bims-enlima Biomed News
on Engineered living materials
Issue of 2024–12–29
thirteen papers selected by
Rahul Kumar, Tallinna Tehnikaülikool
  1. Optogenetic Engineered Living Materials.
  2. Analysis of Light-Controlled Artificial Cell-Cell Adhesions.
  3. A programmable environment for shape optimization and shapeshifting problems.
  4. Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors.
  5. Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia.
  6. Advanced chitin-based composite hydrogels enabled by quercetin-mediated assembly for multifunctional applications.
  7. Programming the elongation of mammalian cell aggregates with synthetic gene circuits.
  8. Click-and-Release Formation of Urea Bonds in Living Cells Enabled by Micelle Nanoreactors.
  9. Decellularized Green and Brown Macroalgae as Cellulose Matrices for Tissue Engineering.
  10. Engineering the 3D structure of organoids.
  11. Adaptable Manufacturing and Biofabrication of Milliscale Organ Chips With Perfusable Vascular Beds.
  12. Interfacial engineering for biomolecule immobilisation in microfluidic devices.
  13. Evaluation of the Biocompatibility of Poly(benzimidazobenzophenanthroline)(BBL) Polymer Films with Living Cells.
  1. Methods Mol Biol. 2025 ;2840 101-114
    Optogenetic Engineered Living Materials.
    Varun Sai Tadimarri, Shrikrishnan Sankaran.
      Engineered living materials (ELM) is a new frontier in materials research that uses living microorganisms to augment nonliving materials with lifelike capabilities, such as responding to external stimuli. This is achieved by genetically programming the microorganisms in an ELM with stimulus-sensing modules. A popular stimulus to remotely control various ELM functions is light, which has been realized thanks to optogenetics. This chapter describes methods to create a simple ELM capable of sensing light and responding to it by producing and releasing a drug. The material component of the ELM will be a Pluronic F127-based hydrogel and the living component will be optogenetically engineered bacteria. Such ELMs are being developed to create smart therapeutic solutions for challenging chronic diseases and variations in the design to improve performance and safety will be mentioned.
    Keywords:  Agarose; Blue light; Drug delivery; E. coli; Engineered living materials; Living therapeutics
    DOI:  https://doi.org/10.1007/978-1-0716-4047-0_8
  2. Methods Mol Biol. 2025 ;2840 245-254
    Analysis of Light-Controlled Artificial Cell-Cell Adhesions.
    Seraphine V Wegner, Christopher A Raab.
      The precise spatial and temporal regulation of cell-cell adhesions is crucial for understanding the underlying biological processes and for assembling multicellular structures in tissue engineering. Traditional approaches have relied on chemical membrane functionalization and regulated gene expression of native cell adhesion molecules (CAMs), but these methods lack the necessary control and can be detrimental to cells. In contrast, engineered photoswitchable cell-cell adhesions offer a reversible and dynamic regulation at a single-cell resolution. This is achieved by expressing different photodimerizers as artificial CAMs on the cell surfaces. Here, we describe a straightforward method for the functional analysis of these photoswitchable cell-cell adhesions in a 3D suspension culture.
    Keywords:  3D clustering; Artificial cell adhesions; Bottom-up tissue engineering; Cell–cell adhesions; Extracellular optogenetics; Photoswitchable; Reversibility
    DOI:  https://doi.org/10.1007/978-1-0716-4047-0_18
  3. Nat Comput Sci. 2024 Dec 27.
    A programmable environment for shape optimization and shapeshifting problems.
    Chaitanya Joshi, Daniel Hellstein, Cole Wennerholm, Eoghan Downey, Emmett Hamilton, Samuel Hocking, Anca S Andrei, James H Adler, Timothy J Atherton.
      Soft materials underpin many domains of science and engineering, including soft robotics, structured fluids, and biological and particulate media. In response to applied mechanical, electromagnetic or chemical stimuli, such materials typically change shape, often dramatically. Predicting their structure is of great interest to facilitate design and mechanistic understanding, and can be cast as an optimization problem where a given energy function describing the physics of the material is minimized with respect to the shape of the domain and additional fields. However, shape-optimization problems are very challenging to solve, and there is a lack of suitable simulation tools that are both readily accessible and general in purpose. Here we present an open-source programmable environment, Morpho, and demonstrate its versatility by showcasing a range of applications from different areas of soft-matter physics: swelling hydrogels, complex fluids that form aspherical droplets, soap films and membranes, and filaments.
    DOI:  https://doi.org/10.1038/s43588-024-00749-7
  4. ACS Synth Biol. 2024 Dec 22.
    Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors.
    Brecht De Paepe, Marjan De Mey.
      Since the description of the lac operon in 1961 by Jacob and Monod, transcriptional regulation in prokaryotes has been studied extensively and has led to the development of transcription factor-based biosensors. Due to the broad variety of detectable small molecules and their various applications across biotechnology, biosensor research and development have increased exponentially over the past decades. Throughout this period, key milestones in fundamental knowledge, synthetic biology, analytical tools, and computational learning have led to an immense expansion of the biosensor repertoire and its application portfolio. Over the years, biosensor engineering became a more multidisciplinary discipline, combining high-throughput analytical tools, DNA randomization strategies, forward engineering, and advanced protein engineering workflows. Despite these advances, many obstacles remain to fully unlock the potential of biosensor technology. This review analyzes the timeline of key milestones on fundamental research (1960s to 2000s) and engineering strategies (2000s onward), on both the DNA and protein level of biosensors. Moreover, insights into the future perspectives, remaining hurdles, and unexplored opportunities of this promising field are discussed.
    Keywords:  biosensors; computational techniques; engineering strategies; historical overview; inducible systems; prokaryotes; transcription factor
    DOI:  https://doi.org/10.1021/acssynbio.4c00689
  5. Nucleic Acids Res. 2024 Dec 27. pii: gkae1256. [Epub ahead of print]
    Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia.
    Abhinav Pujar, Amit Pathania, Corbin Hopper, Amir Pandi, Cristian Ruiz Calderón, Matthias Függer, Thomas Nowak, Manish Kushwaha.
      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.
    DOI:  https://doi.org/10.1093/nar/gkae1256
  6. Int J Biol Macromol. 2024 Dec 20. pii: S0141-8130(24)09854-4. [Epub ahead of print] 139043
    Advanced chitin-based composite hydrogels enabled by quercetin-mediated assembly for multifunctional applications.
    Xinghuan Lin, Hanji Chen, Lin Huang, Shuang Liu, Chunsheng Cai, Yibao Li, Shanshan Li.
      Natural building blocks like chitins for self-assembling into complex materials have garnered significant interest owing to the inherent and diverse functionalities. However, challenges persist in the assembly of chitin-based composites, primarily stemming from chitin's poor solubility and compatibility. Herein, a quercetin-mediated multiple crosslinking strategy was developed to enhance compatibility by quercetin-mediated interfacial interactions between chitin and inorganic materials, achieving a series of chitin-based composite hydrogels with high performances. The quercetin-mediated strategy could effectively modulate the non-covalent interactions within hydrogel, which served as the sacrificial bonds to dissipate large energy, leading to the high toughness of chitin-based composite hydrogels (0.70-1.02 MJ·m-3). Furthermore, through utilizing quercetin-assisted non-covalent interactions, effective dispersion of inorganic materials (e.g., molybdenum disulfide, carbon nanotube and calcium carbonate) within hydrogels was achieved, resulting in composite hydrogels with diverse functionalities. Our quercetin-mediated strategy conceptualized in this work paves the way for the development of a diverse array of chitin-based composite hydrogels which incorporate various functional inorganic materials.
    Keywords:  Chitin; Composite hydrogel; Mediated-assembly; Multifunctionality; Quercetin
    DOI:  https://doi.org/10.1016/j.ijbiomac.2024.139043
  7. bioRxiv. 2024 Dec 11. pii: 2024.12.11.627621. [Epub ahead of print]
    Programming the elongation of mammalian cell aggregates with synthetic gene circuits.
    Josquin Courte, Christian Chung, Naisargee Jain, Catcher Salazar, Neo Phuchane, Steffen Grosser, Calvin Lam, Leonardo Morsut.
      A key goal of synthetic morphogenesis is the identification and implementation of methods to control morphogenesis. One line of research is the use of synthetic genetic circuits guiding the self-organization of cell ensembles. This approach has led to several recent successes, including control of cellular rearrangements in 3D via control of cell-cell adhesion by user-designed artificial genetic circuits. However, the methods employed to reach such achievements can still be optimized along three lines: identification of circuits happens by hand, 3D structures are spherical, and effectors are limited to cell-cell adhesion. Here we show the identification, in a computational framework, of genetic circuits for volumetric axial elongation via control of proliferation, tissue fluidity, and cell-cell signaling. We then seek to implement this design in mammalian cell aggregates in vitro. We start by identifying effectors to control tissue growth and fluidity in vitro. We then combine these new modules to construct complete circuits that control cell behaviors of interest in space and time, resulting in measurable tissue deformation along an axis that depends on the engineered signaling modules. Finally, we contextualize in vitro and in silico implementations within a unified morphospace to suggest further elaboration of this initial family of circuits towards more robust programmed axial elongation. These results and integrated in vitro/in silico pipeline demonstrate a promising method for designing, screening, and implementing synthetic genetic circuits of morphogenesis, opening the way to the programming of various user-defined tissue shapes.
    DOI:  https://doi.org/10.1101/2024.12.11.627621
  8. Angew Chem Int Ed Engl. 2024 Dec 23. e202422627
    Click-and-Release Formation of Urea Bonds in Living Cells Enabled by Micelle Nanoreactors.
    Frédéric Taran, Lea Madegard, Melissa Girard, Estelle Blochouse, Benjamin Riss-Yaw, Alberto Palazzolo, Davide Audisio, Pauline Poinot, Sebastien Papot, Mélanie Laquembe.
      The development of innovative strategies enabling chemical reactions in living systems is of great interest for exploring and manipulating biological processes. Herein, we present a pioneering approach based on both bioorthogonal and confined chemistry for intracellular drug synthesis. Exploiting a click-to-release reaction, we engineered nanoparticles capable of synthesizing drugs within cellular environments through bioorthogonal reactions with cyclooctynes. Proof of concept experiments showed that this new approach could be successfully applied to the synthesis of the FDA-approved Sorafenib within cancer cells. The integration of bioorthogonal and confined chemistry not only offers exciting prospects for advancing therapeutic strategies but also opens up new avenues for exploring non-natural reactions within living systems. This innovative approach represents a fundamental extension of the biorthogonal chemistry concept and holds great promise for pioneering developments in therapeutic applications.
    Keywords:  Cancer; Mesoionics; Nanoreactors; chemical biology; click chemistry
    DOI:  https://doi.org/10.1002/anie.202422627
  9. J Funct Biomater. 2024 Dec 23. pii: 390. [Epub ahead of print]15(12):
    Decellularized Green and Brown Macroalgae as Cellulose Matrices for Tissue Engineering.
    Caitlin Berry-Kilgour, Indrawati Oey, Jaydee Cabral, Georgina Dowd, Lyn Wise.
      Scaffolds resembling the extracellular matrix (ECM) provide structural support for cells in the engineering of tissue constructs. Various material sources and fabrication techniques have been employed in scaffold production. Cellulose-based matrices are of interest due to their abundant supply, hydrophilicity, mechanical strength, and biological inertness. Terrestrial and marine plants offer diverse morphologies that can replicate the ECM of various tissues and be isolated through decellularization protocols. In this study, three marine macroalgae species-namely Durvillaea poha, Ulva lactuca, and Ecklonia radiata-were selected for their morphological variation. Low-intensity, chemical treatments were developed for each species to maintain native cellulose structures within the matrices while facilitating the clearance of DNA and pigment. Scaffolds generated from each seaweed species were non-toxic for human dermal fibroblasts but only the fibrous inner layer of those derived from E. radiata supported cell attachment and maturation over the seven days of culture. These findings demonstrate the potential of E. radiata-derived cellulose scaffolds for skin tissue engineering and highlight the influence of macroalgae ECM structures on decellularization efficiency, cellulose matrix properties, and scaffold utility.
    Keywords:  cellulose; decellularization; fibroblast; macroalgae; matrix; scaffold; seaweed; skin; tissue engineering
    DOI:  https://doi.org/10.3390/jfb15120390
  10. Stem Cell Reports. 2024 Dec 10. pii: S2213-6711(24)00323-0. [Epub ahead of print] 102379
    Engineering the 3D structure of organoids.
    Samuel P Moss, Ezgi Bakirci, Adam W Feinberg.
      Organoids form through the sel f-organizing capabilities of stem cells to produce a variety of differentiated cell and tissue types. Most organoid models, however, are limited in terms of the structure and function of the tissues that form, in part because it is difficult to regulate the cell type, arrangement, and cell-cell/cell-matrix interactions within these systems. In this article, we will discuss the engineering approaches to generate more complex organoids with improved function and translational relevance, as well as their advantages and disadvantages. Additionally, we will explore how biofabrication strategies can manipulate the cell composition, 3D organization, and scale-up of organoids, thus improving their utility for disease modeling, drug screening, and regenerative medicine applications.
    Keywords:  3D bioprinting; biofabrication; organoids; spheroids; stem cells; vascularization
    DOI:  https://doi.org/10.1016/j.stemcr.2024.11.009
  11. Biotechnol J. 2024 Dec;19(12): e202400550
    Adaptable Manufacturing and Biofabrication of Milliscale Organ Chips With Perfusable Vascular Beds.
    Charles Ethan Byrne, Ashley T Martier, Gideon Wills Kpeli, Kevin Michael Conrad, William Bralower, Elisabet Olsen, Gabrielle Fortes, Caroline C Culp, Max Wendell, Keefer A Boone, Matthew R Burow, Mark J Mondrinos.
      Microphysiological systems (MPS) containing perfusable vascular beds unlock the ability to model tissue-scale elements of vascular physiology and disease in vitro. Access to inexpensive stereolithography (SLA) 3D printers now enables benchtop fabrication of polydimethylsiloxane (PDMS) organ chips, eliminating the need for cleanroom access and microfabrication expertise, and can facilitate broader adoption of MPS approaches in preclinical research. Rapid prototyping of organ chip mold designs accelerates the processes of design, testing, and iteration, but geometric distortion and surface roughness of SLA resin prints can impede the development of standardizable manufacturing workflows. This study reports postprocessing procedures for manufacturing SLA-printed molds that produce fully cured, flat, patently bonded, and optically clear polydimethyl siloxane (PDMS) organ chips. Injection loading tests were conducted to identify milliscale membrane-free organ chip (MFOC) designs that allowed reproducible device loading by target end-users, a key requirement for broad nonexpert adoption in preclinical research. The optimized milliscale MFOC design was used to develop tissue engineering protocols for (i) driving bulk tissue vasculogenesis in MFOC, and (ii) seeding the bulk tissue interfaces with a confluent endothelium to stimulate self-assembly of perfusable anastomoses with the internal vasculature. Comparison of rocker- and pump-based protocols for flow-conditioning of anastomosed vascular beds revealed that continuous pump-driven flow is required for reproducible barrier maturation throughout the 3D tissue bulk. Demonstrated applications include nanoparticle perfusion and engineering perfusable tumor vasculature. These easily adaptable methods for designing and fabricating vascularized microphysiological systems can accelerate their adoption in a diverse range of preclinical laboratory settings.
    Keywords:  3D printing; endothelial barrier; organ chips; tissue engineering; tumor vasculature; vascularization
    DOI:  https://doi.org/10.1002/biot.202400550
  12. Biomaterials. 2024 Dec 15. pii: S0142-9612(24)00550-7. [Epub ahead of print]316 123014
    Interfacial engineering for biomolecule immobilisation in microfluidic devices.
    Deepu Ashok, Jasneil Singh, Henry Robert Howard, Sophie Cottam, Anna Waterhouse, Marcela M M Bilek.
      Microfluidic devices are used for various applications in biology and medicine. From on-chip modelling of human organs for drug screening and fast and straightforward point-of-care (POC) detection of diseases to sensitive biochemical analysis, these devices can be custom-engineered using low-cost techniques. The microchannel interface is essential for these applications, as it is the interface of immobilised biomolecules that promote cell capture, attachment and proliferation, sense analytes and metabolites or provide enzymatic reaction readouts. However, common microfluidic materials do not facilitate the stable immobilisation of biomolecules required for relevant applications, making interfacial engineering necessary to attach biomolecules to the microfluidic surfaces. Interfacial engineering is performed through various immobilisation mechanisms and surface treatment techniques, which suitably modify the surface properties like chemistry and energy to obtain robust biomolecule immobilisation and long-term storage stability suitable for the final application. In this review, we provide an overview of the status of interfacial engineering in microfluidic devices, covering applications, the role of biomolecules, their immobilisation pathways and the influence of microfluidic materials. We then propose treatment techniques to optimise performance for various biological and medical applications and highlight future areas of development.
    Keywords:  Biomolecule immobilisation; Biosensing; CTC capture; Microfluidics; Nanostructured; Organs-on-chips; Point-of-care; Surface modification
    DOI:  https://doi.org/10.1016/j.biomaterials.2024.123014
  13. Small. 2024 Dec 23. e2404451
    Evaluation of the Biocompatibility of Poly(benzimidazobenzophenanthroline)(BBL) Polymer Films with Living Cells.
    Claudia Latte Bovio, Paola Campione, Han-Yan Wu, Qifan Li, Ana De La Fuente Durán, Alberto Salleo, Simone Fabiano, Grazia Maria Lucia Messina, Francesca Santoro.
      The integration of organic electronic materials with biological systems to monitor, interface with, and regulate physiological processes is a key area in the field of bioelectronics. Central to this advancement is the development of cell-chip coupling, where materials engineering plays a critical role in enhancing biointerfacing capabilities. Conductive polymers have proven particularly useful in cell interfacing applications due to their favorable biophysical and chemical properties. However, n-type conductive polymers remain underexplored, primarily due to their limited long-term stability. In this study, it is demonstrated that the conductive polymer poly(benzimidazobenzophenanthroline) (BBL), commonly used in organic electronic devices, can effectively support neuronal cell viability and spreading, both as a bare cell culture material and when coated with exracellular matrix proteins. This work provides a preliminary validation of BBL's potential for future integration into bioelectronic devices and in biointerfacing.
    Keywords:  BBL; cell‐chip coupling; in vitro biocompatibility; neuronal cells; organic bioelectronics
    DOI:  https://doi.org/10.1002/smll.202404451
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