Acoustic Biosensors for Noninvasive Imaging of Molecular Processes

Citation

Jin, Zhiyang (2024) Acoustic Biosensors for Noninvasive Imaging of Molecular Processes. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/b51h-q307. https://resolver.caltech.edu/CaltechTHESIS:05152024-052419062

Abstract

Understanding biology in its native context has been a major scientific endeavor. Yet, it is challenging to visualize cellular dynamics at the molecular scale in the context of a living organism at the macroscopic scale. Ultrasound imaging represents a promising candidate to address this challenge, with its unique advantages of large imaging volume, deep penetration, and good spatiotemporal resolution. However, ultrasound was historically limited in retrieving molecular information that biology carries. Until very recently, the discovery of the first ultrasound-interacting biomolecules, gas vesicles (GVs), established a connection between connect cellular function and ultrasound signals, which later enabled ultrasound imaging of gene expression and thus the location of GV-expressing cells. Going beyond location tracking, this thesis describes the engineering of GV-based acoustic biosensors that made it possible to noninvasively image the dynamics of cellular signaling in living organisms.

GVs are genetically encoded intracellular air-filled “balloons” that are encapsulated by protein shells. The acoustic biosensor design leverages the GV surface protein GvpC, which controls GVs' ultrasound scattering by setting the stiffness of their protein shell. We developed the first acoustic biosensors by engineering GvpC to change its confirmation and thereby GVs’ ultrasound contrast in response to the activity or concentration of specific molecules. Specifically, we first built the biosensors for three different types of enzymes and demonstrated noninvasive imaging of enzyme activity inside probiotic cells in the mouse colon in vivo. Next, we engineered the acoustic biosensors for calcium, a ubiquitous signaling molecule that is essential in many cellular processes (e.g., neural activity). With the first generation of this calcium sensor for ultrasound, we demonstrated imaging of receptor-specific calcium signaling deep inside the mouse brain through the intact skull noninvasively, which opened up the possibility of whole-brain neuroimaging that can lead to many breakthroughs in neuroscience. Last, we established a high-throughput engineering platform to develop all these GV-based imaging agents in a much shorter time frame. Collectively, this thesis presents the first demonstration of noninvasively imaging dynamic cellular signaling with acoustic biosensors and the feasibility of efficiently improving them for potential real-world applications with our engineering pipeline, opening up a new route towards understanding biology across scales.

Thesis Files