AxonQuant: A Microfluidic Chamber Culture-Coupled Algorithm That Allows High-Throughput Quantification of Axonal Damage

A Microfluidic Cell Co-Culture Chip for the Monitoring of Interactions between Macrophages and Fibroblasts

Macrophages and fibroblasts are two types of important cells in wound healing. The development of novel platforms for studying the interrelationship between these two cells is crucial for the exploration of wound-healing mechanisms and drug development. In this study, a microfluidic chip composed of two layers was designed for the co-culturing of these two cells. An air valve was employed to isolate fibroblasts to simulate the wound-healing microenvironment. The confluence rate of fibroblasts in the co-culture system with different macrophages was explored to reflect the role of different macrophages in wound healing. It was demonstrated that M2-type macrophages could promote the activation and migration of fibroblasts and it can be inferred that they could promote the wound-healing process. The proposed microfluidic co-culture system was designed for non-contact cell-cell interactions, which has potential significance for the study of cell-cell interactions in biological processes such as wound healing, tumor microenvironment, and embryonic development.

Deep Learning to Decipher the Progression and Morphology of Axonal Degeneration

Axonal degeneration (AxD) is a pathological hallmark of many neurodegenerative diseases. Deciphering the morphological patterns of AxD will help to understand the underlying mechanisms and develop effective therapies. Here, we evaluated the progression of AxD in cortical neurons using a novel microfluidic device together with a deep learning tool that we developed for the enhanced-throughput analysis of AxD on microscopic images. The trained convolutional neural network (CNN) sensitively and specifically segmented the features of AxD including axons, axonal swellings, and axonal fragments. Its performance exceeded that of the human evaluators. In an in vitro model of AxD in hemorrhagic stroke induced by the hemolysis product hemin, we detected a time-dependent degeneration of axons leading to a decrease in axon area, while axonal swelling and fragment areas increased. Axonal swellings preceded axon fragmentation, suggesting that swellings may be reliable predictors of AxD. Using a recurrent neural network (RNN), we identified four morphological patterns of AxD (granular, retraction, swelling, and transport degeneration). These findings indicate a morphological heterogeneity of AxD in hemorrhagic stroke. Our EntireAxon platform enables the systematic analysis of axons and AxD in time-lapse microscopy and unravels a so-far unknown intricacy in which AxD can occur in a disease context.

A Microfluidic Culture Platform to Assess Axon Degeneration

The field of microfluidics allows for the precise spatial manipulation of small amounts of fluids. Within microstructures, laminar flow of fluids can be exploited to control the diffusion of small molecules, creating desired microenvironments for cells. Cellular neuroscience has benefited greatly from devices designed to fluidically isolate cell bodies and axons. Microfluidic devices specialized for neuron compartmentalization are made of polydimethylsiloxane (PDMS) which is gas permeable, is compatible with fluorescence microscopy, and has low cost. These devices are commonly used to study signals initiated exclusively on axons, somatodendritic compartments, or even single synapses. We have also found that microfluidic devices allow for rapid, reproducible interrogation of axon degeneration. Here, we describe the methodology for assessing axonal degeneration in microfluidic devices. We describe several use cases, including enucleation (removal of cell bodies) and trophic deprivation to investigate axon degeneration in pathological and developmental scenarios, respectively.

A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures: Two image analytic approaches using adaptive thresholds or machine learning

BACKGROUND

Assessments of axonal outgrowth and dendritic development are essential readouts in many in vitro models in the field of neuroscience. Available analysis software is based on the assessment of fixed immunolabelled tissue samples, making it impossible to follow the dynamic development of neurite outgrowth. Thus, automated algorithms that efficiently analyse brightfield images, such as those obtained during time-lapse microscopy, are needed.

NEW METHOD

We developed and validated algorithms to quantitatively assess neurite outgrowth from living and unstained spinal cord slice cultures (SCSCs) and dorsal root ganglion cultures (DRGCs) based on an adaptive thresholding approach called NeuriteSegmantation. We used a machine learning approach to evaluate dendritic development from dissociate neuron cultures.

RESULTS

NeuriteSegmentation successfully recognized axons in brightfield images of SCSCs and DRGCs. The temporal pattern of axonal growth was successfully assessed. In dissociate neuron cultures the total number of cells and their outgrowth of dendrites were successfully assessed using machine learning.

COMPARISON WITH EXISTING METHODS

The methods were positively correlated and were more time-saving than manual counts, having performing times varying from 0.5-2 min. In addition, NeuriteSegmentation was compared to NeuriteJ®, that uses global thresholding, being more reliable in recognizing axons in areas of intense background.

CONCLUSION

The developed image analysis methods were more time-saving and user-independent than established approaches. Moreover, by using adaptive thresholding, we could assess images with large variations in background intensity. These tools may prove valuable in the quantitative analysis of axonal and dendritic outgrowth from numerous in vitro models used in neuroscience.

Compartmentalized Microfluidic Platforms: The Unrivaled Breakthrough of In Vitro Tools for Neurobiological Research

Microfluidic technology has become a valuable tool to the scientific community, allowing researchers to study fine cellular mechanisms with higher variable control compared with conventional systems. It has evolved tremendously, and its applicability and flexibility made its usage grow exponentially and transversely to several research fields. This has been particularly noticeable in neuroscience research, where microfluidic platforms made it possible to address specific questions extending from axonal guidance, synapse formation, or axonal transport to the development of 3D models of the CNS to allow pharmacological testing and drug screening. Furthermore, the continuous upgrade of microfluidic platforms has allowed a deeper study of the communication occurring between different neuronal and glial cells or between neurons and other peripheral tissues, both in physiological and pathological conditions. Importantly, the evolution of microfluidic technology has always been accompanied by the development of new computational tools addressing data acquisition, analysis, and modeling.

An on-chip model for investigating the interaction between neurons and cancer cells

Emerging evidence suggests that there is extensive interaction between neurons and cancer cells. However, few model systems have been developed to investigate nerve-cancer cell interaction in vitro. Herein, a high-throughput microfluidic compartmentalized chip is developed to examine the interaction between neurons and cancer cells. The nerve bundles appear to provide a biophysical support for cancer cells and guide their directional migration. The cancers that have high levels of perineural invasion in clinical observations exhibit greater migration along neurites in the on-chip model. The on-chip model allows the screening of compounds which inhibit cancer cell migration along neurites in vitro. The interruption of neurites, the pharmacological blockade of nerve-cancer signaling, effectively attenuates the migration of cancer cells along neurites. This on-chip model provides a useful platform to investigate the dynamic interaction between cancer cells and neurons and can dramatically broaden the chemical space in screening neuron-related drugs for cancers.

A new method for quantifying mitochondrial axonal transport

Axonal transport of mitochondria is critical for neuronal survival and function. Automatically quantifying and analyzing mitochondrial movement in a large quantity remain challenging. Here, we report an efficient method for imaging and quantifying axonal mitochondrial transport using microfluidic-chamber-cultured neurons together with a newly developed analysis package named "MitoQuant". This tool-kit consists of an automated program for tracking mitochondrial movement inside live neuronal axons and a transient-velocity analysis program for analyzing dynamic movement patterns of mitochondria. Using this method, we examined axonal mitochondrial movement both in cultured mammalian neurons and in motor neuron axons of Drosophila in vivo. In 3 different paradigms (temperature changes, drug treatment and genetic manipulation) that affect mitochondria, we have shown that this new method is highly efficient and sensitive for detecting changes in mitochondrial movement. The method significantly enhanced our ability to quantitatively analyze axonal mitochondrial movement and allowed us to detect dynamic changes in axonal mitochondrial transport that were not detected by traditional kymographic analyses.

Quantitative and semi-quantitative measurements of axonal degeneration in tissue and primary neuron cultures

BACKGROUND

Axon viability is critical for maintaining neural connectivity, which is central to neural functionality. Many neurodegenerative diseases (e.g., Parkinson's disease (PD) and Alzheimer's disease) appear to involve extensive axonal degeneration that often precedes somatic loss in affected neural populations. Axonal degeneration involves a number of intracellular pathways and characteristic changes in axon morphology (i.e., swelling, fragmentation, and loss).

NEW METHOD

We describe a relatively simple set of methods to quantify the axonal degeneration using the 6-hydroxydopamine neurotoxin model of PD in rats and a colchicine-induced model in primary rat neurons. Specifically, approaches are described that use the spaceballs stereological probe for tissue sections and petrimetrics stereological probe for cultured neurons, and image analysis techniques in both tissue sections and cultured neurons.

RESULTS

These methods provide a mechanism for obtaining quantitative and semi-quantitative data to track the extent of axonal degeneration and may prove useful as outcome measures in studies aimed at preventing or slowing axonal degeneration in disease models.

COMPARISON WITH EXISTING METHODS

Existing methods of quantification of axonal degeneration use densitometry and manual counts of axonal projections, but they do not utilize the random, unbiased systematic sampling approaches that are characteristic of stereological methods. The ImageJ thresholding analyses described here provide a descriptive method for quantifying the state of axonal degeneration.

CONCLUSIONS

These methods provide an efficient and effective means to quantify the extent and state of axonal degeneration in animal tissue and cultured neurons and can be used in other models for the same purposes.

An integrated microfluidic device for screening the effective concentration of locally applied tacrolimus for peripheral nerve regeneration

The effectiveness of tacrolimus (FK506) for the promotion of nerve regeneration is known. However, at present, due to the fact that systemic application may lead to opportunistic infections and tumors, and that the treatment of peripheral nerve injury with systemic immunosuppression is not generally accepted, FK506 has not been widely used for the treatment of simple or peripheral nerve injury. In this study, a pyramid-shaped microfluidic device was designed and fabricated that was able to analyze the effective concentration of locally applied FK506. After testing the effectiveness of the microfluidic device by measuring the fluorescence intensity of fluorescein isothiocyanate-dextran, rat Schwann cells (SCs) were loaded into the device and cultured for 9 days in the presence of different concentrations of FK506. SC proliferation in the presence of FK506 was concentration-dependent between 0 and 2.5±0.003 ng/ml. The proliferation rate reached a maximum at 1.786±0.014 ng/ml, which was statistically significantly different from the proliferation rate at lower FK506 concentrations. There was no statistically significant difference in the proliferation rate between the 1.786 ng/ml group and groups of higher FK506 concentrations. Furthermore, the SCs in the microfluidic device and a 96-well plate continued to proliferate as the culture time increased. No statistically significant differences were identified between the microfluidic device and a 96-well plate with regard to the proliferation rates in each corresponding group. The results obtained in this study demonstrated that the microfluidic device can be used as an excellent platform for the study of drug concentration at the cellular level, and the effective FK506 concentration for local application is 1.786±0.014 ng/ml.

An ALS-mutant TDP-43 neurotoxic peptide adopts an anti-parallel β-structure and induces TDP-43 redistribution

TDP-43 proteinopathies are clinically and genetically heterogeneous diseases that had been considered distinct from classical amyloid diseases. Here, we provide evidence for the structural similarity between TDP-43 peptides and other amyloid proteins. Atomic force microscopy and electron microscopy examination of peptides spanning a previously defined amyloidogenic fragment revealed a minimal core region that forms amyloid fibrils similar to the TDP-43 fibrils detected in FTLD-TDP brain tissues. An ALS-mutant A315E amyloidogenic TDP-43 peptide is capable of cross-seeding other TDP-43 peptides and an amyloid-β peptide. Sequential Nuclear Overhauser Effects and double-quantum-filtered correlation spectroscopy in nuclear magnetic resonance (NMR) analyses of the A315E-mutant TDP-43 peptide indicate that it adopts an anti-parallel β conformation. When added to cell cultures, the amyloidogenic TDP-43 peptides induce TDP-43 redistribution from the nucleus to the cytoplasm. Neuronal cultures in compartmentalized microfluidic-chambers demonstrate that the TDP-43 peptides can be taken up by axons and induce axonotoxicity and neuronal death, thus recapitulating key neuropathological features of TDP-43 proteinopathies. Importantly, a single amino acid change in the amyloidogenic TDP-43 peptide that disrupts fibril formation also eliminates neurotoxicity, supporting that amyloidogenesis is critical for TDP-43 neurotoxicity.