Biology subjects

Park, S.

Publications and source records attributed to Park, S..

At least 199 records · Page 11Linked to original sources

bioRxiv2023

High-throughput single-nucleus hybrid sequencing reveals genome-transcriptome correlations in cancer

To deepen our understanding of cancer heterogeneity and uncover the dynamic interactions of tumor and host cells, we introduce hybrid BAG-seq: a high-throughput, multi-omic method that simultaneously captures DNA and RNA from tens of thousands of individual single nuclei. This method provides dual molecular layer information: DNA to distinguish tumor from stroma, identify tumor subclones, and detect mutant stromal sub-populations; and RNA to characterize distinct cell types, cell states, and signatures of aberrant expression. Additionally, we developed a suite of analysis tools to illuminate cluster phylogeny and connections between DNA identity and RNA expression. We applied this hybrid protocol to 65,499 single nuclei from samples of five uterine cancer patients, and validated the clustering using RNA-only and DNA-only protocols on 34,651 and 21,432 nuclei, respectively, from the same tissues. Multiple tumor genome or expression clusters were often present within a patient, with different tumor clones projecting into distinct or shared expression states, demonstrating nearly all possible genome-transcriptome correlations across the cohort. While tumor expression profiles were highly unique to each patient, the stromal cell types generally recurred across samples, but certain patients and tissues exhibited unique stromal sub-types characterized by aberrant expression. Moreover, we identified mutant stroma in various cell types from several patients with a significant loss of the X-chromosome. This study reveals the complex landscape of genome and transcriptome interactions at the resolution of single nuclei, providing new insights into mutant stroma and tumor heterogeneity.

genomics↗

bioRxiv2023

A new cell culture resource for investigations of reptilian gene function

The recent establishment of CRISPR/Cas9 gene editing in A. sagrei lizards makes it a powerful model system for studies of reptilian gene function. To enhance the versatility of this model, we developed an immortalized lizard fibroblast cell line (ASEC-1) for the exploration of reptilian gene function in cellular processes. We demonstrate the use of this in vitro system by scrutinizing the role of primary cilia in lizard Hedgehog (Hh) signaling. Through CRISPR/Cas9 mutagenesis we disrupted the ift88 gene, which is required for ciliogenesis in diverse organisms. We find that the loss of itf88 from lizard cells results in an absence of primary cilia, a partial derepression of gli1 transcription, and an inability of the cells to respond to the Smoothened agonist, SAG. Through a cross-species analysis of SAG-induced transcriptional responses in cultured limb bud cells, we further determined that [~]46% of genes induced as a response to Hh pathway activation in A. sagrei, are also SAG-responsive in M. musculus limb bud cells. Our results highlight conserved and diverged aspects of Hh signaling in anoles and establish a new resource for investigations of reptilian gene function.

developmental biology↗

bioRxiv2023

The secreted midbody remnants, MBsomes, as a new class of mRNA nanocarrier applicable to diverse medical fields

The midbodysome (MBsome), a secreted remnant of midbody during cell division, is now known to play a key role in cytokinesis. It was thought that the MBsome is either released into the extracellular space or autophagically degraded by one of its daughter cells. However, recent studies have revealed that MBsomes can be maintained by cells even after cell division is complete, and that they accumulate in the cytoplasm and regulate cell proliferation and survival through integrin and epidermal growth factor receptor-dependent pathways. Here, we examined the ability of MBsomes to act as carriers of mRNAs, a novel function that has not been studied. We found that MBsomes isolated from human lung cancer and stem cells via sucrose cushion ultracentrifugation were 300-400 nm in size and stable for up to 4 days when stored at 4{degrees}C. In addition, we confirmed successful expression of the EGFP protein following incubation of the isolated MBsomes with the EGFP mRNA at room temperature. These results suggest that MBsomes have the potential to serve as mRNA carriers and therapeutic agents capable of delivering a gene-of-interest.

cell biology↗

bioRxiv2023

Effects of visual feedback on corticostriatal activity during continuous de novo motor skill learning

A corticostriatal network plays a pivotal role in visuomotor learning. However, it is unclear to what extent visual feedback for motor learning impacts corticostriatal activity. To address this, we conducted an fMRI experiment in which participants acquired a complex motor skill using either online or offline visual cursor feedback. We found a highly selective response in the entire striatum to visual performance feedback in both conditions and a relatively higher response in the caudate nucleus for the offline feedback. However, the ventromedial prefrontal cortex (vmPFC) response was significant only for online feedback. Furthermore, we also found functional distinctions of the striatal subregions in random versus goal-directed motor control. These findings collectively underscore the substantial impact of such simple visual feedback, as designed in our study, in eliciting corticostriatal responses, thereby elucidating its significance in reinforcement-based motor learning.

neuroscience↗

bioRxiv2023

In Vivo Antiviral Efficacy of LCTG-002, a Pooled, Purified Human Milk Secretory IgA product, Against SARS-CoV-2 in a Murine Model of COVID-19

Immunoglobulin A (IgA) is the most abundant antibody (Ab) in human mucosal compartments including the respiratory tract, with the secretory form of IgA (sIgA) being dominant and uniquely stable in these environments. sIgA is naturally found in human milk, which could be considered a global resource for this biologic, justifying the development of human milk sIgA as a dedicated airway therapeutic for respiratory infections such as SARS-CoV-2. In the present study, methods were therefore developed to efficiently extract human milk sIgA from donors who were either immunologically naive to SARS-CoV-2 (pooled as a control IgA) or had recovered from a PCR-confirmed SARS-CoV-2 infection that elicited high-titer anti-SARS-CoV-2 Spike sIgA Abs in their milk (pooled together to make LCTG-002). Mass spectrometry determined that proteins with a relative abundance of 1.0% or greater were all associated with sIgA. None of the proteins exhibited statistically significant differences between batches. Western blot demonstrated all batches consisted predominantly of sIgA. Compared to control IgA, LCTG-002 demonstrated significantly higher binding to Spike, and was also capable of blocking the Spike - ACE2 interaction in vitro with 6.3x greater potency compared to control IgA (58% inhibition at [~]240ug/mL). LCTG-002 was then tested in vivo for its capacity to reduce viral burden in the lungs of K18+hACE2 transgenic mice inoculated with SARS-CoV-2. LCTG-002 was demonstrated to significantly reduce SARS-CoV-2 titers in the lungs compared to control IgA when administered at either 250ug/day or 1 mg/day, as measured by TCID50, plaque forming units (PFU), and qRT-PCR, with a maximum reduction of 4.9 logs. This innovative study demonstrates that LCTG-002 is highly pure, efficacious, and well tolerated in vivo, supporting further development of milk-derived, polyclonal sIgA therapeutics against SARS-CoV-2 and other mucosal infections.

immunology↗

bioRxiv2023

Immunometabolic cues recompose and reprogram the microenvironment around biomaterials

Circulating monocytes infiltrate and coordinate immune responses in various inflamed tissues, such as those surrounding implanted biomaterials, affecting therapeutic, diagnostic, tissue engineering and regenerative applications. Here, we show that immunometabolic cues in the biomaterial microenvironment govern CCR2- and CX3CR1-dependent trafficking of immune cells, including neutrophils and monocytes; ultimately, this affects the composition and activation states of macrophage and dendritic cell populations. Furthermore, immunometabolic cues around implants orchestrate the relative composition of proinflammatory, transitory and anti-inflammatory CCR2+, CX3CR1+ and CCR2+CX3CR1+ immune cell populations. Consequently, modifying immunometabolism by glycolytic inhibition drives a pro-regenerative microenvironment in part by myeloid cells around amorphous polylactide implants. In addition to, Arginase 1-expressing myeloid cells, T helper 2 cells and {gamma}{delta}+ T-cells producing IL-4 significantly contribute to shaping the metabolically reprogramed, pro-regenerative microenvironment around crystalline polylactide biomaterials. Taken together, we find that local metabolic states regulate inflammatory processes in the biomaterial microenvironment, with implications for translational medicine.

bioengineering↗

bioRxiv2023

Combined representation of visual features in the scene-selective cortex

Visual features of separable dimensions like color and shape conjoin to represent an integrated entity. We investigated how visual features bind to form a complex visual scene. Specifically, we focused on features important for visually guided navigation: direction and distance. Previously, separate works have shown that directions and distances of navigable paths are coded in the occipital place area (OPA). Using functional magnetic resonance imaging (fMRI), we tested how separate features are concurrently represented in the OPA. Participants saw eight different types of scenes, in which four of them had one path and the other four had two paths. In single-path scenes, path direction was either to the left or to the right. In double-path scenes, both directions were present. Each path contained a glass wall located either near or far, changing the navigational distance. To test how the OPA represents paths in terms of direction and distance features, we took three approaches. First, the independent-features approach examined whether the OPA codes directions and distances independently in single-path scenes. Second, the integrated-features approach explored how directions and distances are integrated into path units, as compared to pooled features, using double-path scenes. Finally, the integrated-paths approach asked how separate paths are combined into a scene. Using multi-voxel pattern similarity analysis, we found that the OPAs representations of single-path scenes were similar to other single-path scenes of either the same direction or the same distance. Representations of double-path scenes were similar to the combination of two constituent single-paths, as a combined unit of direction and distance rather than pooled representation of all features. These results show that the OPA combines the two features to form path units, which are then used to build multiple-path scenes. Altogether, these results suggest that visually guided navigation may be supported by the OPA that automatically and efficiently combines multiple features relevant for navigation and represent a navigation file.

neuroscience↗

bioRxiv2023

Multi-modal representation of the size of space in the human brain

To estimate the size of an indoor space, we must analyze the visual boundaries that limit the spatial extent and acoustic cues from reflected interior surfaces. We used fMRI to examine how the brain processes geometric size of indoor scenes when various types of sensory cues are presented individually or together. Specifically, we asked whether the size of space is represented in a modality-specific way or in an integrative way that combines multimodal cues. In a block-design study, images or sounds that depict small and large sized indoor spaces were presented. Visual stimuli were real-world pictures of empty spaces that were small or large. Auditory stimuli were sounds convolved with different reverberation. By using a multi-voxel pattern classifier, we asked whether the two sizes of space can be classified in visual, auditory, and visual-auditory combined conditions. We identified both sensory specific and multimodal representations of the size of space. To further investigate the nature of the multimodal region, we specifically examined whether it contained multimodal information in a coexistent or integrated form. We found that AG and the right IFG pars opercularis had modality-integrated representation, displaying sensitivity to the match in the spatial size information conveyed through image and sound. Background functional connectivity analysis further demonstrated that the connection between sensory specific regions and modality-integrated regions increase in the multimodal condition compared to single modality conditions. Our results suggest that the spatial size perception relies on both sensory specific and multimodal representations, as well as their interplay during multimodal perception.

neuroscience↗

bioRxiv2023

Plant-to-plant reactive oxygen signal transmission via a Cuscuta bridge

Cuscuta, commonly known as dodder, is a parasitic plant that thrives by attaching itself to the stems of other plants. It is found across the globe and is notorious for obstructing crop growth as a weed. Over the past decade, Cuscuta has been used to gain insights into plant-plant interactions and molecular trafficking. Here, we report that two plants connected via a Cuscuta bridge can exchange rapid systemic calcium, electric, and reactive oxygen species signals. These findings suggest that plant interactions with Cuscuta may have beneficial effects to plants, enabling them to rapidly communicate with each other.

plant biology↗

bioRxiv2023

Petascale Homology Search for Structure Prediction

The recent CASP15 competition highlighted the critical role of multiple sequence alignments (MSAs) in protein structure prediction, as demonstrated by the success of the top AlphaFold2-based prediction methods. To push the boundaries of MSA utilization, we conducted a petabase-scale search of the Sequence Read Archive (SRA), resulting in gigabytes of aligned homologs for CASP15 targets. These were merged with default MSAs produced by ColabFold-search and provided to ColabFold-predict. By using SRA data, we achieved highly accurate predictions (GDT_TS > 70) for 66% of the non-easy targets, whereas using ColabFold-search default MSAs scored highly in only 52%. Next, we tested the effect of deep homology search and ColabFolds advanced features, such as more recycles, on prediction accuracy. While SRA homologs were most significant for improving ColabFolds CASP15 ranking from 11th to 3rd place, other strategies contributed too. We analyze these in the context of existing strategies to improve prediction.

bioinformatics↗

bioRxiv2023

Automated Microbial Classification System based on Deep Convolutional Neural Networks using Images from Colony Picker

Colony screening in single and multi-species environments is an essential step for microbiome studies. However, it possesses a high possibility of inaccurately classifying the species of interest and demands a high degree of manpower and time. Thus, automating the classification of microbes is beneficial to minimize the time and inaccuracy in the colony screening/picking step. Here, we developed an automated microbial classification system for five target species, based on deep Convolutional Neural Networks (CNN) using images captured by an automated robotic colony picker. Multiple possible scenarios of colony culture and diverse morphologies of colonies were examined in building the training and test datasets to train and validate the model and performance on real-life implementations. The final model trained using 60,000 training images, with 12,000 images per species and 3-fold cross-validation, achieved a test accuracy of 94.2% and a test loss of 0.154. Upon testing using a deployment dataset of 4,500 images (900 images per species) with different methods of applying cells onto the agar plate, high accuracy of up to 96.6% was obtained. Five evaluation metrics were implemented to evaluate diverse scenarios of the test data to justify the validity of the model in real-life applications. This model forms a foundation for the classification of more species through transfer learning in the future.

synthetic biology↗

bioRxiv2023

The microenvironment dictates glycocalyx construction and immune surveillance

Efforts to identify anti-cancer therapeutics and understand tumor-immune interactions are built with in vitro models that do not match the microenvironmental characteristics of human tissues. Using in vitro models which mimic the physical properties of healthy or cancerous tissues and a physiologically relevant culture medium, we demonstrate that the chemical and physical properties of the microenvironment regulate the composition and topology of the glycocalyx. Remarkably, we find that cancer and age-related changes in the physical properties of the microenvironment are sufficient to adjust immune surveillance via the topology of the glycocalyx, a previously unknown phenomenon observable only with a physiologically relevant culture medium. Key PointsO_LICulture medium dictates cellular mechanoresponse signatures in vitro C_LIO_LIEpithelial glycocalyx construction is mediated by Heat Shock Factor 1 (HSF1) C_LIO_LISialic acid topology dictates Natural Killer cell cytotoxicity C_LIO_LIPhysiological microenvironments reveal distinct glycobiology C_LI

cell biology↗

bioRxiv2023

CRISPR/Cas9 gene editing to generate Drosophila LexA lines in secondary school classes

Genome editing in vivo with CRISPR/Cas9 generates powerful tools to study gene regulation and function. We developed CRISPR-based methods that permitted secondary school student scientists to convert Drosophila GAL4 lines to LexA lines. Our novel curricula implement a new donor strain optimizing Homology-assisted CRISPR knock-in (HACK) that simplifies screening using light microscopy. Successful curricula adoption by a consortium of schools led to the generation and characterization of 16 novel LexA lines. This includes extensive comparative tissue expression analysis between the parental Gal4 and derived LexA lines. From this collaboration, we established a workflow to systematically generate LexA lines from frequently-used GAL4 lines. Modular courses developed from this effort can be tailored to specific secondary school scheduling needs, and serve as a template for science educators to innovate courses and instructional goals. Our unique collaborations highlight that resources and expertise harnessed by university-based research laboratories can transform experiential science instruction in secondary schools while addressing research needs for the community of science.

genetics↗

bioRxiv2023

Periaqueductal gray activates antipredatory neural responses in the amygdala of foraging rats

Pavlovian fear conditioning research suggests that the interaction between the dorsal periaqueductal gray (dPAG) and basolateral amygdala (BLA) acts as a prediction error mechanism in the formation of associative fear memories. However, their roles in responding to naturalistic predatory threats, characterized by less explicit cues and the absence of reiterative trial-and-error learning events, remain unexplored. In this study, we conducted single-unit recordings in rats during an approach food-avoid predator task, focusing on the responsiveness of dPAG and BLA neurons to a rapidly approaching robot predator. Optogenetic stimulation of the dPAG triggered fleeing behaviors and increased BLA activity in naive rats. Notably, BLA neurons activated by dPAG stimulation displayed immediate responses to the robot, demonstrating heightened synchronous activity compared to BLA neurons that did not respond to dPAG stimulation. Additionally, the use of anterograde and retrograde tracer injections into the dPAG and BLA, respectively, coupled with c-Fos activation in response to predatory threats, indicates that the midline thalamus may play an intermediary role in innate antipredatory defensive functioning.

neuroscience↗

bioRxiv2023

Ampk activation by glycogen expenditure primes the exit of naive pluripotency

Embryonic and epiblast stem cells in pre-and post-implantation embryos are characterized by their naive and primed states, respectively, which represent distinct phases of pluripotency. Thus, the cellular transition from naive to primed pluripotency recapitulates a drastic metabolic and cellular remodeling after implantation to adapt to changes in extracellular conditions. Here, we found that inhibition of Ampk occurred during naive transition with two conventional inhibitors (2i) of the Mek1 and Gsk3{beta} pathways. The accumulation of glycogen due to the inhibition of Gsk3{beta} was responsible for Ampk inhibition, which accounted for high de novo fatty acid synthesis in naive embryonic stem cells (ESCs). The knockout of glycogen synthase 1 (Gys1) in naive ESCs (GKO), resulting in a drastic glycogen loss, led to a robust Ampk activation and lowered the level of fatty acids. GKO lost the cellular characteristics of naive ESCs and rapidly transitioned to a primed state, as evidenced by a decrease in pluripotency markers in teratoma from GKO. The characteristics of GKO were restored by the simultaneous knockout of Ampk. These findings suggest that glycogen in naive ESCs within the blastocyst may act as a signaling molecule for the timely activation of Ampk, thus ultimately contributing to the transition to the epiblast stage. Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/541467v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@118ea81org.highwire.dtl.DTLVardef@cbe4bforg.highwire.dtl.DTLVardef@16d5c1org.highwire.dtl.DTLVardef@12b825c_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

Aging-associated Decline in Vascular Smooth Muscle Cell Mechanosensation is Mediated by Piezo1 Channel

Aging of the vasculature is associated with detrimental changes in vascular smooth muscle cell (VSMC) mechanosensitivity to extrinsic forces in their surrounding microenvironment. However, how chronological aging alters VSMCs ability to sense and adapt to mechanical perturbations remains unexplored. Here, we show defective VSMC mechanosensation in aging measured with ultrasound tweezers-based micromechanical system, force instantaneous frequency spectrum and transcriptome analyses. The mechanobiological study reveals that aged VSMCs adapt a relatively inert solid-like state with altered actin cytoskeletal integrity, resulting in an impairment in their mechanosensitivity and dynamic mechanoresponse to mechanical perturbations. The aging-associated decline in mechanosensation behaviors is mediated by hyperactivity of Piezo1-dependent calcium signaling. Inhibition of Piezo1 alleviates vascular aging and partially restores the loss in dynamic contractile properties in aged cells. Altogether, our study reveals the novel signaling pathway underlying aging-associated aberrant mechanosensation in VSMC and identifies Piezo1 as a potential therapeutic mechanobiological target to alleviate vascular aging.

bioengineering↗

bioRxiv2023

Proteasome gene expression is controlled by the coordinated functions of multiple transcription factors

Proteasome activity is crucial for cellular integrity, but how tissues adjust proteasome content in response to catabolic stimuli is uncertain. Here, we demonstrate that transcriptional coordination by multiple transcription factors is required to increase proteasome content and activate proteolysis in catabolic states. Using denervated mouse muscle as a model system for accelerated proteolysis in vivo, we reveal that a two-phase transcriptional program activates genes encoding proteasome subunits and assembly chaperones to boost an increase in proteasome content. Initially, gene induction is necessary to maintain basal proteasome levels, and in a more delayed phase (7-10 d after denervation) it stimulates proteasome assembly to meet cellular demand for excessive proteolysis. Intriguingly, the transcription factors PAX4 and -PALNRF-1 control the expression of proteasome among other genes in a combinatorial manner, driving cellular adaptation to muscle denervation. Consequently, PAX4 and -PALNRF-1 represent new therapeutic targets to inhibit proteolysis in catabolic diseases (e.g. type-2 diabetes, cancer).

cell biology↗

bioRxiv2023

EGFR inhibition in lung adenocarcinoma upregulates cell surface expression of the placental antigen ALPP and enhances efficacy of ALPP-ADC therapy

Alkaline phosphatase placental type (ALPP) and ALPPL2 are closely related and regulated GPI anchored proteins that are known to be expressed on the cell surface in some cancers, whereas normal tissue expression is largely limited to the placenta. Clinical utility of ALPP is potentially limited by heterogenous expression in tumors. Here, we assessed ALPP and ALPPL2 surfaceome protein levels in 158 cancer cell lines and mRNA expression levels in 10,967 tumors representing 32 cancer types from The Cancer Genome Atlas (TCGA), which revealed ALPP, and to a lesser extent ALPPL2, to be variably expressed in several cancer types including lung adenocarcinoma (LUAD). Surface expression of ALPP was confirmed by tissue microarray analysis of 204 lung tumors. Using LUAD as a model system, we demonstrated that treatment with EGFR inhibitors, or induction of cancer cell quiescence via nutrient deprivation greatly enhanced ALPP surface expression. Mechanistic studies revealed that enhancement of surface ALPP expression in LUAD following gefitinib treatment was mediated through repression of EGFR signaling and activation of the transcription factor FoxO3a, which was identified as an upstream transcriptional regulator of ALPP. Using xenograft models of LUAD, we further demonstrated that gefitinib treatment upregulates surface expression of ALPP in LUAD cells but not in normal tissues. Combination therapy with gefitinib and an ALPP antibody conjugated with Monomethylauristatin F (ALPP-ADC-MAF) resulted in superior anti-cancer efficacy compared with gefitinib or ALPP-ADC-MAF alone. Our findings support a novel combination treatment modality that boosts the efficacy of ALPP-ADC directed therapy.

cancer biology↗