A5002633453- Genetics, Aging, and Longevity in Model Organisms
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Circadian rhythm and melatonin
- Autism Spectrum Disorder Research
- Advanced biosensing and bioanalysis techniques
- Microtubule and mitosis dynamics
- PI3K/AKT/mTOR signaling in cancer
- Photosynthetic Processes and Mechanisms
- Cardiomyopathy and Myosin Studies
- Genetics and Neurodevelopmental Disorders
- Chromosomal and Genetic Variations
- Pluripotent Stem Cells Research
- Immune Cell Function and Interaction
- T-cell and B-cell Immunology
- Genetic Neurodegenerative Diseases
- Insect symbiosis and bacterial influences
- Gene Regulatory Network Analysis
- Homelessness and Social Issues
- Gestational Diabetes Research and Management
- Innovative Microfluidic and Catalytic Techniques Innovation
- Neuroendocrine regulation and behavior
- Evolution and Genetic Dynamics
- Electrowetting and Microfluidic Technologies
University of Washington
2021-2025
University of British Columbia
2007-2022
Vancouver Coastal Health
2019-2020
We set out to exhaustively characterize the impact of cis-chromatin environment on prime editing, a precise genome engineering tool. Using highly sensitive method for mapping genomic locations randomly integrated reporters, we discover massive position effects, exemplified by editing efficiencies ranging from ∼0% 94% an identical target site and edit. Position effects efficiency are well predicted chromatin marks, e.g., positively H3K79me2 negatively H3K9me3. Next, developed multiplex...
Adeno-associated viruses (AAVs) have emerged as the foremost gene therapy delivery vehicles due to their versatility, durability, and safety profile. Here we demonstrate extensive chimerism, manifesting pervasive barcode swapping, among complex AAV libraries that are packaged a pool. The observed chimerism is length- homology-dependent but capsid-independent, in some cases affecting majority of genomes. These results implications for design deployment functional both research clinical settings.
A major challenge facing the genetics of autism spectrum disorders (ASDs) is large and growing number candidate risk genes gene variants unknown functional significance. Here, we used Caenorhabditis elegans to systematically functionally characterize ASD-associated in vivo. Using our custom machine vision system, quantified 26 phenotypes spanning morphology, locomotion, tactile sensitivity, habituation learning 135 strains each carrying a mutation an ortholog gene. We identified hundreds...
Abstract Functional variomics provides the foundation for personalized medicine by linking genetic variation to disease expression, outcome and treatment, yet its utility is dependent on appropriate assays evaluate mutation impact protein function. To fully assess effects of 106 missense nonsense variants PTEN associated with autism spectrum disorder, somatic cancer hamartoma syndrome (PHTS), we take a deep phenotypic profiling approach using 18 in 5 model systems spanning diverse cellular...
ABSTRACT Prime editing is a powerful means of introducing precise changes to specific locations in mammalian genomes. However, the widely varying efficiency prime across target sites interest has limited its adoption context both basic research and clinical settings. Here, we set out exhaustively characterize impact cis- chromatin environment on efficiency. Using newly developed highly sensitive method for mapping genomic randomly integrated “sensor”, identify epigenetic features that...
CRISPR-based gene activation (CRISPRa) is a promising therapeutic approach for therapy, upregulating expression by targeting promoters or enhancers in tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsive
Our ability to sequence genomes has vastly surpassed our interpret the genetic variation we discover. This presents a major challenge in clinical setting, where recent application of whole exome and genome sequencing uncovered thousands variants uncertain significance. Here, present strategy for targeted human gene replacement phenomic characterization based on CRISPR-Cas9 engineering model organism Caenorhabditis elegans that will facilitate assessment functional conservation genes...
Abstract CRISPR-based genome editing has revolutionized functional genomics, enabling screens in which thousands of perturbations either gene expression or primary sequence can be competitively assayed single experiments. However, for libraries specific mutations, a challenge screening methods such as saturation is that only one region ( e.g. exon) studied per experiment. Here we describe prime-SGE (“prime editing”), new framework based on prime editing, mutations installed into genes...
Habituation is a ubiquitous form of non-associative learning observed as decrement in responding to repeated stimulation that cannot be explained by sensory adaptation or motor fatigue. One the defining characteristics habituation its sensitivity rate at which training stimuli are presented—animals habituate faster response more rapid stimulation. The molecular mechanisms underlying this interstimulus interval (ISI)-dependent characteristic remain unknown. In article, we use behavioural...
Abstract In this unit, we describe an inexpensive and versatile method for optogenetic stimulation of a large population genetically engineered Caenorhabditis elegans worms while quantitatively analyzing behavior. A custom light‐emitting diode light source is used to deliver blue‐light stimuli, causing direct depolarization neurons expressing the light‐gated cation channel Channelrhodopsin‐2, which in turn evokes behavioral responses. The responses are recorded by high‐throughput machine...
Abstract Our ability to sequence genomes has vastly surpassed our interpret the genetic variation we discover. This presents a major challenge in clinical setting, where recent application of whole exome and genome sequencing uncovered thousands variants uncertain significance. Here, present strategy for targeted human gene replacement phenomic characterization based on CRISPR-Cas9 engineering model organism Caenorhabditis elegans that will facilitate assessment functional conservation genes...
Recent studies have indicated that some phenotypes caused by decreased function of select neurodevelopmental disorder (NDD) risk genes can be reversed restoring gene in adulthood. However, few the hundreds been assessed for adult phenotypic reversibility. We developed a strategy to rapidly assess temporal requirements and reversibility NDD orthologs using conditional protein degradation system machine-vision profiling Caenorhabditis elegans. measured how degrading re-expressing EBF3, BRN3A...
Abstract The ability to learn is an evolutionarily conserved adaptation that remains incompletely understood. Genetically tractable model organisms facilitate mechanistic explanations of learning span genetic, neural circuit, and behavioural levels. Many aspects physiology, including processes underlie ( e.g. neurotransmitter release long-lasting changes in synaptic strength), are regulated by brief local [ μ m] levels free intracellular Ca 2+ . On this scale, [Ca ] activate many -sensors,...
Improved genome engineering methods that enable automation of large and precise edits are essential for systematic investigations function. We adapted peel-1 negative selection to an optimized Dual-Marker Selection (DMS) cassette protocol CRISPR-Cas9 in Caenorhabditis elegans observed robust increases multiple measures efficiency were consistent across injectors four genomic loci. The use Peel-1-DMS killed animals harboring transgenes as extrachromosomal arrays spared genome-edited...
Abstract As the synthetic biology and genome engineering fields mature converge, there is a clear need for “parts list” of components that are diversified with respect to both functional activity (to facilitate design) primary sequence assembly). Here we designed libraries composed extant, ancestral, mutagenized or miniaturized variants Pol III promoters guide RNA (gRNA) scaffolds quantified their ability mediate precise edits mammalian via multiplex prime editing. We identified thousands...
Abstract Genetic variants associated with autoimmune diseases are highly enriched within putative cis -regulatory regions of CD4 + T cells, suggesting that they alter disease risk via changes in gene regulation. However, very few genetic have been shown to affect cell expression or function. We tested >18,000 disease-associated for allele-specific using massively parallel reporter assays primary human cells. The 545 expression-modulating (emVars) identified greatly enrich likely causal...