Self-organizing circuit assembly through spatiotemporally coordinated neuronal migration within geometric constraints

Spatial confinement: A spur for axonal growth

The concept of spatial confinement is the basis of cell positioning and guidance in in vitro studies. In vivo, it reflects many situations faced during embryonic development. In vitro, spatial confinement of neurons is achieved using different technological approaches: adhesive patterning, topographical structuring, microfluidics and the use of hydrogels. The notion of chemical or physical frontiers is particularly central to the behaviors of growth cones and neuronal processes under confinement. They encompass phenomena of cell spreading, boundary crossing, and path finding on surfaces with different adhesive properties. However, the most universal phenomenon related to confinement, regardless of how it is implemented, is the acceleration of neuronal growth. Overall, a bi-directional causal link emerges between the shape of the growth cone and neuronal elongation dynamics, both in vivo and in vitro. The sensing of adhesion discontinuities by filopodia and the subsequent spatial redistribution and size adaptation of these actin-rich filaments seem critical for the growth rate in conditions in which adhesive contacts and actin-associated clutching forces dominate. On the other hand, the involvement of microtubules, specifically demonstrated in 3D hydrogel environments and leading to ameboid-like locomotion, could be relevant in a wider range of growth situations. This review brings together a literature collected in distinct scientific fields such as development, mechanobiology and bioengineering that highlight the consequences of confinement and raise new questions at different cellular scales. Its ambition is to stimulate new research that could lead to a better understanding of what gives neurons their ability to establish and regulate their exceptional size.

Tracking axon initial segment plasticity using high-density microelectrode arrays: A computational study

Despite being composed of highly plastic neurons with extensive positive feedback, the nervous system maintains stable overall function. To keep activity within bounds, it relies on a set of negative feedback mechanisms that can induce stabilizing adjustments and that are collectively termed “homeostatic plasticity.” Recently, a highly excitable microdomain, located at the proximal end of the axon—the axon initial segment (AIS)—was found to exhibit structural modifications in response to activity perturbations. Though AIS plasticity appears to serve a homeostatic purpose, many aspects governing its expression and its functional role in regulating neuronal excitability remain elusive. A central challenge in studying the phenomenon is the rich heterogeneity of its expression (distal/proximal relocation, shortening, lengthening) and the variability of its functional role. A potential solution is to track AISs of a large number of neurons over time and attempt to induce structural plasticity in them. To this end, a promising approach is to use extracellular electrophysiological readouts to track a large number of neurons at high spatiotemporal resolution by means of high-density microelectrode arrays (HD-MEAs). However, an analysis framework that reliably identifies specific activity signatures that uniquely map on to underlying microstructural changes is missing. In this study, we assessed the feasibility of such a task and used the distal relocation of the AIS as an exemplary problem. We used sophisticated computational models to systematically explore the relationship between incremental changes in AIS positions and the specific consequences observed in simulated extracellular field potentials. An ensemble of feature changes in the extracellular fields that reliably characterize AIS plasticity was identified. We trained models that could detect these signatures with remarkable accuracy. Based on these findings, we propose a hybrid analysis framework that could potentially enable high-throughput experimental studies of activity-dependent AIS plasticity using HD-MEAs.

Ligand functionalization of titanium nanopattern enables the analysis of cell-ligand interactions by super-resolution microscopy

The spatiotemporal aspects of early signaling events during interactions between cells and their environment dictate multiple downstream outcomes. While advances in nanopatterning techniques have allowed the isolation of these signaling events, a major limitation of conventional nanopatterning methods is its dependence on gold (Au) or related materials that plasmonically quench fluorescence and, thus, are incompatible with super-resolution fluorescence microscopy. Here we describe a novel method that integrates nanopatterning with single-molecule resolution fluorescence imaging, thus enabling mechanistic dissection of molecular-scale signaling events in conjunction with nanoscale geometry manipulation. Our method exploits nanofabricated titanium (Ti) whose oxide (TiO₂) is a dielectric material with no plasmonic effects. We describe the surface chemistry for decorating specific ligands such as cyclo-RGD (arginine, glycine and aspartate: a ligand for fibronectin-binding integrins) on TiO₂ nanoline and nanodot substrates, and demonstrate the ability to perform dual-color super-resolution imaging on these patterns. Ti nanofabrication is similar to other metallic materials like Au, while the functionalization of TiO₂ is relatively fast, safe, economical, easy to set up with commonly available reagents, and robust against environmental parameters such as humidity. Fabrication of nanopatterns takes ~2-3 d, preparation for functionalization ~1.5-2 d, and functionalization 3 h, after which cell culture and imaging experiments can be performed. We suggest that this method may facilitate the interrogation of nanoscale geometry and force at single-molecule resolution, and should find ready applications in early detection and interpretation of physiochemical signaling events at the cell membrane in the fields of cell biology, immunology, regenerative medicine, and related fields.

Small-world networks of neuroblastoma cells cultured in three-dimensional polymeric scaffolds featuring multi-scale roughness

Understanding the mechanisms underlying cell-surface interaction is of fundamental importance for the rational design of scaffolds aiming at tissue engineering, tissue repair and neural regeneration applications. Here, we examined patterns of neuroblastoma cells cultured in three-dimensional polymeric scaffolds obtained by two-photon lithography. Because of the intrinsic resolution of the technique, the micrometric cylinders composing the scaffold have a lateral step size of ~200 nm, a surface roughness of around 20 nm, and large values of fractal dimension approaching 2.7. We found that cells in the scaffold assemble into separate groups with many elements per group. After cell wiring, we found that resulting networks exhibit high clustering, small path lengths, and small-world characteristics. These values of the topological characteristics of the network can potentially enhance the quality, quantity and density of information transported in the network compared to equivalent random graphs of the same size. This is one of the first direct observations of cells developing into 3D small-world networks in an artificial matrix.

Self-organization of modular network architecture by activity-dependent neuronal migration and outgrowth

The spatial distribution of neurons and activity-dependent neurite outgrowth shape long-range interaction, recurrent local connectivity and the modularity in neuronal networks. We investigated how this mesoscale architecture develops by interaction of neurite outgrowth, cell migration and activity in cultured networks of rat cortical neurons and show that simple rules can explain variations of network modularity. In contrast to theoretical studies on activity-dependent outgrowth but consistent with predictions for modular networks, spontaneous activity and the rate of synchronized bursts increased with clustering, whereas peak firing rates in bursts increased in highly interconnected homogeneous networks. As Ca²⁺ influx increased exponentially with increasing network recruitment during bursts, its modulation was highly correlated to peak firing rates. During network maturation, long-term estimates of Ca²⁺ influx showed convergence, even for highly different mesoscale architectures, neurite extent, connectivity, modularity and average activity levels, indicating homeostatic regulation towards a common set-point of Ca²⁺ influx.

3-D geometry and irregular connectivity dictate neuronal firing in frequency domain and synchronization

The replication of the complex structure and three dimensional (3-D) interconnectivity of neurons in the brain is a great challenge. A few 3-D neuronal patterning approaches have been developed to mimic the cell distribution in the brain but none have demonstrated the relationship between 3-D neuron patterning and network connectivity. Here, we used photolithographic crosslinking to fabricate in vitro 3-D neuronal structures with distinct sizes, shapes or interconnectivities, i.e., milli-blocks, micro-stripes, separated micro-blocks and connected micro-blocks, which have spatial confinement from "Z" dimension to "XYZ" dimension. During a 4-week culture period, the 3-D neuronal system has shown high cell viability, axonal, dendritic, synaptic growth and neural network activity of cortical neurons. We further studied the calcium oscillation of neurons in different 3-D patterns and used signal processing both in Fast Fourier Transform (FFT) and time domain (TD) to model the fluorescent signal variation. We observed that the firing frequency decreased as the spatial confinement in 3-D system increased. Besides, the neuronal synchronization significantly decreased by irregularly connecting micro-blocks, indicating that network connectivity can be adjusted by changing the linking conditions of 3-D gels. Earlier works showed the importance of 3-D culture over 2-D in terms of cell growth. Here, we showed that not only 3-D geometry over 2-D culture matters, but also the spatial organization of cells in 3-D dictates the neuronal firing frequency and synchronicity.

Synthesizing Living Tissues with Microfluidics

In native tissues, various cell types organize and spatiotemporally function and communicate with neighboring or remote cells in a highly regulated way. How can we replicate these amazing functional structures in vitro? From the view of a chemist, the heterogeneous cells and extracellular matrix (ECM) could be regarded as various chemical substrate materials for "synthetic" reactions during tissue engineering. But how can we accelerate these reactions? Microfluidics provides ideal solutions. Microfluidics could be metaphorically regarded as a miniature "biofactory", whereas the on-chip critical chemical cues such as biomolecule gradients and physical cues such as geometrical confinement, topological guidance, and mechanical stimulations, along with the external stimulations such as light, electricity, acoustics, and magnetics, could be regarded as "catalytic cues" which can accelerate the "synthetic reactions" by precisely and effectively manipulating a series of cell behaviors including cell adhesion, migration, growth, proliferation, differentiation, cell-cell interaction, and cell-matrix interaction to reduce activation energy of the "synthetic reactions". Thus, on the microfluidics platform, the "biofactory", various "synthetic" reactions take place to change the substrate materials (cells and ECM) into products (tissues) in a nonlinear way, which is a typical feature of a biological process. By precisely organizing the substrate materials and spatiotemporally controlling the activity of the products, as a "biofactory", the microfluidics system can not only "synthesize" living tissues but also recreate physiological or pathophysiological processes such as immune responses, angiogenesis, wound healing, and tumor metastasis in vitro to bring insights into the mechanisms underlying these processes taking place in vivo. In this Account, we borrow the concept of chemical "synthesis" to describe how to "synthesize" artificial tissues using microfluidics from a chemist's view. Accelerated by the built-in physiochemical cues on microfluidics and external stimulations, various tissues could be "synthesized" on a microfluidics platform. We summarize that there are "step-by-step synthesis" and "one-step synthesis" on microfluidics for creating desired tissues with unprecedented precision, accuracy, and speed. In recent years, researchers developed various microfluidic techniques including creating adhesive domains for mediating reverse and precise adhesion, chemical gradients for directing cell growth, geometrical confinements and topological cues for manipulating cell migration, and mechanics for stimulating cell differentiation. By employing and orchestrating these on-chip tissue "synthetic" conditions, "step-by-step synthesis" could be realized on chips to develop multilayered tissues such as blood vessels. "One-step synthesis" on chips could develop functional three-dimensional tissue structures such as neural networks or nephron-like structures. Based on these on-chip studies, many critical physiological and pathophysiological processes such as wound healing, tumor metastasis, and atherosclerosis could be deeply investigated, and the drugs or therapeutic approaches could also be evaluated or screened conveniently. The "synthetic tissues on microfluidics" system would pave an avenue for precise creation of artificial tissues for not only fundamental research but also biomedical applications such as tissue engineering.

Neural Circuits on a Chip

Neural circuits are responsible for the brain's ability to process and store information. Reductionist approaches to understanding the brain include isolation of individual neurons for detailed characterization. When maintained in vitro for several days or weeks, dissociated neurons self-assemble into randomly connected networks that produce synchronized activity and are capable of learning. This review focuses on efforts to control neuronal connectivity in vitro and construct living neural circuits of increasing complexity and precision. Microfabrication-based methods have been developed to guide network self-assembly, accomplishing control over in vitro circuit size and connectivity. The ability to control neural connectivity and synchronized activity led to the implementation of logic functions using living neurons. Techniques to construct and control three-dimensional circuits have also been established. Advances in multiple electrode arrays as well as genetically encoded, optical activity sensors and transducers enabled highly specific interfaces to circuits composed of thousands of neurons. Further advances in on-chip neural circuits may lead to better understanding of the brain.

The Micro/Nanohybrid Structures Enhancing B35 Cell Guidance on Chitosan

A novel chitosan scaffold with micro- and nano-hybrid structures was proposed in this study. The hemispheric array of the barrier layer of an anodic aluminum oxide (AAO) film was used as the substrate. Microelectromechanical systems and nickel electroforming techniques were integrated for fabricating chitosan scaffolds with different micro/nanohybrid structures. Nerve cells were then cultured on the conduits. It was demonstrated that the scaffold with pure microstructures can guide the nerve cells to grow along the ridges of the microstructure and some cells to grow across the groove in between two ridges of the microstructure. It was also shown that the scaffold with microscale ridges and nanopatterns on the groove between two ridges can more effectively guide the cells to grow along the ridges, thus enhancing the proliferation of nerve cells.

Networks of neuroblastoma cells on porous silicon substrates reveal a small world topology

N2A cells on porous substrates create highly clustered, small world topology patterns.

Emergence of assortative mixing between clusters of cultured neurons

The analysis of the activity of neuronal cultures is considered to be a good proxy of the functional connectivity of in vivo neuronal tissues. Thus, the functional complex network inferred from activity patterns is a promising way to unravel the interplay between structure and functionality of neuronal systems. Here, we monitor the spontaneous self-sustained dynamics in neuronal cultures formed by interconnected aggregates of neurons (clusters). Dynamics is characterized by the fast activation of groups of clusters in sequences termed bursts. The analysis of the time delays between clusters' activations within the bursts allows the reconstruction of the directed functional connectivity of the network. We propose a method to statistically infer this connectivity and analyze the resulting properties of the associated complex networks. Surprisingly enough, in contrast to what has been reported for many biological networks, the clustered neuronal cultures present assortative mixing connectivity values, meaning that there is a preference for clusters to link to other clusters that share similar functional connectivity, as well as a rich-club core, which shapes a 'connectivity backbone' in the network. These results point out that the grouping of neurons and the assortative connectivity between clusters are intrinsic survival mechanisms of the culture.

Local polymer replacement for neuron patterning and in situ neurite guidance

By locally dispensing poly-L-lysine (PLL) molecules with a FluidFM onto a protein and cell resistant poly-L-lysine-graft-polyethylene glycol (PLL-g-PEG) coated substrate, the antifouling layer can be replaced under the tip aperture by the cell adhesive PLL. We used this approach for guiding the adhesion and axonal outgrowth of embryonic hippocampal neurons in situ. Cultures of hippocampal neurons were chosen because they mostly contain pyramidal neurons. The hippocampus is known to be involved in memory formation, and the stages of network development are well characterized, which is an asset to fundamental research. After fabricating diffuse PLL spots with 10-250 μm diameter, seeded hippocampal cells stick preferentially onto the spots migrating toward the spot center along the PLL gradient. Cell clusters were formed depending on the lateral size of the PLL dots and the density of seeded cells. In a second step of this protocol, the FluidFM is used to connect in situ the obtained clusters. The outgrowth of neurites, which are known to grow preferentially on adhesive substrates, is tailored by writing PLL lines. Antibody staining confirms that the outgrowing neurites are mostly axons, while the activity of the neurons is assessed by a calcium indicator, proving cell viability. The calcium signal intensity of two actively interconnected clusters showed to be correlated, corroborating the formation of vectored and polarized interconnections.

Change of laminin density stimulates axon branching via growth cone myosin II-mediated adhesion

Axon branching enables neurons to contact with multiple targets and respond to their microenvironment. Owing to its importance in neuronal network formation, axon branching has been studied extensively during the past decades. The chemical properties of extracellular matrices have been proposed to regulate axonal development, but the effects of their density changes on axon branching are not well understood. Here, we demonstrate that both the sharp broadening of substrate geometry and the sharp change of laminin density stimulate axon branching by using microcontact printing (μCP) and microfluidic printing (μFP) techniques. We also found that the change of axon branching stimulated by laminin density depends on myosin II activity. The change of laminin density induces asymmetric extensions of filopodia on the growth cone, which is the precondition for axon branching. These previously unknown mechanisms of change of laminin density-stimulated axon branching may explain how the extracellular matrices regulate axon branching in vivo and facilitate the establishment of neuronal networks in vitro.

Galvanotactic control of collective cell migration in epithelial monolayers

Many normal and pathological biological processes involve the migration of epithelial cell sheets. This arises from complex emergent behaviour resulting from the interplay between cellular signalling networks and the forces that physically couple the cells. Here, we demonstrate that collective migration of an epithelium can be interactively guided by applying electric fields that bias the underlying signalling networks. We show that complex, spatiotemporal cues are locally interpreted by the epithelium, resulting in rapid, coordinated responses such as a collective U-turn, divergent migration, and unchecked migration against an obstacle. We observed that the degree of external control depends on the size and shape of the cell population, and on the existence of physical coupling between cells. Together, our results offer design and engineering principles for the rational manipulation of the collective behaviour and material properties of a tissue.

Precise control of cell adhesion by combination of surface chemistry and soft lithography

The adhesion of cells on an extracellular matrix (ECM) (in vivo) or the surfaces of materials (in vitro) is a prerequisite for most cells to survive. The rapid growth of nano/microfabrication and biomaterial technologies has provided new materials with excellent surfaces with specific, desirable biological interactions with their surroundings. On one hand, the chemical and physical properties of material surfaces exert an extensive influence on cell adhesion, proliferation, migration, and differentiation. On the other hand, material surfaces are useful for fundamental cell biology research and tissue engineering. In this Review, an overview will be given of the chemical and physical properties of newly developed material surfaces and their biological effects, as well as soft lithographic techniques and their applications in cell biology research. Recent advances in the manipulation of cell adhesion by the combination of surface chemistry and soft lithography will also be highlighted.

Double spiral microchannel for label-free tumor cell separation and enrichment

This work reports on a passive double spiral microfluidic device allowing rapid and label-free tumor cell separation and enrichment from diluted peripheral whole blood, by exploiting the size-dependent hydrodynamic forces. A numerical model is developed to simulate the Dean flow inside the curved geometry and to track the particle/cell trajectories, which is validated against the experimental observations and serves as a theoretical foundation for optimizing the operating conditions. Results from separating tumor cells (MCF-7 and Hela) spiked into whole blood indicate that 92.28% of blood cells and 96.77% of tumor cells are collected at the inner and the middle outlet, respectively, with 88.5% tumor recovery rate at a throughput of 3.33 × 10(7) cells min(-1). We expect that this label-free microfluidic platform, driven by purely hydrodynamic forces, would have an impact on fundamental and clinical studies of circulating tumor cells.

Surface coating as a key parameter in engineering neuronal network structures in vitro

By quantitatively comparing a variety of macromolecular surface coating agents, we discovered that surface coating strongly modulates the adhesion and morphogenesis of primary hippocampal neurons and serves as a switch of somata clustering and neurite fasciculation in vitro. The kinetics of neuronal adhesion on poly-lysine-coated surfaces is much faster than that on laminin and Matrigel-coated surfaces, and the distribution of adhesion is more homogenous on poly-lysine. Matrigel and laminin, on the other hand, facilitate neuritogenesis more than poly-lysine does. Eventually, on Matrigel-coated surfaces of self-assembled monolayers, neurons tend to undergo somata clustering and neurite fasciculation. By replacing coating proteins with cerebral astrocytes, and patterning neurons on astrocytes through self-assembled monolayers, microfluidics and micro-contact printing, we found that astrocyte promotes soma adhesion and astrocyte processes guide neurites. There, astrocytes could be a versatile substrate in engineering neuronal networks in vitro. Besides, quantitative measurements of cellular responses on various coatings would be valuable information for the neurobiology community in the choice of the most appropriate coating strategy.