Self-organising aggregates of zebrafish retinal cells for investigating mechanisms of neural lamination

Emergent Tissue Shapes from the Regulatory Feedback between Morphogens and Cell Growth

Patterning and morphogenesis in multicellular organisms require precise dynamic coordination between cellular behaviors and mechano-chemical signals. However, the mechanisms underlying the pathways that coordinate and integrate these signals into emergent cellular behaviors and tissue shapes remain poorly understood. Here, we present a cell-centered agent-based mathematical approach to shed light on the feedback mechanisms underlying tissue growth and pattern formation. The model includes cell size dynamics governed by both intercellular diffusible morphogen concentrations and mechanical stress between cells to control their spatial organization, and does not require the use of any superimposed lattice, increasing its applicability and performance. The results show how the precise integration of the feedback loop between cellular behaviors and mechano-chemical signaling is essential for the regulation of shape and spatial patterns across the tissue scale. Furthermore, the regulation of cellular dynamics by patterning processes, such as Turing activator-inhibitor systems, can drive the formation of emergent stable tissue shapes, which, in turn, specify the domain for morphogen patterning-closing the self-regulated loop between tissue shape and morphogenetic signals. Overall, this study highlights the importance of the feedback loop between morphogen patterning and cellular behaviors in regulating tissue growth dynamics and stable shape formation. Moreover, this study establishes a framework for further experiments to understand the regulatory dynamics of whole-body development and regeneration using high spatiotemporal resolution models.

Self-Organization of the Retina during Eye Development, Retinal Regeneration In Vivo, and in Retinal 3D Organoids In Vitro

Self-organization is a process that ensures histogenesis of the eye retina. This highly intricate phenomenon is not sufficiently studied due to its biological complexity and genetic heterogeneity. The review aims to summarize the existing central theories and ideas for a better understanding of retinal self-organization, as well as to address various practical problems of retinal biomedicine. The phenomenon of self-organization is discussed in the spatiotemporal context and illustrated by key findings during vertebrate retina development in vivo and retinal regeneration in amphibians in situ. Described also are histotypic 3D structures obtained from the disaggregated retinal progenitor cells of birds and retinal 3D organoids derived from the mouse and human pluripotent stem cells. The review highlights integral parts of retinal development in these conditions. On the cellular level, these include competence, differentiation, proliferation, apoptosis, cooperative movements, and migration. On the physical level, the focus is on the mechanical properties of cell- and cell layer-derived forces and on the molecular level on factors responsible for gene regulation, such as transcription factors, signaling molecules, and epigenetic changes. Finally, the self-organization phenomenon is discussed as a basis for the production of retinal organoids, a promising model for a wide range of basic scientific and medical applications.

CytoCensus, mapping cell identity and division in tissues and organs using machine learning

A major challenge in cell and developmental biology is the automated identification and quantitation of cells in complex multilayered tissues. We developed CytoCensus: an easily deployed implementation of supervised machine learning that extends convenient 2D 'point-and-click' user training to 3D detection of cells in challenging datasets with ill-defined cell boundaries. In tests on such datasets, CytoCensus outperforms other freely available image analysis software in accuracy and speed of cell detection. We used CytoCensus to count stem cells and their progeny, and to quantify individual cell divisions from time-lapse movies of explanted Drosophila larval brains, comparing wild-type and mutant phenotypes. We further illustrate the general utility and future potential of CytoCensus by analysing the 3D organisation of multiple cell classes in Zebrafish retinal organoids and cell distributions in mouse embryos. CytoCensus opens the possibility of straightforward and robust automated analysis of developmental phenotypes in complex tissues.

A Guide to the Development of Human CorneaOrganoids from Induced Pluripotent Stem Cells in Culture

The cornea is the outermost transparent and refractive barrier surface of the eye necessary for vision. Development of the cornea involves the coordinated production of extracellular matrix, epithelial differentiation, and endothelial cell expansion to produce a highly transparent tissue. Here we describe the production of multilayered three-dimensional organoids from human-induced pluripotent stem cells. These organoids have the potential for multiple downstream applications which are currently unattainable using traditional in vitro techniques.

"Necessity Is the Mother of Invention" or Inexpensive, Reliable, and Reproducible Protocol for Generating Organoids

Organoids are three-dimensional (3D) cell cultures that replicate some of the key features of morphology, spatial architecture, and functions of a particular organ. Organoids can be generated from both adult and pluripotent stem cells (PSCs), and complex organoids can also be obtained by combining different types of cells, including differentiated cells. The ability of pluripotent cells to self-organize into organotypic structures containing several cell subtypes specific for a particular organ was used for creating organoids of the brain, eye, kidney, intestine, and other organs. Despite the advantages of using PSCs for obtaining organoids, an essential shortcoming that prevents their widespread use has been a low yield when they are obtained from a PSC monolayer culture and a large variation in size. This leads to great heterogeneity on further differentiation. In this article, we describe our own protocol for generating standardized organoids, with emphasis on a method for generating brain organoids, which allows scaling-up experiments and makes their cultivation less expensive and easier.

Disaggregation and Reaggregation of Zebrafish Retinal Cells for the Analysis of Neuronal Layering

The reaggregation of dissociated cells to form organotypic structures provides an in vitro system for the analysis of the cellular interactions and molecular mechanisms involved in the formation of tissue architecture. The retina, an outgrowth of the forebrain, is a precisely layered neural tissue, yet the mechanisms underlying layer formation are largely unexplored. Here we describe the protocol to dissociate, re-aggregate, and culture zebrafish retinal cells from a transgenic, Spectrum of Fates, line where all main cell types are labelled with a combination of fluorescent proteins driven by fate-specific promoters. These cells re-aggregate and self-organize in just 48 h in minimal culture conditions. We also describe how the patterning in these aggregates can be analyzed using isocontour profiling to compare whether different conditions affect their self-organization.

Differential Expression of Cholinergic System Components in Human Induced Pluripotent Stem Cells, Bone Marrow-Derived Multipotent Stromal Cells, and Induced Pluripotent Stem Cell-Derived Multipotent Stromal Cells

The components of the cholinergic system are evolutionary very old and conserved molecules that are expressed in typical spatiotemporal patterns. They are involved in signaling in the nervous system, whereas their functions in nonneuronal tissues are hardly understood. Stem cells present an attractive cellular system to address functional issues. This study therefore compared human induced pluripotent stem cells (iPSCs; from cord blood endothelial cells), mesenchymal stromal cells derived from iPSCs (iPSC-MSCs), and bone marrow-derived MSCs (BM-MSCs) from up to 33 different human donors with respect to gene expressions of components of the cholinergic system. The status of cells was identified and characterized by the detection of cell surface antigens using flow cytometry. Acetylcholinesterase expression in iPSCs declined during their differentiation into MSCs and was comparably low in BM-MSCs. Butyrylcholinesterase was present in iPSCs, increased upon transition from the three-dimensional embryoid body phase into monolayer culture, and declined upon further differentiation into iPSC-MSCs. In BM-MSCs a notable butyrylcholinesterase expression could be detected in only four donors, but was elusive in other patient-derived samples. Different nicotinic acetylcholine receptor subunits were preferentially expressed in iPSCs and during early differentiation into iPSC-MSCs, low expression was detected in iPS-MSCs and in BM-MSCs. The m2 and m3 variants of muscarinic acetylcholine receptors were detected in all stem cell populations. In BM-MSCs, these gene expressions varied between donors. Together, these data reveal the differential expression of cholinergic signaling system components in stem cells from specific sources and suggest the utility of our approach to establish informative biomarkers.

Neuronal Migration and Lamination in the Vertebrate Retina

In the retina, like in most other brain regions, developing neurons are arranged into distinct layers giving the mature tissue its stratified appearance. This process needs to be highly controlled and orchestrated, as neuronal layering defects lead to impaired retinal function. To achieve successful neuronal layering and lamination in the retina and beyond, three main developmental steps need to be executed: First, the correct type of neuron has to be generated at a precise developmental time. Second, as most retinal neurons are born away from the position at which they later function, newborn neurons have to move to their final layer within the developing tissue, a process also termed neuronal lamination. Third, these neurons need to connect to their correct synaptic partners. Here, we discuss neuronal migration and lamination in the vertebrate retina and summarize our knowledge on these aspects of retinal development. We give an overview of how lamination emerges and discuss the different modes of neuronal translocation that occur during retinogenesis and what we know about the cell biological machineries driving them. In addition, retinal mosaics and their importance for correct retinal function are examined. We close by stating the open questions and future directions in this exciting field.

Organoids: a Special Issue

Summary: This Editorial provides an overview of the entire contents of the Special Issue, highlighting some of the important findings and major themes therein.

Mechanisms of Müller glial cell morphogenesis

Müller Glia (MG), the radial glia cells of the retina, have spectacular morphologies subserving their enormous functional complexity. As early as 1892, the great neuroanatomist Santiago Ramon y Cajal studied the morphological development of MG, defining several steps in their morphogenesis [1,2]. However, the molecular cues controlling these developmental steps remain poorly understood. As MG have roles to play in every cellular and plexiform layer, this review discusses our current understanding on how MG morphology may be linked to their function, including the developmental mechanisms involved in MG patterning and morphogenesis. Uncovering the mechanisms governing glial morphogenesis, using transcriptomics and imaging, may provide shed new light on the pathophysiology and treatment of human neurological disorders.