Matching Items (59)
Description
In an effort to begin validating the large number of discovered candidate biomarkers, proteomics is beginning to shift from shotgun proteomic experiments towards targeted proteomic approaches that provide solutions to automation and economic concerns. Such approaches to validate biomarkers necessitate the mass spectrometric analysis of hundreds to thousands of human samples. As this takes place, a serendipitous opportunity has become evident. By the virtue that as one narrows the focus towards "single" protein targets (instead of entire proteomes) using pan-antibody-based enrichment techniques, a discovery science has emerged, so to speak. This is due to the largely unknown context in which "single" proteins exist in blood (i.e. polymorphisms, transcript variants, and posttranslational modifications) and hence, targeted proteomics has applications for established biomarkers. Furthermore, besides protein heterogeneity accounting for interferences with conventional immunometric platforms, it is becoming evident that this formerly hidden dimension of structural information also contains rich-pathobiological information. Consequently, targeted proteomics studies that aim to ascertain a protein's genuine presentation within disease- stratified populations and serve as a stepping-stone within a biomarker translational pipeline are of clinical interest. Roughly 128 million Americans are pre-diabetic, diabetic, and/or have kidney disease and public and private spending for treating these diseases is in the hundreds of billions of dollars. In an effort to create new solutions for the early detection and management of these conditions, described herein is the design, development, and translation of mass spectrometric immunoassays targeted towards diabetes and kidney disease. Population proteomics experiments were performed for the following clinically relevant proteins: insulin, C-peptide, RANTES, and parathyroid hormone. At least thirty-eight protein isoforms were detected. Besides the numerous disease correlations confronted within the disease-stratified cohorts, certain isoforms also appeared to be causally related to the underlying pathophysiology and/or have therapeutic implications. Technical advancements include multiplexed isoform quantification as well a "dual- extraction" methodology for eliminating non-specific proteins while simultaneously validating isoforms. Industrial efforts towards widespread clinical adoption are also described. Consequently, this work lays a foundation for the translation of mass spectrometric immunoassays into the clinical arena and simultaneously presents the most recent advancements concerning the mass spectrometric immunoassay approach.
ContributorsOran, Paul (Author) / Nelson, Randall (Thesis advisor) / Hayes, Mark (Thesis advisor) / Ros, Alexandra (Committee member) / Williams, Peter (Committee member) / Arizona State University (Publisher)
Created2011
Description
Signal processing techniques have been used extensively in many engineering problems and in recent years its application has extended to non-traditional research fields such as biological systems. Many of these applications require extraction of a signal or parameter of interest from degraded measurements. One such application is mass spectrometry immunoassay (MSIA) which has been one of the primary methods of biomarker discovery techniques. MSIA analyzes protein molecules as potential biomarkers using time of flight mass spectrometry (TOF-MS). Peak detection in TOF-MS is important for biomarker analysis and many other MS related application. Though many peak detection algorithms exist, most of them are based on heuristics models. One of the ways of detecting signal peaks is by deploying stochastic models of the signal and noise observations. Likelihood ratio test (LRT) detector, based on the Neyman-Pearson (NP) lemma, is an uniformly most powerful test to decision making in the form of a hypothesis test. The primary goal of this dissertation is to develop signal and noise models for the electrospray ionization (ESI) TOF-MS data. A new method is proposed for developing the signal model by employing first principles calculations based on device physics and molecular properties. The noise model is developed by analyzing MS data from careful experiments in the ESI mass spectrometer. A non-flat baseline in MS data is common. The reasons behind the formation of this baseline has not been fully comprehended. A new signal model explaining the presence of baseline is proposed, though detailed experiments are needed to further substantiate the model assumptions. Signal detection schemes based on these signal and noise models are proposed. A maximum likelihood (ML) method is introduced for estimating the signal peak amplitudes. The performance of the detection methods and ML estimation are evaluated with Monte Carlo simulation which shows promising results. An application of these methods is proposed for fractional abundance calculation for biomarker analysis, which is mathematically robust and fundamentally different than the current algorithms. Biomarker panels for type 2 diabetes and cardiovascular disease are analyzed using existing MS analysis algorithms. Finally, a support vector machine based multi-classification algorithm is developed for evaluating the biomarkers' effectiveness in discriminating type 2 diabetes and cardiovascular diseases and is shown to perform better than a linear discriminant analysis based classifier.
ContributorsBuddi, Sai (Author) / Taylor, Thomas (Thesis advisor) / Cochran, Douglas (Thesis advisor) / Nelson, Randall (Committee member) / Duman, Tolga (Committee member) / Arizona State University (Publisher)
Created2012
Description
Cancer claims hundreds of thousands of lives every year in US alone. Finding ways for early detection of cancer onset is crucial for better management and treatment of cancer. Thus, biomarkers especially protein biomarkers, being the functional units which reflect dynamic physiological changes, need to be discovered. Though important, there are only a few approved protein cancer biomarkers till date. To accelerate this process, fast, comprehensive and affordable assays are required which can be applied to large population studies. For this, these assays should be able to comprehensively characterize and explore the molecular diversity of nominally "single" proteins across populations. This information is usually unavailable with commonly used immunoassays such as ELISA (enzyme linked immunosorbent assay) which either ignore protein microheterogeneity, or are confounded by it. To this end, mass spectrometric immuno assays (MSIA) for three different human plasma proteins have been developed. These proteins viz. IGF-1, hemopexin and tetranectin have been found in reported literature to show correlations with many diseases along with several carcinomas. Developed assays were used to extract entire proteins from plasma samples and subsequently analyzed on mass spectrometric platforms. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric techniques where used due to their availability and suitability for the analysis. This resulted in visibility of different structural forms of these proteins showing their structural micro-heterogeneity which is invisible to commonly used immunoassays. These assays are fast, comprehensive and can be applied in large sample studies to analyze proteins for biomarker discovery.
ContributorsRai, Samita (Author) / Nelson, Randall (Thesis advisor) / Hayes, Mark (Thesis advisor) / Borges, Chad (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2012
Description
Adaptive therapy utilizes competitive interactions between resistant and sensitive cells by keeping some sensitive cells to control tumor burden with the aim of increasing overall survival and time to progression. The use of adaptive therapy to treat breast cancer, ovarian cancer, and pancreatic cancer in preclinical models has shown significant results in controlling tumor growth. The purpose of this thesis is to draft a protocol to study adaptive therapy in a preclinical model of breast cancer on MCF7, estrogen receptor-positive, cells that have evolved resistance to fulvestrant and palbociclib (MCF7 R). In this study, we used two protocols: drug dose adjustment and intermittent therapy. The MCF7 R cell lines were injected into the mammary fat pads of 11-month-old NOD/SCID gamma (NSG) mice (18 mice) which were then treated with gemcitabine.<br/>The results of this experiment did not provide complete information because of the short-term treatments. In addition, we saw an increase in the tumor size of a few of the treated mice, which could be due to the metabolism of the drug at that age, or because of the difference in injection times. Therefore, these adaptive therapy protocols on hormone-refractory breast cancer cell lines will be repeated on young, 6-week old mice by injecting the cell lines at the same time for all mice, which helps the results to be more consistent and accurate.
ContributorsConti, Aviona (Author) / Maley, Carlo (Thesis director) / Blattman, Joseph (Committee member) / Seyedi, Sareh (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Cancer is a disease acquired through mutations which leads to uncontrolled cell division and destruction of normal tissue within the body. Recent increases in available cross-species data of cancer in mammals, reptiles, birds, and other vertebrates has revealed that the prevalence of cancers varies widely across species. Life-history theory suggests that there could be traits that potentially explain some of that variation. We are particularly interested in species that get very little cancer. How are they preventing cancer and can we learn from them how to prevent cancer in humans? Comparative oncology focuses on the analysis of cancer prevalence and traits in different non-human species and allows researchers to apply their findings to humans with the goal of improving and advancing cancer treatment. We incorporate the predictions that animals with larger bodies have evolved better cancer suppression mechanisms than animals with small bodies. Ruminants in the past were larger in size than modern day ruminants and they may have retained cancer defenses from their large ancestors. The strong cancer defenses and small body size combined may explain the low prevalence of cancer in Ruminants. This paper aims to evaluate the presence of benign and malignant neoplasia prevalence across multiple ruminant species following a time of dramatic decrease in body size across the clade. Our aim is to illuminate the potential impact that these shifts in body size had on their cancer prevalence as well as test the statistical power of other key life history variables to predict cancer prevalence.
ContributorsAustin, Shannon Ruth (Author) / Maley, Carlo (Thesis director) / Boddy, Amy (Committee member) / Compton, Zachary (Committee member) / Historical, Philosophical & Religious Studies (Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Macrostomum lignano is characterized by its elevated regenerative ability conferred by its high percentage of stem cells (the highest recorded for any animal). M. lignano is already used as a model organism for addressing fundamental questions of stem cell biology, aging, regeneration, and reproduction, but not yet cancer.
M. lignano larvae were isolated into separate wells of 24-well plates. After reaching maturity (30 days), the experimental plates were exposed to 5 Gys of X-rays every 4 days for a total of a 25 Gy exposure. We observed phenotypes that may be attributed to the acute effect of irradiation (e.g. blisters) but we recorded two types of phenotypes that may be a result of long-term effects of exposure to radiation. We observed enlarged testis and dark regions/masses that appeared statistically significantly more frequently in the treated animals (Fisher exact test, p=0.0026). Preliminary histological analyses of the enlarged testis suggest a benign testis enlargement due to an aberrant growth of the testes and an accumulation of aberrant spermatozoa. Importantly, we found that, similar to cancer, the dark masses can grow in size over time and the histological analysis confirms that the observed masses are composed of cells completely different from surrounding normal cells. Notably, we observed that those masses can develop and then completely disappear through an observed method of ejection. M. lignano offer the unique possibility to study in vivo cancer development in a simple organism that can easily be cultured in the lab in large numbers.
M. lignano larvae were isolated into separate wells of 24-well plates. After reaching maturity (30 days), the experimental plates were exposed to 5 Gys of X-rays every 4 days for a total of a 25 Gy exposure. We observed phenotypes that may be attributed to the acute effect of irradiation (e.g. blisters) but we recorded two types of phenotypes that may be a result of long-term effects of exposure to radiation. We observed enlarged testis and dark regions/masses that appeared statistically significantly more frequently in the treated animals (Fisher exact test, p=0.0026). Preliminary histological analyses of the enlarged testis suggest a benign testis enlargement due to an aberrant growth of the testes and an accumulation of aberrant spermatozoa. Importantly, we found that, similar to cancer, the dark masses can grow in size over time and the histological analysis confirms that the observed masses are composed of cells completely different from surrounding normal cells. Notably, we observed that those masses can develop and then completely disappear through an observed method of ejection. M. lignano offer the unique possibility to study in vivo cancer development in a simple organism that can easily be cultured in the lab in large numbers.
ContributorsGerman, Adriana (Author) / Fortunato, Angelo (Thesis director) / Maley, Carlo (Committee member) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Cancer rates vary significantly across tissue type and location in humans, driven by clinically relevant distinctions in the risk factors that lead to different cancer types. Despite the importance of cancer location in human health, little is known about tissue-specific cancers in non-human animals. A comparison of cancer prevalence across the tree of life can give insight into how evolutionary history has shaped various mechanisms of cancer suppression. Here, we explore whether species-level life history strategies are associated with differences in mammary neoplasia rates across mammals. We propose that the same patterns of cancer prevalence that have been reported across species will be maintained at the tissue-specific level. We used a phylogenetic regression on 15 life history traits across 112 mammalian species to determine the correlation between a life history trait and how it relates to mammary neoplasia prevalence. A greater risk of mammary neoplasia was found in the characteristics associated with fast life history organisms and a lower risk of mammary neoplasia was found in the characteristics associated with slow life history organisms. With this analysis, a framework is provided for how different life history modalities can influence cancer vulnerability.
ContributorsMajhail, Komal Kaur (Co-author) / Majhail, Komal (Co-author) / Maley, Carlo (Thesis director) / Boddy, Amy (Committee member) / Compton, Zachary (Committee member) / College of Health Solutions (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Cancer is a disease that occurs in many and perhaps all multicellular organisms. Current research is looking at how different life history characteristics among species could influence cancer rates. Because somatic maintenance is an important component of a species' life history, we hypothesize the same ecological forces shaping the life history of a species should also determine its cancer susceptibility. By looking at varying life histories, potential evolutionary trends could be used to explain differing cancer rates. Life history theory could be an important framework for understanding cancer vulnerabilities with different trade-offs between life history traits and cancer defenses. Birds have diverse life history strategies that could explain differences in cancer suppression. Peto's paradox is the observation that cancer rates do not typically increase with body size and longevity despite an increased number of cell divisions over the animal's lifetime that ought to be carcinogenic. Here we show how Peto’s paradox is negatively correlated for cancer within the clade, Aves. That is, larger, long-lived birds get more cancer than smaller, short-lived birds (p=0.0001; r2= 0.024). Sexual dimorphism in both plumage color and size differ among Aves species. We hypothesized that this could lead to a difference in cancer rates due to the amount of time and energy sexual dimorphism takes away from somatic maintenance. We tested for an association between a variety of life history traits and cancer, including reproductive potential, growth rate, incubation, mating systems, and sexual dimorphism in both color and size. We found male birds get less cancer than female birds (9.8% vs. 11.1%, p=0.0058).
ContributorsDolan, Jordyn Nicole (Author) / Maley, Carlo (Thesis director) / Harris, Valerie (Committee member) / Boddy, Amy (Committee member) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
All multicellular organisms are susceptible to developing cancer, but some organisms have varying sensitivities to the disease. One such organism is the Trichoplax adhaerens which has no documented case of cancer development. T. adhaerens cancer resistance was studied by observing physiological and morphological changes of the organism after radiation treatment. Preliminary experiments suggested that this organism is able to survive exposure to 160 gray radiation treatment almost as well as untreated organisms. The T. adhaerens have two genes, TriadG6402 and TriadG5479, similar to the human genes TP53 and MDM2 respectively. TP53 and MDM2 are the two main genes associated with apoptosis in humans: an important cell regulatory checkpoint involved in cancer prevention. PCR analysis, done after radiation treatment, showed an overexpression of the ortholog gene MDM2 in the T. adhaerens. This may suggest that T. adhaerens block apoptosis from occurring and that their ortholog gene is involved in DNA repair. It is significant to study the gene expression of TriadG6402 and TriadG54791 in T. adhaerens because these genes are well conserved in humans. Future studies of these genes in the T. adhaerens can be used to understand the evolution of the function of these genes in more complex organisms and be used for human cancer prevention.
ContributorsKulkarni, Arathi (Author) / Fortunato, Angelo (Thesis director) / Maley, Carlo (Committee member) / Department of Economics (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Trichoplax adhaerens (Placozoa) is the simplest multicellular animal to be described. This organism lacks nervous tissue, muscle tissue and organs, and is composed of only five cell types organized into three layers. Placozoa are gaining popularity as a model organism due to their simple make-up and completely sequenced genome. The complete sequencing of this organism’s genome has revealed the presence of important genes in cancer such as TP53 and MDM2 genes. Along with the presence of these genes, there are also additional pathways commonly deregulated in cancer that are well conserved in this organism. T. adhaerens are able to survive exposure to 160Gy and even 240Gy of X-ray radiation. Though small dark bodies form within the main body, they tend to extrude those masses, and continue to reproduce afterwards. After exposure to both grades of radiation, there was a greater increase in the apparent population size of the treated population than the control population. There was also a greater decrease in surface area of the organisms exposed to 160Gy than the control organisms. This increase in population and decrease in surface area of the treated organisms could be due to the extruded bodies. We hypothesize that the observed extrusion is a novel cancer defense mechanism for ridding the animal of damaged or mutated cells. This hypothesis should be tested through longitudinal observation and genetic analysis of the extruded bodies.
ContributorsYi, Avalon (Author) / Fortunato, Angelo (Thesis director) / Maley, Carlo (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12