Molecular mechanisms controlling vertebrate retinal patterning, neurogenesis, and cell fate specification

Timing neural development and regeneration

Regulation of neural progenitor temporal identity is critical to control the chronological order of cell birth and generation of cell diversity in the developing central nervous system (CNS). Single-cell RNA sequencing studies have identified transcriptionally distinct early and late temporal identity states in mammalian neural progenitors in multiple CNS regions. This review discusses recent advances in understanding the mechanisms underlying regulation of temporal identity in mammalian neural progenitors, the implications of these findings for glia-to-neuron reprogramming strategies, and their potential therapeutic applications. We highlight potential future directions of research, including integrating temporal identity specification with proneural factor overexpression to enhance reprogramming efficiency and broaden the repertoire of neuronal subtypes generated from reprogrammed mammalian glia.

Ontogeny of the spinal cord dorsal horn

The dorsal horn of the mammalian spinal cord is an exquisite example of form serving function. It is comprised of diverse neuronal populations stacked into laminae, each of which receives different circuit connections and plays specialized roles in behavior. An outstanding question is how this organization emerges during development from an apparently homogeneous pool of neural progenitors. Here, we found that dorsal neurons are diversified by time, with families of related cell types born as temporal cohorts, and by a spatial-molecular gradient that specifies the full array of individual cell types. Excitatory dorsal neurons then settle in a chronotopic arrangement that transforms their progressive birthdates into anatomical order. This establishes the dorsal horn laminae, as these neurons are also required for spatial organization of inhibitory neurons and sensory axons. This work reveals essential ontogenetic principles that shape dorsal progenitors into the diverse cell types and architecture that subserve sensorimotor behavior.

Generation of a Double Reporter mES Cell Line to Simultaneously Trace the Generation of Retinal Progenitors and Photoreceptors

Three-dimensional retinal culture systems help to understand eye development and the pathology of disorders. There is a need for reporter stem cell lines to allow in vitro studies on retinal progenitors and photoreceptors and their developmental dynamics or properties and to test therapeutic approaches. The isolation of pure progenitor populations or photoreceptor precursors may serve for drug, gene, and cell therapy development. Here, we generated a dual-reporter mouse embryonic stem cell line Crx-GFP;Rax-mCherry enabling the visualization or isolation of photoreceptors and retinal progenitors from retinal organoid settings. From day 4 organoids, we isolated mCherry-positive cells to assess their early retinal progenitor identity with proliferation tests as well as transcriptomic and proteomic profiling. The timing of eye field transcription factor expression at the transcriptomic and protein levels is in accordance with mouse retinogenesis. This new line will be helpful for rapidly investigating biological questions or testing therapeutics before using human induced pluripotent stem cells (iPSCs), which require a much longer time for retinal organoid formation.

A single-nucleus RNA sequencing atlas of the postnatal retina of the shark Scyliorhinus canicula

The retina, whose basic cellular structure is highly conserved across vertebrates, constitutes an accessible system for studying the central nervous system. In recent years, single-cell RNA sequencing studies have uncovered cellular diversity in the retina of a variety of species, providing new insights on retinal evolution and development. However, similar data in cartilaginous fishes, the sister group to all other extant jawed vertebrates, are still lacking. Here, we present a single-nucleus RNA sequencing atlas of the postnatal retina of the catshark Scyliorhinus canicula, consisting of the expression profiles for 17,438 individual cells from three female, juvenile catshark specimens. Unsupervised clustering revealed 22 distinct cell types comprising all major retinal cell classes, as well as retinal progenitor cells (whose presence reflects the persistence of proliferative activity in postnatal stages in sharks) and oligodendrocytes. Thus, our dataset serves as a foundation for further studies on the development and function of the catshark retina. Moreover, integration of our atlas with data from other species will allow for a better understanding of vertebrate retinal evolution.

Blind But Alive - Congenital Loss of atoh7 Disrupts the Visual System of Adult Zebrafish

Purpose

Vision is the predominant sense in most animal species. Loss of vision can be caused by a multitude of factors resulting in anatomic as well as behavioral changes. In mice and zebrafish, atoh7 mutants are completely blind as they fail to generate retinal ganglion cells (RGCs) during development. In contrast to mice, raising blind zebrafish to adulthood is challenging and this important model is currently missing in the field. Here, we report the phenotype of homozygous mutant adult zebrafish atoh7 mutants that have been raised using adjusted feeding and holding conditions.

Methods

The phenotype of adult mutants was characterized using classical histology and immunohistochemistry as well as optical coherence tomography. In addition, the optokinetic response was characterized.

Results

Adult atoh7 mutants display dark body pigmentation and significantly reduced body length. They fail to form RGCs, the resulting nerve fiber layer as well as the optic nerve, and consequently behave completely blindly. In contrast, increased amounts of other retinal neurons and Müller glia are formed. In addition, the optic tectum is anatomically reduced in size, presumably due to the missing retinal input.

Conclusions

Taken together, we provide a comprehensive characterization of a completely blind adult zebrafish mutant with focus on retinal and tectal morphology, as a useful model for glaucoma and optic nerve aplasia.

Genetic analysis of medaka fish illuminates conserved and divergent roles of Pax6 in vertebrate eye development

Landmark discovery of eye defects caused by Pax6 gene mutations in humans, rodents, and even fruit flies combined with Pax6 gene expression studies in various phyla, led to the master control gene hypothesis postulating that the gene is required almost universally for animal visual system development. However, this assumption has not been broadly tested in genetically trackable organisms such as vertebrates. Here, to determine the functional role of the fish orthologue of mammalian Pax6 in eye development we analyzed mutants in medaka Pax6.1 gene generated by genome editing. We found that transcription factors implicated in vertebrate lens development (Prox1a, MafB, c-Maf, FoxE3) failed to initiate expression in the presumptive lens tissue of Pax6.1 mutant fish resulting in aphakia, a phenotype observed previously in Pax6 mutant mice. Surprisingly, the overall differentiation potential of Pax6.1-deficient retinal progenitor cells (RPCs) is not severely compromised, and the only cell types affected by the absence of Pax6.1 transcription factor are retinal ganglion cells. This is in stark contrast to the situation in mice where the Pax6 gene is required cell-autonomously for the expansion of RPCs, and the differentiation of all retina cell types. Our results provide novel insight into the conserved and divergent roles of Pax6 gene orthologues in vertebrate eye development indicating that the lens-specific role is more evolutionarily conserved than the role in retina differentiation.

New pathways to neurogenesis: Insights from injury-induced retinal regeneration

The vertebrate retina is a tractable system for studying control of cell neurogenesis and cell fate specification. During embryonic development, retinal neurogenesis is under strict temporal regulation, with cell types generated in fixed but overlapping temporal intervals. The temporal sequence and relative numbers of retinal cell types generated during development are robust and show minimal experience-dependent variation. In many cold-blooded vertebrates, acute retinal injury induces a different form of neurogenesis, where Müller glia reprogram into retinal progenitor-like cells that selectively regenerate retinal neurons lost to injury. The extent to which the molecular mechanisms controlling developmental and injury-induced neurogenesis resemble one another has long been unclear. However, a recent study in zebrafish has shed new light on this question, using single-cell multiomic analysis to show that selective loss of different retinal cell types induces the formation of fate-restricted Müller glia-derived progenitors that differ both from one another and from progenitors in developing retina. Here, we discuss the broader implications of these findings, and their possible therapeutic relevance.

Embryonic development of a centralised brain in coleoid cephalopods

The last common ancestor of cephalopods and vertebrates lived about 580 million years ago, yet coleoid cephalopods, comprising squid, cuttlefish and octopus, have evolved an extraordinary behavioural repertoire that includes learned behaviour and tool utilization. These animals also developed innovative advanced defence mechanisms such as camouflage and ink release. They have evolved unique life cycles and possess the largest invertebrate nervous systems. Thus, studying coleoid cephalopods provides a unique opportunity to gain insights into the evolution and development of large centralised nervous systems. As non-model species, molecular and genetic tools are still limited. However, significant insights have already been gained to deconvolve embryonic brain development. Even though coleoid cephalopods possess a typical molluscan circumesophageal bauplan for their central nervous system, aspects of its development are reminiscent of processes observed in vertebrates as well, such as long-distance neuronal migration. This review provides an overview of embryonic coleoid cephalopod research focusing on the cellular and molecular aspects of neurogenesis, migration and patterning. Additionally, we summarize recent work on neural cell type diversity in embryonic and hatchling cephalopod brains. We conclude by highlighting gaps in our knowledge and routes for future research.

Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci

Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) during retinal development and evaluate the contribution of their genomic variation to rare eye diseases, for which pathogenic non-coding variants are emerging. Integration of bulk and single-cell retinal multi-omics data reveals 594 genes under potential cis-regulatory control of UCNEs, of which 45 are implicated in rare eye disease. Mining of candidate cis-regulatory UCNEs in WGS data derived from the rare eye disease cohort of Genomics England reveals 178 ultrarare variants within 84 UCNEs associated with 29 disease genes. Overall, we provide a comprehensive annotation of ultraconserved non-coding regions acting as cCREs during retinal development which can be targets of non-coding variation underlying rare eye diseases.

Expression patterns of CYP26A1, FGF8, CDKN1A, and NPVF in the developing rhesus monkey retina

The fovea centralis (fovea) is a specialized region of the primate retina that plays crucial roles in high-resolution visual acuity and color perception. The fovea is characterized by a high density of cone photoreceptors and no rods, and unique anatomical properties that contribute to its remarkable visual capabilities. Early histological analyses identified some of the key events that contribute to foveal development, but the mechanisms that direct the specification of this area are not understood. Recently, the expression of the retinoic acid-metabolizing enzyme CYP26A1 has become a hallmark of some of the retinal specializations found in vertebrates, including the primate fovea and the high-acuity area in avian species. In chickens, the retinoic acid pathway regulates the expression of FGF8 to then direct the development of a rod-free area. Similarly, high levels of CYP26A1, CDKN1A, and NPVF expression have been observed in the primate macula using transcriptomic approaches. However, which retinal cells express these genes and their expression dynamics in the developing primate eye remain unknown. Here, we systematically characterize the expression patterns of CYP26A1, FGF8, CDKN1A, and NPVF during the development of the rhesus monkey retina, from early stages of development in the first trimester until the third trimester (near term). Our data suggest that some of the markers previously proposed to be fovea-specific are not enriched in the progenitors of the rhesus monkey fovea. In contrast, CYP26A1 is expressed at high levels in the progenitors of the fovea, while it localizes in a subpopulation of macular Müller glia cells later in development. Together these data provide invaluable insights into the expression dynamics of several molecules in the nonhuman primate retina and highlight the developmental advancement of the foveal region.