Rae Cho / July 2026
Our current work focuses on Htra2, a mitochondrial protease, and kindlin-2, a focal adhesion protein. In parallel, we are establishing technological foundations for several future directions.
Depending on your level of experience, you may take ownership of an entire project summarized below (e.g., as a postdoc or PhD student) or be assigned a well-defined, manageable component of one (e.g., as a postbacc or undergrad).
1. Deciphering protease X function in muscle formation: Through activity-based proteomics, we found a protease whose activity goes up ~10-fold during myoblast-to-myotube transition. We first want to determine whether its activity is necessary for myogenesis using cell culture models. We will then generate a muscle-specific KO of protease X in zebrafish to investigate its function in vivo. Ultimately, we want to identify its major substrates and elucidate the molecular mechanisms by which it regulates skeletal muscle development. We also want to examine whether activating protease X – genetically or pharmacologically – could help treat myopathies.
2. Skeletal muscle-specific ECM-ome: We recently developed DrCLIP, a new technology that enables unbiased mapping of protein interactions in zebrafish embryos. Using DrCLIP, we now aim to investigate how the skeletal muscle "ECM-ome" (or "matrisome") evolves during development, whether there are skeletal muscle-specific ECM proteins (versus cardiac muscle-specific or ubiquitous ones), and how the muscle ECM-ome is altered in muscular dystrophy – LGMD R1 specifically. We also plan to extend DrCLIP to mouse and human tissues.
3. Less cooked, but in the pipeline: We are developing approaches to isolate specific cell populations from zebrafish larvae without relying on FACS, which can be labor-intensive and technically challenging. We are also developing new strategies to better visualize the life cycle of muscle stem cells in zebrafish. We anticipate that these tools will become crucial components of future projects.
Modern biology has grown increasingly complex, and many projects now extend beyond what a single trainee can realistically accomplish within one training period (a 4-5-year PhD, excluding rotations, or a postdoctoral fellowship). Success depends not only on the creativity and persistence of individual researchers, but also on a strong foundation of tools, resources, and knowledge built up over time within the lab.
As a PI, I see building this foundation as my primary responsibility: (1) designing projects that synergize with one another both scientifically and logistically, (2) generating, procuring, and validating critical resources in advance (e.g., cell/zebrafish lines, plasmids, and antibodies), and (3) maintaining up-to-date protocols and inventories. My goal is to create a lab environment where new projects can take off quickly, allowing trainees to invest their energy where it matters most – navigating the inevitable "cloud phase" (Uri Alon, Mol Cell, 2009), through which we all struggle but ultimately learn the most.
We will train you to:
Most experiments don’t work (at least not as hoped). Design each experiment so that if it fails (and this is typically a technical rather than a biological failure) you can learn as much as possible. Include controls. Start with pilot experiments. Even differences between experimental and control samples that are real in one experiment may disappear in the next experiment – they were just statistical fluctuation.
Broadly, we welcome two types of scientists: (1) cell and developmental biologists interested in muscle biology and (2) chemists interested in applying their molecular expertise to biological questions.