Biology subjects

Sanders, S.

Publications and source records attributed to Sanders, S..

14 recordsLinked to original sources

bioRxiv2026

The androgen receptor polyglutamine tract sets the transcriptional balance between muscle growth and atrophy

The androgen receptor (AR) mediates the potent anabolic effects of testosterone and other androgens on skeletal muscle, yet the transcriptional mechanisms coupling this hormonal signal to muscle growth remain unresolved. AR is a ligand-inducible transcription factor whose N-terminal transactivation domain (NTD) harbours a polymorphic polyglutamine (polyQ) tract that, when pathologically expanded, causes spinal and bulbar muscular atrophy (SBMA). To define how the NTD and its polyQ tract shape muscle transcription, we combined an engineered AR allelic series in human myogenic cells with super-resolution and single-molecule imaging, genome-wide binding and expression maps, and human population genetics. Under physiological conditions, androgen-activated AR assembles into dynamic transcriptional condensates and drives an anabolic programme in skeletal muscle through activation of the AP-1 pathway. Progressive expansion of the polyQ tract destabilises AR chromatin binding and shifts its occupancy from promoters to low-affinity distal enhancers, tracking with imaging signatures of muscle aging. In SBMA, this culminates in aberrant transactivation of ectodysplasin A2 receptor (EDA2R), a marker of senescence and inflammation, which engages non-canonical NF-{kappa}B signalling to drive muscle atrophy. Silencing Eda2r attenuated muscle wasting in SBMA mice, establishing this axis as therapeutically actionable. Together, these findings reveal a fundamental mechanism of skeletal-muscle homeostasis and open therapeutic avenues for the many conditions in which muscle atrophy is central.

molecular biology↗

bioRxiv2025

Bigger Is Better Than Many: A Strategy to Optimize Multi-Gene Co-Expression

Large plasmids are often avoided in mammalian co-transfection due to the assumption that they transfect poorly, driving the use of multiple smaller plasmids. Here, we pair finite-state-projection modeling with flow cytometry experiments to compare one-, two-, and three-plasmid delivery of GFP/BFP/RFP. Estimated entry rates were size-independent from 4.9 to 16.4 kb, indicating that plasmid length is not the dominant barrier in this range. Our results suggest that using lipofectamine slightly increases co-transfection efficiency due to the ability of lipoplexes to contain multiple plasmids. However, this benefit is limited to only delivering two plasmids. Additionally, we show that contrary to current beliefs, putting all genes onto the same plasmid both increases the probability that a cell will express all genes of interest and results in a tighter correlation of gene expression levels compared to these multi-plasmid systems. Together, these results identify multi-cargo delivery and not plasmid size as the key constraint on co-transfection and show that single-plasmid designs are generally preferable for applications such as viral-vector production. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/675629v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@251928org.highwire.dtl.DTLVardef@196d1cborg.highwire.dtl.DTLVardef@a781e9org.highwire.dtl.DTLVardef@1420928_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

The nuclear egress complex of MHV-68 is not essential for nuclear egress but mediates C-capsid specificity

Herpesvirus capsids must exit the nucleus to undergo additional maturation steps in the cytoplasm, such as secondary envelopment. This process is orchestrated by the nuclear egress complex (NEC), a conserved heterodimer that deforms the inner nuclear membrane and facilitates capsid egress. While NEC proteins are critical for the release of capsids into the cytoplasm and, therefore, efficient replication in [a]-, {beta}-, and {gamma}-herpesviruses, residual infectivity has been observed in NEC-deficient mutants of certain herpesviruses, including the [a]-herpesvirus Pseudorabies virus (PrV). To investigate the role of the NEC in murine gammaherpesvirus 68 (MHV-68), a mutant virus lacking most of the nucleoplasmic NEC component ORF69 ({Delta}ORF69) was generated. Unlike previous studies relying on transfection-based systems, this study demonstrates that NEC-deficient MHV-68 remains replication-competent, albeit with a significant replication defect. Despite the absence of ORF69, the mutant virus produced infectious progeny in non-complementing cells. Quantitative electron microscopy revealed regular nuclear capsid assembly and DNA packaging. However, while the parental virus primarily exported mature, genome-filled C-capsids, the {Delta}ORF69 mutant exhibited cytoplasmic and extracellular emergence of all capsid forms. These findings indicate that the MHV-68 NEC functions as a quality control checkpoint, selectively facilitating the nuclear egress of mature capsids. In the absence of ORF69, some capsids still egress, likely through alternative, less efficient pathways. Inhibition of cyclin-dependent kinases reduced parental and mutant virus spread, suggesting that {gamma}-herpesviruses exploit host-dependent mechanisms for an alternative nuclear egress route. ImportanceGammaherpesviruses, such as Epstein-Barr virus and Kaposis sarcoma-associated herpesvirus, establish lifelong infections and can contribute to cancer. A crucial step in the viral life cycle depends on the nuclear egress of capsids, a process mediated by the viral nuclear egress complex (NEC). Surprisingly, murine gammaherpesvirus 68 (MHV-68) can translocate capsids from the nucleus to the cytoplasm even when a key NEC component, nucleoplasmic ORF69, is disrupted. Deleting most of ORF69 reduced viral replication but did not entirely block nuclear egress. Instead, the mutant virus allowed both mature and immature capsids to leave the nucleus, suggesting that the NEC functions as a quality control checkpoint for mature capsids. Furthermore, host cell kinases seem to enable alternative routes for egress that do not rely on the NEC. These findings further support the notion that NEC is not strictly necessary and suggest the potential exploitation of host-virus interactions for antiviral approaches.

microbiology↗

bioRxiv2024

HerpesFolds: A proteome-wide structural systems approach reveals insights into protein families and activities of all nine human herpesviruses

Structure predictions have become invaluable tools, but viral proteins are absent from the EMBL/DeepMind AlphaFold database. Here, we provide proteome-wide structure predictions for all nine human herpesviruses and analyze them in depth with explicit scoring thresholds. By clustering these predictions into structural similarity groups, we identified new families, such as the HCMV UL112-113 cluster, which is conserved in alpha-and betaherpesviruses. A domain-level search found protein families consisting of subgroups with varying numbers of duplicated folds. Using large-scale structural similarity searches, we identified viral proteins with cellular folds, such as the HSV-1 US2 cluster possessing dihydrofolate reductase folds and the EBV BMRF2 cluster that might have emerged from cellular equilibrative nucleoside transporters. Our HerpesFolds database is available at https://www.herpesfolds.org/herpesfolds and displays all models and clusters through an interactive web interface. Here, we show that system-wide structure predictions can reveal homology between viral species and identify potential protein functions.

microbiology↗

bioRxiv2023

The genome of the colonial hydroid Hydractinia reveals their stem cells use a toolkit of genes shared with all animals

Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinias i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinias stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from non-self.

genomics↗

bioRxiv2023

NECing goes: flexibility of the herpesvirus nuclear egress complex

The nuclear egress complex (NEC) allows herpesvirus capsids to escape from the nucleus without breaking the nuclear envelope barrier. It assembles into a lattice on the inner nuclear membrane enveloping newly assembled nucleocapsids, which bud into the perinuclear space. The primary virion envelope subsequently fuses with the outer nuclear membrane, releasing the capsid into the cytosol. Here we interrogated the NEC in the context of intact cells infected with pseudorabies or herpes simplex virus using focused-ion beam milling and electron cryo- tomography. We determined the structure of NEC in different conformations and show that it consists of a flexible hexameric lattice that generates curvature through a combination of ordered and disordered domains. After interrogating the intermediate stages of capsid formation, we show that capsid vertex binding may initiate envelopment but does not directly induce curvature formation. These data and many examples of the intermediate stages of nuclear egress paint a detailed holistic view of a versatile transport system.

microbiology↗

bioRxiv2022

Single cells tell their own story: An updated framework for understanding stochastic variations in cell cycle progression in bacteria

Our current understanding of the bacterial cell cycle is framed largely by population-based experiments that focus on the behavior of idealized average cells. Most famously, the contributions of Cooper and Helmstetter help to contextualize the phenomenon of overlapping replication cycles observed in rapidly growing bacteria. Despite the undeniable value of these approaches, their necessary reliance on the behavior of idealized average cells washes out the stochasticity inherent in single cell growth and physiology limiting their mechanistic value. To bridge this gap, we propose an updated and agnostic framework, informed by extant single-cell data, that quantitatively accounts for stochastic variations in single-cell dynamics and the impact of medium composition on cell growth and cell cycle progression. In this framework, stochastic timers sensitive to medium composition impact the relationship between cell cycle events, accounting for observed differences in the relationship between cell cycle events in slow and fast growing cells. We conclude with a roadmap for potential application of this framework to longstanding open questions in the bacterial cell cycle field.

biophysics↗

bioRxiv2022

Synaptotagmin 1 mediates toxicity of botulinum neurotoxin type A

The extreme neurotoxicity of botulinum neurotoxins (BoNTs), broadly used as a therapeutics, is mediated by their direct binding to two plasma membrane receptors: polysialogangliosides (PSGs) and serotype-dependently either synaptotagmin 1/2 (Syt1/2) or synaptic vesicle glycoprotein 2 (SV2). Here, we demonstrate that although BoNT/A serotype binds directly to PSG and SV2, its neurotoxicity depends on Syt1. Using single-molecule superresolution microscopy of pathological concentrations of BoNT/A holotoxins, we demonstrate that the toxin binds to a preassembled PSG-Syt1 complex that forms nanoclusters with SV2 on the plasma membrane of hippocampal neurons. This coincidental interaction controls the selective endocytic targeting of BoNT/A into synaptic vesicles, leading to incapacitation of neuronal communication. Our results suggest that Syt1-SV2 plasma membrane nanoclusters may acts as a common target for various BoNT serotypes. One-Sentence SummaryBoNT/A hijacks an intrinsic tripartite PSG-Syt1-SV2 endocytic sorting mechanism to incapacitate neuronal communication

neuroscience↗

bioRxiv2021

Expansion of RNA sequence diversity and RNA editing rates throughout human cortical development

Post-transcriptional modifications by RNA editing are essential for neurodevelopment, yet their developmental and regulatory features remain poorly resolved. We constructed a full temporal view of base-specific RNA editing in the developing human cortex, from early progenitors through fully mature cells found in the adult brain. Developmental regulation of RNA editing is characterized by an increase in editing rates for more than 10,000 selective editing sites, shifting between mid-fetal development and infancy, and a massive expansion of RNA hyper-editing sites that amass in the cortex through postnatal development into advanced age. These sites occur disproportionally in 3UTRs of essential neurodevelopmental genes. These profiles are preserved in non-human primate and murine models, illustrating evolutionary conserved regulation of RNA editing in mammalian cortical development. RNA editing levels are commonly genetically regulated (editing quantitative trait loci, edQTLs) consistently across development or predominantly during prenatal or postnatal periods. Both consistent and temporal-predominant edQTLs co-localize with risk loci associated with neurological traits and disorders, including attention deficit hyperactivity disorder, schizophrenia, and sleep disorders. These findings expand the repertoire of highly regulated RNA editing sites in the brain and provide insights of how epitranscriptional sequence diversity by RNA editing contributes to neurodevelopment.

developmental biology↗

bioRxiv2020

Coupled Control of Distal Axon Integrity and Somal Responses to Axonal Damage by the Palmitoyl Acyltransferase ZDHHC17

After optic nerve crush (ONC), the cell bodies and distal axons of most retinal ganglion cells (RGCs) degenerate. RGC somal and distal axon degeneration were previously thought to be controlled by two distinct pathways, involving activation of the kinase DLK and loss of the axon survival factor NMNAT2, respectively. However, we found that mutual palmitoylation by the palmitoyl acyltransferase ZDHHC17 couples the DLK and NMNAT2 signals, which together form a "trust, but verify system". In healthy optic nerves, ZDHHC17-dependent palmitoylation ensures NMNAT-dependent distal axon integrity, while following ONC, ZDHHC17-dependent palmitoylation is critical for DLK-dependent somal degeneration. We found that ZDHHC17 also controls survival-versus-degeneration decisions in sensory neurons and identified motifs in NMNAT2 and DLK that govern their ZDHHC17-dependent regulation. These findings suggest that the control of somal and distal axon integrity should be considered as a single, holistic process, involving two palmitoylation-dependent pathways acting in concert.

neuroscience↗

bioRxiv2019

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Desiree, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes.

plant biology↗

bioRxiv2019

Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex

Variation in gene expression underlies neurotypical development, while genomic variants contribute to neuropsychiatric disorders. BrainVar is a unique resource of paired whole-genome sequencing and bulk-tissue RNA-sequencing from the human dorsolateral prefrontal cortex of 176 neurotypical individuals across prenatal and postnatal development, providing the opportunity to assay genomic and transcriptomic variation in tandem. Leveraging this resource, we identified rare premature stop codons with commensurate reduced and allele-specific expression of corresponding genes, and common variants that alter gene expression (expression quantitative trait loci, eQTLs). Categorizing eQTLs by prenatal and postnatal effect, genes affected by temporally-specific eQTLs, compared to constitutive eQTLs, are enriched for haploinsufficiency, protein-protein interactions, and neuropsychiatric disorder risk loci. Expression levels of over 12,000 genes rise or fall in a concerted late-fetal transition, with the transitional genes enriched for cell type specific genes and neuropsychiatric disorder loci, underscoring the importance of cataloguing developmental trajectories in understanding cortical physiology and pathology.\n\nHighlightsO_LIWhole-genome and RNA-sequencing across human prefrontal cortex development in BrainVar\nC_LIO_LIGene-specific developmental trajectories characterize the late-fetal transition\nC_LIO_LIIdentification of constitutive, prenatal-specific, postnatal-specific, and rare eQTLs\nC_LIO_LIIntegrated analysis reveals genetic and developmental influences on CNS traits and disorders\nC_LI

neuroscience↗

bioRxiv2018

The autism-associated gene Scn2a plays an essential role in synaptic stability and learning

Autism spectrum disorder (ASD) is strongly associated with de novo gene mutations. One of the most commonly affected genes is SCN2A. ASD-associated SCN2A mutations impair the encoded protein NaV1.2, a sodium channel important for action potential initiation and propagation in developing excitatory cortical neurons. The link between an axonal sodium channel and ASD, a disorder typically attributed to synaptic or transcriptional dysfunction, is unclear. Here, we show NaV1.2 is unexpectedly critical for dendritic excitability and synaptic function in mature pyramidal neurons, in addition to regulating early developmental axonal excitability. NaV1.2 loss reduced action potential backpropagation into dendrites, impairing synaptic plasticity and synaptic stability, even when NaV1.2 expression was disrupted late in development. Furthermore, we identified behavioral impairments in learning and sociability, paralleling observations in children with SCN2A loss. These results reveal a novel dendritic function for NaV1.2, providing insight into cellular mechanisms likely underlying circuit and behavioral dysfunction in ASD.

neuroscience↗

bioRxiv2016

Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

Autism spectrum disorder (ASD) risk is influenced by both common polygenic and de novo variation. The purpose of this analysis was to clarify the influence of common polygenic risk for ASDs and to identify subgroups of cases, including those with strong acting de novo variants, in which different types of polygenic risk are relevant. To do so, we extend the transmission disequilibrium approach to encompass polygenic risk scores, and introduce the polygenic transmission disequilibrium test. Using data from more than 6,400 children with ASDs and 15,000 of their family members, we show that polygenic risk for ASDs, schizophrenia, and greater educational attainment is over transmitted to children with ASDs in two independent samples, but not to their unaffected siblings. These findings hold independent of proband IQ. We find that common polygenic variation contributes additively to risk in ASD cases that carry a very strong acting de novo variant. Lastly, we find evide ...

genetics↗