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Description
Colorectal cancer (CRC) is one of the most highly diagnosed cancers in the United States and accounts for 9.5% of all new cancer cases worldwide. With a 50% five-year prognosis, it is the second highest cancerous cause of death in the U.S. CRC tumors express antigens that are capable of inducing an immune response. The identification of autoantibodies (AAb) against tumor-associated antigens (TAA) may facilitate personalized tumor treatment in the form of targeted immunotherapy. The objective of this study was to observe the AAb expression raised against a 2000 human gene survey in late-stage colorectal cancer using the Nucleic Acid Programmable Protein Arrays (NAPPA). AAbs from serum samples were collected from 80 patients who died within 24 months of their last blood draw and 80 age and gender matched healthy control were profiled using NAPPA. TAA p53, a well-established protein that is one of the most highly mutated across a variety of cancers, was one of the top candidates based on statistical analysis, which, along with its family proteins p63 and p73 (which showed inverse AAb response profiles) warranted further testing via RAPID ELISA. Statistical analysis from these results revealed an inverse differential relationship between p53 and p63, in which p53 seropositivity was higher in patients than in controls, while the opposite was unexpectedly the case for p63. This study involving the AAb immunoprofiling of advanced stage CRC patients is one of the first to shed light on the high-throughput feasibility of immunoproteomic experiments using protein arrays as well as the identification of immunotherapy targets in a more rapid move towards specialized treatment of advanced CRC.
ContributorsSzeto, Emily (Author) / LaBaer, Joshua (Thesis director) / Qiu, Ji (Committee member) / Demirkan, Gokhan (Committee member) / Barrett, The Honors College (Contributor) / T. Denny Sanford School of Social and Family Dynamics (Contributor)
Created2014-12
Description
The pathogenesis of type 1 diabetes (T1D) is still not fully understood in the scientific community. Evidence has shown that viral infections are one of the important environmental factors associated with the disease development. Seven of the top T1D related viruses were selected to study the prevalence of viral humoral response in T1D patients using our innovative protein array platform called Nucleic Acid Programmable Protein Array (NAPPA). In this study, each viral gene was individually captured using various PCR based techniques, cloned into a protein expression vector, and assembled as the first version of T1D viral protein array. Humoral responses of IgG, IgA, and IgM were examined. Although each class of immunoglobulin generated a wide-range of reactivity, responses to various viral proteins from different proteins were observed. In summary, we captured most of the T1D related viral genes, established viral protein expression on the protein array, and displayed the serum response on the viral protein array. The successful progress will help to fulfill the long term goal of testing the viral infection hypothesis in T1D development.
ContributorsDavis, Amy Darlene (Author) / LaBaer, Joshua (Thesis director) / Qiu, Ji (Committee member) / Desi, Paul (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2013-05
Description
AMPylation is a post-translation modification that has an important role in the survival of many bacterial pathogens by affecting the host cell's molecular signaling. In the course of studying this intercellular manipulation, there has only been modest progression in the identification of the enzymes with AMPylation capabilities (AMPylators) and their respective targets. The reason for these minimal developments is the inability to analyze a large subset of these proteins. Therefore, to increase the efficiency of the identification and characterization of the proteins, Yu et al developed a high-throughput non-radioactive discovery platform using Human Nucleic Acid Programmable Protein Arrays (NAPPA) and a validation platform using bead-based assays. The large-scale unbiased screening of potential substrates for two bacterial AMPylators containing Fic domain, VopS and IbpAFic2, had been performed and dozens of novel substrates were identified and confirmed. With the efficiency of this method, the platform was extended to the identification of novel substrates for a Legionella virulence factor, SidM, containing a different adenylyl transferase domain. The screening was performed using NAPPA arrays comprising of 10,000 human proteins, the active AMPylator SidM, and its inactive D110/112A mutant as a negative control. Many potential substrates of SidM were found, including Rab GTPases and non-GTPase proteins. Several of which have been confirmed with the bead-based AMPylation assays.
ContributorsGraves, Morgan C. (Author) / LaBaer, Joshua (Thesis director) / Qiu, Ji (Committee member) / Yu, Xiaobo (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2013-05
Description
Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~10[superscript 11] ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 10[superscript 6] enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients.
ContributorsDomenyuk, Valeriy (Author) / Zhong, Zhenyu (Author) / Stark, Adam (Author) / Xiao, Nianqing (Author) / O'Neill, Heather A. (Author) / Wei, Xixi (Author) / Wang, Jie (Author) / Tinder, Teresa T. (Author) / Tonapi, Sonal (Author) / Duncan, Janet (Author) / Hornung, Tassilo (Author) / Hunter, Andrew (Author) / Miglarese, Mark R. (Author) / Schorr, Joachim (Author) / Halbert, David D. (Author) / Quackenbush, John (Author) / Poste, George (Author) / Berry, Donald A. (Author) / Mayer, Gunter (Author) / Famulok, Michael (Author) / Spetzler, David (Author) / Consortium for Biosocial Complex Systems (Contributor) / Complex Adaptive Systems Initiative (Contributor)
Created2017-02-20
Description
This thesis examines Care Not Cash, a welfare reform measure that replaced traditional cash General Assistance program payments for homeless persons in San Francisco with in-kind social services. Unlike most welfare reform measures, proponents framed Care Not Cash as a progressive policy, aimed at expanding social services and government care for this vulnerable population. Drawing on primary and secondary documents, as well as interviews with homelessness policy experts, this thesis examines the historical and political success of Care Not Cash, and explores the potential need for implementation of a similar program in Phoenix, Arizona.
ContributorsMcCutcheon, Zachary Ryan (Author) / Lucio, Joanna (Thesis director) / Williams, David (Committee member) / Bretts-Jamison, Jake (Committee member) / School of Public Affairs (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
CREB3L1 has been previously shown to auto-acetylate itself when prepared from HeLa cell based in vitro protein expression lysates. To circumvent the concerns of the contamination of co-purified human proteins from HeLa lysates, the protein was purified through insect cell transfection in vitro. The objective of this study was to assay the auto-acetylation activity of CREB3L1 prepared from insect cells using the baculovirus expression vector system (BEVS). To this end, His-tagged CREB3L1 was affinity purified from Hi5 cells using an IMAC column and used for acetylation assay. Samples were taken different time points and auto-acetylation was by western using antibodies specific to acetylated lysines. Auto-acetylation activity was observed after overnight incubation. Future experiments will focus on the improvement of purification yield and the identification of the substrates and interacting proteins of CREB3L1 to better understand the biological functions of this novel acetyltransferase.
ContributorsSchwab, Anna (Author) / LaBaer, Joshua (Thesis director) / Qiu, Ji (Committee member) / Barrett, The Honors College (Contributor)
Created2017-05
Description
ABSTRACTWith the National Aeronautics and Space Administration (NASA) Psyche Mission, humans will soon have the first opportunity to explore a new kind of planetary body: one composed mostly of metal as opposed to stony minerals or ices. Identifying the composition of asteroids from Earth-based observations has been an ongoing challenge. Although optical reflectance spectra, radar, and orbital dynamics can constrain an asteroid’s mineralogy and bulk density, in many cases there is not a clear or precise match with analogous materials such as meteorites. Additionally, the surfaces of asteroids and other small, airless planetary bodies can be heavily modified over geologic time by exposure to the space environment. To accurately interpret remote sensing observations of metal-rich asteroids, it is therefore necessary to understand how the processes active on asteroid surfaces affect metallic materials. This dissertation represents a first step toward that understanding. In collaboration with many colleagues, I have performed laboratory experiments on iron meteorites to simulate solar wind ion irradiation, surface heating, micrometeoroid bombardment, and high-velocity impacts. Characterizing the meteorite surface’s physical and chemical properties before and after each experiment can constrain the effects of each process on a metal-rich surface in space. While additional work will be needed for a complete understanding, it is nevertheless possible to make some early predictions of what (16) Psyche’s surface regolith might look like when humans observe it up close. Moreover, the results of these experiments will inform future exploration beyond asteroid Psyche as humans attempt to understand how Earth’s celestial neighborhood came to be.
ContributorsChristoph, John Morgan M. (Author) / Elkins-Tanton, Linda (Thesis advisor) / Williams, David (Committee member) / Dukes, Catherine (Committee member) / Sharp, Thomas (Committee member) / Bell III, James (Committee member) / Arizona State University (Publisher)
Created2023
Cancer autoantibody biomarker discovery and validation using nucleic acid programmable protein array
Description
Currently in the US, many patients with cancer do not benefit from the population-based screening, due to challenges associated with the existing cancer screening scheme. Blood-based diagnostic assays have the potential to detect diseases in a non-invasive way. Proteins released from small early tumors may only be present intermittently and get diluted to tiny concentrations in the blood, making them difficult to use as biomarkers. However, they can induce autoantibody (AAb) responses, which can amplify the signal and persist in the blood even if the antigen is gone. Circulating autoantibodies is a promising class of molecules that have potential to serve as early detection biomarkers for cancers. This Ph.D thesis aims to screen for autoantibody biomarkers for the early detection of two deadly cancer, basal-like breast cancer and lung adenocarcinoma. First, a method was developed to display proteins in both native and denatured conformation on protein array. This method adopted a novel protein tag technology, called HaloTag, to covalently immobilize proteins on glass slide surface. The covalent attachment allowed these proteins to endure harsh treatment without getting dissociated from slide surface, which enabled the profiling of antibody responses against both conformational and linear epitopes. Next, a plasma screening protocol was optimized to significantly increase signal to noise ratio of protein array based AAb detection. Following this, the AAb responses in basal-like breast cancer were explored using nucleic acid programmable protein arrays (NAPPA) containing 10,000 full-length human proteins in 45 cases and 45 controls. After verification in a large sample set (145 basal-like breast cancer cases / 145 controls / 70 non-basal breast cancer) by ELISA, a 13-AAb classifier was developed to differentiate patients from controls with a sensitivity of 33% at 98% specificity. Similar approach was also applied to the lung cancer study to identify AAbs that distinguished lung cancer patients from computed-tomography positive benign pulmonary nodules (137 lung cancer cases, 127 smoker controls, 170 benign controls). In this study, two panels of AAbs were discovered that showed promising sensitivity and specificity. Six out of eight AAb targets were also found to have elevated mRNA level in lung adenocarcinoma patients using TCGA data. These projects as a whole provide novel insights on the association between AAbs and cancer, as well as general B cell antigenicity against self-proteins.
ContributorsWang, Jie (Author) / LaBaer, Joshua (Thesis advisor) / Anderson, Karen S (Committee member) / Lake, Douglas F (Committee member) / Chang, Yung (Committee member) / Arizona State University (Publisher)
Created2015
Description
The central question of my dissertation is "How old are the inner moons of Saturn?" This question is of critical importance for the refinement of how solar systems and giant planet systems form and evolve. One of the most direct ways to test the ages of a planet's surface is through the use of impact craters. Here I utilize images from the Cassini Imaging Science Subsystem (ISS) to count the craters on the mid-sized moons of Saturn, Tethys and Dione. I present a statistical analysis of the craters and the likely impactor sources that crated these craters. On Tethys I find that the impact craters can be explained by a planetocentric source that is local to the Saturnian system and is not found elsewhere in the outer planets. I also find that the majority of mapped regions are likely close in age. On Dione, I have mapped four areas at a regional-scale resolution ( ~ 200 m/ pix) and have found that resurfacing has greatly affected the small crater population and that the overall size-frequency distribution of craters is most representative of a planetocentric source unique to Saturn. Elliptical craters provide another means of assessing the bombardment environment around Saturn, as they record the primary direction of the object that created the crater upon impact on the surface. I have mapped these craters on Tethys and Dione, to analyze the global distributions of these craters and their orientations. Across both satellites, I find that in the equatorial regions between 30° N and 30°S in latitude, the orientations of the elliptical craters are consistent with an East/West orientation for their direction, which also is suggestive of a local planetocentric source. Throughout the main three studies presented in this dissertation I find that the main impactor source is a planetocentric source that is unique to Saturn and is not seen on the moons of the other giant planets.
ContributorsFerguson, Sierra Nichole (Author) / Rhoden, Alyssa R (Thesis advisor) / Desch, Steven J (Thesis advisor) / Robinson, Mark (Committee member) / Williams, David (Committee member) / Bose, Maitrayee (Committee member) / Arizona State University (Publisher)
Created2021
Description
Deposits of dark material appear on Vesta’s surface as features of relatively low-albedo in the visible wavelength range of Dawn’s camera and spectrometer. Mixed with the regolith and partially excavated by younger impacts, the material is exposed as individual layered outcrops in crater walls or ejecta patches, having been uncovered and broken up by the impact. Dark fans on crater walls and dark deposits on crater floors are the result of gravity-driven mass wasting triggered by steep slopes and impact seismicity. The fact that dark material is mixed with impact ejecta indicates that it has been processed together with the ejected material. Some small craters display continuous dark ejecta similar to lunar dark-halo impact craters, indicating that the impact excavated the material from beneath a higher-albedo surface. The asymmetric distribution of dark material in impact craters and ejecta suggests non-continuous distribution in the local subsurface. Some positive-relief dark edifices appear to be impact-sculpted hills with dark material distributed over the hill slopes.
Dark features inside and outside of craters are in some places arranged as linear outcrops along scarps or as dark streaks perpendicular to the local topography. The spectral characteristics of the dark material resemble that of Vesta’s regolith. Dark material is distributed unevenly across Vesta’s surface with clusters of all types of dark material exposures. On a local scale, some craters expose or are associated with dark material, while others in the immediate vicinity do not show evidence for dark material. While the variety of surface exposures of dark material and their different geological correlations with surface features, as well as their uneven distribution, indicate a globally inhomogeneous distribution in the subsurface, the dark material seems to be correlated with the rim and ejecta of the older Veneneia south polar basin structure. The origin of the dark material is still being debated, however, the geological analysis suggests that it is exogenic, from carbon-rich low-velocity impactors, rather than endogenic, from freshly exposed mafic material or melt, exposed or created by impacts.
ContributorsJaumann, R. (Author) / Nass, A. (Author) / Otto, K. (Author) / Krohn, K. (Author) / Stephan, K. (Author) / McCord, T. B. (Author) / Williams, David (Author) / Raymond, C. A. (Author) / Blewett, D. T. (Author) / Hiesinger, H. (Author) / Yingst, R. A. (Author) / De Sanctis, M. C. (Author) / Palomba, E. (Author) / Roatsch, T. (Author) / Matz, K-D. (Author) / Preusker, F. (Author) / Scholten, F. (Author) / Russell, C. T. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2014-09-15