Biology subjects

Swift, M. B.

Publications and source records attributed to Swift, M. B..

5 recordsLinked to original sources

bioRxiv2024

Multiplexed ultrasound imaging of gene expression

Acoustic reporter genes (ARGs) have enabled the imaging of gene expression with ultrasound, which provides high-resolution access to deep, optically opaque living tissues. However, unlike their fluorescent counterparts, ARGs have so far been limited to a single "color," preventing multiplexed imaging of cellular states or populations. Here, we use rational protein design and directed evolution to develop two novel ARGs that can be distinguished from each other based on their acoustic pressure response profiles, enabling "two-color" ultrasound imaging of gene expression. We demonstrate the utility of multiplexed ARGs for delineating bacterial cell species and cell states in vitro, and then apply them towards imaging distinct subpopulations of probiotics in the mouse gastrointestinal tract and in tumor-colonizing bacterial agents in vivo. Just as the first wavelength-shifted derivatives of fluorescent proteins opened a vivid world for optical microscopy, our next-generation acoustic proteins set the stage for a richer symphony of ultrasound signals from living subjects.

bioengineering↗

bioRxiv2024

Non-invasive imaging of cell-based therapies using acoustic reporter genes

Cell-based therapies are a major emerging category of medicine. The ability of engineered cells to traffic to and function at specific anatomical locations is a major aspect of their performance. However, there is a lack of non-invasive, non-ionizing, cost-accessible methods to track these therapies inside the body and ensure proper function. Here, we establish a platform for in vivo imaging of primary cell therapies using ultrasound - a ubiquitously accessible technology for high-resolution non-invasive imaging. We introduce and optimize a lentiviral delivery system to express acoustic reporter genes based on gas vesicles in primary mammalian cells such as T cells, showing that this results in robust ultrasound contrast. Additionally, we develop genetic circuits making it possible to monitor T cell activation via activity-dependent promoters. We apply this technology to primary human T cells, using it to non-invasively track their accumulation and proliferation as a targeted therapy in a mouse tumor xenograft model and compare it to invasive, terminal measures such as immunohistology. By making it possible to visualize cell-based therapies and their function inside opaque living organs with unprecedented resolution and accessibility, this technology has the potential to significantly accelerate their development and effective use.

bioengineering↗

bioRxiv2023

Gas vesicle-blood interactions enhance ultrasound imaging contrast

Gas vesicles (GVs) are genetically encoded, air-filled protein nanostructures of broad interest for biomedical research and clinical applications, acting as imaging and therapeutic agents for ultrasound, magnetic resonance, and optical techniques. However, the biomedical applications of GVs as a systemically injectable nanomaterial have been hindered by a lack of understanding of GVs interactions with blood components, which can significantly impact in vivo performance. Here, we investigate the dynamics of GVs in the bloodstream using a combination of ultrasound and optical imaging, surface functionalization, flow cytometry, and mass spectrometry. We find that erythrocytes and serum proteins bind to GVs and shape their acoustic response, circulation time, and immunogenicity. We show that by modifying the GV surface, we can alter these interactions and thereby modify GVs in vivo performance. These results provide critical insights for the development of GVs as agents for nanomedicine.

synthetic biology↗

bioRxiv2023

Truly tiny acoustic biomolecules for ultrasound imaging and therapy

Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography has been challenging due to the size and stability constraints of conventional bubble-based agents. Here we describe bicones, truly tiny acoustic contrast agents based on gas vesicles, a unique class of air-filled protein nanostructures naturally produced in buoyant microbes. We show that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.

synthetic biology↗

bioRxiv2021

Genomically Mined Acoustic Reporter Genes Enable On-Demand In Vivo Monitoring of Tumor-Homing Bacteria

A major outstanding challenge in the fields of biological research, synthetic biology and cell-based medicine is visualizing the function of natural and engineered cells noninvasively inside opaque organisms. Ultrasound imaging has the potential to address this challenge as a widely available technique with a tissue penetration of several centimeters and spatial resolution below 100 m. Recently, the first genetically encoded acoustic reporters were developed based on bacterial gas vesicles to link ultrasound signals to molecular and cellular function. However, the properties of these first-generation acoustic reporter genes (ARGs) resulted in limited sensitivity and specificity for imaging gene expression in vivo. Here, we describe second-generation ARGs with greatly improved acoustic properties and expression characteristics, identified through a phylogenetic screen of candidate gene clusters from diverse bacteria and archaea. The resulting constructs offer major qualitative and quantitative improvements, including much stronger ultrasound contrast, the ability to produce nonlinear signals distinguishable from background tissue, and stable long-term expression. We demonstrate the capabilities of these next-generation ARGs by imaging in situ gene expression in mouse models of breast cancer and tumor-homing therapeutic bacteria, noninvasively revealing the unique spatial distributions of tumor growth and colonization by therapeutic cells in living subjects and providing real-time guidance for interventions such as needle biopsies.

bioengineering↗