Synthetic living machines: A new window on life

Abstract

Increased control of biological growth and form is an essential gateway to transformative medical advances. Repairing of birth defects, restoring lost or damaged organs, normalizing tumors, all depend on understanding how cells cooperate to make specific, functional large-scale structures. Despite advances in molecular genetics, significant gaps remain in our understanding of the meso-scale rules of morphogenesis. An engineering approach to this problem is the creation of novel synthetic living forms, greatly extending available model systems beyond evolved plant and animal lineages. Here, we review recent advances in the emerging field of synthetic morphogenesis, the bioengineering of novel multicellular living bodies. Emphasizing emergent self-organization, tissue-level guided self-assembly, and active functionality, this work is the essential next generation of synthetic biology. Aside from useful living machines for specific functions, the rational design and analysis of new, coherent anatomies will greatly increase our understanding of foundational questions in evolutionary developmental and cell biology.

Keywords: bioengineering; developmental biology; synthetic biology.

Graphical abstract

Figure 1

Disciplines and tools that are enabling for development of synthetic functional morphologies and their related impacts on life

Figure 2

Synthetic embryo-like entities (A) Blastoids co-stained with F-actin (red) and Nonog (green). Nanog shows ESC identity (taken with permission from Rivron et al., 2018). (B) Schematic to show strategy for generation of mouse embryonic-like structures via combining mouse ESC (red) and TSCs (blue). Cells are suspended in 3D extracellular matrices and allowed to self-organize (taken with permission from Harrison et al., 2017). (C) ETS-embryo structure. Red shows Oct4 expression from ESCs and cyan is Eomes in TSCs (taken with permission from Harrison et al., 2017). (D) Gastruloids at 120 h after aggregation showing features of mouse embryo at embryonic day 1 and spatially confined presence of signaling cues and markers associated with axis formation such as Brachyury-GFP, WNT signaling activity (TCF/LEF-mCherry), and Nodal-YFP (taken with permission from [Beccari et al., 2018]).

Figure 3

Examples of organoids and multicellular tissues (A) Self-organization of an optic-cup-like structure with differentiating epithelial cells from ES cell aggregates in 3D. Rx-GFP shows retinal analge (taken with permission from Nakano et al., 2012). (B) Left: Bright-field view of cerebral organoid with cavities (arrow) representing ventricle-like structures of brain. Middle: Immunostained cerebral organoid shows tissue morphology with neural progenitors (SOX2, red) and neurons (TUJ1, green). Right: Recorded neural activity using calcium dye (taken with permission from Lancaster et al., 2013). (C) Schematic for genetically guided engineering by using stem cells engineered with inducible genetic circuit to pre-program cell fates associated with different germ layers. Doxycycline (Dox) turns on the expression. (D) Generation of liver bud-like tissue using genetic programming. Immunostained tissue exhibits the presence of subset of cells similar to fetal liver. CD34 marks vasculature, CD45 and HG mark blood cell lineages, DLK1 and Des mark hepatocyte progenitor and pericyte populations, respectively (taken with permission from [Guye et al., 2016]). Part of this figure is created using BioRender (BioRender.com).

Figure 4

Biobots and Xenobots (A) Four layers of body architecture for engineered artificial ray as an example of a biobot. (B and C) (B) Concept of operation and (C) phototactic control via optical stimulation that triggers muscle activation and produces undulatory locomotion and swimming. Asymmetric stimulation controls the direction (taken with permission from Park et al., 2016). (D) Ectodermal and muscle cells from Xenopus embryos are extracted, allowed to re-associate, and then micro-sculpted to remove some cells. (E–H) (E) The remaining cells self-organize a large-scale pattern (with muscle inside, shown by red fluorescent protein signal) to enable forward locomotion of the Xenobot using the available features of the structure. The sculpting is done in accordance with a simulated Xenobot evolved in a virtual computer environment (F), and many different shapes with diverse emergent movement profiles are possible (G). The movement of these synthetic organisms alters their environment by moving materials (H and I) in ways exactly as predicted by the computational model of the swarm behavior.

Figure 5

Integrative analysis and engineering of gene regulatory network (A) Comparison of synthetic tissues with native tissues via quantitative computational analysis and classification algorithms. Genetic circuits to program cell and tissue fates are predicted, engineered, and delivered to synthetic tissue to program developmental trajectories and cellular interactions. (B and C) (B) Example of genetic circuits enabled directing development of liver organoids from pluripotent stem cells; (C) self-vascularized human liver organoids generated via genetic design and engineering (taken with permission from Velazquez et al., 2020). Part of this figure is created using BioRender (BioRender.com).

Figure 6

Developmental bioelectricity (A) Neurons maintain a resting potential via ion channels in their membranes and propagate their electric state to neighbors via gap junctions (electrical synapses). (B and C) (B) Bioelectric signaling using these same molecular components is a property of all cells, which join together into tissues forming networks (C) that enable large-scale electrically mediated computations to regulate distributions of morphogens and control gene expression. (D) Fluorescent voltage dye image showing an example of an instructive bioelectric prepattern—the frog embryo face, showing the future locations of the eye, mouth, and other organs (taken with permission from(Vandenberg et al., 2011)). (E–G) (E) A variety of channel, connexin, and neurotransmitter machinery proteins are available as a parts library, complementing canonical transcriptional modules, which enables synthetic biologists to build bioelectric circuits for control of tissue-level morphogenesis. An example of the plasticity of self-assembly beyond genetic default outcomes are shown in planaria, where normal cells can build wild-type forms (F) or highly altered morphologies (G) if the bioelectric circuit states are modified.