Biology subjects

Hudspeth, A. J.

Publications and source records attributed to Hudspeth, A. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Vangl2 acts in distinct cell types to establish bidirectional hair-bundle polarity and maintains tissue-wide alignment in zebrafish neuromasts

The conserved core planar cell polarity (PCP) pathway orients cells and subcellular structures within an epithelium through asymmetric protein localization and intercellular communication. In vestibular organs and lateral-line neuromasts, mechanosensory hair cells are interspersed among support cells and form opposing hair-bundle orientations along a shared axis, enabling bidirectional sensitivity to head motion and water flow, respectively. In zebrafish neuromasts, Notch-mediated lateral inhibition gives rise to two hair-cell populations, distinguished by differential Emx2 expression, that orient their cell-intrinsic polarity machinery differently relative to a PCP-dependent tissue-wide axis. However, it remains unclear how PCP proteins are organized across hair cells and support cells to achieve both opposing hair-bundle orientations and tissue-wide alignment, and whether PCP signaling remains required after hair-bundle polarity is established. Combining quantitative spatial mapping of the core PCP protein Vangl2 with cell-type-specific and temporally controlled protein degradation, we show that hair cells and support cells make distinct yet coordinated contributions to the polarized Vangl2 organization within neuromasts and to bidirectional hair-bundle polarity. Support-cell Vangl2 facilitates tissue-wide alignment of hair bundles along the anteroposterior axis, whereas hair-cell Vangl2 is required to generate opposing hair-bundle orientations along this axis. Vangl2 degradation after hair bundles have formed disrupts their tissue-wide alignment, showing that planar polarity is actively maintained rather than fixed after establishment. Together, these findings reveal how Vangl2-dependent PCP signaling is distributed across distinct cell types within a heterogeneous epithelium to generate opposing polarity outcomes and remains necessary to preserve tissue-level planar organization.

developmental biology↗

bioRxiv2026

Rocking Without a Tune: Ex vivo and in vivo Responses to Sound in the Basilar Papilla of the Tokay Gecko

Likemammals, some reptiles possess sensitive and frequency-selective hearing at mid- to high-kilohertz frequencies. Both groups employ a place-frequency map within the inner ear to encode sound stimuli, but the mechanisms by which they achieve tuned nerve activation along the cochlea are believed to be distinct. To investigate the mechanical origins of auditory sensation in the reptiles, we measured sound-evoked displacement responses in the hearing organ of the tokay gecko (Gekko gecko), known as the basilar papilla. Using optical coherence tomography, we were able to resolve sub-nanometer-scale vibrations throughout the organ both in vivo and ex vivo. We saw that tuning was not present in the tissue-scale mechanics at any position within the organ; it instead exhibits an untuned rotational motion. We developed a mathematical model which predicted that this motion induces hair-bundle-stimulating fluid displacement, and is due to an anatomical asymmetry seen in many reptile species. These results are consistent with the theory that hair-bundle-level mechanics are primarily responsible for tuning in the tokay gecko cochlea, and we argue that our proposed mechanisms generalize to many other species across the Reptilia class.

biophysics↗

bioRxiv2026

Notch-driven fate asymmetry dictates hair cell behavior via a fate-specific kinase

Cell-cell signaling and cell-fate decisions are essential for organ assembly, but how these molecular events translate into the physical properties and cell behaviors that drive development remains poorly understood. In the zebrafish lateral line, developing pairs of sensory hair cells undergo symmetry-breaking mediated by Notch signaling, leading to one cell becoming Notch-ON (receiver state) and its sibling becoming Notch-OFF (sender state). These cells then undergo coordinated movements that ensure that Notch-OFF cells are always positioned anterior to their Notch-ON sisters, and the Notch state of each sister ultimately determines the direction of hair bundle polarization. However, the cellular mechanisms and molecular programs that guide polarity-specific behaviors remain largely unknown. Here, using time-lapse imaging and a new 3D segmentation and tracking pipeline, we demonstrate that sister cells actively move in opposite directions - Notch-OFF cells migrate anteriorly while Notch-ON cells move posteriorly - enabling robust rotations when cells are initially mispositioned. Using single-cell RNA sequencing, we identify fate-dependent transcriptional programs and show that the differentially expressed kinase stk32a is required for proper navigation and hair bundle placement in Notch-ON cells. Strikingly, loss of stk32a reveals an underlying chiral bias in cell-pair rotations, suggesting the existence of an additional, previously unrecognized axis of symmetry breaking beyond the Notchmediated fate decision.

developmental biology↗

bioRxiv2025

Axonal defasciculation is restricted to specific branching points during regeneration of the lateral line nerve in zebrafish

Peripheral nerve regeneration requires precise selection of the appropriate targets of innervation, often in an environment that differs from that during the developmental wiring of the neural circuit. Severed axons of the zebrafish posterior lateral line nerve have the capacity to reinnervate mechanosensory hair cells clustered in neuromast organs. Regeneration represents a balance between fasciculated regrowth of the axonal bundle and defasciculation of individual axons into the epidermis where neuromasts reside. The cues that guide pathfinding during regeneration of the posterior lateral line nerve are unknown. Here we show that expression of col18a1a, which codes for the secreted heparan sulfate proteoglycan collagen XVIII, biases axonal defasciculation to specific branching points that coincide with circumscribed gaps in the epidermal boundary. We found that col18a1a is expressed by the neuromast and by a subset of Schwann cells that are located at the points of axonal defasciculation. Furthermore, we observed axon branching at inappropriate locations during nerve regeneration in col18a1a mutants. We propose a model in which a collagen XVIII-based axon-guidance cue complex attracts defasciculated axons across the epidermal basement membrane. Summary StatementThe success of nerve regeneration depends on precise axon pathfinding and accurate target selection. We identify neuron-extrinsic factors that guide regeneration in a zebrafish model.

neuroscience↗

bioRxiv2025

Optogenetic interrogation of the lateral-line sensory system reveals mechanisms of pattern separation in the zebrafish brain

The ability of animals to interact with their environment hinges on the brains capacity to distinguish between patterns of sensory information and accurately attribute them to specific sensory organs. The mechanisms by which neuronal circuits discriminate and encode the source of sensory signals remain elusive. To address this, we utilized as a model the posterior lateral line system of larval zebrafish, which is used to detect water currents. This system comprises a series of mechanosensory organs called neuromasts, which are innervated by neurons from the posterior lateral line ganglion. By combining single-neuromast optogenetic stimulation with whole-brain calcium imaging, we developed a novel approach to investigate how inputs from neuromasts are processed. Upon stimulating individual neuromasts, we observed that neurons in the brain of the zebrafish show diverse selectivity properties despite a lack of topographic organization in second-order circuits. We further demonstrated that complex combinations of neuromast stimulation are represented by sparse ensembles of neurons within the medial octavolateralis nucleus (MON) and found that neuromast input can be integrated nonlinearly. Our approach offers an innovative method for spatiotemporally interrogating the zebrafish lateral line system and presents a valuable model for studying whole-brain sensory encoding.

neuroscience↗

bioRxiv2024

ybx1 acts upstream of atoh1a to promote the rapid regeneration of hair cells in zebrafish lateral-line neuromasts

Like the sensory organs of the human inner ear, the lateral-line neuromasts (NMs) of fish such as the zebrafish (Danio rerio) contain mechanosensory hair cells (HCs) that are surrounded by progenitors called supporting cells. Damaged NMs can quickly regenerate new HCs by expressing in the progenitors HC-specific genes such as atoh1a, the master regulator of HC fate. We used the supervised learning algorithm DELAY to infer regenerating NMs early gene-regulatory network (GRN) and identify adaptations that promote the rapid regeneration of lateral-line HCs in larval zebrafish. The central hub in the network, Y-box binding protein 1 (ybx1), is highly expressed in HC progenitors and young HCs and can recognize DNA-binding motifs in cyprinids candidate regeneration-responsive promoter elements for atoh1a. We showed that NMs from ybx1 mutant zebrafish larvae display consistent, regeneration-specific deficits in HC number and initiate both HC regeneration and atoh1a expression 20 % slower than in siblings. By demonstrating that ybx1 promotes rapid HC regeneration through early atoh1a upregulation, the results support DELAYs ability to identify key temporal regulators of gene expression.

genomics↗

bioRxiv2023

Nanomechanics of wild-type and mutant dimers of the tip-link protein protocadherin 15

Mechanical force controls the opening and closing of mechanosensitive ion channels atop the hair bundles of the inner ear. The filamentous tip link connecting transduction channels to the tallest neighboring stereocilium modulates the force transmitted to the channels and thus changes their probability of opening. Each tip link comprises four molecules: a dimer of protocadherin 15 and a dimer of cadherin 23, all of which are stabilized by Ca2+ binding. Using a high-speed optical trap to examine dimeric PCDH15, we find that the proteins configuration is sensitive to Ca2+ and that the molecule exhibits limited unfolding at a physiological Ca2+ concentration. PCDH15 can therefore modulate its stiffness without undergoing large unfolding events in physiological Ca2+ conditions. The experimentally determined stiffness of PCDH15 accords with published values for the stiffness of the gating spring, the mechanical element that controls the opening of mechanotransduction channels. When PCDH15 has a point mutation, V507D, associated with non-syndromic hearing loss, unfolding events occur more frequently under tension and refolding events occur less often than in the wild-type protein. Our results suggest that the maintenance of appropriate tension in the gating spring is critical to the appropriate transmission of force to transduction channels, and hence to hearing.

biophysics↗

bioRxiv2023

Influence of myosin regulatory light chain and myosin light chain kinase on hair cells of the inner ear

In the receptor organs of the inner ear and lateral line, sensory hair cells detect mechanical stimuli such as sounds, accelerations, and water movements. In each instance a stimulus deflects the hair bundle, a hair cells mechanically sensitive organelle. The bundle pivots upon the cells apical surface, which includes an actin meshwork called the cuticular plate and is surrounded by a ring of filamentous actin and non-muscle myosin II (NM2). Myosin regulatory light chain (RLC) is expressed at the apical surfaces of hair cells and RLC is additionally found in hair bundles. NM2 and the phosphorylation of RLC by myosin light chain kinase (MLCK) have earlier been shown to regulate the sizes and shapes of hair cells apical surfaces. We have found that inhibitors of NM2 and MLCK reduce the stiffness of hair bundles from the bullfrogs sacculus. Moreover, MLCK inhibition inhibits the spontaneous oscillation of hair bundles and increases the resting open probability of transduction channels. In addition, MLCK inhibition elevates hearing thresholds in mice. We conclude that NM2 and the phosphorylation of RLC modulate slow adaptation and thereby help to set the normal operating conditions of hair bundles. Statement of significanceSensory hair cells play a key role in mechanoelectrical transduction by the inner ear and lateral-line system. To detect stimuli such as sounds and accelerations, hair cells use an active process to amplify their mechanical inputs. Although amplification is accomplished in part by the activity of the mechanosensitive hair bundles, the molecular mechanism of the active process remains uncertain. The present study shows that non-muscle myosin II (NM2) and the phosphorylation of myosin regulatory right chains (RLC) by myosin light chain kinase (MLCK) regulate the stiffness and spontaneous oscillation of hair bundles as well as the resting open probability of mechanotransduction channels. The results implicate myosin motors in the control of the active process of hair cells.

biophysics↗

bioRxiv2022

Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference

Identifying the causal interactions in gene-regulatory networks requires an accurate understanding of the time-lagged relationships between transcription factors and their target genes. Here we describe DELAY, a convolutional neural network for the inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. We show that combining supervised deep learning with joint-probability matrices of pseudotime-lagged trajectories allows the network to overcome important limitations of ordinary Granger causality-based methods, such as the inability to infer cyclic relationships such as feedback loops. Our network outperforms several common methods for inferring gene regulation and predicts novel regulatory networks from scRNA-seq and scATAC-seq datasets given partial ground-truth labels. To validate this approach, we used DELAY to identify important genes and modules in the regulatory network of auditory hair cells, as well as likely DNA-binding partners for two hair cell cofactors (Hist1h1c and Ccnd1) and a novel binding sequence for the hair cell-specific transcription factor Fiz1. We provide an open-source implementation of DELAY at https://github.com/calebclayreagor/DELAY.

bioinformatics↗

bioRxiv2022

Violation of the fluctuation-response relation from a linear model of hair bundle oscillations

Spontaneous hair-bundle oscillations have been proposed to underlie the ears active process, which amplifies acoustic signals, sharpens frequency selectivity, and broadens the dynamic range. Although this activity is critical for proper hearing, we know very little about its energetics and its nonequilibrium properties. Systems obey fluctuation-response relations, whose violation signals nonequilibrium conditions. Here we demonstrate the violation of the fluctuation-response relation of a linear model for hair bundle oscillations. Combining analytical results with experimental data, we estimate that an energy of at least 146 kBT is dissipated per oscillatory cycle, implying a power output of about 5aW. Our model indicates that this dissipation attains a minimum at a certain characteristic frequency. For high frequencies, we derive a linear scaling behavior of this dissipated energy with the characteristic frequency.

biophysics↗

bioRxiv2022

Development of an improved inhibitor of Lats kinases to promote regeneration of mammalian organs

The Hippo signaling pathway acts as a brake on regeneration in many tissues. This cascade of kinases culminates in the phosphorylation of the transcriptional cofactors Yap and Taz, whose concentration in the nucleus consequently remains low. Various types of cellular stress can reduce phosphorylation, however, resulting in the accumulation of Yap and Taz in the nucleus and subsequently in mitosis. We earlier identified a small molecule, TRULI, that blocks the final kinases in the pathway, Lats1 and Lats2, and thus elicits proliferation of several cell types that are ordinarily post-mitotic and aids regeneration in mammals. In the present study we present the results of chemical modification of the original compound and demonstrate that a derivative, TDI-011536, is an effective blocker of Lats kinases in vitro at nanomolar concentrations. The compound fosters extensive proliferation in retinal organoids derived from human induced pluripotent stem cells. Intraperitoneal administration of the substance to mice suppresses Yap phosphorylation for several hours and induces transcriptional activation of its target genes in the heart, liver, and skin. Moreover, the compound initiates the proliferation of cardiomyocytes in adult mice following cardiac cryolesions. After further chemical refinement, related compounds might prove useful in protective and regenerative therapies. Significance StatementIn humans and other mammals, many organs regenerate through the proliferation of cells that replace those that have succumbed to aging or injury. However, proliferation is largely absent in certain critical organs, including the heart, the central nervous system, and sensory organs such as the inner ear and retina. The Hippo-Yap biochemical signaling pathway, a cascade of proteins that--when active--inhibits cell division, constitutes one impediment to proliferation. We earlier identified a small molecule that interrupts Hippo-Yap signaling and thus relieves this block for some non-proliferating cells in vitro. In the present investigation, we have chemically modified the original substance to yield a more potent analog that is effective for several hours in mammalian tissues in vivo and initiates the proliferation of heart-muscle cells after cryolesioning. After further refinements, compounds of this family might prove useful in regenerative therapies.

cell biology↗

bioRxiv2021

Role of YAP in early ectodermal specification anda Huntington's Disease model of human neurulation

The Hippo pathway, a highly conserved signaling cascade that functions as an integrator of molecular signals and biophysical states, ultimately impinges upon the transcription coactivator Yes-associated protein 1 (YAP). Hippo-YAP signaling has been shown to play key roles both at the early embryonic stages of implantation and gastrulation, and later during neurogenesis. To explore YAPs potential role in neurulation, we used self-organizing neuruloids grown from human embryonic stem cells on micropatterned substrates. We identified YAP activation as a key lineage determinant, first between neuronal ectoderm and non-neuronal ectoderm, and later between epidermis and neural crest, indicating that YAP activity can enhance the effect of BMP4 stimulation and therefore affect ectodermal specification at this developmental stage. Because aberrant Hippo-YAP signaling has been implicated in the pathology of Huntingtons Disease (HD), we used isogenic mutant neuruloids to explore the relationship between signaling and the disease. We found that HD neuruloids demonstrate ectopic activation of gene targets of YAP and that pharmacological reduction of YAPs transcriptional activity can partially rescue the HD phenotype.

developmental biology↗

bioRxiv2021

Rapid mechanical stimulation of inner-ear hair cells by photonic pressure

Hair cells, the receptors of the inner ear, detect sounds by transducing mechanical vibrations into electrical signals. From the top surface of each hair cell protrudes a mechanical antenna, the hair bundle, which the cell uses to detect and amplify auditory stimuli, thus sharpening frequency selectivity and providing a broad dynamic range. Current methods for mechanically stimulating hair bundles are too slow to encompass the frequency range of mammalian hearing and are plagued by inconsistencies. To overcome these challenges, we have developed a method to move individual hair bundles with photonic force. This technique uses an optical fiber whose tip is tapered to a diameter of a few micrometers and endowed with a ball lens to minimize divergence of the light beam. Here we describe the fabrication, characterization, and application of this optical system and demonstrate the rapid application of photonic force to vestibular and cochlear hair cells.

neuroscience↗

bioRxiv2020

Fast recovery of disrupted tip links induced by mechanical displacement of hair bundles

Hearing and balance rely on the capacity of mechanically sensitive hair bundles to transduce vibrations into electrical signals that are forwarded to the brain. Hair bundles possess tip links that interconnect the mechanosensitive stereocilia and convey force to the transduction channels. A dimer of dimers, each of these links comprises two molecules of protocadherin 15 (PCDH15) joined to two of cadherin 23 (CDH23). The "handshake" that conjoins the four molecules can be disrupted in vivo by intense stimulation and in vitro by exposure to Ca2+ chelators. Using hair bundles from the rats cochlea and the bullfrogs sacculus, we observed that extensive recovery of mechanoelectrical transduction, hair-bundle stiffness, and spontaneous bundle oscillation can occur within seconds after Ca2+ chelation, especially if hair bundles are deflected towards their short edges. Investigating the phenomenon in a two-compartment ionic environment that mimics natural conditions, we combined iontophoretic application of a Ca2+ chelator to selectively disrupt the tip links of individual frog hair bundles with displacement clamping to control hair-bundle motion and measure forces. Our observations suggest that, after the normal Ca2+ concentration has been restored, mechanical stimulation facilitates the reconstitution of functional tip links. Significance StatementEach of the sensory receptors responsible for hearing or balance--a hair cell--has a mechanosensitive hair bundle. Mechanical stimuli pull upon molecular filaments--the tip links--that open ionic channels in the hair bundle. Loud sounds can damage hearing by breaking the tip links; recovery by replacement of the constituent proteins then requires several hours. We disrupted the tip links in vitro by removing the calcium ions that stabilize them, then monitored the electrical response or stiffness of hair bundles to determine whether the links could recover. We found that tip links recovered within seconds if their ends were brought back into contact. This form of repair might occur in normal ears to restore sensitivity after damage.

neuroscience↗

bioRxiv2020

Measurement of hindered diffusion in complex geometries for high-speed single-molecule experiments

In a high-speed single-molecule experiment, a protein is tethered between two substrates that are manipulated to exert force on the system. To avoid nonspecific interactions between the protein and nearby substrates, the protein is usually attached to the substrates through long, flexible linkers. This approach precludes measurements of mechanical properties with high spatial and temporal resolution, for rapidly exerted forces are dissipated into the linkers. Because mammalian hearing operates at frequencies reaching tens to hundreds of kilohertz, the mechanical processes that occur during transduction are of very short duration. Single-molecule experiments on the relevant proteins therefore cannot involve long tethers. We previously characterized the mechanical properties of protocadherin 15 (PCDH15), a protein essential for human hearing, by tethering an individual monomer through very short linkers between a probe bead held in an optical trap and a pedestal bead immobilized on a glass coverslip. Because the two confining surfaces were separated by only the length of the tethered protein, hydrodynamic coupling between those surfaces complicated the interpretation of the data. To facilitate our experiments, we characterize here the anisotropic and position-dependent diffusion coefficient of a probe in the presence of an effectively infinite wall, the coverslip, and of the immobile pedestal.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2020

Small-molecule inhibition of Lats kinases promotes Yap-dependent proliferation in postmitotic mammalian tissues

Hippo signaling is an evolutionarily conserved pathway that restricts organ growth during development and suppresses regeneration in mature organs1-3. Using a high-throughput phenotypic screen, we have identified a potent, non-toxic, and reversible inhibitor of Hippo signaling. An ATP-competitive inhibitor of Lats kinases, the compound causes Yap-dependent proliferation of murine supporting cells in the inner ear, murine cardiomyocytes, and human Muller glia in retinal organoids. RNA sequencing indicates that the substance fosters both the G1-S and G2-M checkpoint transitions and yields supporting cells capable of transdifferentiation. Upon withdrawal of the compound, a subset of supporting cells move their nuclei into the hair-cell layer and express genes characteristic of hair cells. Viral transfection of Atoh1 induces the expression of hair cellspecific proteins in progeny. The compound promotes the initial stages of the proliferative regeneration of hair cells, a process thought to be permanently suppressed in the adult mammalian inner ear.

developmental biology↗

bioRxiv2019

Symmetry breaking during morphogenesis of a mechanosensory organ

Actively regulated symmetry breaking, which is ubiquitous in biological cells, underlies phenomena such as directed cellular movement and morphological polarization. Here we investigate how an organ-level polarity pattern emerges through symmetry breaking at the cellular level during the formation of a mechanosensory organ. Combining theory, genetic perturbations, and in vivo imaging assisted by deep learning, we study the development and regeneration of the fluid-motion sensors in the zebrafishs lateral line. We find that two interacting symmetry-breaking events -- one mediated by biochemical signaling and the other by cellular mechanics -- give rise to a novel form of collective cell migration, which produces a mirror-symmetric polarity pattern in the receptor organ.

biophysics↗

bioRxiv2018

The elasticity of individual protocadherin 15 molecules implicates cadherins as the gating springs for hearing

Hair cells, the sensory receptors of the inner ear, respond to mechanical forces originating from sounds and accelerations1,2. An essential feature of each hair cell is an array of filamentous tip links, consisting of the proteins protocadherin 15 (PCDH15) and cadherin 23 (CDH23)3, whose tension is thought to directly gate the cells transduction channels4,5,6. These links are considered far too stiff to represent the gating springs that convert hair-bundle displacement into forces capable of opening the channels7,8, and no mechanism has been suggested through which tip-link stiffness could be varied to accommodate hair cells of distinct frequency sensitivity in different receptor organs and animals. As a consequence, the gating springs identity and mechanism of operation remain central questions in sensory neuroscience. Using a high-precision optical trap, we show that an individual monomer of PCDH15 acts as an entropic spring that is much softer than its enthalpic stiffness alone would suggest7,8. This low stiffness implies that the protein is a significant part of the gating spring that controls a hair cells transduction channels. The tip links entropic nature then allows for stiffness control through modulation of its tension. We find that a PCDH15 molecule is unstable under tension and exhibits a rich variety of reversible unfolding events that are augmented when the Ca2+ concentration is reduced to physiological levels. Tip-link tension and Ca2+ concentration are therefore likely parameters through which nature tunes a gating springs mechanical properties.

biophysics↗