Biology subjects

Huang, W. E.

Publications and source records attributed to Huang, W. E..

3 recordsLinked to original sources

bioRxiv2025

Reprogrammed SimCells for Antimicrobial Therapy

Antimicrobial resistance (AMR) is a critical global health challenge. In this study, we developed a novel platform based on chromosome-free and non-replicating simple cells (SimCells, size 1-2 {micro}m) and mini-SimCells (size 100-400 nm) for targeted pathogen elimination. Engineered with surface-displayed nanobodies, SimCells and mini-SimCells selectively bind bacteria expressing specific antigens (e.g., OmpA in E. coli). The selective interactions facilitate close SimCell-pathogen proximity, enabling two antimicrobial mechanisms: direct injection of toxic effectors into bacterial cytoplasm via a heterologous expression of type VI secretion system (T6SS), and enzymatic conversion of aspirin into catechol by engineered salicylate hydroxylase, leading to sustained local production of hydrogen peroxide (H2O2). Our results demonstrate that both reprogrammed SimCells and mini-SimCells can eliminate target E. coli with high specificity and efficiency. Multi-dose reprogrammed mini-SimCell treatment led to a 103-fold selective reduction of targeted bacteria in mixed microbial communities, with minimal disruption to non-target bacteria. We demonstrate that reprogrammed mini-SimCells, engineered with nanobody targeting outer membrane protein OmpA of the clinically relevant multidrug resistant pathogen E. coli ST131, achieved elimination efficiencies over 97% at 24 and 48 hrs. This modularised plug-and-play antimicrobial platform provides a highly specific, efficient and adaptable solution for combating diverse AMR pathogens. Significance StatementAntimicrobial-resistant (AMR) bacteria cause millions of deaths worldwide annually, representing a critical global health challenge. In this study, we developed a novel therapeutic platform using two types of chromosome-free, non-replicating engineered bacterial cells: SimCells (1-2 {micro}m) and mini-SimCells (100-400 nm). These SimCells were engineered to selectively bind to targeted E. coli, facilitating precise delivery of toxic proteins via a Type VI secretion system (T6SS) and localised generation of hydrogen peroxide from aspirin. We demonstrate that mini-SimCells eliminated over 97% of a targeted AMR strain within 48 hours. Moreover, multiple-dose administration achieved a selective 103-fold reduction of targeted E. coli in mixed microbial communities. This modular plug-and-play platform offers an adaptable solution against diverse multi-drug-resistant pathogens.

synthetic biology↗

bioRxiv2025

Proteome constrained metabolic modeling of Sus scrofa muscle stem cells for cultured meat production

Cultured meat has recently emerged as a sustainable alternative to the traditional livestock farming and gained attention as a promising future protein source. Herein, the Sus scrofa muscle stem cell is a commonly used cell source in the cell proliferation step of cultured meat production. However, a major bottleneck of large-scale cultivation is the inhibition by secreted and accumulated lactate and ammonium in the process of S. scrofa cell proliferation. To simulate the growth and metabolism of S. scrofa muscle stem cells under different lactate and ammonium concentrations, this study constructed the first proteome constrained metabolic model for the core metabolism of S. scrofa muscle stem cells, pcPigGEM2025. The relationship of lactate and ammonium levels with cellular metabolism was derived from growth and metabolomics data of two culture conditions with low and high initial ammonium concentrations, and then incorporated into metabolic flux simulation. Metabolic flux simulations for experimental conditions, along with perturbation simulations considering stressed non-growth associated maintenance and oxygen supply, demonstrated that pcPigGEM2025 could effectively characterize the response of the S. scrofa muscle stem cells growth and metabolism to varying environmental conditions, shedding light on model-aided control and optimization of the cultured meat production process. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/679571v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@a4526aorg.highwire.dtl.DTLVardef@1ee2d1org.highwire.dtl.DTLVardef@1bd4700org.highwire.dtl.DTLVardef@18079e6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe first proteome constrained metabolic model was built for S. scrofa myoblasts. C_LIO_LIThis model effectively simulated myoblast metabolism under lactate and NH4+ stress. C_LIO_LIPerturbation simulations showed that this model could also account for other stress. C_LIO_LIThis model enables in-silico control and optimization of cultured meat production. C_LI

bioengineering↗

bioRxiv2024

Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system

Cupriavidus necator H16 is a promising microbial platform strain for CO2 valorisation. While C. necator is amenable to genome editing, existing tools are often inefficient or rely on lengthy protocols, hindering its rapid transition to industrial applications. In this study, we simplified and accelerated the genome editing pipeline for C. necator by harnessing the Self-splicing Intron-Based Riboswitch (SIBR) system. We used SIBR to tightly control and delay Cas9-based counterselection, achieving >80% editing efficiency at two genomic loci within 48 hours after electroporation. To further increase the versatility of the genome editing toolbox, we upgraded SIBR to SIBR2.0 and used it to regulate the expression of Cas12a. SIBR2.0-Cas12a could mediate gene deletion in C. necator with [~]70% editing efficiency. Overall, we streamlined the genome editing pipeline for C. necator, facilitating its potential role in the transition to a bio-based economy.

bioengineering↗