to the subcutaneous injection in eliciting a strong immune response. The increased neutralizing antibodies observed after IP injection could be due to the advantage that the IP route has of reaching lymphoid tissue faster.
ContributorsDavoudi, Sahar Dawn (Co-author) / Sprout, Jamie (Co-author) / McFadden, Grant (Thesis director) / Rahman, Masmudur (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Lung metastatic cancers represent a major challenge in both basic and clinical cancer research. The ability to treat lung metastases to date has been challenging, current treatment paradigms are a mix of classic radiotherapy, chemotherapies and tumor-targeted therapies, with no one treatment that is effective for all tumors. Oncolytic viruses (OVs) represent a new therapeutic modality for hard-to-treat tumors. However, major questions still exist in the field, especially around how to therapeutically arm and deliver OVs to sites of disseminated tumors. To address this need, oncolytic myxoma viruses (MYXV) that expresses TNF superfamily member transgenes (vMYX-hTNF or vMyx-mLIGHT) were tested in an immunocompetent syngeneic lung metastatic murine osteosarcoma model. Three versions of this model were used; 1-an early intervention model, 2-an established tumor model, defined by both average tumor burden and failure of anti-PD-L1 and vMyx-TNF monotherapies, and 3-a late-stage disease model, defined by the failure the combination of vMyx-hTNF/PBMCs and anti-PD-L1 therapy. These three models were designed to test different questions about therapeutic efficacy of armed MYXV and delivery of MYXV to lung metastases. In the early intervention model, vMyx-hTNF was found to be an effective therapy, especially when delivered by leukocyte carrier cells (either bone marrow or PBMCs). Next, the combination of immune checkpoint inhibitors, including anti-PD-L1, anti-PD-1 and anti-CTLA-4, with vMyx-TNF/PBMCs were found to increase efficacy in treated mice compared to monotherapies. The established model was used to test potential synergy of vMyx-hTNF with anti-PD-L1 therapy. This model was defined by the failure of the monotherapies, however, in combination, treated mice survived significantly longer, and had lower average tumor burden throughout. This model was also used to test tumor specific delivery using ex vivo loaded PBMCs as carrier cells. Using MYXV expressing Tdtomato, PBMCs were found to deliver MYXV to tumors more effectively than free virus. In the most stringent late-stage disease model, vMyx-mLIGHT/PBMCs and vMyx-mLIGHT/PBMCs plus anti-PD-1 were tested and found to be efficacious where combination vMyx-TNF/PBMCs plus PD-1 failed. These results taken together show that TNFSF arming of MYXV, especially when delivered by autologous PBMCs, represents a new potential treatment strategy for lung metastatic tumors.
ContributorsChristie, John Douglas (Author) / McFadden, Grant (Thesis advisor) / Blattman, Joseph (Committee member) / Jacobs, Bertram (Committee member) / Anderson, Karen (Committee member) / Arizona State University (Publisher)
Created2021
Description
Systemic Lupus Erythematosus (SLE) is an autoimmune disease resulting in widespread inflammation of various organ tissues including the lung, heart, kidneys, brain, joints, vasculature, and more. Systemic Lupus Erythematosus (SLE) has at present no cure and therefore, treatments focus on improving quality of life by targeting flare-ups of inflammation (6). Diffuse Alveolar Hemorrhage (DAH) is a rare complication of SLE affecting 1-5% of people diagnosed with SLE. DAH is characterized by bleeding into the lung alveolar spaces and is associated with inflammation, potentially caused by infections and injuries. While the prevalence of DAH is low, the mortality rate is high at 50-80% (5). DAH has no proven effective treatment and many treatments used have severe side effects. Serp-1 is a Myxomavirus derived immune modulating serine protease inhibitor, a serpin, with proven efficacy in a wide range of inflammation-associated disorders (1). Due to the efficacy of Serp-1 in reducing arterial inflammation and lung consolidation in mouse herpes virus infections, Serp-1 treatment in a mouse model of pristane-induced DAH was investigated. Multiple groups were tested including mouse models that were not given pristane as well as mice with pristane-induced DAH treated with saline control, wild-type unmodified Serp-1, and a polyethylene glycol-modified variant of Serp-1 termed PEGSerp-1.
ContributorsAliskevich, Emily (Author) / Lucas, Alexandra (Thesis director) / McFadden, Grant (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution & Social Change (Contributor) / School of Life Sciences (Contributor)
Created2023-05
Description
The innate immune system serves as an immediate response to pathogenic infection and an informant to the adaptive immune system. The 2′,5′-oligoadenylate (2-5A) synthetase (OAS)–RNase-L system is a component of the innate immune system induced by interferons (IFNs) and serves to eliminate viral infections. In humans, three enzymatically active OAS proteins exist, OAS1, OAS2, and OAS3. Recent evidence suggests variations in cellular localization of OAS proteins may influence the impact and influence of those proteins on viral replication. However, viral suppression mechanisms involving specific OAS proteins are still unclear for most viruses. Here, I overexpress different isoforms of OAS and determined that though viruses within the same family have similar replication strategies, the extent to which each OAS protein impacts viral replication for Flaviviruses, and Alphaviruses varies. In contrast to the innate immune system, the adaptive immune system provides specific and long-lived immune responses. In the context of cancer, T cells have been shown to play a prominent role in tumor regression. It has previously been demonstrated that administration α-CTLA-4/α-PD-L1 immune checkpoint blockade (ICB) to mice inoculated with a K7M2 metastatic osteosarcoma (mOS) cell line resulted in ~50% survival. Here, I sought to determine biological differences among murine responders and non-responders to ICB for mOS to understand better what factors could increase ICB efficacy. A prospective culprit is a variance in circulating antibodies (Abs). I have shown that sera from mice, before inoculation with mOS or ICB, display distinct differences in Ab repertoire between responders and non-responders, suggesting the presence or absence of particular Abs may influence the outcome of ICB. Recent studies have also shown that malleable environmental factors, such as differences in microbiome composition, can yield subsequent changes in circulating Abs.
Strong associations have been made between host-microbiome interactions and their effects on health. Here, I study potential associations of microbiome-mediated impacts on ICB efficacy for mOS. Additionally, I sought to determine potential changes in T-cellular response to mOS due to modulations in microbiome composition and showed that ICB efficacy can change in conjunction with microbiome composition changes in a murine model.
ContributorsDi Palma, Michelle Pina (Author) / Blattman, Joseph N (Thesis advisor) / Li, Yize (Thesis advisor) / Anderson, Karen S (Committee member) / McFadden, Grant (Committee member) / Arizona State University (Publisher)
Created2023
Description
Cancer is one of the leading causes of death, globally, with an estimated 9.6 million deaths in 2018, according to the World Health Organization. However, this is not the only impact cancer has on affected individuals, as death rates only capture the mortality of cancer, there are still detrimental effects cancer has on quality of life. Newer therapies for cancer attempt to circumvent these unwanted detriments, such as hormone therapy, stem cell transplants, targeted therapy, etc.3. One such novel therapy being virotherapy, which is the subject of this study. This study follows the observations of the myxoma virus (MYXV), a prototypic poxvirus which belongs to the Leporipoxvirus genus of the Poxviridae family. This method allows larger particles to enter host cells through the process of overriding host cell endocytosis pathways, with a few exceptions. Interestingly, research has shown that MYXV has been able to infect multiple types of tumor cells of non-rabbit species both in vitro and in vivo, in not only humans but murine, rodent, species as well. This allows MYXV to pose as a potential virotherapy for human cancer cells. McFadden research lab has been researching the role of the exportin 1 protein (XPO1), also known as the chromosome maintenance region-1 (CRM-1). It is suspected that the XPO1 pathway may be one of the evasion mechanisms that MYXV utilizes as an antiviral response. KPT-330 (Selinexor) is a selective inhibitor of nuclear transport (SINE) drug that was designed as the first-in-human oral FDA approved cancer treatment. It has been shown effectiveness in inhibiting XPO1 in multiple lines of cancer cells, such as the Lewis Lung Carcinoma (LLC1) cells researched in this study. McFadden research lab has been examining the effects of various Selinexor concentrations along with different multiplicities of infection (MOIs) of MYXV to determine the best combination that can be used to reduce tumor size at the highest effectiveness. Overall, Selinexor is not increasing cell killing through a synergistic means, but rather simply by increasing the ability of MYXV to infect and spread in LLC1 cells. This then causes increased cell killing given that more LLC1 cells are penetrated by the OV and “suffocated” by the prevention of exporting essential proteins from the nucleus to their respectively critical final destinations in the cancer cells.
ContributorsPatel, Hrithik (Author) / Rahman, Masmudur (Thesis director) / McFadden, Grant (Committee member) / Barrett, The Honors College (Contributor) / Department of Management and Entrepreneurship (Contributor) / School of Life Sciences (Contributor)
Created2022-05
Description
Novel biological strategies for cancer therapy have recently been able to generate improved anti-tumor effects in the clinic. Of these new advancements, oncolytic virotherapy is a promising strategy through a dual mechanism of oncolysis and stimulation of tumor immunogenicity against the target cancer cells. Myxoma virus (MYXV) is an oncolytic poxvirus that has a natural tropism for Leporids, being nonpathogenic in humans and all other known vertebrates. MYXV is able to infect cancer cells due to mutations and defects in many innate signaling pathways, such as those involved in anti-viral responses. While MYXV alone infects and kills many classes of human cancer cells, recombinant techniques allow for the implementation of therapeutic transgenes, which have the potential of ‘arming’ the virus to enhance its potential as an oncolytic virus. The implementation of certain transgenes allows improved cancer cell killing and/or promotion of more robust anti-tumor immune responses. To investigate the potential of immune-inducing transgenes in MYXV, in vitro screening experiments were performed with several single transgene-armed recombinant MYXVs. As recent studies have shown the ability of MYXV to uniquely target malignant human hematopoietic stem cells, the potential of oncolytic MYXV armed with individual immune-enhancing transgenes was investigated through in vitro killing analysis using human acute myeloid leukemia (AML) and multiple myeloma (MM) cell lines. Additionally, in vitro experiments were performed using primary bone marrow (BM) cells obtained from human patients diagnosed with MM. Furthermore, the action of an engineered bispecific killer engager (huBIKE) was investigated through co-culture studies between the CD138 surface marker of target MM cells and the CD16 surface marker of primary effector peripheral blood mononuclear cells (PBMCs), particularly NK cells and neutrophils. In this study, several of the test armed MYXV-infected human AML and MM cell lines resulted in increased cell death compared to unarmed MYXV-infected cells. Additionally, increased killing of CD138+ MM cells from primary human BM samples was observed following infection with huBIKE-armed MYXV relative to infection with unarmed MYXV. Furthermore, analysis of co-culture studies performed suggests enhanced killing of target MM cells via engagement of NK cells with U266 MM cells by huBIKE.
ContributorsMamola, Joseph (Author) / McFadden, Grant (Thesis advisor) / Jacobs, Bertram (Committee member) / Blattman, Joseph (Committee member) / Arizona State University (Publisher)
Created2020