Conservation as well as divergence in Mcidas function underlies the differentiation of multiciliated cells in vertebrates

(Zebra)fishing for nephrogenesis genes

Kidney disease is a devastating condition affecting millions of people worldwide, where over 100,000 patients in the United States alone remain waiting for a lifesaving organ transplant. Concomitant with a surge in personalized medicine, single-gene mutations, and polygenic risk alleles have been brought to the forefront as core causes of a spectrum of renal disorders. With the increasing prevalence of kidney disease, it is imperative to make substantial strides in the field of kidney genetics. Nephrons, the core functional units of the kidney, are epithelial tubules that act as gatekeepers of body homeostasis by absorbing and secreting ions, water, and small molecules to filter the blood. Each nephron contains a series of proximal and distal segments with explicit metabolic functions. The embryonic zebrafish provides an ideal platform to systematically dissect the genetic cues governing kidney development. Here, we review the use of zebrafish to discover nephrogenesis genes.

Genetic mechanisms of multiciliated cell development: from fate choice to differentiation in zebrafish and other models

Multiciliated cells (MCCS) form bundles of cilia and their activities are essential for the proper development and physiology of many organ systems. Not surprisingly, defects in MCCs have profound consequences and are associated with numerous disease states. Here, we discuss the current understanding of MCC formation, with a special focus on the genetic and molecular mechanisms of MCC fate choice and differentiation. Furthermore, we cast a spotlight on the use of zebrafish to study MCC ontogeny and several recent advances made in understanding MCCs using this vertebrate model to delineate mechanisms of MCC emergence in the developing kidney.

Visualizing multiciliated cells in the zebrafish

Ciliated cells serve vital functions in the body ranging from mechano- and chemo-sensing to fluid propulsion. Specialized cells with bundles dozens to hundreds of motile cilia known as multiciliated cells (MCCs) are essential as well, where they direct fluid movement in locations such as the respiratory, central nervous and reproductive systems. Intriguingly, the appearance of MCCs has been noted in the kidney in several disease conditions, but knowledge about their contributions to the pathobiology of these states has remained a mystery. As the mechanisms contributing to ciliopathic diseases are not yet fully understood, animal models serve as valuable tools for studying cilia development and how alterations in ciliated cell function impacts disease progression. Like other vertebrates, the zebrafish, Danio rerio, has numerous ciliated tissues. Among these, the embryonic kidney (or pronephros) is comprised of both monociliated cells and MCCs and therefore provides a setting to investigate both ciliated cell fate choice and ciliogenesis. Considering the zebrafish nephron resembles the segmentation and function of human nephrons, the zebrafish provide a tractable model for studying conserved ciliogenesis pathways in vivo. In this chapter, we provide an overview of ciliated cells with a special focus on MCCs, and present a suite of methods that can be used to visualize ciliated cells and their features in the developing zebrafish. Further, these methods enable precise quantification of ciliated cell number and various cilia-related characteristics.

Advances in Understanding the Genetic Mechanisms of Zebrafish Renal Multiciliated Cell Development

Cilia are microtubule-based organelles that project from the cell surface. In humans and other vertebrates, possession of a single cilium structure enables an assortment of cellular processes ranging from mechanosensation to fluid propulsion and locomotion. Interestingly, cells can possess a single cilium or many more, where so-called multiciliated cells (MCCs) possess apical membrane complexes with several dozen or even hundreds of motile cilia that beat in a coordinated fashion. Development of MCCs is, therefore, integral to control fluid flow and/or cellular movement in various physiological processes. As such, MCC dysfunction is associated with numerous pathological states. Understanding MCC ontogeny can be used to address congenital birth defects as well as acquired disease conditions. Today, researchers used both in vitro and in vivo experimental models to address our knowledge gaps about MCC specification and differentiation. In this review, we summarize recent discoveries from our lab and others that have illuminated new insights regarding the genetic pathways that direct MCC ontogeny in the embryonic kidney using the power of the zebrafish animal model.

PCD Genes-From Patients to Model Organisms and Back to Humans

Primary ciliary dyskinesia (PCD) is a hereditary genetic disorder caused by the lack of motile cilia or the assembxly of dysfunctional ones. This rare human disease affects 1 out of 10,000-20,000 individuals and is caused by mutations in at least 50 genes. The past twenty years brought significant progress in the identification of PCD-causative genes and in our understanding of the connections between causative mutations and ciliary defects observed in affected individuals. These scientific advances have been achieved, among others, due to the extensive motile cilia-related research conducted using several model organisms, ranging from protists to mammals. These are unicellular organisms such as the green alga Chlamydomonas, the parasitic protist Trypanosoma, and free-living ciliates, Tetrahymena and Paramecium, the invertebrate Schmidtea, and vertebrates such as zebrafish, Xenopus, and mouse. Establishing such evolutionarily distant experimental models with different levels of cell or body complexity was possible because both basic motile cilia ultrastructure and protein composition are highly conserved throughout evolution. Here, we characterize model organisms commonly used to study PCD-related genes, highlight their pros and cons, and summarize experimental data collected using these models.

Novel Approach Combining Transcriptional and Evolutionary Signatures to Identify New Multiciliation Genes

Multiciliogenesis is a complex process that allows the generation of hundreds of motile cilia on the surface of specialized cells, to create fluid flow across epithelial surfaces. Dysfunction of human multiciliated cells is associated with diseases of the brain, airway and reproductive tracts. Despite recent efforts to characterize the transcriptional events responsible for the differentiation of multiciliated cells, a lot of actors remain to be identified. In this work, we capitalize on the ever-growing quantity of high-throughput data to search for new candidate genes involved in multiciliation. After performing a large-scale screening using 10 transcriptomics datasets dedicated to multiciliation, we established a specific evolutionary signature involving Otomorpha fish to use as a criterion to select the most likely targets. Combining both approaches highlighted a list of 114 potential multiciliated candidates. We characterized these genes first by generating protein interaction networks, which showed various clusters of ciliated and multiciliated genes, and then by computing phylogenetic profiles. In the end, we selected 11 poorly characterized genes that seem like particularly promising multiciliated candidates. By combining functional and comparative genomics methods, we developed a novel type of approach to study biological processes and identify new promising candidates linked to that process.