Biology subjects

Raible, D.

Publications and source records attributed to Raible, D..

6 recordsLinked to original sources

bioRxiv2025

Activity and retinoic acid drive hair cell spatial patterning in the zebrafish utricle

The zebrafish vestibular otolith organs, like those of other vertebrate species, are organized into central (striolar) and peripheral (extrastriolar) zones that drive different vestibular circuits. How and when these spatial hair cell patterns develop in the zebrafish is unknown. We determined that early-developing hair cells (<36 hours) expressed both striolar and extrastriolar transcriptomic markers. After 36 hours, these hair cells become specified as extrastriolar hair cells. Later-developing hair cells (>36 hours) mostly develop directly as striolar or extrastriolar. We observed complementary patterns of RA degrading and synthesizing enzymes that colocalize with striolar and extrastriolar hair cells, respectively, indicating evolutionarily conserved molecular signaling. RA treatment during development increased the proportion of extrastriolar and intermediate-type hair cells, indicating that increased RA reduces striolar development. However, in fish with mechanotransduction dysfunction from a cadherin23 mutation, normal RA patterning is insufficient to finalize the fate of early-born hair cells, which remain transcriptomically unresolved. RA treatment further exacerbates this abnormal patterning. We conclude that hair cell fate, and thus normal zonal patterning, depends on both hair cell activity and the RA gradient. Summary statementThe development of hair cell zonal patterning in the vestibular sensory epithelia depends on a balance of mechanotransduction-driven activity and retinoic acid.

developmental biology↗

bioRxiv2024

Multiple mechanisms of aminoglycoside ototoxicity are distinguished by subcellular localization of action

Mechanosensory hair cells of the inner ears and lateral line of vertebrates display heightened vulnerability to environmental insult, with damage resulting in hearing and balance disorders. An important example is hair cell loss due to exposure to toxic agents including therapeutic drugs such as the aminoglycoside antibiotics such as neomycin and gentamicin and antineoplastic agents. We describe two distinct cellular pathways for aminoglycoside-induced hair cell death in zebrafish lateral line hair cells. Neomycin exposure results in death from acute exposure with most cells dying within 1 hour of exposure. By contrast, exposure to gentamicin results primarily in delayed hair cell death, taking up to 24 hours for maximal effect. Washout experiments demonstrate that delayed death does not require continuous exposure, demonstrating two mechanisms where downstream responses differ in their timing. Acute damage is associated with mitochondrial calcium fluxes and can be alleviated by the mitochondrially-targeted antioxidant mitoTEMPO, while delayed death is independent of these factors. Conversely delayed death is associated with lysosomal accumulation and is reduced by altering endolysosomal function, while acute death is not sensitive to lysosomal manipulations. These experiments reveal the complexity of responses of hair cells to closely related compounds, suggesting that intervention focusing on early events rather than specific death pathways may be a successful therapeutic strategy.

neuroscience↗

bioRxiv2022

Proteostasis governs differential temperature sensitivity across embryonic cell types

The genetic program of embryonic development is remarkably robust, but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped, consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others, the basis of this sensitivity is unknown. Here, we characterize hundreds of individual zebrafish embryos under temperature stress using whole-animal single cell RNA-seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress, which we show is due to a specialized cell type, sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature, leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole-animal single cell RNA-seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points.

genomics↗

bioRxiv2022

Deep molecular, cellular and temporal phenotyping of developmental perturbations at whole organism scale

The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data, however, has been collected from wild type embryos without an appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos, encompassing 19 time points, 23 genetic perturbations, and totaling 3.2M cells. The high degree of replication in our study (8 or more embryos per condition) allows us to estimate the variance in cell type abundance organism-wide and to detect perturbation-dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types, resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons, a cell population that comprises less than 1% of the embryo. Additionally, time-series profiling of individual mutants identified a group of brachyury-independent cells with strikingly similar transcriptomes to notochord sheath cells, leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high-resolution, organism-scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types, while also addressing long-standing challenges in developmental genetics, including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals.

genomics↗

bioRxiv2019

Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores

Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates, derived from embryonic neural crest, are a useful system for elucidating mechanisms of fate specification, pattern formation, and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes, including zebrafish Danio rerio, we identified two populations of white pigment cells--leucophores--one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore-like progenitor. Single-cell transcriptomic, mutational, chemical and ultrastructural analyses of zebrafish leucophores revealed cell-type specific chemical compositions, organelle configurations and genetic requirements. At the organismal level, we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together, our studies revealed new, independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish, and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution.

developmental biology↗

bioRxiv2018

Distinct progenitor populations mediate regeneration in the zebrafish lateral line.

Mechanosensory hair cells of the zebrafish lateral line regenerate rapidly following damage. These renewed hair cells arise from the proliferation of surrounding support cells, which undergo symmetric division to produce two hair cell daughters. Given the continued regenerative capacity of the lateral line, support cells presumably have the ability to replenish themselves. Utilizing novel transgenic lines, we identified support cell populations with distinct progenitor identities. These populations show differences in their ability to generate new hair cells during homeostasis and regeneration. Targeted ablation of support cells reduced the number of regenerated hair cells. Furthermore, progenitors regenerated after targeted support cell ablation in the absence of hair cell damage. We also determined that distinct support cell populations are independently regulated by Notch signaling. The existence of independent progenitor populations could provide flexibility for the continued generation of new hair cells under a variety of conditions throughout the life of the animal.

developmental biology↗