Biology subjects

Jung, Y.

Publications and source records attributed to Jung, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Spatial Transcriptomics Reveals Spatially Diverse Cancer-Associated Fibroblast in Lung Squamous Cell Carcinoma Linked to Tumor Progression

While cancer-associated fibroblasts (CAFs) are crucial in influencing tumor growth and immune responses in lung cancer, we still lack a comprehensive understanding of their spatial organization associated with tumor progression and clinical outcomes. This gap highlights the need to elucidate how the intricate spatial arrangement of CAFs affects their interactions within the tumor microenvironment, ultimately shaping cancer progression and patient prognosis. Here, we unveil the spatial diversity of CAFs in lung squamous cell carcinoma (LUSC), a prevalent and aggressive lung cancer type, elucidating their impact on tumor progression and patient outcomes using spatial transcriptomics (ST). Image-based ST data from 33 LUSC patients demonstrated a significant association of spatial interactions of tumor epithelium and CAFs with tumor size and metabolic activity measured by [18F]fluorodeoxyglucose PET. Furthermore, the proximity of fibroblasts to tumor epithelial cells was linked to recurrence-free survival in LUSC patients. By characterizing CAFs based on their spatial relationship, we identified distinct molecular signatures related to spatially distinct fibroblast subpopulations. In addition, barcode-based ST data from 8 LUSC patients revealed spatially overlapping fibroblast regions characterized by upregulated glycolysis pathways. Our study underscores the importance of the complex spatial dynamics of the tumor microenvironment revealed by ST and its implications for patient outcomes in LUSC.

cancer biology↗

bioRxiv2024

Chemical tools to define and manipulate interferon-inducible Ubl protease USP18

Ubiquitin-specific protease 18 (USP18) is a multifunctional cysteine protease primarily responsible for deconjugating interferon-inducible ubiquitin-like (Ubl) modifier ISG15 from protein substrates. Here, we report the design and synthesis of activity-based probes (ABPs) capable of selectively detecting USP18 activity over other ISG15 cross-reactive deubiquitinases (DUBs) by incorporating unnatural amino acids into the C-terminal tail of ISG15. Combining with a ubiquitin-based DUB ABP, the selective USP18 ABP is employed in a chemoproteomic screening platform to identify and assess inhibitors of DUBs including USP18. We further demonstrate that USP18 ABPs can be utilized to profile differential activities of USP18 in lung cancer cell lines, providing a strategy that will help define the activity-related landscape of USP18 in different disease states and unravel important (de)ISGylation-dependent biological processes.

molecular biology↗

bioRxiv2024

Modeling platinum resistance in a stem-like patient-derived ovarian cancer sample

BackgroundChemoresistance and tumor recurrence remain a significant challenge in ovarian cancer. Particularly in the context of platinum resistance, many mechanisms have been identified, including the activation of cellular processes like epithelial-mesenchymal transition (EMT), which generates cells with stemness characteristics. Current models of platinum resistance are limited or not adequate representations of the heterogeneity of the disease. Thus, to advance our understanding of chemoresistance in the context of cancer stem cells (CSC) in ovarian cancer, this study aims to develop an effective model for cisplatin resistance using a patient-derived cancer stem-like sample. MethodsPDX4, a patient-derived cancer cell line with stem-like properties, was exposed to increasing concentrations of cisplatin in vitro in parallel with vehicle treated cells. Once chemoresistance was established and confirmed, the resistance model was validated through comprehensive molecular profiling through RNA- and miRNA-sequencing, followed by the assessment of alterations in cell morphology, protein expression, and functional properties in the context of EMT and cancer stemness. Moreover, we explored potential signaling pathways involved in cisplatin resistance in these stem-like cancer cells. ResultsOur findings reveal the presence of distinct molecular signatures and phenotypic changes in cisplatin resistant PDX4 compared to their sensitive counterparts. Furthermore, we observed that chemoresistance was not inherently linked with increased stemness. In fact, although resistant cells expressed a combination of EMT and stemness markers, functional assays revealed that they were less proliferative, migratory, and clonogenic. JAK-STAT, hypoxia, and PI3K signaling pathways were enriched in these cells, indicating the activation of pathways that assist in DNA damage tolerance and cellular stress management. ConclusionThis novel, syngeneic model provides a valuable platform for investigating the underlying mechanisms of cisplatin resistance in a clinically relevant context, contributing to the development of targeted therapeutic strategies tailored to combat resistance in stem-like ovarian cancer.

cancer biology↗

bioRxiv2023

Imaging Electrical Activity of Retinal Ganglion Cells with Fluores-cent Voltage and Calcium Indicator Proteins in Retinal Degenera-tive rd1 Blind Mice

In order to understand the retinal network, it is essential to identify functional connectivity among retinal neurons. For this purpose, imaging neuronal activity through fluorescent indicator proteins has been a promising approach offering simultaneous measurements of neuronal activities from different regions of the circuit. In this study, we used genetically encoded voltage and calcium indicators, Bongwoori-R3 and GCaMP6f, to visualize membrane voltage and calcium dynamics in the form of the spatial map within retinal ganglion cells from retina tissues of the photoreceptor degenerated rd1 mice. Retinal voltage imaging confirmed current-evoked responses from somatic spiking and intercellular conduction, while calcium imaging showed current evoked changes in calcium concentrations of presynaptic neurons. These results indicate that the combination of fluorescent protein sensors and high-speed imaging methods permits imaging electrical activity with cellular precision and millisecond resolution. Hence, we expect our method will provide a potent experimental platform for the study of retinal signaling pathways as well as the development of retinal stimulation strategies in visual prosthesis.

neuroscience↗

bioRxiv2023

The CD36 scavenger receptor Bez regulates lipid redistribution from fat body to oocytes in Drosophila

Class B scavenger receptors of the CD36 family are important for lipid mobilization from mammalian adipose tissue. This protein family has 3 members in mammals, but 14 in Drosophila melanogaster. Lipid distribution in Drosophila is mediated by homologs of the LDL receptors, while little is known about the function of scavenger receptors for this process in invertebrates. Here we unravel a role for the so far uncharacterized scavenger receptor Bez in lipid export from Drosophila adipocytes. Bez shares the lipid binding residue with CD36 and is expressed at the plasma membrane of the embryonic, larval and adult fat body. Bez loss-of-function lowers the organismal content of storage lipids while they accumulate in the fat body, concomitant with female sterility and degeneration of ovaries. Using an alkyne-labeled fatty acid tracer, we demonstrate that Bez interacts with the apoB homolog Lipophorin at the plasma membrane of adipocytes, thereby enabling lipid transfer. Our study shows how a scavenger receptor interacts with lipoproteins to distribute storage lipids from the fat body to the ovaries and thereby contributes to the metabolic control of development.

developmental biology↗

bioRxiv2023

Implantable nanophotonic neural probes for integrated patterned photostimulation and electrophysiology recording

Optogenetics has transformed neuroscience by allowing precise manipulation of neural circuits with light [1-5]. However, a central difficulty has been to deliver spatially shaped light and record deep within the brain without causing damage or significant heating. Current approaches form the light beam in free space and record the neural activity using fluorescence imaging or separately inserted electrodes [6-9], but attenuation limits optical penetration to around 1 mm of the brain surface [10]. Here, we overcome this challenge with foundry-fabricated implantable silicon neural probes that combine microelectrodes for electrophysiology recordings with nanophotonic circuits that emit light with engineered beam profiles and minimal thermal impact. Our experiments reveal that planar light sheets, emitted by our neural probes, excited more neurons and induced greater firing rate fatigue in layers V and VI of the motor and somatosensory cortex of Thy1-ChR2 mice at lower output intensities than low divergence beams. In the hippocampus of an epilepsy mouse model, we induced seizures, a network-wide response, with light sheets without exceeding the[~] 1{whitebullet}C limit for thermally induced electrophysiological responses [11-13]. These findings show that optical spatial profiles can be tailored for optogenetic stimulation paradigms and that the probes can photostimulate and record neural activity at single or population levels while minimizing thermal damage to brain tissue. The neural probes, made in a commercial silicon photonics foundry on 200-mm silicon wafers, demonstrate the manufacturability of the technology. The prospect of monolithically integrating additional well-established silicon photonics devices, such as wavelength and polarization multiplexers, temperature sensors, and optical power monitors, into the probes holds the potential of realizing more versatile, implantable tools for multimodal brain activity mapping.

bioengineering↗

bioRxiv2023

Enhanced functionalities of immune cells separated by microfludic lattice: assessment based on holotomography

The isolation of white blood cells (WBCs) from whole blood constitutes a pivotal process for immunological studies, diagnosis of hematologic disorders, and the facilitation of immunotherapy. Despite the ubiquity of density gradient centrifugation in WBC isolation, its influence on WBC functionality remains inadequately understood. This research employs holotomography to explore the effects of two distinct WBC separation techniques, namely conventional centrifugation and microfluidic separation, on the functionality of the isolated cells. We utilize three-dimensional refractive index distribution and time-lapse dynamics to conduct an in-depth analysis of individual WBCs, focusing on their morphology, motility, and phagocytic capabilities. Our observations highlight that centrifugal processes negatively impacts WBC motility and phagocytic capacity, whereas microfluidic separation yields a more favorable outcome in preserving WBC functionality. These findings emphasize the potential of microfluidic separation techniques as a viable alternative to traditional centrifugation for WBC isolation, potentially enabling more precise analyses in immunology research and improving the accuracy of hematologic disorder diagnoses.

biophysics↗

bioRxiv2023

Generalizing deep variant callers via domain adaptation and semi-supervised learning

Deep learning-based variant callers (DVCs) offer state-of-the-art perfor-mance in small variant detection from DNA sequencing data. However, their reliance on supervised learning and the subsequent need for exten-sive labeled data pose a potential hurdle to their generalizability across diverse sequencing methods with varying error profiles. Indeed, even minor discrepancies in error profiles can compromise the robustness of DVCs and impair the variant calling accuracy in the target sequencing method. To mitigate these challenges, we propose RUN-DVC, the first semi-supervised training approach for DVCs that presents two complemen-tary training techniques to the conventional supervised training approach. RUN-DVC leverages semi-supervised learning techniques to learn error profiles from unlabeled datasets of the target sequencing method as well as a domain adaptation technique to aid semi-supervised learning by reducing the domain discrepancy due to different error profiles. We ana-lyze and contrast RUN-DVC against the supervised training approach under various generalization scenarios using nine sequencing methods from Illumina, BGI, PacBio, and Oxford Nanopore sequencing platforms. Remarkably, RUN-DVC significantly improves the variant calling accu-racy of DVC in the target sequencing method even with purely unlabeled datasets in the target domain and enables label-efficient generalization when partially labeled datasets are available. Our results suggest RUN-DVC is a promising semi-supervised training method for DVCs with the potential to broaden the use of DVC across diverse sequencing methods.

bioinformatics↗

bioRxiv2023

Hypothalamic neuronal activation in primates drives naturalistic goal-directed eating behavior

Eating addiction is the primary cause of modern obesity. Although the causal role of the lateral hypothalamic area (LHA) for eating is demonstrated in rodents, there is no evidence in primates regarding naturalistic eating behaviors. We investigated the role of LHA GABAergic (LHAGABA) neurons in eating by chemogenetics in three macaques. LHAGABA neuron activation significantly increased naturalistic goal-directed behaviors and food motivation, which was specific for palatable food. PET and MRS validated the chemogenetic activation. Rs-fMRI result revealed that functional connectivity (FC) between the LHA and frontal areas was increased, while the FC between the frontal cortices was decreased after the LHAGABA neuron activation. Thus, our study elucidates the role of LHAGABA neurons in eating and obesity therapeutics for primates and humans.

neuroscience↗

bioRxiv2023

Darapladib, an inhibitor of Lp-PLA2, sensitizes cancer cells to ferroptosis by remodeling lipid metabolism

Arachidonic and adrenic acids in the membrane play key roles in ferroptosis, but how these fatty acids are manipulated in cells is largely unknown. Here, we reveal that lipoprotein-associated phospholipase A2 (Lp-PLA2) controls intracellular phospholipid metabolism and contributes to ferroptosis resistance. A metabolic drug screen identified that darapladib (SB-480848), an inhibitor of Lp-PLA2, synergistically induced ferroptosis with GPX4 inhibitors. Notably, darapladib was able to enhance ferroptosis under lipoprotein-deficient or serum-free conditions. Furthermore, Lp-PLA2 was located in the membrane and cytoplasm and suppressed ferroptosis, suggesting the critical role of intracellular Lp-PLA2. Lipidomic analysis showed that phosphatidylethanolamine (PE) species were generally enriched, while lysophosphatidylethanolamine (lysoPE) and free fatty acid levels were reduced, upon darapladib treatment. Finally, combination treatment with darapladib and PACMA31, a GPX4 inhibitor, efficiently inhibited tumor growth in a xenograft model. Our study suggests that inhibition of Lp-PLA2 is a potential therapeutic strategy to enhance ferroptosis in cancer treatment.

cancer biology↗

bioRxiv2023

Synthetic lipid rafts formed by cholesterol nano-patch induce T cell activation

Lipid rafts cluster at the immunological synapse during activation and serve as signaling hubs in T cells. While cholesterol plays a crucial role in lipid raft formation, the impact of their spatial configuration remains less understood. Here, we introduce programmable DNA origami, cholesterol nano-patch, for nanoscale spatial control of cholesterols on live T cell membranes, enabling us to elucidate their roles in lipid raft formation, receptor activation, and intracellular signaling. We demonstrate that CNPs with high-density cholesterol arrangements efficiently bind to the T cell plasma membrane and form a large and polarized coalescence, leading to the stabilization of ordered lipid membrane domains by increasing the local concentration of cholesterols. These synthetic lipid rafts colocalize with flotillin-1, a raft-associated protein, and promote the membrane reorganization and physical segregation of key signaling molecules, such as T cell receptors, Lck and LAT kinases, and CD45. Consequently, this leads to early T cell activation in the absence of antigenic stimulation. Our DNA origami approach demonstrates the direct role of cholesterol in lipid raft formation, leading to membrane phase separation and protein reorganization, which are sufficient to induce early T cell activation.

bioengineering↗

bioRxiv2022

Neither sharpened or lost -- the unique role of attention in children's neural representations

One critical feature of childrens cognition is their relatively immature attention. Decades of research have shown that childrens attentional abilities mature slowly over the course of development, including the ability to filter out distracting information. Despite such rich behavioral literature, little is known about how developing attentional abilities modulate neural representations in children. This information is critical to understanding exactly how attentional development shapes the way children process information. One intriguing possibility is that attention might be less likely to impact neural representations in children as compared with adults. In particular, representations of attended items may be less likely to be sharpened relative to unattended items in children as compared to adults. To investigate this possibility, we measured brain activity using fMRI while adults (21-31 years) and children (7-9 years) performed a one-back working memory task in which they were directed to attend to either motion direction or an object in a complex display where both were present. We used multivoxel pattern analysis and compared decoding accuracy of attended and unattended information. Consistent with attentional sharpening, we found higher decoding accuracy for task-relevant information (i.e., objects in the object-attended condition) than for task-irrelevant information (i.e., motion in the object-attended condition) in adults visual cortices. However, in childrens visual cortices, both task-relevant and task-irrelevant information were decoded equally well. Whats more, exploratory whole-brain analysis showed that the children represent task-irrelevant information more than adults in multiple regions across the brain, including the prefrontal cortex. These findings show that 1) attention does not sharpen neural representations in the child visual cortex, and further 2) that the developing brain can represent more information than the adult brain.

neuroscience↗

bioRxiv2022

Single-cell analysis of non-alcoholic fatty livers identifies a role for the constitutive androstane receptor

Non-alcoholic fatty liver disease is a heterogeneous disease with unclear underlying molecular mechanisms. While several genetic risk factors have been identified, the cellular and molecular heterogeneity associated with the development of hepatic steatosis are still not fully understood. Here, we perform single-cell RNA sequencing of hepatocytes and hepatic nonparenchymal cells to map the lipid signatures in mice with non-alcoholic fatty liver disease (NAFLD). We uncover previously unidentified clusters of hepatocytes characterized by either high or low srebp1 expression with unique molecular signatures of lipid synthesis. We find that NAFLD livers have elevated expression of the constitutive androstane receptor (CAR), a gene previously associated with lipid synthesis. Furthermore, nuclear expression of CAR positively correlates with steatohepatitis in humans. These findings demonstrate significant cellular differences in lipid signatures and identify a gene with a high likelihood of being linked to hepatic steatosis in humans.

cell biology↗

bioRxiv2022

Chaperone-Directed Ribosome Repair after Oxidative Damage

Reactive oxygen species are ubiquitous in cells, where they damage RNA and protein. While relief mechanisms, including effects on translation, have been described, whether ribosomes are functionally compromised by oxidation, and how this damage is mitigated, remains unknown. Here we show that cysteines in ribosomal proteins, including Rps26, are readily oxidized and rendered non-functional, which is exacerbated when yeast are exposed to H2O2. Oxidized Rps26 is released from ribosomes by its chaperone Tsr2, which allows for repair of the damaged ribosomes with newly made Rps26. Ribosomes containing damaged Rpl10 or Rpl23 are similarly repaired by their chaperones, Sqt1 and Bcp1. Ablation of this pathway impairs growth, which is exacerbated under oxidative stress. These findings reveal a novel mechanism for chaperone-mediated ribosome repair with implications for aging and health. One-Sentence SummaryChaperones repair thiol-oxidized ribosomes by release of damaged components and incorporation of newly made ribosomal proteins.

molecular biology↗

bioRxiv2022

Whole genome sequencing of hematologically stained cells catapulted from Cell smears

Analyzing archived peripheral blood smears is a potential route towards gaining cell morphology and genome information of blood cell types from various diseases. Yet, acquiring whole genome information from morphologically targeted cells was difficult, especially for rare cell types. The main causes for such difficulty were the inevitable usage of cell stains leading to whole genome amplification inhibition, and insufficient cell isolation performance of previously introduced laser microdissection (LMD) techniques. Here, we introduce a new laser-based cell isolation technique and a whole genome amplification (WGA) protocol optimized for whole genome analysis from minute input of hematologically stained cells. We were able to perform whole genome copy number profiling and SNP analysis from as little as 5 cells.

genomics↗

bioRxiv2021

MetaScore: A novel machine-learning based approach to improve traditional scoring functions for scoring protein-protein docking conformations

Protein-protein interactions play a ubiquitous role in biological function. Knowledge of the three-dimensional (3D) structures of the complexes they form is essential for understanding the structural basis of those interactions and how they orchestrate key cellular processes. Computational docking has become an indispensable alternative to the expensive and timeconsuming experimental approaches for determining 3D structures of protein complexes. Despite recent progress, identifying near-native models from a large set of conformations sampled by docking - the so-called scoring problem - still has considerable room for improvement. We present here MetaScore, a new machine-learning based approach to improve the scoring of docked conformations. MetaScore utilizes a random forest (RF) classifier trained to distinguish near-native from non-native conformations using a rich set of features extracted from the respective protein-protein interfaces. These include physico-chemical properties, energy terms, interaction propensity-based features, geometric properties, interface topology features, evolutionary conservation and also scores produced by traditional scoring functions (SFs). MetaScore scores docked conformations by simply averaging of the score produced by the RF classifier with that produced by any traditional SF. We demonstrate that (i) MetaScore consistently outperforms each of nine traditional SFs included in this work in terms of success rate and hit rate evaluated over the top 10 predicted conformations; (ii) An ensemble method, MetaScore-Ensemble, that combines 10 variants of MetaScore obtained by combining the RF score with each of the traditional SFs outperforms each of the MetaScore variants. We conclude that the performance of traditional SFs can be improved upon by judiciously leveraging machine-learning.

bioinformatics↗

bioRxiv2021

Effect of dietary zinc supplementation on the gastrointestinal microbiota and host gene expression in the Shank3B-/- mouse model of autism spectrum disorder

Shank genes are implicated in ~1% of people with autism and mice with Shank3 knock out mutations exhibit autism-like behaviours. Zinc deficiency and gastrointestinal problems can be common among people with autism, and zinc is a key element required for SHANK protein function and gut development. In Shank3B-/- mice, a supplementary zinc diet reverses autism behaviours. We hypothesise that dietary zinc may alter the gut microbiome, potentially affecting the gut-microbiome-brain axis, which may contribute to changes in autism-like behaviours. To test this, four types of gastrointestinal samples (ileum, caecum, colon, faecal) were collected from wild-type and knock-out Shank3B-/- mice on either control or supplemented-zinc diets. Cage, genotype and zinc diet each contributed significantly to bacterial community variation (accounting for 12.8%, 3.9% and 2.3% of the variation, respectively). Fungal diversity differed significantly between wild-type and knock-out Shank3B-/- mice on the control zinc diet, and the fungal biota differed among gut locations. RNA-seq analysis of host (mouse) transcripts revealed differential expression of genes involved in host metabolism that may be regulated by the gut microbiota and genes involved in anti-microbial interactions. By utilising the Shank3B-/- knock-out mouse model we were able to examine the influence of - and interactions between - dietary zinc and ASD-linked host genotype. These data broaden understanding of the gut microbiome in autism and pave the way towards potential microbial therapeutics for gastrointestinal problems in people with autism. ImportancePreviously, supplemental dietary zinc in the Shank3B-/- mouse model of autism spectrum disorder resulted in observations of ASD behaviours reversal; in this study we also used the Shank3B-/- mouse model to examine the influence of - and interaction between - dietary zinc and ASD-linked host genotype. Sample location along the gastrointestinal tract, genotype and zinc diet explained some of the variation in the microbiota data, with notable bacterial differences between treatment groups. Differential expression of host genes between treatment groups, including antimicrobial interaction genes and gut microbiota-regulated host metabolism genes, suggests that the interplay between gut microbes, the gastrointestinal tract and the brain may play a major role towards the observed amelioration of ASD behaviours seen previously with supplemented dietary zinc. These results widen the scope towards manipulating both dietary zinc and the microbiota itself to ameliorate ASD-related behaviours and associated gastrointestinal issues.

microbiology↗

bioRxiv2021

BWA-MEME: BWA-MEM emulated with a machine learning approach

MotivationThe growing use of next-generation sequencing and enlarged sequencing throughput require efficient short-read alignment, where seeding is one of the major performance bottlenecks. The key challenge in the seeding phase is searching for exact matches of substrings of short reads in the reference DNA sequence. Existing algorithms, however, present limitations in performance due to their frequent memory accesses. ResultsThis paper presents BWA-MEME, the first full-fledged short read alignment software that leverages learned indices for solving the exact match search problem for efficient seeding. BWA-MEME is a practical and efficient seeding algorithm based on a suffix array search algorithm that solves the challenges in utilizing learned indices for SMEM search which is extensively used in the seeding phase. Our evaluation shows that BWA-MEME achieves up to 3.45x speedup in seeding throughput over BWA-MEM2 by reducing the number of instructions by 4.60x, memory accesses by 8.77x, and LLC misses by 2.21x, while ensuring the identical SAM output to BWA-MEM2. AvailabilityThe source code and test scripts are available for academic use at https://github.com/kaist-ina/BWA-MEME/. Contacttom418@kaist.ac.kr, dhan.ee@kaist.ac.kr

bioinformatics↗