Cellular patterns in the inner retina of adult zebrafish: quantitative analyses and a computational model of their formation

Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina

The retina is exquisitely patterned, with neuronal somata positioned at regular intervals to completely sample the visual field. Here, we show that phosphatase and tensin homolog (Pten) controls starburst amacrine cell spacing by modulating vesicular trafficking of cell adhesion molecules and Wnt proteins. Single-cell transcriptomics and double-mutant analyses revealed that Pten and Down syndrome cell adhesion molecule Dscam) are co-expressed and function additively to pattern starburst amacrine cell mosaics. Mechanistically, Pten loss accelerates the endocytic trafficking of DSCAM, FAT3, and MEGF10 off the cell membrane and into endocytic vesicles in amacrine cells. Accordingly, the vesicular proteome, a molecular signature of the cell of origin, is enriched in exocytosis, vesicle-mediated transport, and receptor internalization proteins in Pten conditional knockout (PtencKO) retinas. Wnt signaling molecules are also enriched in PtencKO retinal vesicles, and the genetic or pharmacological disruption of Wnt signaling phenocopies amacrine cell patterning defects. Pten thus controls vesicular trafficking of cell adhesion and signaling molecules to establish retinal amacrine cell mosaics.

Dynamic functional and structural remodeling during retinal regeneration in zebrafish

Introduction

Zebrafish regenerate their retinas following damage, resulting in restoration of visual function. Here we evaluate recovery of retinal function through qualitative and quantitative analysis of the electroretinogram (ERG) over time following retinal damage, in correlation to histological features of regenerated retinal tissue.

Methods

Retinas of adult zebrafish were lesioned by intravitreal injection of 10 μM (extensive lesion; destroys all neurons) or 2 μM (selective lesion; spares photoreceptors) ouabain. Unlesioned contralateral retinas served as controls. Function of retinal circuitry was analyzed at selected timepoints using ERG recordings from live zebrafish, and whole eyes were processed for histological analyses immediately thereafter.

Results

Qualitative and quantitative assessment of waveforms during retinal regeneration revealed dynamic changes that were heterogeneous on an individual level within each sampling time, but still followed common waveform recovery patterns on a per-fish and population-level basis. Early in the regeneration period (13-30 days post injury; DPI), for both lesion types, b-waves were essentially not detected, and unmasked increased apparent amplitudes, implicit times, and half-widths of a-waves (vs. controls). In control recordings, d-waves were not obviously detected, but apparent d-waves (OFF-bipolar responses) from regenerating retinas of several fish became prominent by 30DPI and dominated the post-photoreceptor response (PPR). Beyond 45DPI, b-waves became detectable, and the ratio of apparent d- to b-wave contributions progressively shifted with most, but not all, fish displaying a b-wave dominated PPR. At the latest timepoints (extensive, 90DPI; selective, 80DPI), recordings with measurable b-waves approached a normal waveform (implicit times and half-widths), but amplitudes were not restored to control levels. Histological analyses of the retinas from which ERGs were recorded showed that as regeneration progressed, PKCa + ON-bipolar terminals and parvalbumin + amacrine cell processes became more stereotypically positioned within the deep sublaminae of the INL over recovery time after each lesion type, consistent with the shift in PPR seen in the ERG recordings.

Discussion

Taken together, these data suggest that photoreceptor-OFF-bipolar component/connectivity may functionally recover and mature earlier during regeneration compared to the photoreceptor-ON-bipolar component, though the timeframe in which such recovery happens is heterogeneous on a per-fish basis. Collectively our studies suggest gradual restoration of ON-bipolar functional circuitry during retinal regeneration.

Modeling binary and graded cone cell fate patterning in the mouse retina

Nervous systems are incredibly diverse, with myriad neuronal subtypes defined by gene expression. How binary and graded fate characteristics are patterned across tissues is poorly understood. Expression of opsin photopigments in the cone photoreceptors of the mouse retina provides an excellent model to address this question. Individual cones express S-opsin only, M-opsin only, or both S-opsin and M-opsin. These cell populations are patterned along the dorsal-ventral axis, with greater M-opsin expression in the dorsal region and greater S-opsin expression in the ventral region. Thyroid hormone signaling plays a critical role in activating M-opsin and repressing S-opsin. Here, we developed an image analysis approach to identify individual cone cells and evaluate their opsin expression from immunofluorescence imaging tiles spanning roughly 6 mm along the D-V axis of the mouse retina. From analyzing the opsin expression of ~250,000 cells, we found that cones make a binary decision between S-opsin only and co-expression competent fates. Co-expression competent cells express graded levels of S- and M-opsins, depending nonlinearly on their position in the dorsal-ventral axis. M- and S-opsin expression display differential, inverse patterns. Using these single-cell data, we developed a quantitative, probabilistic model of cone cell decisions in the retinal tissue based on thyroid hormone signaling activity. The model recovers the probability distribution for cone fate patterning in the mouse retina and describes a minimal set of interactions that are necessary to reproduce the observed cell fates. Our study provides a paradigm describing how differential responses to regulatory inputs generate complex patterns of binary and graded cell fates.

The development of a cell in a mammalian tissue is governed by a complex regulatory network that responds to many input signals to give the cell a distinct identity, a process referred to as cell-fate specification. Some of these cell fates have binary on-or-off gene expression patterns, while others have graded gene expression that changes across the tissue. Differentiation of the photoreceptor cells that sense light in the mouse retina provides a good example of this process. Here, we explore how complex patterns of cell fates are specified in the mouse retina by building a computational model based on analysis of a large number of photoreceptor cells from microscopy images of whole retinas. We use the data and the model to study what exactly it means for a cell to have a binary or graded cell fate and how these cell fates can be distinguished from each other. Our study shows how tens-of-thousands of individual photoreceptor cells can be patterned across a complex tissue by a regulatory network, creating a different outcome depending upon the received inputs.

Müller glia: Stem cells for generation and regeneration of retinal neurons in teleost fish

Adult zebrafish generate new neurons in the brain and retina throughout life. Growth-related neurogenesis allows a vigorous regenerative response to damage, and fish can regenerate retinal neurons, including photoreceptors, and restore functional vision following photic, chemical, or mechanical destruction of the retina. Müller glial cells in fish function as radial-glial-like neural stem cells. During adult growth, Müller glial nuclei undergo sporadic, asymmetric, self-renewing mitotic divisions in the inner nuclear layer to generate a rod progenitor that migrates along the radial fiber of the Müller glia into the outer nuclear layer, proliferates, and differentiates exclusively into rod photoreceptors. When retinal neurons are destroyed, Müller glia in the immediate vicinity of the damage partially and transiently dedifferentiate, re-express retinal progenitor and stem cell markers, re-enter the cell cycle, undergo interkinetic nuclear migration (characteristic of neuroepithelial cells), and divide once in an asymmetric, self-renewing division to generate a retinal progenitor. This daughter cell proliferates rapidly to form a compact neurogenic cluster surrounding the Müller glia; these multipotent retinal progenitors then migrate along the radial fiber to the appropriate lamina to replace missing retinal neurons. Some aspects of the injury-response in fish Müller glia resemble gliosis as observed in mammals, and mammalian Müller glia exhibit some neurogenic properties, indicative of a latent ability to regenerate retinal neurons. Understanding the specific properties of fish Müller glia that facilitate their robust capacity to generate retinal neurons will inform and inspire new clinical approaches for treating blindness and visual loss with regenerative medicine.

Candidate molecular mechanisms for establishing cell identity in the developing retina

In the developing nervous system, individual neurons must occupy appropriate positions within circuits. This requires that these neurons recognize and form connections with specific pre- and postsynaptic partners. Cellular recognition is also required for the spacing of cell bodies and the arborization of dendrites, factors that determine the inputs onto a given neuron. These issues are particularly evident in the retina, where different types of neurons are evenly spaced relative to other cells of the same type. This establishes a reiterated columnar circuitry resembling the insect retina. Establishing these mosaic patterns requires that cells of a given type (homotypic cells) be able to sense their neighbors. Therefore, both synaptic specificity and mosaic spacing require cellular identifiers. In synaptic specificity, recognition often occurs between different types of cells in a pre- and postsynaptic pairing. In mosaic spacing, recognition is often occurring between different cells of the same type, orhomotypic self-recognition. Dendritic arborization can require recognition of different neurites of the same cell, or isoneuronal self-recognition. The retina is an extremely amenable system for studying the molecular identifiers that drive these various forms of recognition. The different neuronal types in the retina are well defined, and the genetic tools for marking cell types are increasingly available. In this review we will summarize retinal anatomy and describe cell types in the retina and how they are defined. We will then describe the requirements of a recognition code and discuss newly emerging candidate molecular mechanisms for recognition that may meet these requirements.

Ontogeny of cone photoreceptor mosaics in zebrafish

Cone photoreceptors in fish are typically arranged into a precise, reiterated pattern known as a "cone mosaic." Cone mosaic patterns can vary in different fish species and in response to changes in habitat, yet their function and the mechanisms of their development remain speculative. Zebrafish (Danio rerio) have four cone subtypes arranged into precise rows in the adult retina. Here we describe larval zebrafish cone patterns and investigate a previously unrecognized transition between larval and adult cone mosaic patterns. Cone positions were determined in transgenic zebrafish expressing green fluorescent protein (GFP) in their UV-sensitive cones, by the use of multiplex in situ hybridization labelling of various cone opsins. We developed a "mosaic metric" statistical tool to measure local cone order. We found that ratios of the various cone subtypes in larval and adult zebrafish were statistically different. The cone photoreceptors in larvae form a regular heterotypic mosaic array; i.e., the position of any one cone spectral subtype relative to the other cone subtypes is statistically different from random. However, the cone spectral subtypes in larval zebrafish are not arranged in continuous rows as in the adult. We used cell birth dating to show that the larval cone mosaic pattern remains as a distinct region within the adult retina and does not reorganize into the adult row pattern. In addition, the abundance of cone subtypes relative to other subtypes is different in this larval remnant compared with that of larvae or canonical adult zebrafish retina. These observations provide baseline data for understanding the development of cone mosaics via comparative analysis of larval and adult cone development in a model species.

A three-dimensional analysis of the development of the horizontal cell mosaic in the rat retina: implications for the mechanisms controlling pattern formation

The horizontal cells are known to form a mono-layered mosaic in the adult retina, but are scattered at different retinal depths in early development. To help clarifying when and which spatial constraints appear in the relative positioning of these cells, we have performed a quantitative analysis of the three-dimensional (3D) organization of the horizontal cell mosaic at different developmental stages in the postnatal rat retina. We first analyzed the two-dimensional (2D) distribution of the horizontal cell projections onto a plane parallel to the upper retinal surface in retinal flat-mounts, and thus to the future mature horizontal cell mosaic. We found that this 2D distribution was non random since postnatal day 1 (P1), and had a subsequent stepwise improvement in regularity. This preceded the alignment of cells in a single monolayer, which was observed on P6. We then computed true horizontal cell spacing in 3D, finding non-random 3D positioning already on P1. Simulation studies showed that this order might simply derive from the 2D order observed in the projections of the cells in flat-mount, combined with their limited spread in retinal depth. Throughout the period analyzed, the relative positions of horizontal cells are in good agreement with a minimal spacing rule in which the exclusion zone corresponds to the average size of the inner core of the cell dendritic tree estimated from P1 samples. These data indicate the existence of different phases in the process of horizontal cell 3D spatial ordering, supporting the view that multiple mechanisms are involved in the development of the horizontal cell mosaic.

Visual function in regenerating teleost retina following surgical lesioning

Regeneration of the teleost retina following surgical extirpation of 25% to 100% of the neural retina was investigated in goldfish (Carrasius auratus) and sunfish (Lepomis cyanellus). The retina will regenerate following removal of up to 95% of the neural retina, however complete extirpation prevented regeneration. Visual sensitivity was assessed by examining components of the electroretinogram (ERG) and the dorsal light reflex (DLR) during regeneration. B-wave amplitudes in the experimental eyes increased throughout the study and central connections were reestablished as indicated by the progressive improvement in the dorsal light reflex. The recovery of visual function was closely correlated with retinal regeneration. Visual recovery progressed more slowly than following complete cytotoxic destruction of the mature retina (Mensinger & Powers, 1999) because the surgery removed a large number of the pluripotent cell population and restricted the number and distribution of regenerating foci.

Neurogenesis in the fish retina

The retinas of teleost fish have long been of interest to developmental neurobiologists for their persistent plasticity during growth, life history changes, and response to injury. Because the vertebrate retina is a highly conserved tissue, the study of persistent plasticity in teleosts has provided insights into mechanisms for postembryonic retinal neurogenesis in mammals. In addition, in the past 10 years there has been an explosion in the use of teleost fish-zebrafish (Danio rerio) in particular-to understand the mechanisms of embryonic retinal neurogenesis in a model vertebrate with genetic resources. This review summarizes the key features of teleost retinal neurogenesis that make it a productive and interesting experimental system, and focuses on the contributions to our knowledge of retinal neurogenesis that uniquely required or significantly benefited from the use of a fish model system.

Spatial clustering analysis in neuroanatomy: applications of different approaches to motor nerve fiber distribution

Spatial organization of the nerve fibers in the peripheral nerves may be important for the studies of axonal regeneration, the degenerative nerve diseases and the construction of interfaces with peripheral nerves, such as nerve prostheses. Functional topography of motor axons related to the gastrocnemius muscle was revealed in the ventral spinal roots by retrograde tracing. Gastrocnemius muscles of adult rats were injected with the tracer Fluoro-Gold. After 3 days of survival the animals were sacrificed and their ventral roots were harvested, sectioned, and imaged on a fluorescence microscope. Maps of the traced fibers were automatically analyzed using a novel approach, local spatial clustering statistics, that tested for occurrences of clusters of motor fibers and visualized them. Thresholds indicating the presence of clustering at various scales of observation were computed based on series of Monte Carlo simulations of random spatial point patterns. Clusters were visualized by kernel interpolation. The approach was tested on simulated data and subsequently applied to the motor fiber maps in the ventral roots. Results revealed clustering of the motor fibers innervating the gastrocnemius muscle at the level of the L6 ventral spinal root. The analysis was validated using Voronoi tessellation and nearest neighbor analysis.

Cellular pattern formation during retinal regeneration: a role for homotypic control of cell fate acquisition

A dominant mechanism of cellular patterning in the growing fish retina is control of cell fate acquisition by negative feedback signals arising from differentiated cells. We tested the ability of a computational model of this pattern formation mechanism to simulate cellular patterns in regenerated goldfish retina. The model successfully simulated quantitative features of in vivo regenerated patterns, indicating that regenerating retina has access to and utilizes patterning mechanisms that are operational during normal growth. The atypical patterns of regenerated retina could arise in part from regenerative progenitors that, compared to normal growth progenitors, are less responsive to the feedback patterning signals.

Quantitative in vivo microscopy: the return from the 'omics'

The confluence of recent advances in microscopy instrumentation and image analysis, coupled with the widespread use of GFP-like proteins as reporters of gene expression, has opened the door to high-throughput in vivo studies that can provide the morphological and temporal context to the biochemical pathways regulating cell function. We are now able to quantify the concentration and three-dimensional distribution of multiple spectrally resolved GFP-tagged proteins. Using automatic segmentation and tracking we can then measure the dynamics of the processes in which these elements are involved. In this way, parallel studies are feasible where multiple cell colonies treated with drugs or gene expression repressors can be monitored and analyzed to study the dynamics of relevant biological processes.

Afferents and homotypic neighbors regulate horizontal cell morphology, connectivity, and retinal coverage

Horizontal cells are inhibitory interneurons with laterally oriented dendrites that overlap one another, contacting the pedicles of cone photoreceptors. Because of their regular spacing, the network of horizontal cells provides a uniform coverage of the retinal surface. The developmental processes establishing these network properties are undefined, but cell-intrinsic instructions and interactions with other cells have each been suggested to play a role. Here, we show that the intercellular spacing of horizontal cells is essentially independent of genetic background and is predicted by local density, suggesting that horizontal cell positioning is modulated by proximity to other horizontal cells. Dendritic field area compensates for this variation in intercellular spacing, maintaining constant dendritic coverage between strains. Functional dendritic overlap is achieved anatomically at the level of the pedicles, where horizontal cells interact with one another to establish their connectivity: the number of dendritic terminals contacting a pedicle changes, reciprocally, between neighboring horizontal cells during development based on their relative proximity to each pedicle. Cellular morphology is also shown to be regulated by the afferents themselves: afferent elimination before innervation does not alter dendritic field size nor stratification but compromises dendritic branching and prevents terminal formation. Afferent and homotypic interactions therefore generate the morphology, spacing, and connectivity of horizontal cells underlying their functional coverage of the retina.

Control of cellular pattern formation in the vertebrate inner retina by homotypic regulation of cell-fate decisions

The vertebrate retina is composed of cellular arrays that are nonrandom across two-dimensional space. The determinants of these nonrandom two-dimensional cellular patterns in the inner nuclear layer of the retina were investigated using empirical and computational modeling techniques. In normal and experimental models of goldfish retinal growth, the patterns of tyrosine hydroxylase- and serotonin-positive cells indicated that neither cell death nor lateral migration of differentiated cells were dominant mechanisms of cellular pattern formation. A computational model of cellular pattern formation that used a signaling mechanism arising from differentiated cells that inhibited homotypic cell-fate decisions generated accurate simulations of the empirically observed patterns in normal retina. This model also predicted the principal atypical cellular pattern characteristic, a transient cell-type-specific hyperplasia, which was empirically observed in the growing retina subsequent to selective ablation of differentiated retinal cells, either tyrosine hydroxylase positive or serotonin positive. The results support the hypothesis that inhibitory spatiotemporal regulation of homotypic cell-fate decisions is a dominant mechanistic determinant of nonrandom cellular patterns in the vertebrate retina.

Developmental improvement in the regularity and packing of mouse horizontal cells: implications for mechanisms underlying mosaic pattern formation

The present investigation has sought to determine whether the population of retinal horizontal cells undergoes an increase in the precision of its mosaic patterning during postnatal development, and if so, whether this increase is compatible with three different mechanistic accounts of retinal mosaic formation. Horizontal cells were labeled with antibodies to neurofilaments or calbindin at different developmental stages, and then visualized in retinal wholemounts. Multiple fields were sampled from each retina to determine horizontal cell density, while the X-Y coordinates of each cell in a field were determined. An estimate of total horizontal cell number was calculated for each retina, while the Voronoi domain regularity index and the packing factor were computed for each field. Two strains of mice showing a two-fold difference in the size of their horizontal cell population in maturity were sampled, C57BL/6J and A/J. Horizontal cell number in C57BL/6J was approximately twice that observed in A/J at all postnatal stages, with neither strain showing an effect of age on horizontal cell number. In both strains, however, the Voronoi domain regularity index and the packing factor were significantly lower at P-1 relative to later developmental stages. These results show that accounts of mosaic formation proposing the selective death of irregularly positioned cells, or the periodic occurrence of fate-determining events, are insufficient to establish the final patterning achieved by horizontal cells. Rather, they support the hypothesis that tangential dispersion enhances mosaic patterning during postnatal development.

Regularity and packing of the horizontal cell mosaic in different strains of mice

The present study describes the relationships between mosaic regularity, intercellular spacing, and packing of horizontal cells across a two-fold variation in horizontal cell density in four strains of mice. We have tested the prediction that mosaic patterning is held constant across variation in density following our recent demonstration that intercellular spacing declines as density increases, by further examination of that dataset: Nearest-neighbor and Voronoi-domain analyses were conducted on multiple fields of horizontal cells from each strain, from which their respective regularity indices were calculated. Autocorrelation analysis was performed on each field, from which the density recovery profile was generated, and effective radius and packing factor were calculated. The regularity indexes showed negative correlations with density rather than being held constant, suggesting that the strong negative correlation between intercellular spacing and density exceeded that required to produce a simple scaling of the mosaic. This was confirmed by the negative correlation between packing factor and density. These results demonstrate that the variation in the patterning present in the population of horizontal cells across these strains is a consequence of epigenetic mechanisms controlling intercellular spacing as a function of density.

Targeted effects of retinoic acid signaling upon photoreceptor development in zebrafish

Retinoic acid (RA) is a signaling molecule important for photoreceptor development in vertebrates. The purpose of this study was to examine the mechanisms of the effects of RA upon developing rod and cone photoreceptors in the embryonic zebrafish. Exposure to exogenous RA increased the number of photoreceptors expressing rod opsin and red cone opsin, and decreased the number of photoreceptors expressing the blue and UV cone opsins, suggesting targeted effects of RA on photoreceptor development. RA exposure also increased opsin expression in individual rods and red cones, but decreased opsin expression in individual blue and UV cones, as indicated by differences in the strength of opsin hybridization in identified photoreceptors. RA exposure did not, however, significantly alter quantitative measures of photoreceptor pattern in a manner expected for changes in photoreceptor fate. These observations collectively indicate that RA treatment does not affect photoreceptor fate, but rather differentially influences opsin transcription in determined photoreceptors. An enzyme involved in RA synthesis, RALDH2, was immunocytochemically localized to retinal progenitor cells and the retinal pigmented epithelium (RPE), suggesting the presence of RA in the vicinity of developing photoreceptors. However, expression of an RA response element-driven transgene was restricted to the RPE, retinal progenitors, and a small population of neurons in ventral retina, suggesting that the endogenous RA signaling system is spatially limited within the eye.

Responses of Müller glia to retinal injury in adult zebrafish

In an effort to identify the cellular events that enable neuronal regeneration in the vertebrate retina, the identity and characteristics of mitotic and apoptotic cells were examined in lesioned retinas of adult zebrafish. Following lesion a complex spatiotemporal pattern of mitosis was observed, including a delayed entry of Müller glia into the cell cycle. Characteristics of these proliferative Müller glia indicated they might serve as a stem/precursor cell of regenerated retina. The results suggested a model of retinal regeneration in which lesions are filled, in part, by a localized en place cytogenesis within intact retina surrounding the lesion site.