Biology subjects

Ho, R.

Publications and source records attributed to Ho, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Generation of human iPSC-derived motor neurons with defined regional identities across the rostrocaudal axis

This study establishes a unified pipeline for generating human induced pluripotent stem cell (iPSC)-derived motor neurons (iMNs) with defined hindbrain, cervical, and lumbar identities to support anatomically resolved studies of motor neuron development and degeneration. Conventional differentiation methods can efficiently produce iMNs but provide limited control over rostrocaudal identity and frequently generate populations with heterogeneous HOX profiles. We addressed this limitation by optimizing developmental morphogen combinations and treatment windows, establishing three complementary protocols that reproducibly generated hindbrain/rhombomere-associated motor neurons (RiMNs), cervical motor neurons (CiMNs), and lumbar motor neurons (LiMNs) across iPSC lines from six non-diseased donors balanced by sex. Transcriptomic and protein analyses demonstrated graded rostrocaudal specification from RiMNs through CiMNs to LiMNs, together with region-appropriate motor neuron subtype features. These identities showed the expected relationships to human week 9 fetal rostrocaudal HOX programs. High-density multielectrode array analysis further revealed synchronized network firing, electrically active neurite networks, and enhanced axonal signal propagation in the regional iMN populations compared with conventionally differentiated iMNs. Spike-sorted recordings additionally revealed protocol-associated differences in single-neuron electrophysiological profiles. Together, this three-protocol pipeline enables the reproducible generation and comparative analysis of anatomically defined human motor neuron populations and provides region-matched cellular models for investigating motor neuron development, selective degeneration, and therapeutic responses.

neuroscience↗

bioRxiv2026

Electron microscopy reveals water networks inside hydrated cellulose fibers

Cellulose is a highly abundant linear glucose polymer that exists in amorphous and fibrillar forms1-3. Primarily produced by vascular plants but also microbes and tunicates, cellulose predominantly performs architectural functions by stabilizing cell walls, tissues, and multicellular communities4-9. Owing to its association with other cell surface materials, physiological higher-order structures of cellulose have been difficult to obtain. Here, we describe a never-dried tunicate cellulose fibril structure by cryogenic electron microscopy, which resolves a fiber of more than 360 cellulose strands. Our data reveals linear and severely twisted fiber segments that are interspersed with solvent channels. Solid-state NMR analyses and molecular dynamics simulations indicate the presence of structural water molecules that form a network connecting neighboring cellulose chains. Confocal and super-resolution MINFLUX fluorescence imaging using cellulose-specific probes as well as biochemical analyses demonstrate shared surface and material properties of plant and tunicate cellulose fibers. Combined, our data suggest that architectural water molecules may be common features of cellulose fibers and likely other polysaccharide assemblies in their hydrated physiological states.

molecular biology↗

bioRxiv2026

A molecular description of plant cellulose biosynthesis inhibition

Dictating cell growth and morphology, cellulose biosynthesis is intrinsic to plant cell biology. Accordingly, cellulose biosynthesis inhibitors (CBIs) are important herbicides, toxins, and experimental tools. We currently lack mechanistic understanding of CBI activity, preventing engineering of herbicide selectivity and disease immunity. Contrasting classical inhibitors, we unexpectedly identify the unusual Streptomyces phytotoxin thaxtomin A as the only in vitro-active CBI, with unprecedentedly broad-spectrum activity against various cellulose synthase enzymes. High-resolution cryo-electron microscopy reveals that thaxtomin A leverages exotic nitroaromatic chemistry to target a strictly conserved site in cellulose synthases polysaccharide secretion channel. Strikingly, in vitro biosynthesis and biophysical assays demonstrate thaxtomin As near-picomolar efficacy. Plant and algal systems reveal that its global arrest of cellulose biosynthesis produces an osmotically driven crisis in expanding cells. Finally, site-directed mutagenesis generates the first toxin-resistant cellulose synthase. Our results underscore celluloses critical function in plant lifeforms and inform efforts to inhibit related enzymes across kingdoms.

plant biology↗

bioRxiv2026

A region-delineated snRNA-seq atlas of mouse spinal cord across lifespan resolves the interaction of normative aging programs with SOD1-G93A ALS

Aging is the strongest risk factor for amyotrophic lateral sclerosis (ALS), yet how normative aging programs intersect with disease mechanisms remain unclear. Here we generated a lifespan-resolved, cell type-and region-specific single-nucleus RNA-sequencing atlas of the mouse spinal cord spanning embryonic development through advanced age in WT mice and end-stage disease in the SOD1-G93A ALS model. This resource enabled systematic comparison of physiological aging trajectories with disease-associated transcriptional changes across spinal cord cell types and rostrocaudal regions. We found that SOD1-G93A transcript and protein states differed markedly across spinal regions during disease onset and progression, and these molecular patterns paralleled the relative resilience of cervical regions and the heightened vulnerability of lumbar regions to degeneration in this transgenic mouse model. Prior to disease onset, we identified reduced ubiquitin expression that primed region-specific disruption of proteostasis in the SOD1-G93A spinal cord. Despite these disease-associated changes, aging-related transcriptional programs were largely preserved across most cell types, arguing against a global acceleration of aging in ALS. Instead, microglia emerged as a key exception, exhibiting accelerated and rewired aging- and disease-associated gene expression modules regulated by MITF and NRF2. Together, these findings provide an anatomically, cellularly, and temporally resolved framework for understanding how aging programs interact with disease-specific pathways to shape regional dysfunction and neurodegeneration in ALS.

neuroscience↗

bioRxiv2025

Autophagy-Dependent Regulation of YAP1 by STK38 Governs Recruitment of Differentiated Cells as Progenitor Cells During Regeneration

Paligenosis is a conserved cellular plasticity program that allows mature cells to reenter the cell cycle in response to tissue injury. Paligenosis progresses via three stages: autodegradation (with dramatic increase in autophagy and lysosomes), induction of metaplastic or fetal-like genes, and cell cycle entry. Hippo signaling, particularly the downstream effector YAP1, regulates cellular plasticity, but its role in paligenosis has not been studied. Here we first examine paligenosis in digestive-enzyme-secreting chief cells in mouse stomach. We identify Serine/Threonine Kinase 38 (STK38) as a non-canonical YAP1 kinase that phosphorylated and deactivated YAP1 in uninjured chief cells. During paligenosis, STK38 was degraded by autophagy in stage 1, dephosphorylating and activating YAP1. YAP1 activation was necessary and sufficient for the paligenosis that converts chief cells into metaplastic, proliferating progenitors. Additionally, we show STK38, like canonical Hippo kinases, interact with NF2. We also observed the same pattern of YAP1 induction via autophagic destruction of STK38 in other tissues and cell types, suggesting a universal logic model for how the massive autophagy activated in differentiated cells during tissue damage can consequently activate Hippo effectors to induce plasticity for tissue regeneration.

developmental biology↗

bioRxiv2024

Delineating sex-dependent and anatomic decline of motor functions in the SOD1G93A mouse model of amyotrophic lateral sclerosis

The transgenic SOD1G93A mouse model is the most widely used animal model of amyotrophic lateral sclerosis (ALS), a fatal disease of motor neuron degeneration. While genetic background influences onset and progression variability of motor dysfunction, the C57BL/6 background most reliably exhibits robust ALS phenotypes; thus, it is the most widely used strain in mechanistic studies. In this model, paresis begins in the hindlimbs and spreads rostrally to the forelimbs. Males experience earlier onset, greater disease severity, and shorter survival than females. However, the influence of sex on patterns of declining motor function between forelimbs and hindlimbs as well as among distinct, spinal-innervated muscle groups within each limb are not fully understood. To provide a higher resolution framework of degenerating motor function across the body, we conducted more comprehensive, limb-dependent and independent measures of motor decline over the course of disease. Subsequently, we compared the timing and intensity of these features across sex, and we consider to what extent these patterns are conserved in clinical observations from human ALS patients. We found male mice experienced earlier and less localized onset than females. We also report distinct motor features decline at different rates between sexes. Finally, mice showed differences in correlation between the decline of left- and right-side measures of the hindlimb. Consequently, our findings reinforce and refine the utility of the SOD1 mouse in modeling more highly resolved, sex-specific differences in ALS patient motor behavior. This may better guide preclinical studies in stratifying patients by sex and anatomical site of onset.

animal behavior and cognition↗

bioRxiv2024

CD47 predominates over CD24 as a macrophage immune checkpoint in cancer.

Macrophages hold tremendous promise as effectors of cancer immunotherapy, but the best strategies to provoke these cells to attack tumors remain unknown. Here, we evaluated the therapeutic potential of targeting two distinct macrophage immune checkpoints: CD47 and CD24. We found that antibodies targeting these antigens could elicit maximal levels of phagocytosis when combined together in vitro. However, to our surprise, via unbiased genome-wide CRISPR screens, we found that CD24 primarily acts as a target of opsonization rather than an immune checkpoint. In a series of in vitro and in vivo genetic validation studies, we found that CD24 was neither necessary nor sufficient to protect cancer cells from macrophage phagocytosis in most mouse and human tumor models. Instead, anti-CD24 antibodies exhibit robust Fc-dependent activity, and as a consequence, they cause significant on-target hematologic toxicity in mice. To overcome these challenges and leverage our findings for therapeutic purposes, we engineered a collection of 77 novel bispecific antibodies that bind to a tumor antigen with one arm and engage macrophages with the second arm. We discovered multiple novel bispecifics that maximally activate macrophage-mediated cytotoxicity and reduce binding to healthy blood cells, including bispecifics targeting macrophage immune checkpoint molecules in combination with EGFR, TROP2, and CD71. Overall, our findings indicate that CD47 predominates over CD24 as a macrophage immune checkpoint in cancer, and that the novel bispecifics we created may be optimal immunotherapies to direct myeloid cells to eradicate solid tumors.

cancer biology↗

bioRxiv2024

Pancreatic islet alpha cells regulate microtubule stability in neighboring beta cells to tune insulin secretion and induce functional heterogeneity in individual mouse and human islets

We have reported that the microtubule (MT) network in {beta} cells attenuates this function by withdrawing insulin secretory granules (ISGs) away from the plasma membrane. Thus, high glucose-induced MT remodeling is required for robust glucose-stimulated insulin secretion (GSIS). We now show that -cell secreted hormones, Gcg and/or Glp1, regulate the MT stability in {beta} cells. Activating the receptors of Gcg or Glp1 (GcgR or Glp1R) with chemical agonists induces MT destabilization in {beta} ells in the absence of high glucose. In contrast, inhibiting these receptors with antagonists attenuates high glucose-induced MT destabilization. Supporting the significance of this regulation, the MT networks in {beta} cells of islets with higher /{beta} cell ratio are less stable than those with lower /{beta} cell ratio. Within each individual islet, {beta} cells that are located close to cells show faster MTs remodeling upon glucose stimulation than those away. Consequently, islets with higher /{beta} cell ratio secrete more insulin in response to high glucose and plasma membrane depolarization, which is recapitulated by direct Gcg stimulation. These combined results reveal a new MT-dependent pathway by which cells, using Gcg and or Glp1-mediated paracrine signaling, tune {beta}-cell secretion. In addition, the different -{beta} cell ratios in individual islets lead to their heterogeneous secretory responses, which may be important for handling secretory function needs under different physiological conditions. HighlightsO_LIGcg sensitizes glucose-induced MT remodeling in mouse and human {beta} cells C_LIO_LIMT density in single islets anti-correlates with /{beta} cell ratio C_LIO_LIGSIS levels in single islets positively correlate with /{beta} cell ratio C_LIO_LIDifferent /{beta} cell ratio contributes to heterogeneity of single islet GSIS C_LI

cell biology↗

bioRxiv2024

The myokine FGF21 associates with enhanced survival in ALS and mitigates stress-induced cytotoxicity

Amyotrophic lateral sclerosis (ALS) is an age-related and fatal neurodegenerative disease characterized by progressive muscle weakness. There is marked heterogeneity in clinical presentation, progression, and pathophysiology with only modest treatments to slow disease progression. Molecular markers that provide insight into this heterogeneity are crucial for clinical management and identification of new therapeutic targets. In a prior muscle miRNA sequencing investigation, we identified altered FGF pathways in ALS muscle, leading us to investigate FGF21. We analyzed human ALS muscle biopsy samples and found a large increase in FGF21 expression with localization to atrophic myofibers and surrounding endomysium. A concomitant increase in FGF21 was detected in ALS spinal cords which correlated with muscle levels. FGF21 was increased in the SOD1G93A mouse beginning in presymptomatic stages. In parallel, there was dysregulation of the co-receptor, {beta}-Klotho. Plasma FGF21 levels were increased and high levels correlated with slower disease progression, prolonged survival, and increased body mass index. In NSC-34 motor neurons and C2C12 muscle cells expressing SOD1G93A or exposed to oxidative stress, ectopic FGF21 mitigated loss of cell viability. In summary, FGF21 is a novel biomarker in ALS that correlates with slower disease progression and exerts trophic effects under conditions of cellular stress.

neuroscience↗

bioRxiv2024

Dissecting the oncogenic mechanisms of POT1 cancer mutations through deep scanning mutagenesis

Mutations in the shelterin protein POT1 are associated with diverse cancers, but their role in cancer progression remains unclear. To resolve this, we performed deep scanning mutagenesis in POT1 locally haploid human stem cells to assess the impact of POT1 variants on cellular viability and cancer-associated telomeric phenotypes. Though POT1 is essential, frame-shift mutants are rescued by chemical ATR inhibition, indicating that POT1 is not required for telomere replication or lagging strand synthesis. In contrast, a substantial fraction of clinically-validated pathogenic mutations support normal cellular proliferation, but still drive ATR-dependent telomeric DNA damage signaling and ATR-independent telomere elongation. Moreover, this class of cancer-associated POT1 variants elongates telomeres more rapidly than POT1 frame-shifts, indicating they actively drive oncogenesis and are not simple loss-of-function mutations.

cancer biology↗

bioRxiv2024

Molecular insights into phosphoethanolamine cellulose formation and secretion

Phosphoethanolamine (pEtN) cellulose is a naturally occurring modified cellulose produced by several Enterobacteriaceae. The minimal components of the E. coli cellulose synthase complex include the catalytically active BcsA enzyme, an associated periplasmic semicircle of hexameric BcsB, as well as the outer membrane (OM)-integrated BcsC subunit containing periplasmic tetratricopeptide repeats (TPR). Additional subunits include BcsG, a membrane-anchored periplasmic pEtN transferase associated with BcsA, and BcsZ, a conserved periplasmic cellulase of unknown biological function. While events underlying the synthesis and translocation of cellulose by BcsA are well described, little is known about its pEtN modification and translocation across the cell envelope. We show that the N-terminal cytosolic domain of BcsA positions three copies of BcsG near the nascent cellulose polymer. Further, the terminal subunit of the BcsB semicircle tethers the N-terminus of a single BcsC protein to establish a trans-envelope secretion system. BcsCs TPR motifs bind a putative cello-oligosaccharide near the entrance to its OM pore. Additionally, we show that only the hydrolytic activity of BcsZ but not the subunit itself is necessary for cellulose secretion, suggesting a secretion mechanism based on enzymatic removal of mislocalized cellulose. Lastly, we introduce pEtN modification of cellulose in orthogonal cellulose biosynthetic systems by protein engineering.

biophysics↗

bioRxiv2024

Sexual Dimorphism in Age-Dependent Neurodegeneration After Mild Head Trauma in Drosophila: Unveiling the Adverse Impact of Female Reproduction

Environmental insults, including mild head trauma, significantly increase the risk of neurodegeneration. However, it remains challenging to establish a causative connection between early-life exposure to mild head trauma and late-life emergence of neurodegenerative deficits, nor do we know how sex and age compound the outcome. Using a Drosophila model, we demonstrate that exposure to mild head trauma causes neurodegenerative conditions that emerge late in life and disproportionately affect females. Increasing age-at-injury further exacerbates this effect in a sexually dimorphic manner. We further identify Sex Peptide (SP) signaling as a key factor in female susceptibility to post-injury brain deficits. RNA sequencing highlights a reduction in innate immune defense transcripts specifically in mated females during late life. Our findings establish a causal relationship between early head trauma and late-life neurodegeneration, emphasizing sex differences in injury response and the impact of age-at-injury. Finally, our findings reveal that reproductive signaling adversely impacts female response to mild head insults and elevates vulnerability to late-life neurodegeneration.

neuroscience↗

bioRxiv2024

Cognate Antigen Engagement Induces HIV-1 Expression In CD4+ T Cells From People On Long-Term ART

Despite antiretroviral therapy (ART), HIV-1 persists in latently-infected CD4+ T cells, preventing cure. Antigens drive the proliferation of infected cells, precluding latent reservoir decay. However, the relationship between antigen recognition and HIV-1 gene expression is poorly understood since most studies of latency reversal use agents that induce non-specific global T cell activation. Here, we isolated rare CD4+ T cells responding to cytomegalovirus (CMV) or HIV-1 Gag antigens from participants on long-term ART and assessed T cell activation and HIV-1 RNA expression upon co-culture with autologous dendritic cells (DCs) presenting cognate antigens. Physiological presentation of cognate antigens induced broad T cell activation (median 42-fold increase in CD154+CD69+ cells) and significantly increased HIV-1 transcription (median 4-fold), mostly through the induction of rare cells with higher viral expression. Thus, despite low proviral inducibility, physiologic antigen recognition can promote HIV-1 expression, potentially contributing to spontaneous reservoir activity on ART and viral rebound upon ART interruption.

immunology↗

bioRxiv2024

In vitro function, assembly, and interaction of primary cell wall cellulose synthase homotrimers

Plant cell walls contain a meshwork of cellulose fibers embedded into a matrix of other carbohydrate and non-carbohydrate-based biopolymers. This composite material exhibits extraordinary properties, from stretchable and pliable cell boundaries to solid protective shells. Cellulose, a linear glucose polymer, is synthesized and secreted across the plasma membrane by cellulose synthase (CesA), of which plants express multiple isoforms. Different subsets of CesA isoforms are necessary for primary and secondary cell wall biogenesis. Here, we structurally and functionally characterize the Glycine max (soybean) primary cell wall CesAs CesA1, CesA3, and CesA6. The CesA isoforms exhibit robust in vitro catalytic activity. Cryo-electron microscopy analyses reveal their assembly into homotrimeric complexes in vitro in which each CesA protomer forms a cellulose-conducting transmembrane channel with a large lateral opening. Biochemical and co-purification analyses demonstrate that different CesA isoforms interact in vitro, leading to synergistic cellulose biosynthesis. Interactions between CesA trimers are only observed between different CesA isoforms and require the class-specific region (CSR). The CSR forms a hook-shaped extension of CesAs catalytic domain at the cytosolic water-lipid interface. Negative stain and cryo-electron microscopy analyses of mixtures of different CesA isoform trimers reveal their side-by-side arrangement into loose clusters. Our data suggest a model by which CesA homotrimers of different isoforms assemble into cellulose synthase complexes to synthesize and secrete multiple cellulose chains for microfibril formation. Inter-trimer interactions are mediated by fuzzy interactions between their CSR extension.

plant biology↗

bioRxiv2023

Multivalent DNA-encoded lectins on phage enable detecting compositional glycocalyx differences

Selective detection of disease-associated changes in the cellular glycocalyx is a foundation of modern targeted therapies. Detecting minor changes in the density and identity of glycans on the cell surface is a technological challenge exacerbated by lack of 1:1 correspondence between cellular DNA/RNA and glycan structures on cell surface. We demonstrate that multivalent displays of up to 300 lectins on DNA-barcoded M13 phage on a liquid lectin array (LiLA), detects subtle differences in composition and density of glycans on cells ex vivo and in immune cells or organs in animals. For example, constructs displaying 73 copies of diCBM40 lectin per 700x5 nm virion ({varphi}-CBM73) exhibit non-linear ON/OFF-like recognition of sialoglycans on the surface of normal and cancer cells. In contrast, a high-valency {varphi}-CBM290 display, or soluble diCBM40, exhibit canonical progressive scaling in binding with increased epitope density; these constructs cannot amplify the subtle differences detected by {varphi}-CBM73. Similarly, multivalent displays of diCBM40 and Siglec-7 detect differences in the glycocalyx between stem-like and non-stem populations in cancer cells that are not detected with soluble lectins. Multivalent display of lectins on M13 scaffold with protected DNA inside the phage offer non-destructive detection of minor differences in glycocalyx in cells in vitro and in vivo not feasible to currently available technologies.

biochemistry↗

bioRxiv2023

scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular building blocks of the primary pacemaker

The heart is comprised of a variety of specialized cell types that work in unison to maintain blood flow. Here we utilized scRNA-seq analysis to delineate the diversity of cardiac cell types in the zebrafish. With the growing use of the zebrafish to model human heart biology, a deeper insight into its complex cellular composition is critical for a better understanding of heart function, development, and associated malformations. We present a high resolution atlas of zebrafish heart single cells transcriptomics, consisting of over 50 000 cells representing the building blocks of the zebrafish heart at 48 and 72 hpf. We defined 18 discrete cell populations comprising major cell lineages and sublineages of the developing heart. We pinpointed a population of cells likely to be the primary pacemaker and identified the transcriptome profile defining this critical cell type. Our analyses identified two genes, atp1b3b and colec10, which were enriched in the sinoatrial pacemaker cells. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate which is accompanied by arrhythmia or morphological defects, suggesting their novel function in cardiac development and conduction. Additionally, we describe other subpopulations of cardiac cell lineages, including the endothelial and neural cells, whose expression profiles we provide as a resource for further investigations into the cellular and molecular mechanisms of this organ.

developmental biology↗

bioRxiv2023

Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8

Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrates glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loop with the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation. HighlightsO_LICryo-EM structures of substrate and product bound poplar cellulose synthase provide insights into substrate selectivity C_LIO_LISite directed mutagenesis signifies a critical function of the gating loop for catalysis C_LIO_LIMolecular dynamics simulations support persistent gating loop - substrate interactions C_LIO_LIGating loop helps in positioning the substrate molecule to facilitate cellulose elongation C_LIO_LIConserved cellulose synthesis substrate binding mechanism across the kingdoms C_LI

biochemistry↗

bioRxiv2021

Single-cell Atlas Unveils Cellular Heterogeneity and Novel Markers in Human Neonatal and Adult Intervertebral Discs

The origin, composition, distribution, and function of cells in the human intervertebral disc (IVD) has not been fully understood. Here, cell atlases of both human neonatal and adult IVDs have been generated and further assessed by gene ontology pathway enrichment, pseudo-time trajectory, histology, and immunofluorescence. Comparison of cell atlases revealed the presence of two sub-populations of notochordal cells (NCs) and their associated markers in both the neonatal and adult IVDs. Developmental trajectories predicted 7 different cell states that describe the developmental process from neonatal to adult cells in IVD and analyzed the NCs role in the IVD development. A high heterogeneity and gradual transition of annulus fibrosus cells (AFCs) in the neonatal IVD was detected and their potential relevance in IVD development assessed. Collectively, comparing single-cell atlases between neonatal and adult IVDs delineates the landscape of IVD cell biology and may help discovering novel therapeutic targets for IVD degeneration.

developmental biology↗