Biology subjects

Heo, D.

Publications and source records attributed to Heo, D..

9 recordsLinked to original sources

bioRxiv2026

MorphoStat: A Statistics-Aware Pipeline for Morphological Profiling Analysis

High-content imaging produces thousands of morphological measurements per cell. Interpreting these measurements requires normalization to remove plate effects, statistical tests selected on the basis of data distribution, and control over false discoveries across many features tested at once. MorphoStat is an open-source Python pipeline that applies this sequence of steps automatically. Given a CSV file from CellProfiler or a compatible imaging platform, it removes low-quality wells, normalizes each plate against DMSO controls using a MAD-scaled z-score, routes each feature to a parametric or nonparametric test based on a distributional check, applies Benjamini-Hochberg correction, and writes out results and publication-ready figures. On the BBBC021 benchmark (MCF-7 breast-cancer cells, 632 wells, 473 features), MorphoStat recovered 12 of 13 known mechanism-of-action classes in principal component space, confirming that the normalization and statistical routing work as intended. The tool is available at https://github.com/Almunthir334/morphostat (DOI: 10.5281/zenodo.20354069) under the MIT license.

bioinformatics↗

bioRxiv2026

All-in-one, Cas13d-based cell-specific gene knockdown system for zebrafish

Cell type-specific genetic manipulation is essential for dissecting neural circuits and glial biology in vivo; however, methods for achieving and validating cell-specific gene knockdown in zebrafish remain limited. Here, we introduce a CRISPR-Cas13d-based mRNA knockdown platform for zebrafish that leverages RNA targeting, rather than DNA editing, to enable efficient and flexible perturbation of gene function in defined cell types of interest. We engineered an all-in-one vector system for cell type-specific RfxCas13d expression and ubiquitous expression of crispr RNAs (crRNAs) and validated its utility across the major classes of CNS glia: astrocytes, oligodendrocytes, and microglia. Cas13d-mediated knockdown consistently achieved target mRNA depletion and produced heritable reproducible morphological and functional phenotypes, demonstrating the robustness of the approach. This approach complements permanent genome-editing methods such as CRISPR-Cas9 by providing a reliable, efficient, and scalable strategy for RNA-level perturbation. Our Cas13d toolkit expands the repertoire of zebrafish genetic technologies, offering a powerful resource for in vivo cell type-specific studies to uncover cell-autonomous mechanisms and possibility for cell type-specific genetic screens in development and disease.

neuroscience↗

bioRxiv2026

PIEZOs regulate oligodendrocyte sheath formation, expansion, and myelination potential

Myelination requires precise integration of physical cues by oligodendrocyte lineage cells (OLCs), but the molecular sensors that detect these cues remain incompletely understood. Here, we demonstrate that oligodendrocyte progenitor cells (OPCs) are sensitive to sub-micron changes in membrane displacement. Based on channel properties, RNA expression, and protein abundance, we find that the mechanosensitive ion channel PIEZO1 contributes to OPC mechanosensitivity. In vivo, zebrafish with oligodendrocyte (OL)-specific disruption of piezo1 have fewer sheaths per OL. Zebrafish with OL-specific piezo2 disruption also have fewer sheaths as well as decreased total myelin capacity over time. OL-specific disruption of both piezo1 and piezo2 caused more severe phenotypes, with reduced OPC volume, and in myelinating OLs, reduced sheath number, sheath length, and total myelin output. Furthermore, piezo1/piezo2 disruption leads to sporadic sheath formation outside the normal developmental window. Our findings indicate that OLs use Piezo channels in vivo to influence sheath formation, expansion, and retractions.

neuroscience↗

bioRxiv2024

Transcriptional profiles of murine oligodendrocyte precursor cells across the lifespan

Oligodendrocyte progenitor cells (OPCs) are highly dynamic, widely distributed glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. By also generating new oligodendrocytes in the adult CNS, OPCs allow formation of new myelin sheaths in response to environmental and behavioral changes and play a crucial role in regenerating myelin following demyelination (remyelination). However, the rates of OPC proliferation and differentiation decline dramatically with aging, which may impair homeostasis, remyelination, and adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses membrane-anchored EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP) and performed high-throughput single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation across the lifespan. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1 and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged animals restored their ability to differentiate, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages help to define the molecular changes guiding their behavior in various physiological and pathological contexts.

neuroscience↗

bioRxiv2024

Freeing P300-Based Brain-Computer Interfaces from Daily Calibration by Extracting Daily Common ERPs

When people use brain-computer interfaces (BCIs) based on event-related potentials (ERPs) over different days, they often need to repeatedly calibrate BCIs every day using ERPs acquired on the same day. This cumbersome recalibration procedure would make it difficult to use BCIs on a daily basis. We aim to address the daily calibration issue by examining across-day variation of the BCI performance and proposing a method to avoid daily calibration. To this end, we implemented a P300-based BCI system designed to control a home appliance over five days in nineteen healthy subjects. We first examined how the BCI performance varied across days with or without daily calibration. On each day, P300-based BCIs were tested using calibration-based and calibration-free decoders (CB and CF), with a CB or a CF decoder being built on the training data on each day or those on the first day, respectively. Using the CF decoder resulted in lower BCI performance on subsequent days compared to the CB decoder. Then, we developed a method to extract daily common ERP patterns from observed ERP signals using the sparse dictionary learning algorithm. We applied this method to the CF decoder and retested the BCI performance over days. Using the proposed method improved the CF decoder performance on subsequent days; the performance was closer to the level of the CB decoder, with improvement of accuracy by 2.28%, 1.93%, 1.75%, and 3.86 % on the subsequent four days, respectively, compared to the original CF decoder. The method proposed by our study may provide a novel approach to addressing the daily-calibration issue for P300-based BCIs, which is essential to implementing BCIs into daily life.

bioengineering↗

bioRxiv2022

MHC class I and MHC class II reporter mice enable analysis of immune oligodendroglia in mouse models of multiple sclerosis

Oligodendrocytes and their progenitors upregulate MHC pathways in response to inflammation, but the frequency of this phenotypic change is unknown and the features of these immune oligodendroglia are poorly defined. We generated MHC class I and II transgenic reporter mice to define their dynamics in response to inflammatory demyelination, providing a means to monitor MHC activation in diverse cell types in living mice and define their roles in aging, injury and disease.

neuroscience↗

bioRxiv2021

Stage-specific control of oligodendrocyte survival and morphogenesis by TDP-43

Generation of oligodendrocytes in the adult brain enables both adaptive changes in neural circuits and regeneration of myelin sheaths destroyed by injury, disease, and normal aging. This transformation of oligodendrocyte precursor cells (OPCs) into myelinating oligodendrocytes requires processing of distinct mRNAs at different stages of cell maturation. Although mislocalization and aggregation of the RNA binding protein TDP-43 occur in both neurons and glia in neurodegenerative diseases, the consequences of TDP-43 loss within different stages of the oligodendrocyte lineage are not well understood. By performing stage-specific genetic inactivation of Tardbp in vivo, we show that oligodendrocyte lineage cells are differentially sensitive to loss of TDP-43. While OPCs depend on TDP-43 for survival, with conditional deletion resulting in cascading cell loss followed by rapid regeneration to restore their density, oligodendrocytes become less sensitive to TDP-43 depletion as they mature. Deletion of TDP-43 early in the maturation process led to eventual oligodendrocyte degeneration, seizures and premature lethality, while oligodendrocytes that experienced late deletion survived and mice exhibited a normal lifespan. At both stages, TDP-43 deficient oligodendrocytes formed fewer and thinner myelin sheaths and extended new processes that inappropriately wrapped neuronal somata and blood vessels. Transcriptional analysis revealed that in the absence of TDP-43, key proteins involved in oligodendrocyte maturation and myelination were misspliced leading to aberrant incorporation of cryptic exons. Inducible deletion of TDP-43 from oligodendrocytes in the adult CNS induced the same progressive morphological changes and mice acquired profound hindlimb weakness, suggesting that loss of TDP-43 function in oligodendrocytes may contribute to neuronal dysfunction in neurodegenerative disease.

neuroscience↗

bioRxiv2020

Modulating Intra-Nuclear LC3 with Small Molecules Rescues Cells from a Docetaxel-Induced Phenotype

Nucleus-associated autophagy has been described as a cellular metabolic response by which nuclear material is actively degraded. This degradation occurs after stress, such as nuclear damage or the onset of tumorigenesis. Here we describe a nucleus-associated autophagic process distinct from other forms of selective autophagy in human cell lines. We found that although nuclear localization of MAP1LC3B (LC3) is not dependent on particular nuclear importins, knockdown of nuclear importins, which causes nuclear stress, can induce a nuclear autophagic response. Our characterization of this autophagic phenomenon was facilitated by chemical modulation of the process via two compounds discovered previously in a high content analysis. These small molecules bidirectionally regulate nuclear LC3 in human renal, pancreatic, and bladder cell lines. One molecule (NSC31762 or DTEP) enhances nuclear LC3 puncta and increases lysosomal targeting of LC3. This compound also decreases the nuclear envelope protein LaminB1. Another molecule (NSC279895 or DIHI) reduces the nuclear localization of LC3. Finally, we applied these chemical tools in the setting of mitotic-disruptor induced nuclear stress. The compound DIHI, shown to reduce nuclear autophagic puncta, diminished the mitotic disruptor effect. These new tools will allow for deeper exploration of nucleus-associated autophagies, and could serve as proof-of-principle in guiding new therapies for diseases involving nuclear stress.

molecular biology↗

bioRxiv2020

3D bioprinting of co-cultured osteogenic spheroids for bone tissue fabrication

Conventional top-down approaches in tissue engineering involving cell seeding on scaffolds have been widely used in bone engineering applications. However, scaffold-based bone tissue constructs have had limited clinical translation due to constrains in supporting scaffolds, minimal flexibility in tuning scaffold degradation, and low achievable cell seeding density as compared with native bone tissue. Here, we demonstrate a pragmatic and scalable bottom-up method, inspired from embryonic developmental biology, to build three-dimensional (3D) scaffold-free constructs using spheroids as building blocks. Human umbilical vein endothelial cells (HUVECs) were introduced to human mesenchymal stem cells (hMSCs) (hMSC/HUVEC) and spheroids were fabricated by an aggregate culture system. Bone tissue was generated by induction of osteogenic differentiation in hMSC/HUVEC spheroids for 10 days, with enhanced osteogenic differentiation and cell viability in the core of the spheroids compared to hMSC-only spheroids. Aspiration-assisted bioprinting (AAB) is a new bioprinting technique which allows precise positioning of spheroids (11% with respect to the spheroid diameter) by employing aspiration to lift individual spheroids and bioprint them onto a hydrogel. AAB facilitated bioprinting of scaffold-free bone tissue constructs using the pre-differentiated hMSC/HUVEC spheroids. These constructs demonstrated negligible changes in their shape for two days after bioprinting owing to the reduced proliferative potential of differentiated stem cells. Bioprinted bone tissues showed interconnectivity with actin-filament formation and high expression of osteogenic and endothelial-specific gene factors. This study thus presents a viable approach for 3D bioprinting of complex-shaped geometries using spheroids as building blocks, which can be used for various applications including but not limited to, tissue engineering, organ-on-a-chip and microfluidic devices, drug screening and, disease modeling.

bioengineering↗