Biology subjects

Harimoto, T.

Publications and source records attributed to Harimoto, T..

7 recordsLinked to original sources

bioRxiv2026

Engineered probiotics target granulomas to treat mycobacterial infection

Granulomas are a pathological niche for mycobacteria that remain difficult to access with conventional therapies. Here we show that probiotic Escherichia coli Nissle 1917 (EcN) infiltrates and colonizes granulomas and can be engineered as a delivery system that senses the local microenvironment and releases antimycobacterial payloads. Specifically, we leveraged the hypoxic microenvironment of necrotic granulomas to restrict bacterial growth, and developed a dual-mode lysis circuit combining intracellular and extracellular killing for sustained payload release with limited evolutionary escape. We further engineered EcN to express a mycobacteriophage-derived enzyme, generating a strain that suppressed drug-sensitive and drug-resistant mycobacteria in vitro and potentiated conventional antibiotic activity. Engineered probiotics also reduced mycobacterial burden in vivo, and in a murine model of rifampicin-resistant infection, combination treatment with pretomanid achieved greater bacterial reduction than either monotherapy. Together, these results establish a synthetic biology framework for targeting granulomatous infections with programmable living microbes.

synthetic biology↗

bioRxiv2025

Implantable Living Materials Autonomously Deliver Therapeutics from Contained Engineered Bacteria

Microbes are increasingly utilized as living therapeutic vehicles, yet their uncontrolled dissemination in the body has long remained a roadblock to clinical development. Physical containment, while widely used for mammalian cells, remains largely unattainable due to eventual bacteria escape. Here, we present an implantable material platform that encapsulates and confines bacteria, wherein synthetically engineered microbes produce therapeutic payloads from within. To prevent microbial escape, we developed a hydrogel scaffold with dual mechanical features: high stiffness to regulate bacterial proliferation and high toughness to resist material fracture under physiological stress. This design achieved complete bacterial containment for over six months and withstood multiple forms of mechanical loading that otherwise caused catastrophic material failure. By genetically engineering embedded bacteria, we endowed the material with environmental sensing and on-demand therapeutic release capabilities and demonstrated autonomous treatment in a murine prosthetic joint infection model. This multimodal strategy provides a safe and generalizable framework for deploying microbial medicines in vivo and supports their use as autonomous drug depots across a range of disease settings.

bioengineering↗

bioRxiv2024

Tumor-selective treatment of metastatic pancreatic cancer with an engineered, probiotic living drug

Pancreatic ductal adenocarcinoma (PDAC) poses significant challenges for effective treatment, with systemic chemotherapy often proving inadequate due to poor drug delivery and the tumors immunosuppressive microenvironment. Engineered bacteria present a novel approach to target PDAC, leveraging their ability to colonize tumors and deliver therapeutic payloads. Here, we engineered probiotic Escherichia coli Nissle 1917 (EcN) to produce the pore-forming Theta toxin (Nis-Theta) and evaluated its efficacy in a preclinical model of PDAC. Probiotic administration resulted in selective colonization of tumor tissue, leading to improved overall survival compared to standard chemotherapy. Moreover, this strain exhibited cytotoxic effects on both primary and distant tumor lesions while sparing normal tissues. Importantly, treatment also modulated the tumor microenvironment by increasing anti-tumor immune cell populations and reducing immunosuppressive markers. These findings demonstrate the potential of engineered probiotic bacteria as a safe and effective therapeutic approach for PDAC, offering promise for improved patient outcomes.

cancer biology↗

bioRxiv2021

A programmable probiotic encapsulation system enhances therapeutic delivery in vivo

Recent advances in therapeutic modulation of human microbiota have driven new efforts to engineer living microbial medicines using synthetic biology. However, a long-standing challenge for live bacterial therapies is balancing the high dose required to achieve robust efficacy with the potential for sepsis. Here, we developed a genetically encoded microbial encapsulation system with tunable and dynamic expression of surface capsular polysaccharides to enhance therapeutic delivery. Following a synthetic small RNA knockdown screen of the capsular biosynthesis pathway, we constructed synthetic gene circuits that regulate bacterial encapsulation based on sensing the levels of environmental inducer, bacterial density, and blood pH. The induced encapsulation system enabled tunable immunogenicity and survivability of the probiotic Escherichia coli, resulting in increased maximum tolerated dose and enhanced efficacy in murine cancer models. Furthermore, triggering in situ encapsulation was found to increase microbial translocation between mouse tumors, leading to efficacy in distal tumors. The programmable encapsulation system demonstrates a new approach to control microbial therapeutic profiles in vivo using synthetic biology.

synthetic biology↗

bioRxiv2020

Injectable therapeutic organoids using sacrificial hydrogels

Organoids, by promoting self-organization of cells into native-like structures, are becoming widespread in drug-screening technologies, but have so far been used sparingly for cell therapy as current approaches for producing self-organized cell clusters lack scalability or reproducibility in size and cellular organization. We introduce a method of using hydrogels as sacrificial scaffolds, which allow cells to form self-organized clusters followed by gentle release, resulting in highly reproducible multicellular structures on a large scale. We demonstrated this strategy for endothelial cells and mesenchymal stem cells to self-organize into blood-vessel units, which were injected into mice using hypodermic needles, and observed in real time to rapidly form perfusing vasculature. As cell therapy transforms into a new class of therapeutic modality, this simple method - by making use of the dynamic nature of hydrogels - could offer high yields of self-organized multicellular aggregates with reproducible sizes and cellular architectures.

bioengineering↗

bioRxiv2019

Multiplexed biosensors for precision bacteria tropism in vivo

The engineering of microbes spurs biotechnological innovations, but requires control mechanisms to confine growth within defined environments for translation. Here we engineer bacterial growth tropism to sense and grow in response to specified oxygen, pH, and lactate signatures. Coupling biosensors to drive essential gene expression reveals engineered bacterial localization within upper or lower gastrointestinal tract. Multiplexing biosensors in an AND logic-gate architecture reduced bacterial off-target colonization in vivo.

synthetic biology↗

bioRxiv2018

Rapid screening of engineered microbial therapies in a 3-D multicellular model

Synthetic biology is transforming therapeutic paradigms by engineering living cells and microbes to intelligently sense and respond to diseases including inflammation1,2, infections3-5, metabolic disorders6,7, and cancer8,9. However, the ability to rapidly engineer new therapies far outpaces the throughput of animal-based testing regimes, creating a major bottleneck for clinical translation10,11. In vitro approaches to address this challenge have been limited in scalability and broad-applicability. Here, we present a bacteria-in-spheroid co-culture (BSCC) platform that simultaneously tests host species, therapeutic payloads and synthetic gene circuits of engineered bacteria within multicellular spheroids over a timescale of weeks. Long-term monitoring of bacterial dynamics and disease progression enables quantitative comparison of critical therapeutic parameters such as efficacy and biocontainment. Specifically, we screen S. typhimurium strains expressing and delivering a library of antitumor therapeutic molecules via several synthetic gene circuits. We identify novel candidates exhibiting significant tumor reduction and demonstrate high similarity in their efficacies using a syngeneic mouse model. Lastly, we show that our platform can be expanded to dynamically profile diverse microbial species including L. monocytogenes, P. mirabilis, and E. coli in various host cell types. This high-throughput framework may serve to accelerate synthetic biology for clinical applications and understanding the host-microbe interactions in disease sites.

synthetic biology↗