Biology subjects

Huh, D.

Publications and source records attributed to Huh, D..

8 recordsLinked to original sources

bioRxiv2025

SpaceSequest: A unified pipeline for spatial transcriptomics data analysis

BackgroundSpatial transcriptomics has emerged as one of the most powerful tools for gaining biological insights, enabling researchers to uncover intricate relationships between gene expression patterns and tissue architecture. Recent advances in the field have resulted in a variety of new platforms, including Visium, Visium HD, and Xenium from 10x Genomics, as well as GeoMx and CosMx from NanoString Technologies, which has now been acquired by the Bruker Corporation. However, the existence of diverse spatial transcriptomics platforms and various data formats poses challenges in standardizing data analysis. Thus, there remains a critical gap in the availability of a comprehensive pipeline capable of conducting end-to-end analysis that is necessary to extract biological insights from multiple spatial transcriptomics platforms. ResultsHere, we present SpaceSequest, a tailored pipeline that utilizes cutting-edge computational methodologies to conduct a thorough analysis, enabling the extraction of crucial biological insights from five major spatial transcriptomics technologies. SpaceSequest performs (1) standardized quality control and general data processing, (2) key analyses customized for each spatial platform, (3) automated cell type annotation and deconvolution, and (4) high-quality figure and analysis result generation. In addition, SpaceSequest allows for smooth integration with cellxgene VIP and Quickomics for user-friendly data access and interactive visualization. ConclusionsSpaceSequest is a unified and comprehensive pipeline designed for the analysis, visualization, and publication of spatial transcriptomics data from various platforms. The source code is available at https://github.com/interactivereport/SpaceSequest. To facilitate seamless installation and usage, we have also created a detailed Bookdown tutorial that can be accessed through https://interactivereport.github.io/SpaceSequest/tutorial/docs/index.html.

bioinformatics↗

bioRxiv2025

Comparative snRNAseq study of C9orf72, SOD1, and sALS spinal cord

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by the loss of motor neurons, yet the cell-type specific molecular alterations within the spinal cords are not well characterized. In this study, we conducted deep molecular profiling of spinal cord tissues donated by people living with sporadic, C9orf72, and SOD1-ALS using single-nucleus RNA sequencing (snRNAseq). We observed numerous distinct gene expression patterns and enriched pathways among ALS types. However, when focusing on common features, we identified activation of stress-response and inflammatory pathways in specific microglia subtypes, as well as disrupted vesicle transport and synaptic function in a ventral inhibitory neuronal subtype. Notably, CPLX3, a SNARE regulator, was uniquely expressed in alpha-motor neurons and was commonly downregulated across all ALS types. While this study uncovers the molecular heterogeneity underlying ALS, it also highlights shared pathways within specific cell types, especially in the ventral inhibitory neurons that have been less explored in ALS research.

neuroscience↗

bioRxiv2024

Cyr61 delivery promotes angiogenesis during bone fracture repair

Compromised vascular supply and insufficient neovascularization impede bone repair, increasing risk of non-union. Cyr61, Cysteine-rich angiogenic inducer of 61kD (also known as CCN1), is a matricellular growth factor that is regulated by mechanical cues during fracture repair. Here, we map the distribution of endogenous Cyr61 during bone repair and evaluate the effects of recombinant Cyr61 delivery on vascularized bone regeneration. In vitro, Cyr61 treatment did not alter chondrogenesis or osteogenic gene expression, but significantly enhanced angiogenesis. In a mouse femoral fracture model, Cyr61 delivery did not alter cartilage or bone formation, but accelerated neovascularization during fracture repair. Early initiation of ambulatory mechanical loading disrupted Cyr61-induced neovascularization. Together, these data indicate that Cyr61 delivery can enhance angiogenesis during bone repair, particularly for fractures with stable fixation, and may have therapeutic potential for fractures with limited blood vessel supply.

bioengineering↗

bioRxiv2023

Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning

Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes 1,2. However, the mechanisms that govern their sorting and secretion are still not well understood. In this study, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequence. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis, and confirmed that primary RNA sequence is a major determinant in small RNA secretion. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins, e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. We used exoCLIP to reveal the RNA interactome of HNRNPA2B1 and RBM24 in extracellular vesicles. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into complex processes such as small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.

systems biology↗

bioRxiv2023

Autistic kinematics diverge from the power laws that typically govern movement

Extant work reliably demonstrates that autistic individuals move with increased jerk (where jerk concerns change in acceleration). Although it follows that autistic movement may therefore diverge from fundamental power laws that govern movement, this hypothesis has not been directly tested to date. This lack of insight holds back progress in understanding the mechanisms underpinning differences in autism in motor control particularly with respect to movement jerkiness. Here we investigated whether movements executed by autistic adults diverged from the typical power law relationship that links movement speed and curvature. x and y position of the stylus tip was recorded at 133 Hz while 21 autistic and 19 non-autistic age-, intelligence quotient- and sex-matched adults traced, on a tablet device, a range of shapes that varied in angular frequency from 2/33 (spiral-like shapes) to 4 (square-like shapes). The gradient of the relationship between speed and curvature for each angular frequency-defined shape is reliably predicted by a set of mathematical equations often referred to as fundamental power laws thus, to assess deviations from power laws, we compared autistic and non-autistic participants in terms of speed-curvature gradients. To gain insight into potential mechanisms underpinning any differences we also used fast Fourier transform to explore amplitude spectral density across all angular frequencies. Compared to non-autistic adults, autistic adults exhibited significantly steeper speed-curvature gradients. Fast Fourier transform further revealed that non-autistic participants exhibited highly precise modulation of speed oscillations around the target frequency. For example, when drawing an ellipse their speed profile was dominated by speed changes in a band centred around the angular frequency 2 with minimal changes in other bands. Autistic adults, in contrast, exhibited less precise modulation of speed oscillations around the target frequency, a result that is reminiscent of a literature reporting broader auditory filters in autistic individuals. These results evidence, in autistic adults, a deviation from the power laws that typically govern movement and suggest differences in motor cortical control policies and/or biomechanical constraints.

neuroscience↗

bioRxiv2023

Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration

BackgroundMicroglia are the resident immune cells in the brain that play a key role in driving neuroinflammation, a hallmark of neurodegenerative disorders. Inducible microglia-like cells have been developed as an in vitro platform for molecular and therapeutic hypothesis generation and testing. However, there has been no systematic assessment of similarity of these cells to primary human microglia along with their responsiveness to external cues expected of primary cells in the brain. MethodsIn this study, we performed transcriptional characterization of commercially available human inducible pluripotent stem cell (iPSC)-derived microglia-like (iMGL) cells by bulk and single cell RNA sequencing to assess their similarity with primary human microglia. To evaluate their stimulation responsiveness, iMGL cells were treated with Liver X Receptor (LXR) pathway agonists and their transcriptional responses characterized by bulk and single cell RNA sequencing. ResultsBulk transcriptome analyses demonstrate that iMGL cells have a similar overall expression profile to freshly isolated human primary microglia and express many key microglial transcription factors and functional and disease-associated genes. Notably, at the single-cell level, iMGL cells exhibit distinct transcriptional subpopulations, representing both homeostatic and activated states present in normal and diseased primary microglia. Treatment of iMGL cells with LXR pathway agonists induces robust transcriptional changes in lipid metabolism and cell cycle at the bulk level. At the single cell level, we observe heterogeneity in responses between cell subpopulations in homeostatic and activated states and deconvolute bulk expression changes into their corresponding single cell states. ConclusionsIn summary, our results demonstrate that iMGL cells exhibit a complex transcriptional profile and responsiveness, reminiscent of in vivo microglia, and thus represent a promising model system for therapeutic development in neurodegeneration.

genomics↗

bioRxiv2020

A split methyl halide transferase AND gate that reports by synthesizing an indicator gas

It is challenging to detect microbial reactions in highly opaque or autofluorescent environments like soils, seawater, and wastewater. To develop a simple approach for monitoring post-translational reactions within microbes situated in environmental matrices, we designed a methyl halide transferase (MHT) fragment complementation assay that reports by synthesizing an indicator gas. We show that backbone fission within regions of high sequence variability in the Rossmann-fold domain yields split MHT (sMHT) AND gates whose fragments cooperatively associate to synthesize CH3Br. Additionally, we identify a sMHT whose fragments require fusion to pairs of interacting partner proteins for maximal activity. We also show that sMHT fragments fused to FKBP12 and the FKBP-rapamycin binding domain of mTOR display significantly enhanced CH3Br production in the presence of rapamycin. This gas production is reversed in the presence of the competitive inhibitor of FKBP12/FKPB dimerization, indicating that sMHT is a reversible reporter of post-translational reactions. This sMHT represents the first genetic AND gate that can report on protein-protein interactions via an indicator gas. Because indicator gases can be measured in the headspaces of complex environmental samples, this protein fragment complementation assay should be useful for monitoring the dynamics of diverse molecular interactions within microbes situated in hard-to-image marine and terrestrial matrices.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗

bioRxiv2018

An adaptive stress-induced tRNA depletion response mediates codon-based gene repression and growth suppression

Eukaryotic transfer RNAs can become selectively fragmented upon various stresses, generating tRNA-derived small RNA fragments. Such fragmentation has been reported to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that oxidative stress can rapidly generate tyrosine tRNAGUA fragments in human cells--causing significant depletion of the precursor tRNA. Tyrosine tRNAGUA depletion impaired translation of growth and metabolic genes enriched in cognate tyrosine codons. Depletion of tyrosine tRNAGUA or its translationally regulated targets USP3 and SCD repressed proliferation--revealing a dedicated tRNA-regulated growth suppressive pathway for oxidative stress response. Tyrosine fragments are generated in a DIS3L2 exoribonuclease-dependent manner and inhibit hnRNPA1-mediated transcript destabilization. Moreover, tyrosine fragmentation is conserved in C. elegans. Thus, tRNA fragmentation can coordinately generate trans-acting small-RNAs and functionally deplete a tRNA. Our findings reveal the existence of an underlying adaptive codon-based regulatory response inherent to the genetic code.

molecular biology↗