BIOTECHNOLOGY TRAINING PROGRAM

Doctoral Research Project:  Cell-based therapies represent an emerging arena of novel disease-targeting strategies enabled by increasingly sophisticated genetic programs. To achieve this, it is imperative to investigate and ultimately repurpose the naturally occurring tools and mechanisms of action inherent to the processes involved in gene expression. Through my research, I aim to characterize the influence of chromatin regulators and the related promoter architecture on mammalian transcription in order to elucidate underlying features that may prove useful to synthetic biologists. In doing this, I aim to help provide additional layers of tunability to current cell-based therapies that will enhance their safety, effectiveness, and versatility. 

Doctoral Research Project:  Protein therapeutics have shown great success, especially in the treatment of cancer and immune disorders. However, protein therapeutics typically cannot cross cellular membranes, which prevents them from reaching targets inside the cell's cytosol. Overcoming this limitation would greatly expand the use of protein therapeutics to new targets within the cytosol, including protein-protein interactions that are difficult to target using small molecules. Designed miniproteins may be able to overcome this barrier as some have the ability to enter the cytosol by escaping from endosomes after endocytosis. However, only a few cell-penetrating miniproteins have been discovered, and current methods to screen for cell-penetrating miniproteins are slow and costly, limiting the number that can be screened per experiment. This small scale does not generate adequate data to develop "design rules'' for cell-penetrating miniproteins, so we lack a strong understanding of what molecular characteristics confer this capability. My project aims to develop a new high-throughput approach to measure cell penetration for thousands of miniproteins with diverse structures. Using these large-scale data, we will create a model to identify structural properties that lead to efficient cell penetration.

Doctoral Research Project:  Genome-wide association studies (GWAS) allow us to identify genomic loci statistically associated with a phenotypic trait. GWAS are a powerful genetic tool that have allowed us to better understand the biology of human disease by correlating genetic variants with risk loci. In the model organism Caenorhabditis elegans we can use GWAS to identify naturally segregating variants in complex traits like response to chemotherapeutics, anti-parasitic resistance, and viral sensitivity. GWAS of natural populations of C. elegans have revealed the genetic and molecular underpinnings of phenotypic variation for many traits and unveiled evolutionary forces shaping trait adaptation and divergence across the species. However, GWAS are limited by false discoveries and low power to detect small-effect loci, which play important evolutionary roles. Therefore, we must evaluate the performance of GWAS across natural populations to identify how we can develop and improve our current techniques. One aim of my work is to evaluate and optimize the empirical performance of GWA in three Caenorhabditis species. Using simulation frameworks, I am exploring how the genomic architecture of traits and each species' evolutionary history sets the constraints of discovery for GWAS.  By creating more robust GWAS pipelines, I can start to compare and explore traits across related species. Altogether I will develop a comparative framework for GWAS in Caenorhabditis species to identify orthologous genetic loci responsible for trait variation across the three species. This approach will enhance our genetic toolkit by increasing our power to identify genetic variants and the evolutionary forces shaping trait variation across species

Doctoral Research Project:  Natural products are a diverse source of potential therapeutics and bioactive molecules. Many natural products are bioactive and can act as therapeutics such as antibiotics, anticancer agents, and immunomodulatory agents. Although actinomycete natural products have been widely explored, secondary metabolites from fungi are an untapped source of interesting molecules and biosynthetic chemistry that can be adapted for uses in biotechnology. In the Kelleher Research Group, my doctoral research involves i) using our unique correlation algorithm to link secondary metabolites to their biosynthetic gene clusters using mass spectrometry and bioinformatics in concert, ii) investigating the bioactivity of these metabolites, and iii) elucidating the biosynthetic machinery and enzyme-catalyzed reactions that produce these natural products.

Doctoral Research Project:  Control over the human immune response is at the forefront of medical research. Targeting both innate and adaptive immune systems in a regulated and reproducible manner is incredibly challenging when considering the complexity of overlapping immune pathways and variations between individuals. When created properly, immune therapies produce potent and long lasting protective effects contributing to increased lifespans and better quality of life. My work  focuses around the therapeutic qualities of nanoparticles known as spherical nucleic acids (SNAs). SNAs have minimal components to reduce the risk of off target effects while maintaining high cellular uptake for maximal immune targeting. Currently, I'm expanding upon vaccine scaffolds that incorporate SNAs with lipid antigens, late-stage HPV oncogenes, and virus-like particle cores in multiple preclinical disease models.

Doctoral Research Project:  Infections with the gram-negative bacteria Pseudomonas aeruginosa (PA) are increasingly difficult to treat due to antibiotic resistance. A major concern is the lack of new antibiotic treatments for resistant infections.  The goal of my PhD thesis in the laboratory of Dr. Egon Ozer is to identify novel antibiotic resistance mechanisms in PA by utilizing state-of the art machine learning approach based on whole genome sequencing (WGS) and transposon insertion sequencing (INseq).  We aim to elucidate novel antibiotic resistance factors in drug-insensitive clinical isolates by identifying the involved genes and pathways that might subsequently be targeted for the development of novel antimicrobial therapeutics.

Doctoral Research Project:  Engineered cell therapies expressing a chimeric antigen receptor (CAR) in human T cells have demonstrated success in the treatment of hematological malignancies. However, the success of these therapies has proven difficult to translate to solid tumors due to the lack of specific tumor antigens present on solid tumor cells, as well as the presence of immunosuppressive microenvironments surrounding solid tumors. The hypoxic microenvironment ubiquitous to solid tumors can be used as a biomarker to restrict CAR expression within a tumor, improving the safety and specificity of solid tumor CAR T cell therapy. However, current strategies engineered for this targeting have only provided an effective anti-tumor response at levels of profound hypoxia. Thus, strategies are needed to provide specific, anti-tumor responses in tumors exhibiting modest levels of hypoxia that are not addressed by current approaches. My objective is to engineer microenvironment-responsive CAR T cells containing hypoxia biosensor circuits sensitive to modest levels of hypoxia to improve the safety and potency of CAR T cell therapy for solid tumors.

Doctoral Research Project:  Virus-Like Particles (VLPs) are protein structures with potential application for targeted drug delivery, gene therapy, and imaging diagnostics. However, the capacity to selectively deliver VLPs to specific targets in vivo remains an ongoing challenge. Such hindrances exist because these macromolecule carriers do not have sufficient time for tissue-specific uptake before immunologic agents and/or enzymes clear them from circulation. Our research group has been exploring ways to engineer VLPs to obtain characteristics necessary for the aforementioned applications. My efforts are divided into three main research fronts: first, I am exploring how single and epistatic mutations impact VLP properties, such as pH stability, thermostability, and size; second, I am using cell-free expression systems to “decorate” the VLP shell with functional groups that enhance efficacy for biomedical applications, such as glycans and peptides; third, I am incorporating non-canonical amino acids in the VLP structure to increase the capacity to append/encapsidate more than one functional molecule simultaneously. These research fronts should increase VLP specificity in cells. In the future, my research efforts will target ways to reduce the rapid clearing of the VLPs by proteases and the immune system. 

Doctoral Research Project:  Protein synthesis is the mechanism by which the information carried by messenger RNA (mRNA) is translated into functional proteins. Though translation is a tightly-regulated process, it is commonly dysregulated in cancers. Cancer cells often readapt to adverse conditions such as anti-tumor therapies by aberrantly initiating translation in cancer-driver genes. Notably, cancer-driver genes harbor alternative translation initiation sites that result in protein isoforms with oncogenic or tumor suppressor activity. Thus, targeting oncogenic-specific initiation sites while preserving tumor suppressor activity is a potential avenue for cancer treatment. I aim to understand how epitranscriptomic modifications can be leveraged to guide and reprogram translation. We hope to provide a basis for mRNA epitranscriptomic strategies to sensitize cancers to anti-tumor therpies.