Abstract
Theses reviewed in this issue include “Bowties, Barcodes, and DNA Origami: A Novel Approach for Paired-Chain Immune Receptor Repertoire Analysis,” “Development of Canine Chimeric Antigen Receptor T Cell Therapy for Treatment & Translation,” “Endocytic Vesicle Rupture in the Pathogenesis and Propagation of Neurodegenerative Proteinopathies,” “Exploring Mechanisms of Metastasis Suppression in Metastatic Melanoma,” “Polymer and Nucleic Acid Self-Assemblies: Properties and Applications at the Biological Interface,” and “Towards a Scalable, Biomimetic, Antibacterial Coating.”
I
Bowties, Barcodes, and DNA Origami: A Novel Approach for Paired-Chain Immune Receptor Repertoire Analysis
There are many biological questions that require single-cell analysis of gene sequences, including analysis of clonally distributed dimeric immunoreceptors on lymphocytes (T cells and B cells) and/or the accumulation of driver/accessory mutations in polyclonal tumors. Lysis of bulk cell populations results in mixing of gene sequences, making it impossible to know which pairs of gene sequences originated from any particular cell and obfuscating analysis of rare sequences within large populations. Although current single-cell sorting technologies can be used to address some of these questions, such approaches are expensive, require specialized equipment, and lack the necessary high-throughput capacity for comprehensive analysis. Water-in-oil emulsion approaches for single-cell sorting have been developed but droplet-based single-cell lysis and analysis have proven inefficient and yield high rates of false pairings. Ideally, molecular approaches for linking gene sequences from individual cells could be coupled with next-generation high-throughput sequencing to overcome these obstacles, but conventional approaches for linking gene sequences, such as by transfection with bridging oligonucleotides, result in activation of cellular nucleases that destroy the template, precluding this strategy. Recent advances in the synthesis and fabrication of modular deoxyribonucleic acid (DNA) origami nanostructures have resulted in new possibilities for addressing many current and long-standing scientific and technical challenges in biology and medicine. One exciting application of DNA nanotechnology is the intracellular capture, barcode linkage, and subsequent sequence analysis of multiple messenger RNA (mRNA) targets from individual cells within heterogeneous cell populations. DNA nanostructures can be transfected into individual cells to capture and protect mRNA for specific expressed genes, and incorporation of origami-specific bowtie-barcodes into the origami nanostructure facilitates pairing and analysis of mRNA from individual cells by high-throughput next-generation sequencing. This approach is highly modular and can be adapted to virtually any two (and possibly more) gene target sequences, and, therefore, has a wide range of potential applications for analysis of diverse cell populations such as understanding the relationship between different immune cell populations, development of novel immunotherapeutic antibodies, or improving the diagnosis or treatment for a wide variety of cancers.
Development of Canine Chimeric Antigen Receptor T Cell Therapy for Treatment and Translation
Chimeric antigen receptor (CAR) T cell therapy has had remarkable success targeting B cell leukemias in human patients, but unexpected toxicities and failures in other disease demonstrate the need for more predictive preclinical animal models than the murine ones currently used. Dogs develop spontaneous malignancies similar to humans in their tissues of origin, gene expression profiles, treatments, and disease courses, and have long been used as models for immunotherapy. I hypothesize that the development of CAR T cell therapy for dogs with spontaneous disease and that the treatment of these canine patients will recapitulate the observations found in human patients, and provide new insights into the safety and efficacy of this breakthrough therapy. To achieve this, I first established methods for growing primary canine T cells from healthy and disease-bearing donors to clinically relevant scale, developed RNA electroporation protocols to transiently express a CAR targeting the canine tumor-associated antigen CD20, demonstrated its function in vitro, and treated a relapsed canine B cell lymphoma patient with autologous CAR T cells as a proof of feasibility. I then developed methods to permanently express a second-generation cCD20-8-28-ζ CAR in canine T cells using lentiviral transduction, showed in vitro antigen-specific function and proliferation of CAR T cells, and treated four canine B cell lymphoma patients with CAR T cells. Based on my observations from those patients, I made iterative improvements to the T cell culture system and CAR construct, and treated a canine B cell lymphoma patient with cCD20-8-BB-ζ CAR T cells, whose tumor cells lost target antigen expression to avoid immune pressure. These results prove that it is not only possible to generate canine CAR T cell therapy, but that it recapitulates observations found until now only in human patients. In addition, novel findings regarding the recovery of T cells during ex vivo culture and the host immune response to the CAR demonstrate that this model can already inform human medicine.
Endocytic Vesicle Rupture in the Pathogenesis and Propagation of Neurodegenerative Proteinopathies
Numerous pathological amyloid proteins spread from cell-to-cell during neurodegenerative disease, facilitating the propagation of cellular pathology and disease progression. Understanding the mechanism by which disease-associated amyloid protein assemblies enter target cells and induce cellular dysfunction is, therefore, key to understanding the progressive nature of such neurodegenerative proteinopathies. In this study, we utilized an imaging-based assay to monitor the ability of disease-associated amyloid assemblies to induce the rupture of intracellular vesicles following endocytosis, as well as to elucidate the cellular consequences of this damaging mechanism of invasion. We observed that the ability to induce vesicle rupture is a conserved feature of fibrillar amyloid assemblies of alpha-synuclein, tau, and polyglutamine-expanded huntingtin. In the case of alpha-synuclein amyloid assemblies, we determined that Serine 129 phosphorylation and strain conformation dictate the potency of endocytic vesicle rupture. We also demonstrated that vesicles ruptured by alpha-synuclein are lysosomes, and that these damaged vesicles are targeted to the autophagic degradation pathway. We observed that vesicles ruptured by alpha-synuclein can accumulate and fuse into large intracellular structures resembling Lewy bodies in vitro, and showed that the same markers of vesicle rupture surround Lewy bodies in brain sections from PD patients. These data underscore the importance of this conserved endocytic vesicle rupture event as a damaging mechanism of cellular invasion by amyloid assemblies of multiple neurodegenerative disease-associated proteins, and suggest that proteinaceous inclusions such as Lewy bodies form as a consequence of continued fusion of autophagic vesicles in cells unable to degrade ruptured vesicles and their amyloid contents.
Exploring Mechanisms of Metastasis Suppression in Metastatic Melanoma
Melanoma is responsible for 76% of deaths from skin cancer, making it the deadliest form of commonly diagnosed skin cancer. The deadly nature of melanoma is due to its tendency towards rapid early metastasis. Metastasis, the process of cells exiting the primary tumor and forming secondary tumors in other parts of the body, accounts for the majority of morbidity and mortality associated with cancer. Therapeutically targeting and treating melanoma metastases is a challenging clinical goal, as metastatic cells are heterogeneous and can be morphologically and genetically distinct from the primary tumor. This dissertation examines two approaches for prevention or treatment of disseminated melanoma metastases: (1) reintroduction of metastasis suppressor protein fragments to prevent metastatic colonization and (2) treating disseminated metastases with a targeted small molecule treatment. By examining two discrete approaches of treating metastatic melanoma, this work sheds light on the clinical viability of using metastasis suppressors or metastasis-targeting drugs in patients with metastatic melanoma.
To examine strategies for metastasis suppression through metastasis suppressor proteins, we examined cleavage products of the metastasis suppressor KISS1, a metastasis suppressor protein. Expression of KISS1 inhibits metastatic colonization at secondary sites, rendering disseminated cells dormant. KISS1 must be secreted outside of the cell to suppress metastasis, where furin cleaves KISS1 into kisspeptins at three dibasic sites. This cleavage liberates an internal kisspeptin, Kisspeptin-54 (KP54, amino acid K67 to F121), which is amidated and can bind a Gq/11-coupled protein receptor KISS1R. The mechanism of action for KISS1 metastasis suppression has long been assumed to be KP54 interacting with KISS1R. However, expression of KISS1R is not necessary for KISS1 metastasis suppression, and the extracellular processing of KISS1 hints at an alternative hypothesis: a different kisspeptin may be responsible for suppressing metastasis. To test this hypothesis, all possible kisspeptins (KISS1 Manufactured Peptides, or KMP) were generated based on known dibasic cleavage sites (M1–Q145; M1–R56; M1–R67; M1–R124; R56–R66; R67–F121; R56–F121; R56–Q145; R67–Q145; R124–Q145) and were used in an experimental metastasis assay to characterize their abilities to suppress metastasis. We found that while KP54 suppressed metastasis, additional KMP lacking the KISS1R binding site (LRF-NH2) were able to completely suppress metastasis (p < 0.05). In particular, one kisspeptin (KMP2, M1–R56) suppressed metastatic traits in vitro as well as completely suppressing metastasis in vivo. To identify the signaling pathways used by KMP2 to suppress metastasis, a genome-wide CRISPR/Cas9 screen was performed in KMP2-expressing B16-F10 melanoma cells. As a whole, these data suggest that metastasis suppression by KISS1 is not necessarily contingent on KISS1R activation, and also supports investigation into additional receptors.
To investigate the efficacy of targeting metastases with small molecules, we also investigated the impact of ML246 (also known as metarrestin). Metarrestin was discovered by a high throughput assay for molecules which disassemble the perinucleolar compartment (PNC). PNCs are structures composed of RNA and RNA binding proteins near the nucleolus. These structures are enriched in metastatic cells and are druggable targets which target metastases and not normal epithelium. We examined the impact of metarrestin treatment on orthotopic tumor growth, microscopic metastasis formation, and macroscopic metastasis formation. We found that metarrestin treatment had no significant impact on metastatic outgrowth, but suppressed intradermal tumor growth. Based on these data, we can infer that PNC-positive metastases may be too small a population to effectively target in this model. This treatment paradigm may be more effective in conjunction with a more potent approach to metastasis suppression. Overall, the work in this dissertation identified a potent metastasis suppressing fragment of KISS1, KMP2, and described the efficacy of metarrestin treatment of disseminated metastases. The metastasis suppression induced by KMP2 expression was far more potent than the effects of metarrestin treatment on suppressing metastatic colonization and outgrowth, suggesting that treatment deliveries and targets are critical considerations in the development of antimetastatic therapeutics.
Polymer and Nucleic Acid Self-Assemblies: Properties and Applications at the Biological Interface
Ring opening metathesis polymerization (ROMP) was used to generate a variety of self-assembled nanostructures, including purely synthetic and biohybrid materials. The properties of polynorbornene amphiphilic block copolymer structures and their relationship to resulting morphology were explored, paving the way for nanoparticle design at the structural and processing level. In the context of biosynthetic polymer amphiphiles, hydrophobic ROMP polymers were attached to hydrophilic DNA strands to produce self-assembly micelles on the order of 20 nm in diameter. Herein, we explored the self-assembly properties, stability, and applications of these assemblies in pristine conditions and cellular environments.
Morphology plays an important yet poorly understood role in dictating how nanomaterials interact with cells and tissues. Uncovering this relationship relies on working out how to control particle morphology in the first place. We prepared purely synthetic amphiphiles using ROMP to prepare aqueous phase diagrams of block copolymer assemblies. By preparing polymers with varying properties, such as block lengths, block identity, and block ratios, the relationship between polymer structure and the resulting self-assembly nanostructure could be observed under certain conditions. Furthermore, by manipulating the assembly conditions of these polymers, we have shown that multiple stable morphologies can be generated from the same block copolymer starting material. This represents the first study of its kind for ROMP-derived amphiphilic assemblies, which exhibit variations in self-assembly dynamics compared with more traditional block copolymers.
Adding a level of complexity to our block copolymer system, we next explored more therapeutically relevant systems by conjugating DNA to a hydrophobic ROMP homopolymer and assembling them into DNA-displaying micelles. We determined the stability of the DNA on the micelle surface by treating the structures with various nucleases and human serum. The stability of the DNA on the micelle corona resisted degradation by nucleases in some circumstances, but not all, relative to the free DNA control, highlighting the importance of careful design of the amphiphile for a given application.
After determining the stability of DNA polymer assemblies (DPAs), antisense DPAs were designed against a known therapeutic target in cancer cells, MDR1. Importantly, these materials were designed with sequences not containing chemical modifications, such as locked nucleic acids or other backbone alterations. After treating MDR1-dependent doxorubicin-resistant cells with the antisense micelles, sensitivity to the chemotherapeutic could be restored to near-parental cell line IC50 values.
Despite many desirable properties nanoparticles have in therapeutic applications, a major bottleneck in their development is the fact that very little is known about how they interact with cells and tissues. Next, a high-throughput whole-genome approach to elucidate the pathways responsible for nanomaterial uptake by cells was developed and tested using DPAs as a proof-of-concept. Using GeCKO, a population of cells representing knockouts across the entire genetic spectrum was tested against uptake of cyanine 5 labeled DPAs. Using this approach, we have identified the transmembrane protein SLC18B1, among a handful of other proteins, as candidate for mediating uptake; a previously unknown interaction by DNA-displaying nanomaterials with cell surfaces. By expanding this technique to other categories of nanoparticle medicines with different structures and surface modifications, the generation of new design rules for nanomaterial therapeutics may be prepared to help researchers avoid off-target accumulation and advance many more nanotherapies to the clinic.
Towards a Scalable Biomimetic Antibacterial Coating
Corneal afflictions are the second leading cause of blindness worldwide. When a corneal transplant is unavailable or contraindicated, an artificial cornea device is the only chance to save sight. Bacterial or fungal biofilm buildup on artificial cornea devices can lead to serious complications, including the need for systemic antibiotic treatment and even explantation. As a result, much emphasis has been placed on antiadhesion chemical coatings and antibiotic leeching coatings. These methods are not long-lasting, and microorganisms can eventually circumvent these measures. Thus, I have developed a surface topographical antimicrobial coating. Various surface structures including rough surfaces, superhydrophobic surfaces, and the natural surfaces of insects' wings and sharks' skin are promising antibiofilm candidates; however, none meet the criteria necessary for implementation on the surface of an artificial cornea device.
In this thesis I (1) developed scalable fabrication protocols for a library of biomimetic nanostructure polymer surfaces, (2) assessed the potential theses for poly(methyl methacrylate) (PMMA) nanopillars to kill or prevent formation of biofilm by Escherichia coli bacteria and species of Pseudomonas and Staphylococcus bacteria and improved upon a proposed mechanism for the rupture of Gram-negative bacterial cell walls, (3) developed a scalable commercially viable method for producing antibacterial nanopillars on a curved PMMA artificial cornea device, and (4) developed scalable fabrication protocols for implantation of antibacterial nanopatterned surfaces on the surfaces of thermoplastic polyurethane materials, commonly used in catheter tubings. This project constitutes a first step towards fabrication of the first entirely PMMA artificial cornea device.
The major finding of this work is that by precisely controlling the topography of a polymer surface at the nanoscale, we can kill adherent bacteria and prevent biofilm formation of certain pathogenic bacteria, without the use of any chemical antibiotic agents. Such nanotopographic coatings can be applied to implantable polymer medical devices with scalable commercializable processes, and may deter or delay biofilm formation, potentially improving patient outcomes. This thesis also opens the door for adaptation of antibacterial nanopillared surfaces for other applications, including other medical devices, marine applications, and environmental surfaces.
