Biology subjects

Wheeler, G.

Publications and source records attributed to Wheeler, G..

9 recordsLinked to original sources

bioRxiv2026

Sequestration of growth cone surface proteins by cytoplasmic Lrrtm2 induces de novo amygdala innervation by cerebral cortex associative neurons

Precise establishment of distinct cerebral cortex circuits is essential for sensorimotor function, high-level cognition, and cross-modality integration and association. Although an increasing set of molecular controls over subtype-specific cortical wiring have been identified, much less is known about how molecules in growth cones (GCs) regulate precise long-range projection of axons through complex environments, or how dysregulation of GC molecular machinery disrupts precision of circuit formation. Here, we discover a generalizable mechanism for regulation of precise circuit wiring by focusing on callosal projection neurons (CPN), which link cortical hemispheres via the corpus callosum. CPN are centrally involved in associative and cognitive function, and are often disrupted in people with autism spectrum disorders (ASD) and intellectual disabilities (ID). We identify dysregulated subcellular CPN GC proteomes in vivo after CPN-specific deletion of Bcl11a/Ctip1, a transcription factor (TF) with variants that cause ASD/ID in humans, and validate localization of dysregulated proteins to CPN GCs ex vivo. We identify that disruption of Lrrtm2 - a canonically postsynaptic transmembrane protein - in CPN GCs specifically induces de novo innervation of the amygdala, an evolutionarily ancient regulator of social behavior, cognition, and anxiety that is abnormally activated in humans with ASD. Mechanistically, we identify that deletion of Bcl11a from CPN disrupts targeting of Lrrtm2 to CPN GC membranes, causing cytoplasmic sequestration of key CPN GC surface proteins, and resulting in aberrant innervation of basolateral amygdala (BLA), which is typically targeted by evolutionarily older archicortex. Together, this work connects deletion of a causal ASD/ID TF, dysregulation of a non-canonical control over GC surface protein remodeling, and formation of a de novo, subtype-specific circuit between cerebral cortex and BLA - similar mechanisms likely generalize across neuron subtypes. These results expand conceptual understanding of how diverse circuits are precisely constructed and potentially evolve, and how coordinated dysregulation of GC molecules can disrupt precise subtype-specific circuitry, contributing to diverse neurodevelopmental and neuropsychiatric disorders.

neuroscience↗

bioRxiv2025

REMEDY: REpair of heterozygous Mutations independent of Exogenous Donor template with high efficiency using allele specific CRISPR targeting and HDR enhancers

We report the development of REMEDY (REpair of heterozygous Mutations independent of Exogenous Donor template with high efficiencY), a genome editing strategy that allows efficient repair of heterozygous mutations in human and mouse cells without necessitating an exogenous donor DNA template. Here, we used in-PAM or near-PAM CRISPR strategies to induce a double-strand break (DSB) in mutant alleles. Following the DSB, the wild-type homologous chromosome itself serves as an endogenous DNA donor template and initiates the correction of the mutant allele. Concurrently treating the cells with HDR enhancers, such as AZD7648, further improved the efficiency of the correction. We demonstrated the utility of REMEDY in the context of six different diseases with heterozygous mutations such as IBMPFD, cystic fibrosis, progeria, ITPR3-associated combined immunodeficiency, ACTA1, and TBCD in human patient derived primary cells and complementary mouse model cell lines. O_FIG O_LINKSMALLFIG WIDTH=91 HEIGHT=200 SRC="FIGDIR/small/641201v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@5f6c41org.highwire.dtl.DTLVardef@bc50d5org.highwire.dtl.DTLVardef@15edca2org.highwire.dtl.DTLVardef@e74ada_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

genetics↗

bioRxiv2025

Histone Deacetylase Inhibitor Largazole Deactivates A Subset of Superenchancers and Causes Mitotic Chromosome Mis-alignment by Suppressing SP1 and BRD4

Histone deacetylase inhibitors have been investigated as potential therapeutic agents for cancer and other diseases. HDIs are known to promote histone acetylation, resulting in an open chromatin conformation and generally increased gene expression. In previous work, we reported that a subset of genes, particularly those regulated by superenhancers, can be suppressed by the HDAC inhibitor largazole. To elucidate the molecular mechanisms underlying gene repression by largazole, we conducted transposase-accessible chromatin sequencing, ChIP-seq, and RNA-seq studies. Our findings revealed that while largazole treatment generally enhances chromatin accessibility, it selectively decreases the accessibility of a subset of superenhancer regions. These genomic regions, showing the most significant changes in the presence of largazole, were enriched with transcription factor binding motifs for SP1, BRD4, CTCF, and YY1. ChIP-seq analysis confirmed reduced binding of BRD4 and SP1 at their respective sites on chromatin, particularly at superenhancers regulating genes such as ID1, c-Myc and MCMs. Largazole exerts its effects by inhibiting DNA replication, RNA processing, and cell cycle progression, partially through the suppression of SP1 expression. Depletion of SP1 by shRNA mimics several key biological effects of largazole and increases cellular sensitivity to the drug. Specific to cell cycle regulation, we demonstrated that largazole disrupts G/M transition by interfering with chromosome alignment during metaphase, a phenotype also observed with SP1 depletion. Our results suggest that largazole exerts its growth-inhibitory effect by suppressing BRD4 and SP1 at super-enhancers, leading to cytostatic responses and mitotic dysfunction.

cancer biology↗

bioRxiv2024

Nutrient addition in grasslands worldwide reveals proportional plant diversity decline across spatial scales but little change in beta diversity

Nutrient enrichment typically causes local plant diversity declines. A common but untested expectation is that nutrient enrichment also reduces variation in nutrient conditions among localities and selects for a smaller pool of species, causing greater diversity declines at larger than local scales and thus biotic homogenization. Here we apply a framework that links changes in species richness across scales to changes in the numbers of spatially restricted and widespread species for a standardized nutrient addition experiment across 72 grasslands on six continents. Overall, we find proportionally similar species loss at local and larger scales, suggesting similar declines of spatially restricted and widespread species, and no biotic homogenization after 4 years and up to 14 years of treatment. These patterns of diversity changes are generally consistent across species groups. Thus, nutrient enrichment poses threats to plant diversity, including for widespread species that are often critical for ecosystem functions.

ecology↗

bioRxiv2024

Brain-wide neuronal circuit connectome of human glioblastoma

Glioblastoma (GBM), a universally fatal brain cancer, infiltrates the brain and can be synaptically innervated by neurons, which drives tumor progression1-6. Synaptic inputs onto GBM cells identified so far are largely short-range and glutamatergic7-9. The extent of integration of GBM cells into brain-wide neuronal circuitry is not well understood. Here we applied a rabies virus-mediated retrograde monosynaptic tracing approach10-12 to systematically investigate circuit integration of human GBM organoids transplanted into adult mice. We found that GBM cells from multiple patients rapidly integrated into brain-wide neuronal circuits and exhibited diverse local and long-range connectivity. Beyond glutamatergic inputs, we identified a variety of neuromodulatory inputs across the brain, including cholinergic inputs from the basal forebrain. Acute acetylcholine stimulation induced sustained calcium oscillations and long-lasting transcriptional reprogramming of GBM cells into a more invasive state via the metabotropic CHRM3 receptor. CHRM3 downregulation suppressed GBM cell invasion, proliferation, and survival in vitro and in vivo. Together, these results reveal the capacity of human GBM cells to rapidly and robustly integrate into anatomically and molecularly diverse neuronal circuitry in the adult brain and support a model wherein rapid synapse formation onto GBM cells and transient activation of upstream neurons may lead to a long-lasting increase in fitness to promote tumor infiltration and progression.

cancer biology↗

bioRxiv2020

Genome-wide binding analysis of 195 DNA Binding Proteins reveals "reservoir" promoters and human specific SVA-repeat family regulation

A key aspect in defining cell state is the complex choreography of DNA binding events in a given cell type, which in turn establishes a cell-specific gene-expression program. In the past two decades since the sequencing of the human genome there has been a deluge of genome-wide experiments which have measured gene-expression and DNA binding events across numerous cell-types and tissues. Here we re-analyze ENCODE data in a highly reproducible manner by utilizing standardized analysis pipelines, containerization, and literate programming with Rmarkdown. Our approach validated many findings from previous independent studies, underscoring the importance of ENCODEs goals in providing these reproducible data resources. This approach also revealed several new findings: (i) 1,362 promoters, termed reservoirs, have up to 111 different DNA binding-proteins localized on one promoter yet do not have any expression of steady-state RNA (ii) The human specific SVA repeat element may have been co-opted for enhancer regulation. Collectively, this study performed by the students of a CU Boulder computational biology class (BCHM 5631 - Spring 2020) demonstrates the value of reproducible findings and how resources like ENCODE that prioritize data standards can foster new findings with existing data in a didactic environment.

genomics↗

bioRxiv2020

A novel Ca2+ signalling pathway co-ordinates environmental phosphorus sensing and nitrogen metabolism in marine diatoms

Diatoms are a diverse and globally important phytoplankton group, responsible for an estimated 20% of carbon fixation on Earth. They frequently form spatially extensive phytoplankton blooms, responding rapidly to increased availability of nutrients including phosphorus and nitrogen. Although it is well established that diatoms are common first-responders to nutrient influxes in aquatic ecosystems, little is known of the sensory mechanisms that they employ for nutrient perception. Here we show that diatoms use a novel and highly-sensitive Ca2+-dependent signalling pathway, not previously described in eukaryotes, to sense and respond to the critical macronutrient phosphorus. We demonstrate that phosphorus-Ca2+ signalling is essential for regulating diatom recovery from phosphorus limitation, by controlling rapid and substantial increases in nitrogen assimilation. Phosphorus-Ca2+ signalling thus mediates fundamental cross-talk between the vital nutrients P and N to maximise resource competition, and likely governs the success of diatoms as major bloom formers in regions of pulsed nutrient supply. Importantly, our study demonstrates that distinct mechanisms for nutrient sensing have evolved in photosynthetic eukaryotes.

microbiology↗

bioRxiv2020

A novel single-domain Na+-selective voltage-gated channel in photosynthetic eukaryotes

The evolution of Na+-selective four-domain voltage-gated channels (4D-Navs) in animals allowed rapid Na+-dependent electrical excitability, and enabled the development of sophisticated systems for rapid and long-range signalling. Whilst bacteria encode single-domain Na+-selective voltage-gated channels (BacNav), they typically exhibit much slower kinetics than 4D-Navs, and are not thought to have crossed the prokaryote-eukaryote boundary. As such, the capacity for rapid Na+-selective signalling is considered to be confined to certain animal taxa, and absent from photosynthetic eukaryotes. Certainly, in land plants, such as the Venus Flytrap where fast electrical excitability has been described, this is most likely based on fast anion channels. Here, we report a unique class of eukaryotic Na+-selective single-domain channels (EukCatBs) that are present primarily in haptophyte algae, including the ecologically important calcifying coccolithophores. The EukCatB channels exhibit very rapid voltage-dependent activation and inactivation kinetics, and sensitivity to the highly selective 4D-Nav blocker tetrodotoxin. The results demonstrate that the capacity for rapid Na+-based signalling in eukaryotes is not restricted to animals or to the presence of 4D-Navs. The EukCatB channels therefore represent an independent evolution of fast Na+-based electrical signalling in eukaryotes that likely contribute to sophisticated cellular control mechanisms operating on very short time scales in unicellular algae. One Sentence SummaryThe capacity for rapid Na+-based signalling has evolved in ecologically important coccolithophore species via a novel class of voltage-gated Na+ channels, EukCatBs.

microbiology↗

bioRxiv2019

Chytrid rhizoid morphogenesis is adaptive and resembles hyphal development in ‘higher’ fungi

Fungi are major components of the Earths biosphere [1], sustaining many critical ecosystem processes [2, 3]. Key to fungal prominence is their characteristic cell biology, our understanding of which has been principally based on higher dikaryan hyphal and yeast forms [4-6]. The early-diverging Chytridiomycota (chytrids) are ecologically important [2, 7, 8] and a significant component of fungal diversity [9-11], yet their cell biology remains poorly understood. Unlike dikaryan hyphae, chytrids typically attach to substrates and feed osmotrophically via anucleate rhizoids [12]. The evolution of fungal hyphae appears to have occurred from lineages exhibiting rhizoidal growth [13] and it has been hypothesised that a rhizoid-like structure was the precursor to multicellular hyphae and mycelial feeding in fungi [14]. Here we show in a unicellular chytrid, Rhizoclosmatium globosum, that rhizoid development has equivalent features to dikaryan hyphae and is adaptive to resource availability. Rhizoid morphogenesis exhibits analogous properties with growth in hyphal forms, including tip production, branching and decreasing fractal geometry towards the growing edge, and is controlled by {beta}-glucan-dependent cell wall synthesis and actin polymerisation. Chytrid rhizoids from individual cells also demonstrate adaptive morphological plasticity in response to substrate availability, developing a searching phenotype when carbon starved and exhibiting spatial differentiation when interacting with particulate substrates. Our results show striking similarities between unicellular early-diverging and dikaryan fungi, providing insights into chytrid cell biology, ecological prevalence and fungal evolution. We demonstrate that the sophisticated cell biology and developmental plasticity previously considered characteristic of hyphal fungi are shared more widely across the Kingdom Fungi and therefore could be conserved from their most recent common ancestor.

developmental biology↗