Biology subjects

Choi, J. J.

Publications and source records attributed to Choi, J. J..

12 recordsLinked to original sources

bioRxiv2026

Regulatory divergence and functional diversification of a c-di-GMP-controlled sigma factor in Actinomycetota

Members of the {sigma}28 family of alternative {sigma} factors typically regulate genes involved in flagellar biosynthesis. However, the only member of the {sigma}28 family present in the actinobacterial genus Streptomyces, WhiG, controls the differentiation of aerial hyphae into spores. WhiG activity is regulated by the second messenger c-di-GMP, which arms its cognate anti-{sigma}, RsiG, to bind and sequester the {sigma} factor. Understanding WhiG evolution can thus shed light on the diversity of processes regulated by c-di-GMP across Phylum Actinomycetota. Members of Actinomycetota comprise highly diverse filamentous and unicellular, flagellated and non-flagellated species, and the actinobacterial ancestor is predicted to have been motile. Here, our systematic analysis reveals that WhiG homologs are broadly distributed throughout the Actinomycetota and form two distinct clades: WhiG1, whose members have retained the ancestral association with the flagellar biosynthesis cluster and are not regulated by an RsiG anti-{sigma}, and WhiG2, whose members are typically regulated by RsiG via c-di-GMP. Bioinformatic analysis of their target regulons suggests that this {sigma} factor has significantly diversified in function to control various processes, including motility, chemotaxis, Type IV pili synthesis, sporulation, antibiotic biosynthesis, and c-di-GMP metabolism across diverse actinobacterial species. These findings highlight a phylogenetic split in the regulation and function of this key transcription factor throughout the phylum. ImportanceMounting global responses to dynamic environmental conditions is a crucial function that bacterial cells must perform. Global regulatory networks are most often studied in individual species, however, understanding how regulatory networks have evolved in distinct bacterial lineages remains an outstanding question. The alternative factor WhiG, which is found in the actinobacterial genus Streptomyces, is a dedicated sporulation , yet has long been known to have a close evolutionary relationship to factors that are responsible for regulation of flagellar biosynthesis. Analysis of the distribution of WhiG in Phylum Actinomycetota reveals that homologs typically co-occur with either a flagellar cluster or the c-di-GMP-binding anti- RsiG. Functional predictions of WhiG target genes across the Actinomycetota further reveal that diverse biological processes are controlled by these transcription factors, most notably motility, chemotaxis, Type IV pili biosynthesis, regulation of gene expression, c-di-GMP metabolism, and specialized metabolite biosynthesis.

microbiology↗

bioRxiv2025

Inferring virtual cell environments using multi-agent reinforcement learning

1Single cells interact continuously to form a cell environment that drives key biological processes. Cells and cell environments are highly dynamic across time and space, fundamentally governed by molecular mechanisms, such as gene expression. Recent sequencing techniques measure single-cell-level gene expression under specific conditions, either temporally or spatially. Using these datasets, emerging works, such as virtual cells, can learn biologically useful representations of individual cells. However, these representations are typically static and overlook the underlying cell environment and its dynamics. To address this, we developed CellTRIP, a multi-agent reinforcement learning method that infers a virtual cell environment to simulate the cell dynamics and interactions underlying given single-cell data. Specifically, cells are modeled as individual agents with dynamic interactions, which can be learned through self-attention mechanisms via reinforcement learning. CellTRIP also applies novel truncated reward boot-strapping and adaptive input rescaling to stabilize training. We can in-silico manipulate any combination of cells and genes in our learned virtual cell environment, predict spatial and/or temporal cell changes, and prioritize corresponding genes at the single-cell level. We applied and benchmarked CellTRIP on various simulated and real gene expression datasets, including recapitulating cellular dynamic processes simulated by gene regulatory networks and stochastic models, imputing spatial organization of mouse cortical cells, predicting developmental gene expression changes after drug treatment in cancer cells, and spatiotemporal reconstruction of Drosophila embryonic development, demonstrating its outperformance and broad applicability. Interactive manipulation of those virtual cell environments, including in-silico perturbation, can prioritize spatial and developmental genes for single-cell-level changes, enabling the generation of new insights into cell dynamics over time and space. CellTRIP is open source as a general tool and available at github.com/daifengwanglab/CellTRIP.

bioinformatics↗

bioRxiv2025

Dynamic landscapes of gene regulatory networks in early mammalian neurogenesis: Insights into brain evolution and disorder risk

Neurogenesis--the process of generating neurons--is governed by dynamic transcriptional programs that vary across time, brain regions, and cell types, forming regionally specialized neuronal circuits. To understand these dynamics, we constructed a comprehensive gene regulatory network (GRN) resource encompassing 22 neurogenic lineages from human, macaque, and mouse, enabling cross-species and cross-regional comparisons. Leveraging state-of-the-art trajectory analysis and GRN inference, we characterized temporal regulatory dynamics and introduced a "dynamic score" to identify key subnetworks with lineage-specific dynamics, including hundreds of regulons and co-regulatory modules. Our analysis uncovered both known and novel candidate regulators driving neuronal differentiation and regional identity, spanning the entire human brain, as well as evolutionary divergence in neurogenic GRNs distinguishing human brains. Mapping risk genes to the resource helped understand associated early gene regulatory dynamics with 35 neurodevelopmental disorders and traits including autism, schizophrenia, severe intellectual disability, and microcephaly. This resource is publicly available as an interactive online platform.

developmental biology↗

bioRxiv2025

Aberrant Fibro-Adipogenic Progenitor Subpopulations Drive Volumetric Muscle Loss-Induced Fibrosis

Volumetric muscle loss (VML) injuries result in chronic fibrosis, inflammation, and persistent functional deficits. Fibro-adipogenic progenitor (FAP) cells are a heterogeneous, muscle-resident stromal cell population that play a crucial role in muscle regeneration, but also contribute to fibrosis in muscle disease. The role of FAPs in VML is not well established and may be critical target to ensure functional muscle regeneration after VML. We utilized a VML model in the mouse quadriceps to study the location, secretome, surface marker distribution, gene expression, and single-cell transcriptional profile of FAPs after VML. After VML, a subpopulation of FAPs highly expressed {beta}1-integrin and were elevated in the post-VML muscle tissue; these FAPs had increased fibrotic gene expression and increased myofibroblast differentiation potential. Transforming growth factor-{beta}1 (TGF-{beta}1) and tissue inhibitor of matrix metalloproteinase 1 (TIMP1) were identified as secreted proteins from VML derived FAPs that produced both pro-fibrotic and anti-myogenic signaling. These data establish an aberrant FAP sub-population that are elevated in VML injury and provides novel targets for future scarless muscle regeneration in VML.

pathology↗

bioRxiv2025

COSIME: Cooperative multi-view integration and Scalable and Interpretable Model Explainer

Single-omics approaches often provide a limited perspective on complex biological systems, whereas multi-omics integration enables a more comprehensive understanding by combining diverse data views. However, integrating heterogeneous data types and interpreting complex relationships between biological features--both within and across views--remains a major challenge. To address these challenges, we introduce COSIME (Cooperative Multi-view Integration with a Scalable and Interpretable Model Explainer). COSIME applies the backpropagation of a learnable optimal transport algorithm to deep neural networks, thus enabling the learning of latent features from several views to predict disease phenotypes. It also incorporates Monte Carlo sampling to enable interpretable assessments of both feature importance and pairwise feature interactions for both within and across views. We applied COSIME to both simulated and real-world datasets--including single-cell transcriptomics, spatial transcriptomics, epigenomics and metabolomics--to predict Alzheimers disease-related phenotypes. Benchmarking of existing methods demonstrated that COSIME improves prediction accuracy and provides interpretability. For example, it reveals that synergistic interactions between astrocyte and microglia genes associated with Alzheimers disease are more likely to localize at the edges of the middle temporal gyrus. Finally, COSIME is also publicly available as an open source tool.

bioinformatics↗

bioRxiv2024

Single-cell multi-omics analysis reveals cooperative transcription factors for gene regulation in oligodendrocytes

Oligodendrocytes are the myelinating cells within the central nervous system. Many oligodendrocyte genes have been associated with brain disorders. However, how transcription factors (TFs) cooperate for gene regulation in oligodendrocytes remains largely uncharacterized. To address this, we integrated scRNA-seq and scATAC-seq data to identify the cooperative TFs that co-regulate the target gene (TG) expression in oligodendrocytes. First, we identified co- binding TF pairs whose binding sites overlapped in oligodendrocyte-specific regulatory regions. Second, we trained a deep learning model to predict the expression level of each TG using the expression levels of co-binding TFs. Third, using the trained models, we computed the TF importance and TF-TF interaction scores for predicting TG expression by the Shapley interaction scores. We found that the co-binding TF pairs involving known important TF pairs for oligodendrocyte differentiation, such as SOX10-TCF12, SOX10-MYRF, and SOX10-OLIG2, exhibited significantly higher Shapley scores than others (t-test, p-value < 1e-4). Furthermore, we identified 153 oligodendrocyte-associated eQTLs that reside in oligodendrocyte-specific enhancers or promoters where their eGenes (TGs) are regulated by cooperative TFs, suggesting potential novel regulatory roles from genetic variants. We also experimentally validated some identified TF pairs such as SOX10-OLIG2 and SOX10-NKX2.2 by co-enrichment analysis, using ChIP-seq data from rat peripheral nerve.

bioinformatics↗

bioRxiv2023

Microbubble dynamics in brain microvessels

BackgroundFocused ultrasound stimulation of microbubbles is being tested in clinical trials for its ability to deliver drugs across the blood-brain barrier (BBB). This technique has the potential to treat neurological diseases by preferentially delivering drugs to targeted regions. Yet despite its potential, the physical mechanisms by which microbubbles alter the BBB permeability remain unclear, as direct observations of microbubbles oscillating in cerebral capillaries have never been previously recorded. The purpose of this study was to reveal how microbubbles respond to ultrasound when within the microvessels of living brain tissue. MethodsMicrobubbles in acute brain slices acquired from juvenile rats perfused with a concentrated solution of SonoVue(R) and dye were exposed to ultrasound pulses typically used in BBB disruption (center frequency: 1 MHz, peak-negative pressure: 0.2-1 MPa, pulse length: up to 10 ms) and observed using high-speed microscopy at up to 10 million frames per second. ResultsWe observed that microbubbles can exert mechanical stresses on a wide region of tissue beyond their initial location and immediate surroundings. A single microbubble can apply mechanical stress to parenchymal tissues several micrometers away from the vessel. Microbubbles can travel at high velocities within the microvessels, extending their influence across tens of micrometers during a single pulse. With longer pulses and higher pressures, microbubbles could penetrate the vessel wall and move through the parenchyma, refuting a previous assumption that microbubbles are confined to vessels. The probability of extravasation scales approximately with mechanical index, being rare at low pressures, but much more common at a mechanical index [≥] 0.6. ConclusionsThese observations provide important insight into microbubble dynamics in microvessels, and are critical leads into ultimately identifying the microbubble activities that lead to both safe drug delivery and into activities we seek to avoid, such as petechiae and other bioeffects.

bioengineering↗

bioRxiv2020

Single Cell Deconstruction of Muscle Stem Cell Heterogeneity During Aging Reveals Sensitivity to the Neuromuscular Junction

During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function in that impacts mobility and quality of life. Muscle loss is often associated with denervation and a loss of resident muscle stem cells (satellite cells or MuSCs), but the relationship between MuSCs and neural control has not been established. Herein, using a combination of single-cell transcriptomic analysis, high-resolution immunofluorescence imaging and transgenic young and aged mice as well as from mice with neuromuscular degeneration (Sod1-/-), a compensatory neuro-responsive function for a subset of MuSCs was identified. Genetic rescue of motor neurons in Sod1-/- mice reduced this subset of MuSCs and restored integrity of the neuromuscular junction (NMJ) in a manner akin to young muscle. Administration of severe neuromuscular trauma induced young MuSCs to specifically engraft in a position proximal to the NMJ but in aging, this behavior was abolished. Contrasting the expression programs of young and aged MuSCs after muscle injury at the single cell level, we observed distinctive gene expression programs between responses to neuro-muscular degeneration and muscle trauma. Collectively, these data reveal MuSCs sense synaptic perturbations during aging and neuro-muscular deterioration, and can exert support for the NMJ, particularly in young muscle. HighlightsO_LITranscriptional landscapes of single satellite cells from different ages before and after injury as well as neurodegenerative models before and after nervous rescue C_LIO_LIA population of satellite cells reside in close proximity to neuromuscular synapse, which are lost with age C_LIO_LIDenervation promotes satellite cell engraftment into post-synaptic regions of young as opposed to aged muscle C_LI

cell biology↗

bioRxiv2020

Regenerating motor neurons prime muscle stem cells for myogenesis by enhancing protein synthesis and mitochondrial bioenergetics

Throughout life, skeletal muscle, the arbiter of voluntary movements, is maintained by a population of skeletal muscle-dedicated stem cells, called muscle satellite cells (MuSCs). Similar to other adult stem cells, the function of MuSCs is tightly coordinated by the cellular and acellular components of their microenvironment, or the niche. While the processes that control the coupling of neurotransmission and muscle contraction have been well characterized, little is known on the reciprocal crosstalk between neural cells and MuSCs within the muscle microenvironment. Here, we report that mild peripheral nerve injury enhances MuSC myogenic function and muscle regeneration by synergistically augmenting MuSC mitochondrial bioenergetics and upregulating anabolic protein synthesis pathways. We also demonstrate that chronic disruption or degeneration of neuromuscular synapses, such as in muscular dystrophy and biological aging, abolishes MuSC and motor neuron interactions, causing significant deficits in muscle regeneration following injury. These results underscore the importance of neuromuscular junction and neural network as an essential niche of MuSCs. Determining the significance of MuSC-nerve interactions and their functional outcomes, as well as the possibility of modulating these connections, have important implications for our understanding of neuromuscular disease pathology and development of therapeutic interventions. HighlightsO_LIMild peripheral nerve injury increases muscle stem cell bioavailability of healthy muscle. C_LIO_LINerve perturbation stimulates myogenesis by enhancing protein synthesis and mitochondrial metabolism in young, healthy muscle. C_LIO_LISynergistic crosstalk within neuromuscular niche boosts muscle regeneration in young, healthy muscle. C_LIO_LIPositive influences from the neural network on muscle stem cells are abolished in pathological denervation manifested in dystrophic and aging muscle. C_LI

cell biology↗

bioRxiv2020

Transplantation of muscle stem cell mitochondria rejuvenates the bioenergetic function of dystrophic muscle

Mitochondrial dysfunction has been implicated in various pathologies, including muscular dystrophies. During muscle regeneration, resident stem cells, also known as muscle satellite cells (MuSCs), undergo myogenic differentiation to form de novo myofibers or fuse to existing syncytia. Leveraging this cell-cell fusion process, we postulated that mitochondria stemming from MuSCs could be transferred to myofibers during muscle regeneration to remodel the mitochondrial network and restore bioenergetic function. Here, we report that dystrophic MuSCs manifest significant mitochondrial dysfunction and fuse with existing dystrophic myofibers to propagate mitochondrial dysfunction during muscle repair. We demonstrate that by transplanting healthy donor MuSCs into dystrophic host muscle, the mitochondrial network (reticulum) and bioenergetic function can be rejuvenated. Conversely, when bioenergetically-compromised donor MuSCs are transplanted, improvements in mitochondrial organization and bioenergetic function were ablated in the dystrophic recipient. Overall, these data reveal a unique role of muscle stem cells as an essential regulator of myofiber mitochondrial homeostasis and a potential therapeutic target against mitochondrial myopathies.

cell biology↗

bioRxiv2020

Engineered Heterochronic Parabiosis in 3D Microphysiological System for Identification of Muscle Rejuvenating Factors

Exposure of aged mice to a young systemic milieu revealed remarkable rejuvenation effects on aged tissues, including skeletal muscle. Although some candidate factors have been identified, the exact identity and the underlying mechanisms of putative rejuvenating factors remain elusive, mainly due to the complexity of in vivo parabiosis. Here, we present an in vitro muscle parabiosis system that integrates young- and old-muscle stem cell vascular niche on a three-dimensional microfluidic platform designed to recapitulate key features of native muscle stem cell microenvironment. This innovative system enables mechanistic studies of cellular dynamics and molecular interactions within the muscle stem cell niche, especially in response to conditional extrinsic stimuli of local and systemic factors. We demonstrate that vascular endothelial growth factor (VEGF) signaling from endothelial cells and myotubes synergistically contribute to the rejuvenation of the aged muscle stem cell function. Moreover, with the adjustable on-chip system, we can mimic both blood transfusion and parabiosis and detect the time-varying effects of anti-geronic and pro-geronic factors in a single organ or multi-organ systems. Our unique approach presents a complementary in vitro model to supplement in vivo parabiosis for identifying potential anti-geronic factors responsible for revitalizing aging organs.

cell biology↗

bioRxiv2018

Critical Limb Ischemia Induces Remodeling of Skeletal Muscle Motor Unit and Myonuclear- and Mitochondrial-Domains

Critical limb ischemia, the most severe form of peripheral artery disease, leads to extensive damage and alterations in skeletal muscle homeostasis. Although recent developments towards revascularization therapies have been introduced, there has been limited research into treatments for ischemic myopathy. To elucidate the regenerative mechanism of the muscle stem cell and its niche components in response to ischemic insults, we explored interactions between the vasculature, motor neuron, muscle fiber, and the muscle stem cell. We first investigated changes in the neuromuscular junction and motor neuron innervation following a surgical hindlimb ischemia model of critical limb ischemia in mice. Along with previous findings that support remodeling of the neuromuscular junction, we report that ischemic injury also causes significant alterations to the myofiber through a muscle stem cell-mediated increase of myonuclei number per fiber, a concomitant decrease in myonuclear domain size, and an increase in relative mitochondrial content per myonucleus. These results indicate that as a regenerative response to critical limb ischemia, myofibers exhibit myonuclear expansion to allow enhanced transcriptional support and an increase in mitochondrial content for bioenergetic need of the energy-demanding tissue regeneration.

physiology↗