Biology subjects

Kim, M.

Publications and source records attributed to Kim, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Fractionated proton and photon FLASH irradiation mitigates radiation-induced lymphopenia through kinetic sparing of circulating lymphocytes

Background and purpose: Radiation-induced lymphopenia is associated with adverse outcomes in thoracic malignancies. FLASH radiotherapy delivers radiation over a timescale of hundreds of milliseconds, potentially reducing the fraction of irradiated circulating lymphocytes. In this study, we investigated whether FLASH mitigates lymphopenia after thoracic irradiation delivered with protons or photons. Materials and methods: C57BL/6 mice received three 13.5-Gy whole-heart fractions at 48-hour intervals using FLASH or standard dose-rate proton irradiation at the University of Pennsylvania (n=15), with photon validation at Queen's University Belfast (n=72). Leukocytes and CD4 T cells, CD8 T cells, B cells, and NK cells were quantified by hemocytometer and flow cytometry. A continuous-time Markov model simulated lymphocyte trafficking, dose accumulation, and post-irradiation recovery. Results: FLASH attenuated leukocyte depletion across both proton and photon irradiation modalities. In the proton cohort, white blood cell counts were significantly higher after FLASH at D1, D3, D7, and D14; CD4 T cells and NK cells were preserved through D14, while CD8 T cell sparing persisted through D21. Photon FLASH preserved CD45 leukocytes at D1, D3, D7, and D21, with sustained CD8 sparing at D21. Modeling showed that FLASH shifted the lymphocyte dose distribution toward lower exposures, increasing the proportion of lymphocytes receiving <1 Gy from 2.4% to 16.4%, and reduced the proportion of lymphocytes repeatedly irradiated across all three fractions from 36.3% at standard dose rate to 9.18%, despite similar median cumulative doses. The spleen contributed substantially to cumulative lymphocyte dose, and marrow-entering lymphocytes displayed a more high-dose-enriched distribution after FLASH irradiation. Conclusion: FLASH consistently mitigated radiation-induced lymphopenia for proton and photon modalities, with durable CD8 T cell preservation. These findings support a kinetic mechanism and provide a rationale for combining FLASH radiotherapy with immune-sparing planning and immunotherapy.

cell biology↗

bioRxiv2026

Predicting Macroscopic Axon Topology from Microscopic Kinematics: An Interactive Tracking and Random Walk Pipeline for Substrate-Dependent Cortical Neurospheres

The cortical neuron is a fundamental building block of the mammalian brain, and the morphology of its axonal projections is central to how functional circuits assemble. The trajectory along which an axon grows is a key determinant of connectivity, yet the kinematics of cortical axon outgrowth remain poorly quantified. Characterizing these dynamics is most tractable in vitro, where axonal growth can be measured directly and under controlled, reproducible conditions. Even in culture, however, this remains challenging because cortical neurons require dense plating for viability, and their soma is motile, so growth behavior is highly sensitive to local density and population context, complicating reproducible measurement of intrinsic dynamics. To overcome these limitations, we used size-controlled cortical neurospheres, which provide a fixed spatial origin and a reproducible environment, together with a custom semi-automated tracking pipeline to quantify single-axon kinematics across two functionalized substrates and two developmental phases. This approach revealed a substrate-dependent divergence in outgrowth: during the later developmental phase, axons on poly-D-lysine with laminin (PDL-LA) substrate grew faster than those on PDL, with a mean step size of 0.436 versus 0.339 {micro}m /min. Decomposing trajectories into Katz dynamic states, we built a generative biased random walk model that reproduces axonal behavior at both microscopic (single-axon) and macroscopic (network topology) scales. This open, reproducible framework links single-axon kinematics to network architecture, enabling the structural connectivity of neurospherebased circuits in vitro to be predicted from measurable growth dynamics, a necessary foundation for future studies linking circuit structure to emergent function.

bioengineering↗

bioRxiv2026

Dynamic Nanoparticle Assembly-Based Biomedical Microrobots

Precise drug delivery within anatomically complex tissues demands systems capable of both active navigation and deep tissue access, properties that have remained difficult to reconcile in existing nanocarriers and microrobots. Here we introduce Dynabots, a dynamic microrobotic assembly constructed from multifunctional nanoparticles covalently linked by thermally cleavable molecular connectors. This nanoparticle-rich architecture enables the integration of magnetic, imaging, and therapeutic components while preserving a high content of functional material. Collective assembly imparts enhanced magnetic responsiveness and maneuverability, enabling controlled navigation through tortuous biological environments. Upon exposure to mild thermal stimuli, the assemblies undergo programmed disassembly, releasing individual nanoparticles that can diffuse through tissue for localized therapeutic action. We establish the programmable transitions, biocompatibility, and therapeutic efficacy of this process across in vitro and in vivo models, including real-time fluoroscopic guidance within anatomically realistic phantoms and live rodent and porcine systems. By integrating magnetic control, reconfigurable architecture, and stimulus-triggered disassembly, Dynabots unite navigational precision with tissue permeability, providing a versatile platform for adaptive and deep-tissue drug delivery.

bioengineering↗

bioRxiv2026

Lysyl oxidase drives ccRCC progression by coordinating HIF-2α transcription program with tumor microenvironment

Clear cell renal cell carcinoma (ccRCC) is driven by persistent HIF-2 transcription program initiated by VHL loss, yet molecular mediators sustaining this program are poorly defined. Using single-cell transcriptomics, we identified lysyl oxidase (LOX) as a driver of ccRCC progression, selectively enriched in a hypoxia/epithelial-mesenchymal transition (EMT) gene program associated with poor outcome. While LOX oxidizes and stabilizes HIF-2 by antagonizing HUWE1-mediated ubiquitination and degradation, thereby sustaining HIF-2-driven transcription in cancer cells, it also remodels extracellular matrix (ECM) and promotes angiogenesis in the tumor microenvironment (TME). Genetic or pharmacological inhibition of LOX destabilizes HIF-2, disrupts ECM, inhibits angiogenesis, and suppresses tumor initiation, growth, and metastasis in vivo. LOX inhibition enhances anti-angiogenic therapy response and remains effective in belzutifan-resistant HIF-2 G323E-mutant tumors. Nuclear LOX protein correlates with nuclear HIF-2 in high-grade patient tumors. Together, LOX coordinates HIF-2 transcription program with TME and is a therapeutic target in ccRCC.

cancer biology↗

bioRxiv2026

Structure-affinity correlations and separable optical activity in carbon nanotube protein coronas

Biomolecular corona on nanoparticle surfaces enriches low-abundance proteins and compresses the dynamic range of the plasma proteome. Single-walled carbon nanotubes are particularly attractive because their surface chemistry is highly tunable, and their near-infrared fluorescence directly reports corona modulation. However, how surface chemistry shapes the corona and how the corona relates to the fluorescence response remain unclear. We profiled protein enrichment patterns and the resulting fluorescence in a library of 25 chemically modified carbon nanotubes by quantitative proteomics and near-infrared fluorescence spectroscopy. We found that polymer and quantum-defect chemistry orthogonally modulate corona composition and dispersion forces are the dominant, universal driver of protein-nanotube binding. Proteomics and fluorescence correlation analyses indicate that enrichment and fluorescence response are partially decoupled. A subset of corona proteins stays optically silent, but where responses occur, enriched proteins respond at lower, physiologically relevant ranges than depleted ones. Our findings inform design principles for carbon nanomaterial-based sensors and biomarker discovery platforms.

biochemistry↗

bioRxiv2026

Drosophila melanogaster lactate dehydrogenase deficiency recapitulates the exercise intolerance of human glycogen storage disease type XI

Lactate dehydrogenase A (LDHA) is a key glycolytic enzyme that commonly exhibits altered expression in human diseases such as cancers and neurodegeneration, making it a valuable disease biomarker and putative therapeutic target. However, any treatment targeting LDHA will also disrupt normal metabolism, underscoring the need to investigate physiological consequences of inhibiting this enzyme. We previously established the fruit fly Drosophila melanogaster as a genetic model for studying LDH function in the context of growth, metabolism, and development. Here we expand upon those studies by investigating a serendipitous observation that Ldh mutant larvae exhibit diet-dependent lethality. Using a multiomic approach, we discovered this diet-dependent phenotype is independent of nutritional composition. Instead, Ldh mutant larvae are exercise intolerant and display reduced mobility, rendering mutant larvae sensitive to food consistency. Moreover, tissue-specific analysis reveals that LDH activity within muscle and peripheral glia are essential for larval viability raised on solid food. Intriguingly, these phenotypes mirror the pathophysiology of LDHA deficiency (Glycogen Storage Disease Type XI; GSD Type XI) in humans, where mild symptoms are exacerbated by physical exertion and environmental stress. Together, our findings further highlight the value of using Drosophila to explore the developmental and physiological consequences of Ldh inhibition. SUMMARY STATEMENTLoss of lactate dehydrogenase in Drosophila causes exercise intolerance and diet-dependent lethality, revealing conditional phenotypes that mirror those associated with human LDH-A deficiency.

developmental biology↗

bioRxiv2026

Combinatorial regulation of cellular rotation by CUL-3-actomyosin-dependent oriented division, eggshell geometry, and Ras–MAPK signaling during dorsal–ventral axis establishment in Caenorhabditis elegans

Cellular rotation is an understudied mechanism that regulates animal morphogenesis. In C. elegans, the dorsal-ventral axis is established when the two-cell-stage AB cell rotates within the eggshell as it divides, generating the diamond-shaped blastomere arrangement at the four-cell stage that enables distinct cell fate specification. Multiple mechanisms, including actomyosin-dependent oriented division, chiral cortical flow, and eggshell shape, have been proposed to regulate this arrangement, but whether these represent conflicting hypotheses or co-acting mechanisms remains unclear. Here, we show that CUL-3-actomyosin-dependent oriented division, eggshell geometry, and the Ras-MAPK signaling pathway regulate distinct steps of cellular rotation. AB cell rotation occurred in two distinct phases: Phase I during AB cytokinesis and Phase II during cytokinesis of the neighboring P1 cell. Quantitative analysis revealed that CUL-3-actomyosin-dependent oriented division is the only one of these three pathways that regulates the AB division axis before anaphase. Actomyosin-dependent oriented division and eggshell geometry were both required for Phase I rotation, whereas Phase II rotation was independent of eggshell geometry. We further identified the Ras-MAPK signaling pathway as a regulator of AB cell rotation that acts independently of eggshell geometry. Strikingly, the CUL-3-actomyosin-dependent pathway may have two distinct roles: first, specifying the AB division axis, and second, correcting the division axis in all cell types during cytokinesis. Together, these functions contribute significantly to cellular rotation and dorsal-ventral axis establishment.

Cell Biology↗

bioRxiv2026

Primary-Level Meta-Analysis of Diversity Outbred Mice Identifies a Fasting Plasma Trimethylamine N-Oxide (TMAO) Locus Modified by Sex and Diet

Trimethylamine n-oxide (TMAO) is a plasma metabolite linked to adverse cardiometabolic health with complex regulation involving diet, sex, and host genetics. We explored the role of these factors in the genetic regulation of TMAO by performing a primary-level meta-analysis in 1,482 female and male Diversity Outbred (DO) mice from five distinct studies conducted in various regions of the United States. We identified a quantitative trait locus (QTL) associated with TMAO concentration at [~]86 megabase pairs on mouse chromosome 12 with a highly significant LOD score of 67.67. Alleles at the chromosome 12 QTL inherited from the Cast/EiJ (CAST) and PWK/PhJ (PWK) mouse strains primarily drove the association with reduced TMAO concentrations. The chromosome 12 QTL remained significant in sex-stratified analyses and the mode of inheritance appeared additive; furthermore, the QTL was regulated by sex-by-genotype and sex-by-diet interactions. Using a CAST/EiJ X C57BL/6J F2 cross, positional candidates were prioritized by eQTL analysis. Further analysis in a study utilizing the eight DO founding strains identified that Acyp1 was differentially expressed in hepatic tissue from CAST mice, prompting investigation into its genetic regulation. Acyp1 demonstrated relevant cis- and trans-regulation and was significantly correlated with TMAO and hepatic Fmo3. However, no significant relationships between Acyp1 and TMAO were identified in mice inactivated for Acyp1 or with AAV overexpression of Acyp1 in the liver. Genes within the chromosome 12 QTL have synteny with humans and may translate to the genetic regulation of human plasma TMAO concentrations and atherosclerosis. Author SummaryWe explored the roles of diet, sex, and genetics on the regulation of fasting plasma trimethylamine n-oxide (TMAO) concentration by performing a meta-analysis in 1,482 female and male Diversity Outbred (DO) mice from five unique studies. We identified a QTL associated with TMAO concentration on chromosome 12 at [~]86 mega base pair (Mb) with a highly significant LOD score of 67.67. The locus is modified by both sex and diet.

genetics↗

bioRxiv2026

Context-dependent Foxa2 activity maintains floor plate fate and tunes Sonic hedgehog signaling to regulate neural progenitor differentiation

The developing spinal cord contains both neural and non-neural tissues that arise within a shared morphogen signaling environment, raising the question of how distinct lineage identities are established and maintained. A striking example of this is the floor plate (FP), a mesoderm-derived, non-neural midline structure that functions as a critical signaling center adjacent to neural progenitor domains. Here, using zebrafish, we show that the pioneer transcription factor foxa2 is expressed in the FP, adjacent p3 neural progenitors, and p3-derived Kolmer-Agduhr" (KA") interneurons. Loss of foxa2 results in a complete loss of canonical FP identity and an expansion of p3 progenitors. Lineage tracing reveals that, in the absence of foxa2, FP cells undergo a fate transformation into neuron-producing p3-like cells, indicating that Foxa2 functions as a lineage barrier to preserve non-neural FP identity. In contrast, within the neural lineage, loss of foxa2 leads to elevated Sonic hedgehog (Shh) pathway activity and impaired KA" differentiation, suggesting that Foxa2 negatively regulates Shh responsiveness. Conversely, Foxa2 overexpression induces ectopic FP and KA" marker expression in a stage-dependent manner. Together, our findings reveal a dual role for Foxa2 in maintaining the non-neural FP lineage while fine-tuning morphogen responsiveness in neighboring neural progenitors during spinal cord development.

Developmental Biology↗

bioRxiv2026

Holotomography reveals biophysical remodeling of mouse oocytes during post-ovulatory aging

Routine assessment of oocyte state in reproductive biology and clinical embryology still relies largely on two-dimensional transmitted-light morphology, leaving the underlying three-dimensional intracellular organization largely unmeasured. Here, we use holotomography to reconstruct volumetric refractive index (RI) distributions in unlabeled live mouse oocytes and combine this imaging with sparse-annotation, AI-assisted compartment segmentation and multidimensional feature extraction across geometry, RI statistics, dry-mass density, and intracellular texture. Applied to an in vitro model of post-ovulatory aging, holotomography-derived biophysical profiles separated fresh and aged oocytes more strongly than two-dimensional brightfield-derived features, and feature-family ablation indicated that non-morphological descriptors contributed substantially to this separation. At the population level, aged oocytes showed coordinated ooplasmic remodeling, including reduced volume, increased RI heterogeneity, and increased dry-mass density while total dry mass was broadly conserved. These findings demonstrate a label-free quantitative framework for detecting post-ovulatory aging-associated biophysical remodeling in intact mammalian oocytes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/733271v1_ufig1.gif" ALT="Figure 1"> View larger version (89K): org.highwire.dtl.DTLVardef@c7257aorg.highwire.dtl.DTLVardef@6d92f0org.highwire.dtl.DTLVardef@1c9f7eborg.highwire.dtl.DTLVardef@b36637_HPS_FORMAT_FIGEXP M_FIG C_FIG

Developmental Biology↗

bioRxiv2026

Simultaneous regeneration of skin and bone in full-thickness cranial composite defects

Traumatic cranial defects often involve concurrent loss of soft and hard tissues and can progress to chronic defects due to delayed healing associated with infection or other co-morbidities. Despite autologous reconstruction remaining the clinical standard, it requires staged procedures using heterogeneous tissues, increasing operative time, costs, and surgical risks. Moreover, current tissue engineering approaches focus on single tissues or acute tissue defect models, limiting their clinical applications. Herein, we describe an acellular, material-driven 3D-printed composite scaffold designed to regenerate both bone and skin within composite cranial defects. The scaffold integrates controlled copper ion release from both organic and inorganic components with 3D-printed citrate polymer and citrate polymer-ceramic composites. Integrated thermoresponsive citrate-based hydrogels further enable spatially defined dermoconductive and osteoconductive properties, supporting a one-step surgical approach. At 12 weeks post-implantation, our scaffold enhanced keratinocyte organization, collagen deposition, and defect coverage with mature bone, achieving histological outcomes comparable to autografts. Furthermore, the system suppressed bacterial burden. Thus, this acellular platform represents a clinically promising synchronized strategy to address the complex demands of traumatic craniofacial composite defects.

bioengineering↗

bioRxiv2026

Chemically Engineered Carbon Nanotubes Map Class-Selective Metabolite Enrichment from Human Plasma

The spontaneous adsorption of biomolecules onto nanoparticle surfaces has been extensively characterized at the protein level, but the metabolite corona remains poorly defined while being physicochemically and biologically distinctive. Herein, we report the first class-level mapping of metabolite corona composition across 25 chemically modified carbon nanotubes in human plasma using untargeted liquid chromatography-mass spectrometry. Complementary analytical conditions detected approximately 9,000 metabolite features, of which over 5,000 yielded valid corona-versus-plasma enrichment measurements. Machine learning classifiers extended metabolite class annotations from 10-45% to the full detected set, enabling systematic analysis of class-level enrichment patterns. We find that polymer wrapping dominates corona composition, with DNA wrapping selectively enriching nonpolar lipids and PEG wrapping favoring polar metabolites. Within each polymer background, covalent quantum well defects further modulate class-level enrichment in a structure- and chemistry-dependent manner. Carboxyl aryl defects broadly enhance amphiphilic lipid recruitment, while trifluoro aryl defects suppress single-chain amphiphilic species but attenuate depletion of double-chain phospholipids. Our findings demonstrate that engineered nanotubes can serve as chemically tunable, selective scaffolds for metabolite enrichment, potentially enhancing the capability of nanotube-based platforms to recruit and detect structurally diverse, low-abundance small molecules in complex biofluids.

biochemistry↗

bioRxiv2026

Engineering Carbon Nanotube Quantum Well Defects with Recognition Tripeptides for Optical Detection of Extracellular Vesicles in Plasma

Extracellular vesicles (EVs) carry molecular signatures of their originating cells and have thus emerged as promising biomarkers. However, their clinical utility remains limited due to their low abundance and the modest sensitivity of current EV detection methods in complex biological environments. Here, we present a quantum well defect functionalized carbon nanotube sensor coupled with integrin-recognition RGD tripeptide for EV detection in human plasma. Leveraging the abundance of integrins on EV surfaces, we targeted 5{beta}1, V{beta}1, and V{beta}3 subtypes. The nanosensor exhibited robust hypsochromic shifts in defect emission upon integrin binding, achieving sub-picomolar detection limits for integrin subunits and quantifying EVs at concentrations as low as 104 EVs{middle dot}mL-1 for glioblastoma, ovarian cancer, and fibroblast cell-derived EV types. Molecular dynamics simulation indicated that integrin docking at the RGD-coupled quantum defect can substantially reshape the interfacial environments of the quantum defects, explaining the high sensitivity in EV detection in complex biological media. Finally, transmembrane protein analysis validated the expression of surface integrins across the tested EV types. The modular nanosensor construct can be targeted to detect disease-associated EV subpopulations, advancing EV-based diagnostics.

biochemistry↗

bioRxiv2026

Biomimetic MRI Nanoprobe for Mapping Cerebrovascular Inflammation After Traumatic Brain Injury

Cerebrovascular inflammation is a critical driver of secondary injury following traumatic brain injury (TBI), yet no noninvasive tool currently exists to map its spatial heterogeneity across the injured brain. Here, we report MoNP-SPION, a monocyte-mimetic nanoprobe that selectively targets activated cerebrovascular endothelium after TBI and enables quantitative MRI of spatiotemporally heterogeneous cerebrovascular inflammation. MoNP-SPION binding to inflamed brain endothelium scaled with activation state, enabling rapid, spatially heterogeneous targeting of injured cerebral vasculature. MoNP-SPION-enhanced MRI revealed dynamic reductions in T2* throughout the brain that extended beyond the injury penumbra and captured both subacute vascular injury and therapy-induced recovery. Importantly, spatiotemporal reductions in T2* strongly correlated with VCAM1 upregulation, supporting MoNP-SPION as a molecularly specific readout of endothelial activation. Together, these findings establish MoNP-SPION as a promising platform for longitudinal, noninvasive monitoring of cerebrovascular inflammation in TBI and other neurological disorders involving vascular dysfunction. TEASERCell-mimicking MRI nanoprobe maps cerebrovascular injury and recovery dynamics following brain trauma.

bioengineering↗

bioRxiv2026

Early Spatiotemporal Deficits Become Competitive Advantages During Collective Expansion

Rapid spatial expansion into new territory is fundamental to population persistence, ecological dominance, and evolutionary success. Every race for space is initiated by founding populations, yet how their initial spatiotemporal conditions shape the outcome remains unclear. Here, by combining nonlinear theory with quantitative microbial experiments, we show that collective motility can overturn the classical logic of priority effects. Populations expanding by individual motility retain the expected advantage of an earlier start or a larger initial footprint. By contrast, under collective motility, nonlinear density-dependent feedback enables initially lagging populations to accelerate, transforming early deficits into long-term competitive advantage. Optimization predicts that this advantage is maximized when the delay scales log-linearly with initial density. We validate this scaling behavior across diverse swarming microbes, revealing a general regulatory strategy for competitive range expansion. Competition and evolution experiments further show that this behavior is adaptive and robustly preserved. Together, our results establish a quantitative framework linking the initial organization of founding populations to final spatial outcomes, helping explain how organisms regulate early dynamics to shape ecological success in space. SignificanceRapid expansion into new territory often decides who will dominate. To understand this contest, we focused on how the race begins. We built a theoretical framework linking the initial conditions of founding populations to long-run competitive outcomes, then tested its predictions experimentally in microbial populations by controlling inoculum, quantifying range expansion, competing strains head-to-head, and performing laboratory evolution. Our results show that history is not merely the starting point of range expansion, but part of the regulatory strategy for winning space. This work provides a mechanistic framework for quantitatively thinking about range expansion across systems, from microbial colonization and biological invasions to infection spread, cancer metastasis and developmental migration.

ecology↗

bioRxiv2026

Long-Lasting Electrohydrodynamically Printed Transparent Soft Microelectrode for Implantable Biointerfaces

Reliable and scalable soft implantable neural interface fabrication remains a key challenge for chronic bioelectronic applications. Here, we present a transparent soft microelectrode fabricated with electrohydrodynamic (EHD) printing, utilizing the fluorinated polymer poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) and poly (3, 4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT: PSS) to form seamless, selectively patterned multilayer structures with low impedance and long-term stability. Controlled in situ curing during printing yields dense, void-free substrate and encapsulation layers, suppressing interfacial defects and ionic pathways, while maintaining high optical transparency (>60%) with PEDOT:PSS. The printed microelectrodes exhibit low impedance, high charge storage and injection capacities, and stable electrochemical behavior under biomimetic conditions. In addition, the devices demonstrate robust mechanical and electromechanical stability under cyclic deformation in both dry and wet environments, as well as under prolonged electrical stimulation. Accelerated aging studies project multi-year operational lifetimes, and in vitro/in vivo biocompatibility assessments confirm excellent tissue integration. These results establish EHD-printed fluorinated polymer-based microelectrodes as a scalable and durable platform for chronic implantable biointerfaces. ToC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/726391v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@f4f717org.highwire.dtl.DTLVardef@8a34a1org.highwire.dtl.DTLVardef@185540dorg.highwire.dtl.DTLVardef@51462a_HPS_FORMAT_FIGEXP M_FIG C_FIG This report presents an electrohydrodynamically printed transparent soft microelectrode for chronic purposes. Electrohydrodynamic printing promotes seamless multilayer structures with selective deposition and long-term mechanical stability. The devices show low impedance, high charge capacity, and robust electrochemical/electromechanical properties. Accelerated aging projects [~]7.2 year lifetimes, and XPS/SEM-EDS confirm strong ion barrier properties and biocompatibility for chronic implantation.

bioengineering↗

bioRxiv2026

A pipeline for cell migration analysis in live-cell imaging data from human iPSC-derived forebrain assembloids.

During forebrain development, inhibitory interneurons and oligodendrocyte progenitor cells migrate long distances into the developing dorsal cortex. Human induced pluripotent stem cell-derived forebrain assembloids (FAs) provide direct experimental access to this migratory process in vitro. Using viral labeling to express yellow fluorescent protein (EYFP) and tandem-dimer tomato (tdTomato) driven by EF1 or SOX10 promoters, respectively, we tracked cells in FAs over 15-17h using spinning disk confocal microscopy. We developed an end-to-end processing pipeline for 4D volumetric imaging data, consisting of background subtraction and drift correction, manual cell coordinate tracking, and an analysis workflow to describe migratory cell behavior. Image preprocessing significantly improved data quality for subsequent manual tracking in datasets with heterogeneous labeling density and brightness. Trajectory analysis of 336 EYFP- and 337 tdTomato-labeled cells from twelve FAs indicates that most cells show super-diffusive directed motility. Our pipeline represents a key resource for cell tracking in FAs and similar three-dimensional platforms. This pipeline represents the first open tracking resource for iPSC-derived FAs and can be used as a ground-truth resource for the development of automated cell detection and tracking algorithms.

neuroscience↗

bioRxiv2026

Stage-specific exposure to an activity-permissive media enhances neuronal maturation in oligodendrocyte-enriched cortical organoids

Oligodendrocyte-enriched cortical organoids (OCOs) are a powerful platform for modeling oligodendrogenesis in a human cellular context. However, neuronal activity is impaired in conventional culture media, limiting assessment of neuronal function in conjunction with oligodendrocyte biology. To address this, we used a modified BrainPhys medium termed neuronal activity medium (NAM) and defined the optimal developmental window for NAM exposure to generate OCOs with robust neuronal activity (NAM-OCOs). Stage-specific exposure to NAM, prior to oligodendrocyte expansion, leads to enhanced structural maturation, as evidenced by increased organoid size, heightened synaptogenesis, and upregulation of transcripts associated with neuronal complexity. Further, NAM-OCOs display increased cellular heterogeneity, including greater representation of GABAergic interneurons while preserving oligodendrocyte development and maturation. Altogether, our studies demonstrate that stage-specific exposure to an activity-permissive environment enhances neuronal activity, establishing an OCO model which integrates neuronal activity with oligodendrocyte development and maturation. HighlightsO_LIIncreased neuronal activity in oligodendrocyte-enriched cortical organoids (OCOs) C_LIO_LIStage-specific Neuronal Activity Medium (NAM) optimizes activity C_LIO_LINAM-OCOs display increased cellular heterogeneity and neuronal maturation C_LIO_LIOligodendrogenesis is preserved in NAM-OCOs C_LI eTOC blurbIn this article, Chung et al enhance neuronal activity in oligodendrocyte-enriched cortical organoids (OCOs) through stage-specific exposure to Neuronal Activity Medium (NAM). OCOs exposed to NAM display elevated cellular heterogeneity, structural maturation, and synaptogenesis, while preserving oligodendrocyte development and maturation. These results establish an increasingly comprehensive OCO model for studying neuronal function and oligodendrogenesis.

neuroscience↗