People

Diverse CRISPR-Cas systems are now known to function as integral components of the immune repertoire of many microorganisms, with the currently known catalog of systems spanning two of the three domains of life and contributing to the capacity of these bacteria and archaea to thwart viral infection. Eukaryotes conspicuously lack endogenous CRISPR-Cas systems, but it is not yet known if these molecular surveillance complexes can be co-opted to achieve therapeutically relevant inhibition of viral infection in humans through direct interference with the genomes of human viruses. While investigating strategies to improve the therapeutic potential of CRISPR-Cas components, I will also examine our ability to temporally control the editing activity of diverse CRISPR effectors.

CRISPR-Cas-based genome editing tools enable the control of gene expression in cells, tissues and whole organisms. Although invaluable for experimental studies, translation of these advances into clinical therapeutics requires delivery of CRISPR-Cas proteins and guide RNA to disease-relevant organs in the body. All current in vivo delivery strategies have drawbacks including ineffective delivery to target tissue, prolonged nuclease expression leading to off-target damage, and clearance of edited cells by adaptive immune responses. I posit that viral infection strategies can be harnessed to overcome the challenges faced by the in vivo delivery of genome editing tools. In the Doudna laboratory, I am applying my background in viral engineering to create the next-generation of CRISPR-Cas delivery vehicles and translate these technologies into therapeutics. By merging virology with bioengineering, I aim to make these revolutionary genome-based treatments accessible to all people who can benefit.

CRISPR-Cas systems are an ancient and widespread RNA-guided adaptive immune system in bacteria and archaea. My research focuses on how multisubunit Type III CRISPR-Cas complexes target transcriptionally active DNA and RNA of invading phages and plasmids. Using a combination of biochemistry and single-particle electron microscopy, I aim to uncover the mechanism of transcription-coupled target recognition by Type III complexes. Understanding how they find and destroy their targets will provide fundamental insights into RNA-guided immunity in prokaryotes, and could potentially lead to a tool that can detect or target actively expressed genes in heterologous systems, such as eukaryotic cells.

CRISPR-Cas (clustered regularly interspaced short palindromic repeats – CRISPR-associated proteins) systems typically provide bacteria and archaea with an adaptive immunity against foreign nucleic acids. Interestingly, many mobile genetic elements (MGEs, e.g bacteriophages and transposons) have recently been shown to possess their own CRISPR-Cas systems. Those MGE-borne CRISPR-Cas systems are believed to eliminate competing MGEs and some variants have been shown to sequence-specifically guide transposition events of their associated transposons. My research focuses on the biochemical and structural characterization of novel MGE-borne CRISPR-Cas systems, to understand their biological role and to eventually allow their translation into tools for genome editing and biotechnological applications.

CRISPR-Cas in Uncultured Microbes: The large majority of life has never been cultivated within the laboratory. This life can both be mined for new CRISPR-Cas systems and manipulated by these systems to facilitate understanding. My research focuses on the development of genetics, enabled by CRISPR-Cas, in communities of uncultured microorganisms. Secondarily, I look for new CRISPR-CAS and CRISPR-Cas-like defense systems within these same communities.

Glioblastoma (GBM) is a deadly disease that most people with this cancer died within two years of diagnosis despite decades of research on finding more effective treatments. With the recent development of CRISPR (clustered regularly interspaced short palindromic repeats) and CRISPR-associated (Cas) proteins as easily accessible and programmable means of editing and regulating genes, I propose to directly leverage CRISPR-Cas as a therapeutic modality to eliminate GBM cells. I have two main research focuses 1) use CRISPR-Cas system to dissect mechanisms of tumorigenesis and identify therapeutic targets, and 2) develop in vivo delivery tools to target GBM stem-like cells, the main population responsible for tumor recurrence, using intracranial xenograft model of GBM.

Abby is a postdoctoral scholar in the California Institute for Quantitative Biosciences. She began studying the host immune response to bioengineered materials during her time as a graduate student at the University of Pittsburgh McGowan Institute for Regenerative Medicine. She now studies how the immune system responds to Cas proteins and delivery vectors to improve the efficacy of gene editing and to further translate the use of CRISPR systems for in vivo applications.

While protein structures are commonly represented as a single set of 3D coordinates, most biological macromolecules rely heavily on conformational flexibility to effect their functions in solution. Cas effector complexes in particular undergo dramatic conformational movements during the process of RNA-guided nucleic acid targeting. I am broadly probing the energetic landscape of these dynamic interference complexes to better understand how their nuclease activity is regulated.