Characterizing Genetic Drivers of Lymphoma through High-Throughput Sequencing

The advent of next-generation sequencing, now nearing a decade in age, has enabled, among other capabilities, measurement of genome-wide sequence features at unprecedented scale and resolution.

In this dissertation, I describe work to understand the genetic underpinnings of non-Hodgkin’s lymphoma through exploration of the epigenetics of its cell of origin, initial characterization and interpretation of driver mutations, and finally, a larger-scale, population-level study that incorporates mutation interpretation with clinical outcome.

In the first research chapter, I describe genomic characteristics of lymphomas through the lens of their cells of origin. Just as many other cancers, such as breast cancer or lung cancer, are categorized based on their cell of origin, lymphoma subtypes can be examined through the context of their normal B Cells of origin, Naïve, Germinal Center, and post-Germinal Center. By applying integrative analysis of the epigenetics of normal B Cells of origin through chromatin-immunoprecipitation sequencing, we find that differences in normal B Cell subtypes are reflected in the mutational landscapes of the cancers that arise from them, namely Mantle Cell, Burkitt, and Diffuse Large B-Cell Lymphoma.

In the next research chapter, I describe our first endeavor into understanding the genetic heterogeneity of Diffuse Large B Cell Lymphoma, the most common form of non-Hodgkin’s lymphoma, which affects 100,000 patients in the world. Through whole-genome sequencing of 1 case as well as whole-exome sequencing of 94 cases, we characterize the most recurrent genetic features of DLBCL and lay the groundwork for a larger study.

In the last research chapter, I describe work to characterize and interpret the whole exomes of 1001 cases of DLBCL in the largest single-cancer study to date. This highly-powered study enabled sub-gene, gene-level, and gene-network level understanding of driver mutations within DLBCL. Moreover, matched genomic and clinical data enabled the connection of these driver mutations to clinical features such as treatment response or overall survival. As sequencing costs continue to drop, whole-exome sequencing will become a routine clinical assay, and another diagnostic dimension in addition to existing methods such as histology. However, to unlock the full utility of sequencing data, we must be able to interpret it. This study undertakes a first step in developing the understanding necessary to uncover the genomic signals of DLBCL hidden within its exomes. However, beyond the scope of this one disease, the experimental and analytical methods can be readily applied to other cancer sequencing studies.

Thus, this dissertation leverages next-generation sequencing analysis to understand the genetic underpinnings of lymphoma, both by examining its normal cells of origin as well as through a large-scale study to sensitively identify recurrently mutated genes and their relationship to clinical outcome.

Role of ABL Family Kinases in Breast Cancer

The ABL family of non-receptor tyrosine kinases, ABL1 (also known as c-ABL) and ABL2 (also known as Arg), links diverse extracellular stimuli to signaling pathways that control cell growth, survival, adhesion, migration and invasion. ABL tyrosine kinases play an oncogenic role in human leukemias. However, the role of ABL kinases in solid tumors including breast cancer progression and metastasis is just emerging.

To evaluate whether ABL family kinases are involved in breast cancer development and metastasis, we first analyzed genomic data from large-scale screen of breast cancer patients. We found that ABL kinases are up-regulated in invasive breast cancer patients and high expression of ABL kinases correlates with poor prognosis and early metastasis. Using xenograft mouse models combined with genetic and pharmacological approaches, we demonstrated that ABL kinases are required for regulating breast cancer progression and metastasis to the bone. Using next generation sequencing and bioinformatics analysis, we uncovered a critical role for ABL kinases in promoting multiple oncogenic pathways including TAZ and STAT5 signaling networks and the epithelial to mesenchymal transition (EMT). These findings revealed a role for ABL kinases in regulating breast cancer tumorigenesis and bone metastasis and provide a rationale for targeting breast tumors with ABL-specific inhibitors.

Nanostructured Metal Oxide Coatings for Electrochemical Energy Conversion and Storage Electrodes

The realization of an energy future based on safe, clean, sustainable, and economically viable technologies is one of the grand challenges facing modern society. Electrochemical energy technologies underpin the potential success of this effort to divert energy sources away from fossil fuels, whether one considers alternative energy conversion strategies through photoelectrochemical (PEC) production of chemical fuels or fuel cells run with sustainable hydrogen, or energy storage strategies, such as in batteries and supercapacitors. This dissertation builds on recent advances in nanomaterials design, synthesis, and characterization to develop novel electrodes that can electrochemically convert and store energy.

Chapter 2 of this dissertation focuses on refining the properties of TiO2-based PEC water-splitting photoanodes used for the direct electrochemical conversion of solar energy into hydrogen fuel. The approach utilized atomic layer deposition (ALD); a growth process uniquely suited for the conformal and uniform deposition of thin films with angstrom-level thickness precision. ALD’s thickness control enabled a better understanding of how the effects of nitrogen doping via NH3 annealing treatments, used to reduce TiO2’s bandgap, can have a strong dependence on TiO2’s thickness and crystalline quality. In addition, it was found that some of the negative effects on the PEC performance typically associated with N-doped TiO2 could be mitigated if the NH3-annealing was directly preceded by an air-annealing step, especially for ultrathin (i.e., < 10 nm) TiO2 films. ALD was also used to conformally coat an ultraporous conductive fluorine-doped tin oxide nanoparticle (nanoFTO) scaffold with an ultrathin layer of TiO2. The integration of these ultrathin films and the oxide nanoparticles resulted in a heteronanostructure design with excellent PEC water oxidation photocurrents (0.7 mA/cm2 at 0 V vs. Ag/AgCl) and charge transfer efficiency.

In Chapter 3, two innovative nanoarchitectures were engineered in order to enhance the pseudocapacitive energy storage of next generation supercapacitor electrodes. The morphology and quantity of MnO2 electrodeposits was controlled by adjusting the density of graphene foliates on a novel graphenated carbon nanotube (g-CNT) scaffold. This control enabled the nanocomposite supercapacitor electrode to reach a capacitance of 640 F/g, under MnO2 specific mass loading conditions (2.3 mg/cm2) that are higher than previously reported. In the second engineered nanoarchitecture, the electrochemical energy storage properties of a transparent electrode based on a network of solution-processed Cu/Ni cores/shell nanowires (NWs) were activated by electrochemically converting the Ni metal shell into Ni(OH)2. Furthermore, an adjustment of the molar percentage of Ni plated onto the Cu NWs was found to result in a tradeoff between capacitance, transmittance, and stability of the resulting nickel hydroxide-based electrode. The nominal area capacitance and power performance results obtained for this Cu/Ni(OH)2 transparent electrode demonstrates that it has significant potential as a hybrid supercapacitor electrode for integration into cutting edge flexible and transparent electronic devices.

Selective Preparation of Semiconducting Single-Walled Carbon Nanotubes: From Fundamentals to Applications

Aligned single-walled carbon nanotubes (SWNTs) synthesized by the chemical vapor deposition (CVD) method have exceptional potential for next-generation nanoelectronics. However, there are considerable challenges in the preparation of semiconducting (s-) SWNTs with controlled properties (e.g., density, selectivity, and diameter) for their application in solving real-world problems. This dissertation describes research that aims to overcome the limitations by novel synthesis strategies and post-growth treatment. The application of as-prepared SWNTs as functional devices is also demonstrated. The dissertation includes the following parts: 1) decoupling the conflict between density and selectivity of s-SWNTs in CVD growth; 2) investigating the importance of diameter control for the selective synthesis of s-SWNTs; 3) synthesizing highly conductive SWNT thin film by thiophene-assisted CVD method; 4) eliminating metallic pathways in SWNT crossbars by gate-free electrical breakdown method; 5) enhancing the density of SWNT arrays by strain-release method; 6) studying the sensing mechanism of SWNT crossbar chemical sensors.

Other Than a Citizen: Vernacular Poetics in Postwar America

Few symbols of 1950s-1960s America remain as central to our contemporary conception of Cold War culture as the iconic ranch-style suburban home. While the house took center stage in the Nixon/Khrushchev kitchen debates as a symbol of modern efficiency and capitalist values, its popularity depended largely upon its obvious appropriation of vernacular architecture from the 19th century, those California haciendas and Texas dogtrots that dotted the American west. Contractors like William Levitt modernized the historical common houses, hermetically sealing their porous construction, all while using the ranch-style roots of the dwelling to galvanize a myth of an indigenous American culture. At a moment of intense occupational bureaucracy, political uncertainty and atomized social life, the rancher gave a self-identifying white consumer base reason to believe they could master their own plot in the expansive frontier. Only one example of America’s mid-century love affair with commodified vernacular forms, the ranch-style home represents a broad effort on the part of corporate and governmental interest groups to transform the vernacular into a style that expresses a distinctly homogenous vision of American culture. “Other than a Citizen” begins with an anatomy of that transformation, and then turns to the work of four poets who sought to reclaim the vernacular from that process of standardization and use it to countermand the containment-era strategies of Cold War America.

In four chapters, I trace references to common speech and verbal expressivity in the poetry and poetic theory of Charles Olson, Robert Duncan, LeRoi Jones/Amiri Baraka and Gwendolyn Brooks, against the historical backdrop of the Free-Speech Movement and the rise of mass-culture. When poets frame nonliterary speech within the literary page, they encounter the inability of writing to capture the vital ephemerality of verbal expression. Rather than treat this limitation as an impediment, the writers in my study use the poem to dramatize the fugitivity of speech, emphasizing it as a disruptive counterpoint to the technologies of capture. Where critics such as Houston Baker interpret the vernacular strictly in terms of resistance, I take a cue from the poets and argue that the vernacular, rooted etymologically at the intersection of domestic security and enslaved margin, represents a gestalt form, capable at once of establishing centralized power and sparking minor protest. My argument also expands upon Michael North’s exploration of the influence of minstrelsy and regionalism on the development of modernist literary technique in The Dialect of Modernism. As he focuses on writers from the early 20th century, I account for the next generation, whose America was not a culturally inferior collection of immigrants but an imperial power, replete with economic, political and artistic dominance. Instead of settling for an essentially American idiom, the poets in my study saw in the vernacular not phonetic misspellings, slang terminology and fragmented syntax, but the potential to provoke and thereby frame a more ethical mode of social life, straining against the regimentation of citizenship.

My attention to the vernacular argues for an alignment among writers who have been segregated by the assumption that race and aesthetics are mutually exclusive categories. In reading these writers alongside one another, “Other than a Citizen” shows how the avant-garde concepts of projective poetics and composition by field develop out of an interest in black expressivity. Conversely, I trace black radicalism and its emphasis on sociality back to the communalism practiced at the experimental arts college in Black Mountain, North Carolina, where Olson and Duncan taught. In pressing for this connection, my work reveals the racial politics embedded within the speech-based aesthetics of the postwar era, while foregrounding the aesthetic dimension of militant protest.

Not unlike today, the popular rhetoric of the Cold War insists that to be a citizen involves defending one’s status as a rightful member of an exclusionary nation. To be other than a citizen, as the poets in my study make clear, begins with eschewing the false certainty that accompanies categorical nominalization. In promoting a model of mutually dependent participation, these poets lay the groundwork for an alternative model of civic belonging, where volition and reciprocity replace compliance and self-sufficiency. In reading their lines, we become all the more aware of the cracks that run the length of our load-bearing walls.

Bioengineered Approaches to Prevent Hypertrophic Scar Contraction

Burn injuries in the United States account for over one million hospital admissions per year, with treatment estimated at four billion dollars. Of severe burn patients, 30-90% will develop hypertrophic scars (HSc). Current burn therapies rely upon the use of bioengineered skin equivalents (BSEs), which assist in wound healing but do not prevent HSc. HSc contraction occurs of 6-18 months and results in the formation of a fixed, inelastic skin deformity, with 60% of cases occurring across a joint. HSc contraction is characterized by abnormally high presence of contractile myofibroblasts which normally apoptose at the completion of the proliferative phase of wound healing. Additionally, clinical observation suggests that the likelihood of HSc is increased in injuries with a prolonged immune response. Given the pathogenesis of HSc, we hypothesize that BSEs should be designed with two key anti-scarring characterizes: (1) 3D architecture and surface chemistry to mitigate the inflammatory microenvironment and decrease myofibroblast transition; and (2) using materials which persist in the wound bed throughout the remodeling phase of repair. We employed electrospinning and 3D printing to generate scaffolds with well-controlled degradation rate, surface coatings, and 3D architecture to explore our hypothesis through four aims.

In the first aim, we evaluate the impact of elastomeric, randomly-oriented biostable polyurethane (PU) scaffold on HSc-related outcomes. In unwounded skin, native collagen is arranged randomly, elastin fibers are abundant, and myofibroblasts are absent. Conversely, in scar contractures, collagen is arranged in linear arrays and elastin fibers are few, while myofibroblast density is high. Randomly oriented collagen fibers native to the uninjured dermis encourage random cell alignment through contact guidance and do not transmit as much force as aligned collagen fibers. However, the linear ECM serves as a system for mechanotransduction between cells in a feed-forward mechanism, which perpetuates ECM remodeling and myofibroblast contraction. The electrospinning process allowed us to create scaffolds with randomly-oriented fibers that promote random collagen deposition and decrease myofibroblast formation. Compared to an in vitro HSc contraction model, fibroblast-seeded PU scaffolds significantly decreased matrix and myofibroblast formation. In a murine HSc model, collagen coated PU (ccPU) scaffolds significantly reduced HSc contraction as compared to untreated control wounds and wounds treated with the clinical standard of care. The data from this study suggest that electrospun ccPU scaffolds meet the requirements to mitigate HSc contraction including: reduction of in vitro HSc related outcomes, diminished scar stiffness, and reduced scar contraction. While clinical dogma suggests treating severe burn patients with rapidly biodegrading skin equivalents, these data suggest that a more long-term scaffold may possess merit in reducing HSc.

In the second aim, we further investigate the impact of scaffold longevity on HSc contraction by studying a degradable, elastomeric, randomly oriented, electrospun micro-fibrous scaffold fabricated from the copolymer poly(l-lactide-co-ε-caprolactone) (PLCL). PLCL scaffolds displayed appropriate elastomeric and tensile characteristics for implantation beneath a human skin graft. In vitro analysis using normal human dermal fibroblasts (NHDF) demonstrated that PLCL scaffolds decreased myofibroblast formation as compared to an in vitro HSc contraction model. Using our murine HSc contraction model, we found that HSc contraction was significantly greater in animals treated with standard of care, Integra, as compared to those treated with collagen coated-PLCL (ccPLCL) scaffolds at d 56 following implantation. Finally, wounds treated with ccPLCL were significantly less stiff than control wounds at d 56 in vivo. Together, these data further solidify our hypothesis that scaffolds which persist throughout the remodeling phase of repair represent a clinically translatable method to prevent HSc contraction.

In the third aim, we attempt to optimize cell-scaffold interactions by employing an anti-inflammatory coating on electrospun PLCL scaffolds. The anti-inflammatory sub-epidermal glycosaminoglycan, hyaluronic acid (HA) was used as a coating material for PLCL scaffolds to encourage a regenerative healing phenotype. To minimize local inflammation, an anti-TNFα monoclonal antibody (mAB) was conjugated to the HA backbone prior to PLCL coating. ELISA analysis confirmed mAB activity following conjugation to HA (HA+mAB), and following adsorption of HA+mAB to the PLCL backbone [(HA+mAB)PLCL]. Alican blue staining demonstrated thorough HA coating of PLCL scaffolds using pressure-driven adsorption. In vitro studies demonstrated that treatment with (HA+mAB)PLCL prevented downstream inflammatory events in mouse macrophages treated with soluble TNFα. In vivo studies using our murine HSc contraction model suggested positive impact of HA coating, which was partiall impeded by the inclusion of the TNFα mAB. Further characterization of the inflammatory microenvironment of our murine model is required prior to conclusions regarding the potential for anti-TNFα therapeutics for HSc. Together, our data demonstrate the development of a complex anti-inflammatory coating for PLCL scaffolds, and the potential impact of altering the ECM coating material on HSc contraction.

In the fourth aim, we investigate how scaffold design, specifically pore dimensions, can influence myofibroblast interactions and subsequent formation of OB-cadherin positive adherens junctions in vitro. We collaborated with Wake Forest University to produce 3D printed (3DP) scaffolds with well-controlled pore sizes we hypothesized that decreasing pore size would mitigate intra-cellular communication via OB-cadherin-positive adherens junctions. PU was 3D printed via pressure extrusion in basket-weave design with feature diameter of ~70 µm and pore sizes of 50, 100, or 150 µm. Tensile elastic moduli of 3DP scaffolds were similar to Integra; however, flexural moduli of 3DP were significantly greater than Integra. 3DP scaffolds demonstrated ~50% porosity. 24 h and 5 d western blot data demonstrated significant increases in OB-cadherin expression in 100 µm pores relative to 50 µm pores, suggesting that pore size may play a role in regulating cell-cell communication. To analyze the impact of pore size in these scaffolds on scarring in vivo, scaffolds were implanted beneath skin graft in a murine HSc model. While flexural stiffness resulted in graft necrosis by d 14, cellular and blood vessel integration into scaffolds was evident, suggesting potential for this design if employed in a less stiff material. In this study, we demonstrate for the first time that pore size alone impacts OB-cadherin protein expression in vitro, suggesting that pore size may play a role on adherens junction formation affiliated with the fibroblast-to-myofibroblast transition. Overall, this work introduces a new bioengineered scaffold design to both study the mechanism behind HSc and prevent the clinical burden of this contractile disease.

Together, these studies inform the field of critical design parameters in scaffold design for the prevention of HSc contraction. We propose that scaffold 3D architectural design, surface chemistry, and longevity can be employed as key design parameters during the development of next generation, low-cost scaffolds to mitigate post-burn hypertrophic scar contraction. The lessening of post-burn scarring and scar contraction would improve clinical practice by reducing medical expenditures, increasing patient survival, and dramatically improving quality of life for millions of patients worldwide.

Design, Fabrication, and Characterization of Carbon Nanotube Field Emission Devices for Advanced Applications

Carbon nanotubes (CNTs) have recently emerged as promising candidates for electron field emission (FE) cathodes in integrated FE devices. These nanostructured carbon materials possess exceptional properties and their synthesis can be thoroughly controlled. Their integration into advanced electronic devices, including not only FE cathodes, but sensors, energy storage devices, and circuit components, has seen rapid growth in recent years. The results of the studies presented here demonstrate that the CNT field emitter is an excellent candidate for next generation vacuum microelectronics and related electron emission devices in several advanced applications.

The work presented in this study addresses determining factors that currently confine the performance and application of CNT-FE devices. Characterization studies and improvements to the FE properties of CNTs, along with Micro-Electro-Mechanical Systems (MEMS) design and fabrication, were utilized in achieving these goals. Important performance limiting parameters, including emitter lifetime and failure from poor substrate adhesion, are examined. The compatibility and integration of CNT emitters with the governing MEMS substrate (i.e., polycrystalline silicon), and its impact on these performance limiting parameters, are reported. CNT growth mechanisms and kinetics were investigated and compared to silicon (100) to improve the design of CNT emitter integrated MEMS based electronic devices, specifically in vacuum microelectronic device (VMD) applications.

Improved growth allowed for design and development of novel cold-cathode FE devices utilizing CNT field emitters. A chemical ionization (CI) source based on a CNT-FE electron source was developed and evaluated in a commercial desktop mass spectrometer for explosives trace detection. This work demonstrated the first reported use of a CNT-based ion source capable of collecting CI mass spectra. The CNT-FE source demonstrated low power requirements, pulsing capabilities, and average lifetimes of over 320 hours when operated in constant emission mode under elevated pressures, without sacrificing performance. Additionally, a novel packaged ion source for miniature mass spectrometer applications using CNT emitters, a MEMS based Nier-type geometry, and a Low Temperature Cofired Ceramic (LTCC) 3D scaffold with integrated ion optics were developed and characterized. While previous research has shown other devices capable of collecting ion currents on chip, this LTCC packaged MEMS micro-ion source demonstrated improvements in energy and angular dispersion as well as the ability to direct the ions out of the packaged source and towards a mass analyzer. Simulations and experimental design, fabrication, and characterization were used to make these improvements.

Finally, novel CNT-FE devices were developed to investigate their potential to perform as active circuit elements in VMD circuits. Difficulty integrating devices at micron-scales has hindered the use of vacuum electronic devices in integrated circuits, despite the unique advantages they offer in select applications. Using a combination of particle trajectory simulation and experimental characterization, device performance in an integrated platform was investigated. Solutions to the difficulties in operating multiple devices in close proximity and enhancing electron transmission (i.e., reducing grid loss) are explored in detail. A systematic and iterative process was used to develop isolation structures that reduced crosstalk between neighboring devices from 15% on average, to nearly zero. Innovative geometries and a new operational mode reduced grid loss by nearly threefold, thereby improving transmission of the emitted cathode current to the anode from 25% in initial designs to 70% on average. These performance enhancements are important enablers for larger scale integration and for the realization of complex vacuum microelectronic circuits.

Public-Private Partnership Design for Inclusive Cocoa Global Value Chains in Ghana

Within 10 years, there could be a severe global shortage in the supply of cocoa, according to industry practitioners and other experts. Due to global population growth and the emergence of a growing global middle class, by 2025 the cocoa crop would need to increase by nearly 50 per cent to keep up with projected demand. A potential shortage of supply is a direct threat to the business model of lead firms – including cocoa grinders and processors, chocolate confectioners, and retail distributors. But these international firms – the ones that will suffer the most if there is a shortage of cocoa supply – are helping create the market failure that is stifling sustainability. Functioning as a two-tiered consolidated oligopoly with a combined market share of approximately 89%, these firms enjoy the largest portion of value capture in the cocoa-chocolate global value chain (GVC). The smallholder cocoa producers, conversely, are trapped in low value-add segments of the GVC. In fact, most smallholder farmers survive on less than $1.00 per day per capita, on average in many cocoa exporting countries. In Ghana - the second largest producer of cocoa in the world - the government has accomplished little to help these smallholders upgrade and make cocoa an attractive sector for the next generation to inherit. The result – both in Ghana and around the world – is a lack of sustainability of the supply of cocoa. Demand is already beginning to outstrip supply. As a result of these underlying circumstances, the United States Agency for International Development (USAID) has posed the following policy question: "Under what conditions could USAID, as a development agency, support and enhance potential public-private partnerships in order to improve the bargaining power (and financial wherewithal) of smallholder organizations and farmers in the context of the global value chain for cocoa in Ghana?"