Emory University  |  Under the advisement of Professor Manoj K. Bhasin

I am currently a Cancer Biology PhD candidate under the advisement of Professor Manoj Bhasin, leveraging big data and bioinformatics to probe the pathogenesis of disease and identify targets for therapeutic intervention. My work primarily centers on single-cell and spatial transcriptomic analyses of vascular disease (CABG graft failure, sickle cell anemia) and cancers (pediatric leukemias, pediatric brain cancers, multiple myeloma). Utilizing these approaches, my work aims to profile the genomic and cellular landscape of the disease microenvironment to uncover the genetic regulation of intracellular pathways and intercellular interactions underlying disease pathogenesis.

Integrated single-cell and spatial transcriptomic investigations of cardiac bypass procedures | My work on cardiac bypass graft failures in collaboration with a team of surgeon-scientists at Harvard University has centered on the integration of single-cell and spatial transcriptomic analysis to probe the cellular landscape underlying graft failure. I designed and performed this integrated analysis to reveal that the vascular endothelium becomes severely injured during the implantation of the graft, ultimately leading to the upregulation of maladaptive pathways that underlie graft failure, published in Circulation Research. The results of our collaborative studies have led to additional funding, in which I am currently leading a temporally-resolved integrated single-cell and spatial analysis of prosthetic atrial bypass grafting,  under preparation for submission to Circulation Research.

Profiling tumor microenvironments | My thesis work centers on the application of single-cell and spatial transcriptomics to map the tumor microenvironment (TME) across various cancers, primarily multiple myeloma (MM) and medulloblastoma (MB). Through my work on multiple myeloma, I am a member of the national Immune Atlas consortium team led by the Multiple Myeloma Research Foundation (MMRF) focused on generating the first multiple myeloma single-cell immune atlas from the largest cancer dataset in the world. My work analyzing the intercellular communication networks within the MM-TME has been included in the immune-atlas manuscript submitted to Nature Medicine. Currently, I am expanding upon this work to lead an expanded single-cell analysis of ~500 MM patient samples, specifically investigating how ncRNA networks regulate malignant phenotypes, ultimately shaping the immune landscape in MM. 

For my work on medulloblastoma, I led the spatial transcriptomic analysis of pediatric MB samples in collaboration with physician-scientists Dr. Frank Chien and Dr. Tobey MacDonald at Emory. Our analyses revealed inter- and intra-tumoral heterogeneity within the TME, comprised of tumor-associated astrocytes (TAAs), macrophages (TAMs), stromal components, and distinct subpopulations of MB cells at different stages of neuronal differentiation and cell cycle progression. Notably, my analysis identified dense regions of quiescent progenitor MB cells enriched in patients with high-risk (HR) disease and an increase in TAAs, TAMs, and dysregulated vascular endothelium following relapse. Our study presents novel insights into the spatial architecture and cellular landscape of the medulloblastoma TME, highlighting spatial patterns linked to HR features and relapse, which may serve as potential therapeutic targets.

Developing bioinformatic tools | In addition to the application of bioinformatic tools to address biological questions, my PhD work also includes the development of these tools. Over the past two years, I have collaborated with Chenbin Huag, a Computer Science PhD student in the Bhasin Lab, to develop an interactive web-based platform for conducting survival analysis across publicly available cancer datasets. The inherent complexity of public datasets and the requisite bioinformatic skills to perform detailed analyses preclude the use of these datasets to their full potential. To address this challenge, our web-based tool facilitates individual gene-, gene set-, gene ratio-, and cluster marker-based survival analyses through a user-friendly interface. Moreover, the tool facilitates more complex analyses based on cell-cell communication, transcriptional factors, long non-coding RNA (lncRNA), and co-expression networks from user-provided single-cell data. The tool, launched in December 2023, has already been accessed by users across the globe and is currently under review.

Emory University  |  Under the advisement of Professor William M. Wuest

I completed my Master of Science in the Wuest Lab at Emory University, which centers on the total synthesis and biological investigation of natural products with antimicrobial properties. Utilizing our next-generation disinfectants as tool compounds, I probed structure-activity and structure-resistance relationships to ultimately further our understanding of bacterial processes and resistance, identify new targets, and synthesize novel molecules with enhanced antimicrobial activity. Through my research, I employed my background and interests in synthesis, microbiology, and computation in a multifaceted approach to the development and investigation of antimicrobials. 

Summary of thesis work:

Experts estimate that the number of global deaths associated with antimicrobial resistance rose to 4.95 million in 2019. Moreover, the World Health Organization predicts that without intervention, this toll will surpass 50 million annual deaths globally by the year 2050, eclipsing current leading causes of mortality. To address this rapid rise of AMR and forestall a post-antibiotic era, there is a crucial need for the development of novel antimicrobial compounds to treat and prevent the spread of infection. Disinfectant compounds, such as quaternary ammonium compounds (QACs), present an economical and accessible first line of defense against a broad-spectrum of pathogens. The essential role of disinfectants in modern healthcare has been further underscored by the COVID-19 pandemic, wherein QACs have comprised the largest share of active ingredients in EPA-approved disinfectants against SARS-CoV-2.

While QACs have become a mainstay in disinfectant formulations, a lack of structural diversity, disinfectant misuse, and an over-reliance on select compounds have propelled the emergence and spread of resistance. In fact, Chng and coworkers recently reported that pathogens harboring both antibiotic and QAC resistance were widely distributed through healthcare settings and persisted in biofilms and niche microbiomes for over eight years. Although previous work has elucidated the primary mechanisms mediating QAC resistance, examination of the relationship between these QAC resistance mechanisms and antibiotic resistance has received little attention. Furthermore, sub-inhibitory concentrations of QACs have been demonstrated to select for the spread of resistance plasmids encoding both QAC and antibiotic resistance genes. Despite the significant healthcare implications, antibiotic and QAC co- and cross-resistance mechanisms still remain poorly understood. Moreover, as these mechanisms are elucidated, there is a paucity of investigations into next-generation disinfectant compounds that can specifically evade resistance while maintaining potent broad-spectrum activity.

Accordingly, the Wuest Lab, in collaboration with Professor Kevin Minbiole at Villanova University, has sought to develop next-generation disinfectant compounds that evade resistance and preserve broad-spectrum efficacy. To this end, the Wuest and Minbiole Labs have developed a growing library comprised of over 725 amphiphilic compounds that expand beyond canonical QAC structures by varying the cationic moiety and hydrophobic tail(s). These next-generation molecules have been subsequently evaluated by the Wuest Lab for their antimicrobial activity against clinically relevant Gram-positive and -negative pathogens. Through these studies, the structure-activity-relationships (SAR) for these novel disinfectant subclasses have been elucidated, and in 2021 we unveiled that quaternary phosphonium compounds (QPCs) possess potent antimicrobial activities over leading QACs. Furthermore, we observed that our best-in-class QPC uniquely evades QAC resistance mechanisms to maintain its potency, underscoring the promise of QPCs as potential replacements for commercial QACs. However, prior works have only centered on the diverse properties of QPCs, leaving a gap in knowledge as to how these molecules exhibit their potency and evade resistance. Therefore, through my thesis research, I sought to leverage our library of novel QPCs as tool compounds to interrogate the mechanism of action for this nascent disinfectant subclass and its ability to evade QAC resistance mechanisms, providing insight for the rational design of potent next-generation disinfectants.

To this end, I led several investigations in this area, which culminated in a co-first author and first author publications in ACS Infectious Diseas, and two additional publications. Specifically, in the first investigation, I assessed the antimicrobial activity of QPCs against a panel of bacterial pathogens to provide novel insight into the SAR of this understudied disinfectant class. Notably, our best-in-class QPC (P6P-10,10) was found to maintain potency against pathogens refractory to QAC treatment. Therefore, harnessing P6P-10,10 as a tool compound, I then utilized a combination of bioinformatics, microscopy, and fluorescence microassays to elucidate the structure-resistance relationship (SRR) of QPCs. To build upon these findings through a second investigation, we next evaluated the translational potential of P6P-10,10 against a panel of 35 highly-resistant A. baumannii clinical isolates. Excitingly, P6P-10,10 illustrated overall improved activity compared to the leading commercial and next-generation QACs, including against a strain exhibiting pan-resistance to both QACs and antibiotics. Moreover, this QPC displayed a four-fold increase in biofilm eradication activity against this pan-resistant isolate compared to the commercial QAC combination. Together, these results have provided a strong foundation for the continued investigation of next-generation QPC-based disinfectants and resulted in external funding and collaborations to pursue more in-depth studies of the mechanisms and commercialization of these antimicrobial compounds. 

North Carolina State University  |  Under the advisement of Professors Joshua G. Pierce, Elon Ison, and Elena Jakubikova  

Thiazolines are a class of nitrogen-heterocyclic scaffolds present in numerous biologically active natural products that have been demonstrated as effective anticancer (curacin A and largazole), antimicrobial (marthiapeptide A), and antiviral (thiangazole) agents. Furthermore, thiazolines offer a utile route for access to a variety of other synthetically relevant functional groups such as aldehydes, ketones, thiazoles, thiazolidines, amino alcohols, and amino thiols, in addition to their employment as chiral ligands in stereoselective catalysis. 

During my NSF-REU fellowship at North Carolina State University, under the advisement of Professor Josh Peirce, I sought novel photochemical access to these versatile scaffolds through a computationally guided synthetic approach. Through my research, I investigated a series of photocatalysts and photosensitizers to cyclize S-allyl-O-alkyl thiohydroximic acid derivatives via iminyl radical intermediates produced by the homolytic cleavage of the weak N–O bond. Under the advisement of Professors Elon Ison and Elena Jakubikova, I designed and performed an in-depth computational study to predict relative N–O bond dissociation energies among the substrate scope of oxime ethers and esters. The results of my computational studies elucidated an apparent relationship between Hammett constants of the oxime substrates and the bond dissociation energy of the N–O bond involved in iminyl radical formation. This theoretically derived relationship then served as a model to guide the empirical exploration of the photochemically induced synthesis of thizaoline scaffolds.  

Georgia Southern University  |  Under the advisement of Professor Hans-Jörg Schanz

In 2014, traumatic brain injury (TBI) accounted for more than 2.53 million emergency department visits, 288,000 hospitalizations, and 56,000 mortalities annually, making it a leading and growing cause of morbidity and mortality in the United States. The primary obstacle in mitigating the severe complications associated with TBI arises in the timely treatment of cerebral ischemia and inflammation that often result from the deleterious combination of cortical impact and hemorrhaging at the time of the injury. The use of hemoglobin-based oxygen carriers (HBOCs) addresses this challenge by providing a universal blood substitute derived from extracellular hemoglobin (Hb) molecules which can infiltrate and oxygenate the inflamed ischemic tissue, owing to their reduced size and oxygen-carrying heme core. While promising for the treatment of TBI and other hematological-related diseases, previous generations of HBOCs have failed to pass the clinical trial stage due to renal toxicity. This nephrotoxicity arises from the dissociation of extracellular hemoglobin protein into its dimeric units, which undergo glomerular filtration due to their decreased Mw, and subsequently induce oxidative stress and vasoconstriction through the generation of radical oxygen species (ROS) and nitric oxide (NO) scavenging. 

Our group seeks to develop a next-generation HBOC that reduces nephrotoxicity through modification of extracellular Hb with multifunctional polymers that mimic the regulatory properties of the erythrocyte membrane, preserving the tetrameric protein morphology and reducing NO scavenging and the generation of ROS. This is accomplished through the grafting of polyacrylates functionalized with polyethylene glycol 5 (PEG) and (2,2,6,6-Tetramethylpiperidin-1-yl)oxyl (TEMPO) moieties to the surface of Hb proteins. Through binding groups that conjugate these multifunctional polyacrylates to the surface cysteine residues of the Hb, a shell is effectively formed around the protein that conserves the tetrameric structure, increases Mw, and neutralizes ROS. 

This project laid the groundwork for my undergraduate honors thesis in which I focused on the controlled synthesis of well-defined polyacrylates through RAFT polymerization, the post-polymerization functionalization of these polyacrylates with PEG and TEMPO moieties, and the design of a binding group for the conjugation of the functionalized polymers to the cysteine residues of the Hb protein surface. 

Georgia Southern University  |  Under the advisement of Professor Hans-Jörg Schanz

Owing to their versatile nature, polyelectrolytes have found diverse applications in material science, especially in materials that interface with biological systems. Of prominent and pertinent interest is their efficacy in drug-delivery systems and as antimicrobials, prompting the exploration of polyelectrolytes with tailored properties. Seeking access to a diverse set of polyelectrolytes through an industrially scalable and economical synthetic route, our group developed a novel polyaddition technique via the hydroamination of various amines. Using this technique, maleimide derivatives can be polymerized through a hydroamination mechanism in high yields. The preliminary research on the project conducted by myself and two student mentees led to our group receiving a grant from the ACS Petroleum Research Fund to continue our explorations of this novel polymerization methodology.