BIOTECHNOLOGY TRAINING PROGRAM

Doctoral Research Project:  Cell and gene therapies are a growing modality to treat previously incurable diseases. Delivery of these therapies to target cells requires platforms that can achieve therapeutic efficacy while minimizing safety risks. Engineered virus-like particles (eVLPs) are an emerging delivery vehicle that offer the delivery efficiency of viruses while lacking the capacity for viral replication. However, one of the challenges in the translation of eVLPs lies in their manufacturing and scale-up. Current approaches employ simultaneous expression of multiple plasmids, resulting in cell-to-cell variability in the expression of eVLP components. Moreover, this standard biomanufacturing method differs fundamentally from the natural viral replication cycle, in which gene expression is temporally regulated. During the viral replication cycle, genes encoding catalytic and regulatory proteins are expressed prior to genes encoding structural proteins, enabling the assembly of viral components. My research aims to improve eVLP biomanufacturing by engineering genetic circuits that coordinate and temporally regulate eVLP component expression.

Doctoral Research Project:  Glioblastoma (GBM) is an aggressive brain cancer with a dismal 6.9% five-year survival rate, primarily due to frequent GBM cell migration, leading to secondary tumor formation in the brain. Migrasomes, a recently discovered type of matrix-bound extracellular vesicle (EV), may influence this malignant cell migration. As cells migrate, migrasomes are formed at the intersections and tips of the retraction fibers which are left in trails in their wake. Trailing cells can then internalize these “breadcrumbs,” originally deposited by the leading cells, through an unclear and understudied process. This form of intercellular communication suggests that migrasomes could play a significant role in modulating tumor cell migration and other important processes within the microenvironment. However, inefficiencies in migrasome isolation, characterization, and in vitro biomimicry have hindered researchers in fully understanding their impact on disease progression and their potential as therapeutics. My project aims to optimize both migrasome isolation and a micropatterning technology to develop a high-throughput platform for studying GBM cell migration in response to migrasomes.

Doctoral Research Project:  High blood sugar (hyperglycemia) is a major driver of diabetes. Blood sugar levels are regulated in part by the proximal tubule cells in the kidney that express sodium glucose cotransporter 2 (SGLT2) proteins. Several FDA-approved small molecule drugs lower blood sugar by inhibiting SGLT2. Although these inhibitors are effective, they often lack target specificity, resulting in broad systemic circulation and off-target effects. Biologics such as antisense oligonucleotides (ASOs), which have been approved to treat several diseases, offer a promising alternative by enabling sequence-specific gene knockdown through mRNA degradation. However, their clinical translation is constrained by nuclease degradation, organ targeting, and cellular uptake, particularly for renal hyperglycemia treatment. Nucleic acid dendron nanostructures present an attractive platform due to their programmability, cellular uptake properties, and molecularly precise architecture. As a result, my project aims to design ASO dendrons for kidney localization and uptake by proximal tubule cells to achieve SGLT2 knockdown. By systematically varying dendron structure, this work will investigate how molecular architecture influences kidney targeting, cellular uptake, and gene silencing, establishing structure-function relationships that govern their biological activity.

Doctoral Research Project:  Polyketide synthases (PKSs) are multifunctional enzymes composed of covalently linked domains that facilitate enzymatic transformations in an assembly line fashion to synthesize elongated carbon scaffolds. As one of the few systems capable of recursively forming carbon-carbon bonds, PKSs are particularly useful for constructing molecular backbones that can later be modified using monofunctional enzymes or synthetic chemistry. The modularity and deterministic nature of PKSs make them a promising candidate for engineering the synthesis of structurally and functionally diverse molecules. Integrating enzymatic machinery with synthetic modifications and pathway engineering holds significant potential for overcoming key bottlenecks in biomanufacturing. My project focuses on developing and advancing computational methods for engineering novel molecular syntheses, using PKSs as the primary platform. Through this work, I aim to improve the utility of these systems in enhancing downstream bioproduct production and supporting the pursuit of a bio-based economy.

Doctoral Research Project:  Biologic therapies, such as antibodies and CAR-T cells, represent 35% of the U.S. drug market but are expensive to produce and often require frequent, high-dose administration, tethering patients to routine hospital visits. Biohybrid pharmacies, consisting of implanted cells that produce biologic therapies on demand, could provide a more cost-effective and untethered alternative by allowing drug production to respond directly to changes in the body. A key challenge is coupling real-time biomarker sensing with tunable therapeutic output. My proposed research will develop a closed-loop system that combines an electrochemical aptamer-based sensor with an electrogenetic cell-based therapy actuator to regulate in vitro production of albumin, a plasma protein whose levels decrease in diseases such as hepatic cirrhosis and chronic kidney disease. These sensor and therapeutic actuator will interface using a proportional-integrative-derivative controller, allowing the system to adjust albumin production in response to continuously-measured changes in albumin concentration.

Doctoral Research Project:  Plastic pollution continues to be an existential ecological and human health issue because current plastic recycling and upcycling methods are not economically viable. Biological upcycling could serve as an effective method of converting plastic waste into valuable products such as specialty chemicals, biofuels, and biopolymers. The current challenge with developing those processes is enabling microorganisms to break down and assimilate these non-biodegradable plastics, especially non-hydrolysable polyolefins like polyethylene (PE). Chemical oxidation of PE creates dicarboxylate degradation products that can be converted by engineered organisms like P. putida into polyhydroxyalkanoates (PHAs), a biopolymer that is biodegradable and has tunable properties based on monomer side chain length. This two-stage PE to PHA process can be improved by using Comamonas testosteroni for dicarboxylate conversion because it is a PHA-producing organism that can uptake and catabolize dicarboxylates without the same engineering that P. putida required. My project instead focuses on engineering C. testosteroni for tailored PHA production, enabling us to control the chain length of monomers and therefore the material properties of the resulting biopolymer. I employ multi-omic (proteomic, transcriptomic, metabolomic, 13-C fluxomic) analysis to identify major proteins and metabolic pathways responsible for dicarboxylate conversion into PHAs. I utilize cell-free protein expression systems to perform enzyme engineering campaigns in and to prototype C. testosteroni engineered metabolic pathways high throughput. Combining these methods, I can efficiently engineer target enzymes and correct metabolic bottlenecks in C. testosteroni to improve both PHA yield and monomer selectivity when fed dicarboxylates and create an engineered strain for industrial plastic waste management.