Bioengineering Research Articles

Recommendations for mitochondria transfer and transplantation nomenclature and characterization.

Intercellular mitochondria transfer is an evolutionarily conserved process in which one cell delivers some of their mitochondria to another cell in the absence of cell division. This process has diverse functions depending on the cell types involved and physiological or disease context. Although mitochondria transfer was first shown to provide metabolic support to acceptor cells, recent studies have revealed diverse functions of mitochondria transfer, including, but not limited to, the maintenance of mitochondria quality of the donor cell and the regulation of tissue homeostasis and remodelling. Many mitochondria-transfer mechanisms have been described using a variety of names, generating confusion about mitochondria transfer biology. Furthermore, several therapeutic approaches involving mitochondria-transfer biology have emerged, including mitochondria transplantation and cellular engineering using isolated mitochondria. In this Consensus Statement, we define relevant terminology and propose a nomenclature framework to describe mitochondria transfer and transplantation as a foundation for further development by the community as this dynamic field of research continues to evolve.

Potential and development of cellular vesicle vaccines in cancer immunotherapy.

Cancer vaccines are promising as an effective means of stimulating the immune system to clear tumors as well as to establish immune surveillance. In this paper, we discuss the main platforms and current status of cancer vaccines and propose a new cancer vaccine platform, the cytosolic vesicle vaccine. This vaccine has a unique structure that can integrate antigen and adjuvant carriers to improve the delivery efficiency and immune activation ability, which brings new ideas for cancer vaccine design. Tumor exosomes carry antigens and MHC-peptide complexes, which can provide tumor antigens to antigen-processing cells and increase the chances of recognition of tumor antigens by immune cells. DEVs play a role in amplifying the immune response by acting as carriers for the dissemination of antigenic substances in dendritic cells. OMVs, with their natural adjuvant properties, are one of the advantages for the preparation of antitumor vaccines. This paper presents the advantages of these three bacteria/extracellular vesicles as cancer vaccines and discusses the potential applications of functionally modified extracellular vesicles as cancer vaccines after cellular engineering or genetic engineering, as well as current clinical trials of extracellular vesicle vaccines. In summary, extracellular vesicle vaccines are a promising direction for cancer vaccine research.

Toward risk analysis of the impact of artificial intelligence on the deliberate biological threat landscape.

The perception that the convergence of biological engineering and artificial intelligence (AI) could enable increased biorisk has recently drawn attention to the governance of biotechnology and AI. The 2023 Executive Order, Executive Order on the Safe, Secure, and Trustworthy Development and Use of Artificial Intelligence, requires an assessment of how AI can increase biorisk. Within this perspective, quantitative and qualitative frameworks for evaluating biorisk are presented. Both frameworks are exercised using notional scenarios and their benefits and limitations are then discussed. Finally, the perspective concludes by noting that assessment and evaluation methodologies must keep pace with advances of AI in the lifesciences.

Modifications to rhesus macaque TCR constant regions improve TCR cell surface expression.

T cell immunotherapy success is dependent on effective levels of antigen receptor expressed at the surface of engineered cells. Efforts to optimize surface expression in T cell receptor (TCR)-based therapeutic approaches include optimization of cellular engineering methods and coding sequences, and reducing the likelihood of exogenous TCR α and β chains mispairing with the endogenous TCR chains. Approaches to promote correct human TCR chain pairing include constant region mutations to create an additional disulfide bond between the two chains, full murinization of the constant region of the TCR α and β sequences, and a minimal set of murine mutations to the TCR α and β constant regions. Preclinical animal models are valuable tools to optimize engineering designs and methods, and to evaluate the potential for off-target tissue injury. To further develop rhesus macaque models for TCR based cellular immunotherapy, we tested methods for improving cell surface expression of rhesus macaque TCR in rhesus macaque primary cells by generating five alternative TCRαβ constant region constructs in the context of a SIV Gag-specific TCR: 1. human codon optimized rhesus macaque (RH); 2. RH TCR with an additional disulfide linkage; 3. rhesus macaque constant sequences with minimal murine amino acid substitutions; 4. murinized constant sequences; and 5. murinized constant sequences with a portion of the exposed FG loop in the β constant sequence replaced with rhesus macaque sequence to reduce potential immunogencity. Murinization or mutation of a minimal set of amino acids to the corresponding murine sequence of the constant region resulted in the greatest increase in rhesus macaque TCR surface expression relative to wild type. All novel TCR constructs retained the ability to induce production of cytokines in response to cognate peptide antigen specific stimulation. This work can inform the design of TCRs selected for use in rhesus macaque models of TCR-based cellular immunotherapy.

Development of Microorganisms Capable of Absorbing Environmental Pollutants through Synthetic Biological Engineering

In Indonesia, environmental pollution is a major concern, especially in industrialised and urban areas. The use of synthesised microorganisms can be an innovative solution to rehabilitate the damaged ecosystems in this region. In this research, an innovative approach based on synthetic biological engineering will be developed to create microbes that have an optimal capacity to absorb and decompose various types of environmental pollutants, such as heavy metals (Pb and Hg), hydrocarbons (benzene), and organic waste (phenol). The results show that the engineered bacteria Escherichia coli, Pseudomonas putida, Bacillus subtilis, and Alcaligenes eutrophus showed high pollutant removal efficiency (85-93%) under laboratory conditions. These results support the potential of synthetic biology technology as an innovative solutions in bioremediation of polluted environments. This research makes a real contribution to green technology innovation in environmental pollution mitigation, supporting the implementation of Sustainable Development Goals (SDGs), especially on points 6 (Clean Water) and 15 (Land Ecosystems).

Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia.

Coordinated actions of cells in microbial communities and multicellular organisms enable them to perform complex tasks otherwise difficult for single cells. This has inspired biological engineers to build cellular consortia for larger circuits with improved functionalities while implementing communication systems for coordination among cells. Here, we investigate the signalling dynamics of a phage-mediated synthetic DNA messaging system and couple it with CRISPR interference to build distributed circuits that perform logic gate operations in multicellular bacterial consortia. We find that growth phases of both sender and receiver cells, as well as resource competition between them, shape communication outcomes. Leveraging the easy programmability of DNA messages, we build eight orthogonal signals and demonstrate that intercellular CRISPRi (i-CRISPRi) regulates gene expression across cells. Finally, we multiplex the i-CRISPRi system to implement several multicellular logic gates that involve up to seven cells and take up to three inputs simultaneously, with single- and dual-rail encoding: NOT, YES, AND and AND-AND-NOT. The communication system developed here lays the groundwork for implementing complex biological circuits in engineered bacterial communities, using phage signals for communication.

Biomimetic Anisotropic-Functionalized Platelet-Membrane-Coated Polymeric Particles for Targeted Drug Delivery to Human Breast Cancer Cells.

Biomimetic particles that can replicate aspects of natural biological cell function are useful for advanced biological engineering applications. Engineering such particles requires mimicking the chemical complexity of the surface of biological cells, and this can be achieved by coating synthetic particles with naturally derived cell membranes. Past research has demonstrated the feasibility of utilizing cell membrane coatings from a variety of cell types to achieve extended blood circulation half-life. A particle's shape can also be designed to mimic a biological cell or virus, and this physical attribute can cause particular transport and biodistribution properties. However, the potential synergy between engineering a biomimetic particle's core shape in combination with functionalizing its surface with cell membranes to achieve targeted drug delivery has not been well-investigated. Here, anisotropic poly(lactic-co-glycolic acid) (PLGA) particles are coated with platelet membranes to engineer particles with enhanced stealth properties that are biomimetic in size, shape, and surface composition to natural platelets. The natural ability of platelets to target tumor cells was harnessed to develop a particulate system for targeted dual delivery of a small molecule and protein to cancer cells. The particles had targeted binding to metastatic human breast cancer cells, leading to enhanced killing of these cells in a mouse model through codelivery of TRAIL and doxorubicin. This system can be used for cancer cell killing and could potentially be utilized in preventing breast cancer metastasis. By engineering both the physical and chemical properties of the particles, biomimicry and therapeutic promise can be best achieved.

Numerical treatments for peristaltic transport of Johnson‐Segalman nanofluid through a vertical divergence irregular channel in the presence of inclined magnetic field and double‐diffusive

AbstractThis paper presents a computational study for the peristaltic pumping within vertical irregular divergence channels filled with magnetic Johnson—Segalman nanofluid. Various configurations of the outer boundaries are considered, namely, square wave, multi‐sinusoidal wave, trapezoidal wave, and triangular wave. An inclined magnetic field together with nanoparticles and mass concentrations is considered. Influences of the Dufour and Soret numbers are examined, and the cases of low Reynolds number and long wavelength are applied. All the computations are obtained numerically using Mathematica symbolical software (ND‐Solve), and the obtained results are presented in terms of the axial velocity , heat transfer rate , nanoparticle fraction profile , concentration profile , temperature profile , extra stress tensor , pressure gradient , pressure rise , and stream function . The major outcomes revealed that the square wave shape gives higher pressure gradients near the inlet and outlet parts while the multi‐sinusoidal wave gives periodic behaviors of . Also, the maximizing in thermophoresis parameter is better to obtain a higher rate of heat transfer while the increase in thermo‐diffusion and diffusion thermo effects causes a reduction in the rate of heat transfer. The discipline of biological and medical engineering, particularly for nanofluid peristaltic pumps, can benefit from the practical uses of such a model, which can be used to simulate the small vessel transport of particles in hemodynamics.

Abstract IA010: Bioengineering cell-based therapeutics

Abstract Cell-based therapeutics are an emerging modality that can potentially treat many currently intractable diseases through uniquely powerful modes of action. Our group is innovating new biomaterials and cellular constructs for medicine and biology by combining chemical biology, cellular engineering, and multi-scale fabrication. We have pioneered innovative approaches to synthesizing and in vivo screening of large libraries of biomaterial formulations for tailored applications in immunology and medicine. In my talk, I will describe our advances in discovering immunomodulatory biomaterials that can interact appropriately with the host immune system for localized immunomodulation. I will highlight our efforts to develop “cytokine factories” locally activating the innate and adaptive immune response to generate systemic immunotherapy and eradicate metastatic cancer. This approach has advanced to phase I/II human clinical trials for treating recurrent, refractory ovarian cancer. Citation Format: Omid Veiseh. Bioengineering cell-based therapeutics [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Optimizing Therapeutic Efficacy and Tolerability through Cancer Chemistry; 2024 Dec 9-11; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(12_Suppl):Abstract nr IA010.

Dynamic Diselenide Hydrogels for Controlled Tumor Organoid Culture and Dendritic Cell Vaccination.

Dynamic hydrogels are emerging as advanced materials for engineering tissue-like environments that mimic cellular microenvironments. We introduce a diselenide-cross-linked hydrogel system with light-responsive properties, designed for precise control of tumor organoid growth and light-initiated radical inactivation, particularly for dendritic cell (DC) vaccines. Diselenide exchange enables stress relaxation and hydrogel remodeling, while recombination and quenching of seleno radicals (Se•) reduce cross-linking density, leading to controlled degradation. We demonstrate a 2D to 3D growth strategy, where tumor cells inoculate on the hydrogel surface, expand, and gradually form spherical organoids within the 3D hydrogel. These tumor organoids show significantly higher drug resistance compared to 2D-cultured cells. High-density light irradiation enhances diselenide exchange, inducing hydrogel degradation, tumor cell death, and release of functional antigens. This system serves as a dynamic platform for tumor organoid culture and antigen release, offering significantly advanced approaches for in vitro tumor modeling and immunological research. Our findings position diselenide-cross-linked hydrogels as versatile materials for precision cellular engineering, with broad applications in cancer research and beyond.

Dismantling Silos: Academia, Industry, and a Science Museum Working Together

ABSTRACT A partnership between four universities, an industrial research lab, and a public science museum, created as a National Science Foundation Science and Technology Center, offers diverse collaboration and learning opportunities in cellular engineering. Each institution plays a vital role: universities advance science education, industry develops and commercializes technologies based on basic research, and science museums educate and engage the public. However, differences in the culture, values, and focus of these institutions create collaboration challenges. Three workshops highlight how consistent funding, intellectual property agreements, shared facilities, and long-term collaborations can harness the strengths of each institution to promote rapid prototyping, confront global problems, and encourage commercial applications from research.

EccDNA in plant-stress and biotechnological solutions in agriculture

Extrachromosomal circular DNA (eccDNA) is genetic material that exists outside of chromosomes and holds potential for next-generation genetic engineering in plant biology. By improving plant resilience, growth, and productivity, eccDNA offers a promising solution to global challenges in food security and environmental sustainability, making this a transformative era in agricultural biotechnology.

A massively parallel reporter assay library to screen short synthetic promoters in mammalian cells

Cellular responses to stimuli underpin discoveries in drug development, synthetic biology, and general life sciences. We introduce a library comprising 6144 synthetic promoters, each shorter than 250 bp, designed as transcriptional readouts of cellular stimulus responses in massively parallel reporter assay format. This library facilitates precise detection and amplification of transcriptional activity from our promoters, enabling the systematic development of tunable reporters with dynamic ranges of 50−100 fold. Our library proved functional in numerous cell lines and responsive to a variety of stimuli, including metabolites, mitogens, toxins, and pharmaceutical agents, generating robust and scalable reporters effective in screening assays, biomarkers, and synthetic circuits attuned to endogenous cellular activities. Particularly valuable in therapeutic development, our library excels in capturing candidate reporters to signals mediated by drug targets, a feature we illustrate across nine diverse G-protein coupled receptors (GPCRs), critical targets in drug development. We detail how this tool isolates and defines discrete signaling pathways associated with specific GPCRs, elucidating their transcriptional signatures. With its ease of implementation, broad utility, publicly available data, and comprehensive documentation, our library will be beneficial in synthetic biology, cellular engineering, ligand exploration, and drug development.

AtLEC2-Mediated Enhancement of Endoplasmic Reticulum-Targeted Foreign Protein Synthesis in Nicotiana benthamiana Leaves: Insights From Transcriptomic Analysis.

Many proteins used in industrial and pharmaceutical applications are typically synthesized within the secretory pathway. While yeast and mammalian cells have been engineered to enhance the production of endomembrane-targeted proteins, similar strategies in plant cells remain underexplored. This study investigates the potential of arabidopsis leafy cotyledon 2 (AtLEC2), a key regulator of seed development, to enhance the production of proteins targeted to the endoplasmic reticulum (ER) in Nicotiana benthamiana leaves. Through transient expression experiments, we demonstrate that AtLEC2 selectively increases the production of ER-targeted GUS without affecting its cytosolic variant. Moreover, leaves agroinfiltrated with AtLEC2 show a significant increase in ER-GFP accumulation compared to controls lacking AtLEC2. Transcriptomic analysis reveals that AtLEC2 promotes ribosome and chloroplast biogenesis, along with the upregulation of genes involved in photosynthesis, translation, and membrane synthesis. Notably, seed-specific poly(A) binding proteins involved in RNA stability and translation initiation, as well as 3-hydroxy-3-methylglutaryl coenzyme A reductase-linked to ER hypertrophy-are highly upregulated. This study establishes a novel connection between AtLEC2 and the enhancement of ER-targeted foreign protein synthesis, paving the way for innovative strategies in plant cellular engineering.

Rapid in silico directed evolution by a protein language model with EVOLVEpro.

Directed protein evolution is central to biomedical applications but faces challenges like experimental complexity, inefficient multi-property optimization, and local maxima traps. While in silico methods using protein language models (PLMs) can provide modeled fitness landscape guidance, they struggle to generalize across diverse protein families and map to protein activity. We present EVOLVEpro, a few-shot active learning framework that combines PLMs and regression models to rapidly improve protein activity. EVOLVEpro surpasses current methods, yielding up to 100-fold improvements in desired properties. We demonstrate its effectiveness across six proteins in RNA production, genome editing, and antibody binding applications. These results highlight the advantages of few-shot active learning with minimal experimental data over zero-shot predictions. EVOLVEpro opens new possibilities for AI-guided protein engineering in biology and medicine.

Layered Bio-Inorganic MXene Membranes: A Green Approach for Uranium Extraction from Seawater Using Genetically Modified E. coli.

With the growing demand for clean energy, efficient uranium extraction technologies are needed, especially from seawater, where uranium reserves are huge. Here, we developed a composite membrane by inserting Escherichia coli engineered with super uranyl-binding protein (SUP) within a two-dimensional (2D) MXene (Ti3C2Tx) layer. SUP endowed the bioinorganic hybrid membrane with ultrahigh selectivity for uranyl ions, while the engineered E. coli improved the mechanical strength and economy of the membranes. Experimental results showed that the membranes achieved precise recognition of uranyl ions and excellent ion screening performance (SFU/V ≈ 43, SFNa/U ≈ 158). Excellent separation performance and cyclic stability tests demonstrated the industrial application potential of the membrane. This method offers a green and sustainable solution, combining biological engineering and nanomaterial innovation, providing an environmentally friendly and efficient approach for uranium extraction from seawater, marking a significant advancement in the field of clean energy resource development.

Haitham Amal: Nitric oxide is a shared molecular mechanism of multiple neurodevelopmental and neurodegenerative disorders

Haitham Amal is an internationally recognized expert in cell signaling and brain disorders who heads the Laboratory of Neuromics, Cell Signaling, and Translational Medicine at the Hebrew University of Jerusalem. His research program integrates proteomics with systems biology, combining biochemical, pharmacological, and behavioral approaches. Currently a Visiting Professor at Boston Children's Hospital and Harvard Medical School, Dr. Amal previously conducted his postdoctoral studies at the Massachusetts Institute of Technology (MIT), where he served as a Senior Postdoctoral Associate in the Biological Engineering Department and was affiliated with the Stanley Center for Psychiatric Research at the Broad Institute of MIT and Harvard. His innovative research has been supported by numerous competitive grants, including awards from the German DFG, Israel Science Foundation, and the US Department of Defense, with his contributions recognized through the Krill Prize from the Wolf Foundation and the Eagles Autism Foundation Research Grant as its first international recipient. His research established essential connections between nitric oxide and autism spectrum disorder (ASD), while also revealing significant pathological overlaps between ASD and Alzheimer's disease. Building on these discoveries, Dr. Amal has co-founded Point6 Bio Ltd, developing biological diagnostic tools for ASD, and NeuroNOS Ltd., focused on nitric oxide synthase inhibitors for treating neurological disorders. In this Genomic Press interview, Dr. Amal shares his insights on the path to these discoveries and his vision for advancing our understanding of neurological disorders.

AI in Biomedical Imaging and Diagnostics

Advances in artificial intelligence (AI) and synthetic biology have profoundly influenced biomedical research, creating transformative opportunities in imaging, diagnostics, and therapeutic engineering. In biomedical imaging, AI-driven algorithms enhance precision and accuracy, enabling automated analysis of complex datasets, real-time imaging insights, and identification of disease biomarkers. Meanwhile, synthetic biology redefines cellular engineering, particularly in T-cell research, by enabling customized functionalities, such as precision-targeted antigen recognition and tunable immune responses. The integration of AI into T-cell engineering amplifies these capabilities, facilitating the design and optimization of synthetic circuits, predictive modeling of cellular behaviors, and dynamic monitoring of therapeutic outcomes. This interdisciplinary approach is revolutionizing diagnostics and immunotherapy by streamlining the identification of disease-specific markers, improving diagnostic accuracy, and enabling real-time modulation of T-cell functionality within the tumor microenvironment. By combining AI-powered insights with synthetic biology's ability to engineer living systems, this research aims to address critical challenges in disease treatment, including tumor heterogeneity and immune evasion. This work explores the synergistic application of AI and synthetic biology in biomedical imaging and T-cell engineering, highlighting state-of-the-art technologies, their therapeutic potential, and the future landscape of personalized medicine.

Development of a specific biosensor for sesquiterpene based on SELEX and directed evolution platforms

Biosensors are essential in synthetic biology, particularly for detecting compounds without distinct visual markers. In this study, a riboswitch biosensor specifically responsive to a sesquiterpene — amorpha-4,11-diene was developed for the first time. Through SELEX-SMB, a high-affinity aptamer library comprising 81,520 sequences was generated. Subsequent screening via the TBG-directed evolution platform identified riboswitch5, which downregulates downstream gene expression in response to amorpha-4,11-diene within a concentration range of 10–100 mg/L, achieving a log₂Foldchange of −0.51 at 100 mg/L. Structural predictions, combined with molecular docking and molecular dynamics simulations, revealed that ligand binding induced conformational changes that stabilize the riboswitch and enhance its repressive effect. This biosensor represents a powerful tool for the detection and regulation of small molecules, with broad applications in strain engineering, pathway regulation, and metabolic optimization in synthetic biology.

Hydrogen Sulfide‐Triggered Artificial DNAzyme Switches for Precise Manipulation of Cellular Functions

AbstractThe development of synthetic molecular tools responsive to biological cues is crucial for advancing targeted cellular regulation. A significant challenge is the regulation of cellular processes in response to gaseous signaling molecules such as hydrogen sulfide (H2S). To address this, we present the design of Gas signaling molecule‐Responsive Artificial DNAzyme‐based Switches (GRAS) to manipulate cellular functions via H2S‐sensitive synthetic DNAzymes. By incorporating stimuli‐responsive moieties to the phosphorothioate backbone, DNAzymes are strategically designed with H2S‐responsive azide groups at cofactor binding locations within the catalytic core region. These modifications enable their activation through H2S‐reducing decaging, thereby initiating substrate cleavage activity. Our approach allows for the flexible customization of various DNAzymes to regulate distinct cellular processes in diverse scenarios. Intracellularly, the enzymatic activity of GRAS promotes H2S‐induced cleavage of specific mRNA sequences, enabling targeted gene silencing and inducing apoptosis in cancer cells. Moreover, integrating GRAS with dynamic DNA assembly allows for grafting these functional switches onto cell surface receptors, facilitating H2S‐triggered receptor dimerization. This extracellular activation transmits signals intracellularly to regulate cellular behaviors such as migration and proliferation. Collectively, synthetic switches are capable of rewiring cellular functions in response to gaseous cues, offering a promising avenue for advanced targeted cellular engineering.