Description of Research Expertise

RESEARCH INTERESTS
* Subcellular compartmentalization, including condensation of disordered proteins and RNAs into mesoscale assemblies such as stress granules and germ granules
* Cell biology of early embryo development, including functional adaptations to cell size variation and assembly of embryo-specific organelles
* Mechanism regulating zygotic genome activation in space and time
* Synthetic biology and immune cell engineering
* Biomaterials and drug delivery
* Technological development: construction of cell-like compartments, aka ‘synthetic cells’, designer biomolecular condensates, optochemical and optogenetic tools for cell and developmental biology

KEY WORDS: condensates, membraneless organelles, disordered proteins, early embryo development, zygotic genome activation, cell size regulation, organelle scaling, optogenetics, cell-free systems, microfluidics, synthetic cells

DESCRIPTION OF RESEARCH

TOPIC 1: Membraneless Organelles and Disordered Protein Condensation.
Our lab is interested in understanding mechanisms that control the spatial organization and functional insulation of biochemical reactions within a cell. We study germ granule and stress granules assemblies that function to partition specific targets within a cell, as well protein condensates that govern genome integrity. We have uncovered fundamental rules governing membraneless organelle assembly through reconstitution of condensates including from the germ granule protein LAF-1 (Schuster et al, PNAS 2020) and stress granule component FUS (Welles et al, Nature Chemistry 2024). We aim to understand how the material properties of these condensed phases contributes to their function. We have also developed custom platforms of self-assembling protein that form membraneless compartments in protocells and cells (Schuster et al, Nature Comm 2018). A primary function of membraneless organelles, such as stress granules and germ granules, is to sequester and insulate select proteins and RNAs. Inspired by this concept, we developed synthetic a condensate platform to regulate cellular behavior through sequestration and release of native protein targets, which can operate in a wide variety of cells (Garabedian et al, Nature Chemical Biology 2021). Our research has significance toward understanding cellular dysfunction in senescence and aging and applications toward reprogramming cell behavior.

TOPIC 2: Unique Cell Biology of Early Development, and Embryonic Genome Activation.
The dimensions of cells and their organelles are cell-type specific, coupled to function and dysregulated in senescent cells and cancer. Eggs are remarkably large cells, which divide in the absence of cell growth upon fertilization. This results in a rapid reduction in embryo blastomere cell size, which triggers key events in development including repartitioning of factors from the cytosol to nucleus in blastomeres and widespread zygotic genome activation (ZGA). Building from my work on how organelles adapt to blastomere size (Good et al, Science 2013), our lab has discovered a number of control systems that regulate the onset of large-scale gene expression in embryogenesis (Chen et al, Dev Cell 2019; Chen et al Curr Biol 2022). A watershed event in early development is transition from maternal to zygotic control of embryogenesis, requiring awakening of genomes in pluripotent blastomeres and expression of 1000s of nascent transcripts in a process termed zygotic genome activation (ZGA). We developed specialized techniques to image and quantify the nascent transcriptome in embryos (Chen et al, Methods Enz 2020). Prior to ZGA, zygotic nuclei of pluripotency blastomeres are largely transcriptionally dormant. Once ZGA occurs, the zygote takes control of development by replacing RNA deposited maternally. Recently, we identified that blastula embryos can undergo a spatially graded ZGA pattern essential for normal development. ZGA onset is a highly stereotyped process within a species, but the timing can differ widely across model embryonic systems. We are broadly interested in the molecular mechanisms that determine the onset of ZGA.

TOPIC 3: Synthetic Biology and Biomaterials, and Immune Cell Engineering.
We are interested in developing tools to augment the function of living cells, as well as generating biomimetics of living cells. (1) We have developed a synthetic organelle toolkit (Schuster et al, Nature Comm 2018) (Garabedian et al, Biochemistry 2022) that is deployable genetically to control cell behaviors. (2) We have generated synthetic cell-like compartments that carry out aspects of the cell division cycle in vitro (Good et al, Science 2019), and patterned them create mechanical deformation (Bermudez et at, ACS Syn Biol 2021), and tested new chemistries to expand the functionalities and durability of synthetic compartments (Torre et al, PNAS 2019) (Li et al, ACS Nano 2020). We are currently using these platforms and tools to programmably control cell behavior (Garabedian et al, Nature Chem Biol 2021), and for applications in immune cell therapies. Separately, we are developing coacervate materials that enable synthetic condensates or hubs to be delivered to cells without the requirement for viral transduction.

TOPIC 4: Regulation of Cell Size and Dysregulation In Disease.
We are interested in cell and tissue size regulation and its contribution to intracellular organization and cellular function. We have investigated cell division and growth in giant cells of the early embryo and developed tools to spatially control the blastula cell size gradient (Qian et al, manuscript in prep 2024). Separately we have been interested in cell size dysregulation in cancer. We revealed the loss of epithelial cell size homeostasis and altered organelle sizes in lung adenocarcinoma (Sandlin et al, 2022).