FRET imaging and in silico simulation: analysis of the signaling network of nerve growth factor-induced neuritogenesis

Establishing neuronal polarity: microtubule regulation during neurite initiation

The initiation of nascent projections, or neurites, from the neuronal cell body is the first stage in the formation of axons and dendrites, and thus a critical step in the establishment of neuronal architecture and nervous system development. Neurite formation relies on the polarized remodelling of microtubules, which dynamically direct and reinforce cell shape, and provide tracks for cargo transport and force generation. Within neurons, microtubule behaviour and structure are tightly controlled by an array of regulatory factors. Although microtubule regulation in the later stages of axon development is relatively well understood, how microtubules are regulated during neurite initiation is rarely examined. Here, we discuss how factors that direct microtubule growth, remodelling, stability and positioning influence neurite formation. In addition, we consider microtubule organization by the centrosome and modulation by the actin and intermediate filament networks to provide an up-to-date picture of this vital stage in neuronal development.

Two New FRET Imaging Measures: Linearly Proportional to and Highly Contrasting the Fraction of Active Molecules

We developed two new FRET imaging measures for intramolecular FRET biosensors, called linearly proportional (LP) and highly contrasting (HC) measures, which can be easily calculated by the fluorescence intensities of donor and acceptor as a ratio between their weighted sums. As an alternative to the conventional ratiometric measure, which non-linearly depends on the fraction of active molecule, we first developed the LP measure, which is linearly proportional to the fraction of active molecules. The LP measure inherently unmixes bleed-through signals and is robust against fluorescence noise. By extending the LP measure, we furthermore designed the HC measure, which provides highly contrasting images of the molecular activity, more than the ratiometric measure. In addition to their advantages, these measures are insensitive to the biosensor expression level, which is a fundamental property of the ratiometric measure. Using artificial data and FRET imaging data, we showed that the LP measure effectively represents the fraction of active molecules and that the HC measure improves visual interpretability by providing high contrast images of molecular activity. Therefore, the LP and HC measures allow us to gain more quantitative and qualitative insights from FRET imaging than the ratiometric measure.

Mechanism for neurotropic action of vorinostat, a pan histone deacetylase inhibitor

In this study we investigated the neurotrophic actions of vorinostat (suberoylanilide hydroxamic acid, SAHA), a class I and class II HDAC inhibitor, on the differentiation of Neuroscreen-1 (NS-1) cells. NS-1 cell is a subclone of the rat pheochromocytoma cell line (PC 12). Vorinostat independently induced neurite outgrowth in NS-1 cells. The NS-1 cells were further interrogated for the effects of vorinostat on intracellular neurotrophin signaling pathways, to understand its mechanism of neurotrophic action. Selective inhibitors of MEK1/2 (PD98059 and U0126), phosphoinositide 3-kinase (PI3K) (LY294002) and tyrosine kinase A (TrkA) (GW441756) were employed for these interrogations. Our results suggest that neurite outgrowth mediated by both nerve growth factor (NGF), an intrinsic neurotrophin, and vorinostat were blocked by the inhibitors of MEK1/2 & PI3K. Vorinostat induced phosphorylation of ERK1/2 occurs at 2h post treatment. Phosphorylation of ERK was abolished in presence of U0126, further confirming the role of ERK pathway in vorinostat-induced differentiation of NS-1 cells. Vorinostat-induced neurite outgrowth also involves the activation of upstream extracellular kinase TrkA, as both vorinostat mediated neurite outgrowth and activation of ERK were attenuated in presence of the TrkA inhibitor, GW441756. Vorinostat also stimulated hyperacetylation of α-tubulin and histones H3/H4 in NS-1 cells. The results suggest that vorinostat exerts a positive effect on the neuritogenesis via activation of MEK1/2 & PI3K pathways involving an upstream kinase, TrkA. Bioactive small molecules with neurotrophic and neuritogenic actions, like vorinostat identified in the present study, hold great promise as therapeutic agents for treatment of neurodegenerative diseases and neuronal injuries by virtue of their ability to stimulate neuritic outgrowth.

Cytoskeletal and signaling mechanisms of neurite formation

The formation of a neurite, the basis for axons and dendrites, begins with the concerted accumulation and organization of actin and microtubules. Whereas much is known about the proteins that play a role in these processes, because they perform similar functions in axon branching and filopodia formation, much remains to be discovered concerning the interaction of these individual cytoskeletal regulators during neurite formation. Here, we review the literature regarding various models of filopodial formation and the way in which proteins that control actin organization and polymerization induce neurite formation. Although several different regulators of actin polymerization are involved in neurite initiation, redundancy occurs between these regulators, as the effects of the loss of a single regulator can be mitigated by the addition of neurite-promoting substrates and proteins. Similar to actin dynamics, both microtubule stabilizing and destabilizing proteins play a role in neurite initiation. Furthermore, interactions between the actin and microtubule cytoskeleton are required for neurite formation. Several lines of evidence indicate that the interactions between these two components of the cytoskeleton are needed for force generation and for the localization of microtubules at sites of nascent neurites. The general theme that emerges is the existence of several central regulatory pathways on which extracellular cues converge to control and organize both actin and microtubules to induce the formation of neurites.

Optogenetic reporters: Fluorescent protein-based genetically encoded indicators of signaling and metabolism in the brain

Fluorescent protein technology has evolved to include genetically encoded biosensors that can monitor levels of ions, metabolites, and enzyme activities as well as protein conformation and even membrane voltage. They are well suited to live-cell microscopy and quantitative analysis, and they can be used in multiple imaging modes, including one- or two-photon fluorescence intensity or lifetime microscopy. Although not nearly complete, there now exists a substantial set of genetically encoded reporters that can be used to monitor many aspects of neuronal and glial biology, and these biosensors can be used to visualize synaptic transmission and activity-dependent signaling in vitro and in vivo. In this review, we present an overview of design strategies for engineering biosensors, including sensor designs using circularly permuted fluorescent proteins and using fluorescence resonance energy transfer between fluorescent proteins. We also provide examples of indicators that sense small ions (e.g., pH, chloride, zinc), metabolites (e.g., glutamate, glucose, ATP, cAMP, lipid metabolites), signaling pathways (e.g., G protein-coupled receptors, Rho GTPases), enzyme activities (e.g., protein kinase A, caspases), and reactive species. We focus on examples where these genetically encoded indicators have been applied to brain-related studies and used with live-cell fluorescence microscopy.

The design of Förster (fluorescence) resonance energy transfer (FRET)-based molecular sensors for Ran GTPase

The application of FRET-based molecular biosensors provided confirmation of the central model of Ran GTPase function and led to important new insights into its physiological role. In many fields of cell biology, methods employing FRET are a standard approach that is becoming increasingly accessible due to advances in instrumentation and available fluorophores. However, the optimal design of a FRET sensor remains to be the cornerstone of any successful FRET application. Utilizing the recent literature on FRET applications and our studies on Ran, we outline the basic considerations involved in designing molecular FRET sensors. We point to several broadly applicable principles that were used in many different FRET sensors that can detect a wide range of molecular events. Using the FRET sensors for Ran that we created as examples, we then focus on the practical aspects of FRET assays. We describe the preparation of a bipartite FRET sensor consisting of ECFP-Ran and EYFP-importin beta and its validation as a reporter for FRET-based high throughput screening in small molecule libraries. Finally, we review the design and optimization of monomolecular FRET sensors that monitor the RanGTP-RanBP1 interaction, and of sensors detecting the RanGTP-regulated importin beta cargo release.