Biology subjects

Smith, R. G.

Publications and source records attributed to Smith, R. G..

12 recordsLinked to original sources

bioRxiv2026

DNMT1-Mediated Epigenetic Reprogramming Drives KMT2A Amplifications and Rearrangements

MLL/KMT2A amplifications and rearrangements are prevalent in infant, adult, and therapy-induced leukemia; however, the molecular contributors controlling these alterations remain elusive. Here, we reveal that rapid CTCF degradation generates local genome structure alterations at KMT2A and copy gains and rearrangements. We then established a conserved, coordinated interplay between DNA and histone methylation pathways that control CTCF occupancy, and in turn, KMT2A locus stability. For example, DNMT1 overexpression promotes increased H3K9 methylation, reduced CTCF occupancy, and causes KMT2A alterations. However, DNMT1 inhibition suppresses these events and KMT2A alterations caused by topoisomerase II inhibition. Locus-specific epigenome targeting demonstrated that DNA or H3K9 methylation promotes KMT2A copy gains and rearrangement, whereas targeted TET activity suppresses these events upon methylation perturbation or doxorubicin treatment. These findings identify a conserved, coordinated DNA-histone methylation axis governing KMT2A amplifications and rearrangement susceptibility, revealing biomarkers and therapeutic targets to predict and intercept these events in cancer.

cancer biology↗

bioRxiv2026

Integrating epigenomic features reveals principles of chromatin-state organization

The coordinated activities of histone modifications and chromatin-associated proteins establish chromatin states that regulate genome function and cellular identity. However, the organizational principles that distinguish chromatin states across cell types remain incompletely understood. Here, we integrated genome-wide profiles of CTCF, H3K27ac, H3K9ac, H3K27me3, and H3K9me3 at 1-kb resolution to generate a unified representation of chromatin organization in human cells. Unsupervised embedding resolved five principal chromatin states corresponding to constitutive heterochromatin, CTCF-associated architectural chromatin, transcriptionally active chromatin, mixed repressive chromatin, and Polycomb-associated chromatin. Comparative analyses of HCT116 and K562 cells revealed that cell-type-specific epigenomic differences arise predominantly through remodeling of Polycomb-associated chromatin, whereas the remaining chromatin states exhibit broadly similar epigenomic signatures and comparatively limited remodeling. Consistent with this observation, principal component analysis identified H3K27me3 as the primary contributor to genome-wide epigenomic divergence, whereas CTCF represented a secondary contributor. Integration with Hi-C data further demonstrated that CTCF-associated chromatin is strongly enriched at chromatin loop anchors and other local architectural features, linking chromatin-state organization to three-dimensional genome architecture. Together, our findings identify distinct chromatin-state classes that organize the human epigenome and reveal Polycomb-associated chromatin as a key determinant of cell-type-specific epigenomic differences.

genomics↗

bioRxiv2026

Cohesin residence time gates 3D genome response to histone hyperacetylation

Cohesin-mediated loop extrusion and chromatin state-dependent compartmentalization are major drivers of three-dimensional (3D) genome organization. Although epigenomic perturbations are widely assumed to reshape chromatin architecture, the mechanisms that determine how changes in chromatin state are translated into structural reorganization remain poorly understood. Here, we identify cohesin residence time as a key regulator of the genomes architectural response to histone hyperacetylation induced by histone deacetylase inhibition (HDACi). Acute depletion of RAD21 or CTCF weakens chromatin loops but preserves HDACi-induced changes in compartmentalization, contact-scaling behavior, and loop density. In contrast, perturbation of cohesin loading or release produces opposing effects: NIPBL depletion sensitizes and amplifies architectural responses to HDACi, whereas WAPL loss renders the genome largely refractory to HDACi-induced remodeling, suppressing changes in compartments and loop density while stabilizing CTCF-anchored loops. These distinct architectural outcomes occur despite comparable levels of HDACi-induced histone hyperacetylation across genotypes, indicating that differential epigenomic input is not responsible for the observed effects. Together, our findings demonstrate that dynamic cohesin turnover, rather than cohesin chromatin association alone, governs whether epigenomic perturbations are converted into higher-order genome reorganization. These results establish cohesin residence time as a molecular gate linking chromatin state to 3D genome architecture and reveal a previously unrecognized principle underlying chromatin architecture plasticity.

genomics↗

bioRxiv2025

Systemic infections alter cortical transcriptional signatures in Alzheimer's disease

Alzheimers disease (AD) is characterized by neuroinflammation, yet the impact of concurrent systemic infections on the AD brain remains poorly understood. We investigated the molecular mechanisms underlying the central nervous system response to systemic infections in AD by analyzing RNA sequencing data generated in the prefrontal cortex from 202 post-mortem donors (113 AD, 89 controls), where we stratified by the presence of a respiratory infection at the time of death. We identified 763 significantly differentially expressed genes (DEGs) between AD and controls without infection, which were enriched for oxidative phosphorylation and neurodegenerative pathways. In contrast, 122 DEGs distinguished AD from controls during infection, with 57 genes uniquely altered in AD in the presence of infection, including MAPK4, VAV3, and POU3F4, implicating infection-dependent mechanisms of vascular and immune regulation. Pathway activity analysis revealed that infection in AD suppresses some immune and vascular pathways, while enhancing transcriptional and developmental programs. Weighted gene co-expression network analysis uncovered three key modules: one module strongly associated with AD, enriched for aging and signal transduction; one module linked to both AD and infection, highlighting cytoskeletal remodelling and host-pathogen interactions; and one module specific to infection, enriched in astrocytes, pericytes, and endothelial cells, implicating blood-brain barrier dysfunction. These findings suggest that systemic respiratory infections reshape transcriptional programs in the AD brain, dampening immune effector pathways and engaging vascular and host-pathogen processes in blood-brain-barrier-associated cell types. Our results highlight the complex interplay between systemic infection, neuroinflammation, and vascular responses in AD.

neuroscience↗

bioRxiv2025

Exploring the functions of JAKMIP1 in neuronal IL-6/STAT3 signaling and its relevance to chromosome 15q-duplication syndrome

Growing evidence supports neuroinflammation as a risk factor for neurodevelopmental and psychiatric disorders. Interleukin 6 (IL-6), a classical pro-inflammatory cytokine, has been associated with autism spectrum disorder (ASD)-related phenotypes. To better understand molecular factors that modify neuronal cytokine responses in ASD, we investigated potential roles for JAKMIP1, a gene linked to chromosome 15q-duplication syndrome (Dup15q; a form of syndromic ASD), in regulating IL-6/STAT3 signaling. We observe that JAKMIP1 deficiency impairs IL-6/STAT3 signaling and IL-6-induced neuritogenesis in SH-SY5Y cells; and discover that JAKMIP1 may regulate STAT3 expression via its C-terminus, which exhibits nucleoplasmic localization. Additionally, we find that IL-6/STAT3 signaling is altered in Dup15q hiPSCs-derived cortical neurons, which display heightened responsiveness to IL-6; though it is unclear whether and how JAKMIP1 contributes to this. Overall, our findings identify JAKMIP1 as a modulator of neuronal IL-6/STAT3 signaling and support that ASD-linked genetic variants can alter the inflammatory landscape of ASD.

neuroscience↗

bioRxiv2025

Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions

The cohesin complex structures the interphase genome by extruding loops and organizing topologically associating domains (TADs). While cohesin engages chromatin in context- dependent modes, the regulatory influence of chromatin state on these interactions remains unclear. Here, we show that histone hyperacetylation, induced by the histone deacetylase inhibitor trichostatin A (TSA), preferentially disrupts short-range interactions within TADs but spares CTCF-anchored loops, despite reduced cohesin occupancy at these sites. These findings point to two functionally distinct cohesin populations: a TSA- sensitive pool within TADs, likely representing extruding, non-topologically bound cohesin, and a TSA-resistant population at CTCF-CTCF anchors that maintains loops through topological entrapment. Using a semi-in vitro system with TEV-cleavable RAD21, we show that TSA-resistant cohesin at CTCF sites becomes TSA-sensitive after proteolytic cleavage that opens the cohesin ring, showing that it is the topological engagement with DNA that makes cohesin, and CTCF-CTCF loops, TSA-resistant. Notably, we also detect TSA-sensitive cohesin at CTCF sites, suggesting the presence of transient, non-encircling cohesin that either precedes conversion to the stable form or is halted by pre-existing encircling cohesin. Together, our results suggest that cohesin exists in distinct biochemical states: an extruding form found within TADs and at CTCF sites, that is sensitive to hyperacetylation, and a topologically bound form specifically at CTCF-CTCF loops that is insensitive. The former may allow dynamic changes in chromatin loops, while latter ensures robustness of CTCF-anchored loops in response to chromatin state changes.

genomics↗

bioRxiv2025

Visual pathway origins: an electron microscopic volume for connectomic analysis of the human foveal retina

The fovea is a unique specialization of the primate retina and is a promising site for obtaining the first complete connectome of a human central nervous system (CNS) structure. Within the fovea, neural cells and circuits have been miniaturized and compressed during evolution to sample the visual image at highest spatial resolution and begin the neural processing that serves human form, color, and motion perception. Here we present a comprehensive analysis of a sample of human foveal retina using deep learning-based segmentation to reconstruct all cells and synaptic connections at nanoscale resolution. We classified [~]3,000 cells into 51 distinct morphological types based on their structural features and connectivity patterns. Our observations reveal novel synaptic pathways absent in non-human primates, suggesting specialized circuits contribute uniquely to human trichromatic color vision. A biophysical model of the distinct connectomes made by gap junctions (electrical synapses) between short- (S) and medium-long- (ML) wavelength-sensitive cone photoreceptors, suggests chromatic interactions between S and ML cones prior to the first chemical synapse. Segmentation of retinal ganglion cells (RGCs) suggests the presence of only 11 visual pathways, with 5 high-density RGC pathways accounting for over 95% of foveal output to the brain: a dramatic contrast to the 40+ ganglion cell types recognized in mouse retina. Our connectomic analysis reveals distinctive features of human neural circuitry and demonstrates how AI-based computational approaches can advance understanding of human brain structure and function. Significant statementVision begins in the retina, an accessible outpost of the brain located at the back of the eye. When we directly view an object, we use the fovea--a tiny region containing over 50 distinct, densely packed neuron types. How these diverse cells interconnect through synapses to transmit visual information has been difficult to determine. Here, we used artificial intelligence-based computational methods to create a complete wiring diagram--a connectome--mapping every neuron and synapse in a sample of human fovea. This connectomic resource will be freely available to researchers worldwide. Discoveries so far include synaptic circuits linked to human color vision, demonstrating how connectomics can reveal what makes the human nervous system unique.

neuroscience↗

bioRxiv2023

Epigenetic insights into neuropsychiatric and cognitive symptoms in Parkinson's disease: A DNA co-methylation network analysis

Parkinsons disease is a highly heterogeneous disorder, encompassing a complex spectrum of clinical presentation including motor, sleep, cognitive and neuropsychiatric symptoms. We aimed to investigate genome-wide DNA methylation networks in post-mortem Parkinsons disease brain samples and test for region-specific association with common neuropsychiatric and cognitive symptoms. Of traits tested, we identify a co-methylation module in the substantia nigra with significant correlation to depressive symptoms and with ontological enrichment for terms relevant to neuronal and synaptic processes. Notably, expression of the genes annotated to the methylation loci present within this module are found to be significantly enriched in neuronal subtypes within the substantia nigra. These findings highlight the potential involvement of neuronal-specific changes within the substantia nigra with regard to depressive symptoms in Parkinsons disease.

neuroscience↗

bioRxiv2021

Visual stimulation induces distinct forms of sensitization of On-Off direction-selective ganglion cell responses in the dorsal and ventral retina

Experience-dependent modulation of neuronal responses is a key attribute in sensory processing. In the mammalian retina, the On-Off direction-selective ganglion cell (On-Off DSGC) is well known for its robust direction selectivity. However, how the On-Off DSGC light responsiveness dynamically adjusts to the changing visual environment is underexplored. Here, we report that the On-Off DSGC can be transiently sensitized by prior stimuli. Notably, distinct sensitization patterns are found in dorsal and ventral DSGCs that receive visual inputs from lower and upper visual fields respectively. Although responses of both dorsal and ventral DSGCs to dark stimuli (Off responses) are sensitized, only dorsal cells show sensitization of responses to bright stimuli (On responses). Visual stimulation to the dorsal retina potentiates a sustained excitatory input from Off bipolar cells, leading to tonic depolarization of dorsal DSGCs. Such tonic depolarization propagates from the Off to the On dendritic arbor of the DSGC to sensitize its On response. We also identified a previously overlooked feature of DSGC dendritic architecture that can support direct electrotonic propagation between On and Off dendritic layers. By contrast, ventral DSGCs lack a sensitized tonic depolarization and thus do not exhibit sensitization of their On responses. Our results highlight a topographic difference in Off bipolar cell inputs underlying divergent sensitization patterns of dorsal and ventral On-Off DSGCs. Moreover, substantial crossovers between dendritic layers of On-Off DSGCs suggest an interactive dendritic algorithm for processing On and Off signals before they reach the soma.

neuroscience↗

bioRxiv2021

Gain control by sparse, ultra-slow glycinergic synapses

SO_SCPLOWUMMARYC_SCPLOWRetinal ON starburst amacrine cells (SACs) play a critical role in computing stimulus direction, partly in service of image stabilization by optokinetic nystagmus. ON SAC responses are sculpted by rich GABAergic innervation, mostly from neighbouring SACs. Surprisingly, however, we find that glycinergic narrow field amacrine cells (NACs) serve as their dominant source of inhibition during sustained activity. Although NAC inputs constitute only [~]5% of inhibitory synapses to ON SACs, their distinct input patterns enable them to drive glycine inhibition during the both light increments and decrements. NAC-to-ON-SAC inhibition appears to be mediated by ultra-slow non-canonical glycine receptors containing the 4 subunit, which effectively summate during repetitive stimulation. Glycinergic inhibition strongly decreases the output gain of the SACs, ensuring that their direction-selective output is maintained over their operating range. These results reveal an unexpected role for glycinergic pathways and receptor kinetics in modulating direction selectivity in the retina.

neuroscience↗

bioRxiv2020

Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics

Multicompartment models have long been used to study the biophysical mechanisms underlying neural information processing. However, it has been challenging to infer the parameters of such models from data. Here, we build on recent advances in Bayesian simulation-based inference to estimate the parameters of detailed models of retinal neurons whose anatomical structure was based on electron microscopy data. We demonstrate how parameters of a cone, an OFF- and an ON-cone bipolar cell model can be inferred from standard two-photon glutamate imaging with simple light stimuli. The inference method starts with a prior distribution informed by literature knowledge and yields a posterior distribution over parameters highlighting parameters consistent with the data. This posterior allows determining how well parameters are constrained by the data and to what extent changes in one parameter can be compensated for by changes in another. To demonstrate the potential of such data-driven mechanistic neuron models, we created a simulation environment for external electrical stimulation of the retina as used in retinal neuroprosthetic devices. We used the framework to optimize the stimulus waveform to selectively target OFF- and ON-cone bipolar cells, a current major problem of retinal neuroprothetics. Taken together, this study demonstrates how a data-driven Bayesian simulation-based inference approach can be used to estimate parameters of complex mechanistic models with high-throughput imaging data.

neuroscience↗

bioRxiv2019

Retinal horizontal cells use different synaptic sites for global feedforward and local feedback signaling

In the outer plexiform layer (OPL) of the mouse retina, two types of cone photoreceptors (cones) provide input to more than a dozen types of cone bipolar cells (CBCs). This transmission is modulated by a single horizontal cell (HC) type, the only interneuron in the outer retina. Horizontal cells form feedback synapses with cones and feedforward synapses with CBCs. However, the exact computational role of HCs is still debated. Along with performing global signaling within their laterally coupled network, HCs also provide local, cone-specific feedback. Specifically, it has not been clear which synaptic structures HCs use to provide local feedback to cones and global forward signaling to CBCs.\n\nHere, we reconstructed in a serial block-face electron microscopy volume the dendritic trees of five HCs as well as cone axon terminals and CBC dendrites to quantitatively analyze their connectivity. In addition to the fine HC dendritic tips invaginating cone axon terminals, we also identified \"bulbs\", short segments of increased dendritic diameter on the primary dendrites of HCs. These bulbs are located well below the cone axon terminal base and make contact to other cells mostly identified as other HCs or CBCs. Using immunolabeling we show that HC bulbs express vesicular gamma-aminobutyric acid transporters and co-localize with GABA receptor {gamma}2 subunits. Together, this suggests the existence of two synaptic strata in the mouse OPL, spatially separating cone-specific feedback and feedforward signaling to CBCs. A biophysics-based computational model of a HC dendritic branch supports the hypothesis that the spatial arrangement of synaptic contacts allows simultaneous local feedback and global feedforward signaling.

neuroscience↗