Biology subjects

Choi, H.

Publications and source records attributed to Choi, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2022

Targeted protein degradation reveals BET bromodomains as the cellular target of Hedgehog Pathway Inhibitor-1

Target deconvolution of small molecule hits from phenotypic screens presents a major challenge. Illustrative of these are the many screens that have been conducted to find inhibitors for the Hedgehog (Hh) signaling pathway - a major developmental pathway with many implications in health and disease - with many hits but very few identified cellular targets. We here present a strategy for target identification based on Proteolysis-Targeting Chimeras (PROTACs), combined with label-free quantitative proteomics. We developed a PROTAC based on the downstream Hedgehog Pathway Inhibitor-1 (HPI-1), a phenotypic screen hit with unknown cellular target. Using our Hedgehog Pathway PROTAC (HPP) we identified and validated BET bromodomains to be the cellular targets of HPI-1. Furthermore, we found that HPP-9 has a unique mechanism of action as a long-acting Hh pathway inhibitor through prolonged BET bromodomain degradation. Collectively, we provide a powerful PROTAC-based approach for target deconvolution, that has answered the longstanding question of the cellular target of HPI-1 and yielded the first PROTAC that acts on the Hh pathway.

cell biology↗

bioRxiv2022

CD3e-immunotoxin spares CD62L(lo) Tregs and reshapes organ-specific T-cell composition by preferentially depleting CD3e(hi) T cells.

CD3-epsilon(CD3e) immunotoxins (IT), a promising precision reagent for various clinical conditions requiring effective depletion of T cells, often shows limited treatment efficacy for largely unknown reasons. Tissue-resident T cells that persist in peripheral tissues have been shown to play pivotal roles in local and systemic immunity, as well as transplant rejection, autoimmunity and cancers. The impact of CD3e-IT treatment on these local cells, however, remains poorly understood. Here, using a new murine testing model, we demonstrate a substantial enrichment of tissue-resident Foxp3+ Tregs following CD3e-IT treatment. Differential surface expression of CD3e among T-cell subsets appears to be a main driver of Treg enrichment in CD3e-IT treatment. The surviving Tregs in CD3e-IT-treated mice were mostly the CD3edimCD62Llo effector phenotype, but the levels of this phenotype markedly varied among different lymphoid and nonlymphoid organs. We also found notable variations in surface CD3e levels among tissue-resident T cells of different organs, and these variations drive CD3e-IT to uniquely reshape T-cell compositions in local organs. The functions of organs and anatomic locations (lymph nodes) also affected the efficacy of CD3e-IT. The multi-organ pharmacodynamics of CD3e-IT and potential treatment resistance mechanisms identified in this study may generate new opportunities to further improve this promising treatment.

immunology↗

bioRxiv2022

Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection

Zika virus (ZIKV) and dengue virus (DENV) are two closely related flaviviruses with similar symptoms; understanding differences in their molecular impact on the host is therefore of high interest. Viruses interact with the hosts post-translational modifications, inducing changes visible in serum. As modifications are diverse and of low abundance, they typically require additional sample processing which is not feasible for large cohort studies. Therefore, we tested the potential of next-generation proteomics data in its ability to prioritize specific modifications for later targeted analysis. We re-mined published mass spectra from 122 unenriched serum samples from ZIKV and DENV patients for the presence of phosphorylated, methylated, oxidized, glycosylated/glycated, sulfated, and carboxylated peptides. We identified 272 modified peptides with significantly differential abundance in ZIKV and DENV patients. Amongst these, methionine-oxidized peptides from apolipoproteins and glycosylated peptides from immunoglobulin proteins were more abundant in ZIKV patient serum and generate hypotheses on the potential roles of the modification in the infection. The results demonstrate how data-independent acquisition techniques can help prioritize future analyses of peptide modifications.

molecular biology↗

bioRxiv2022

spSeudoMap: Cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data

With advances in computational models, the cellular landscape can be tracked in various tissues using spatial transcriptomics. Since many single-cell RNA-seq (scRNA-seq) data have been obtained after cell sorting, such as when investigating immune cells, integrating these singlecell data with spatial data is limited due to a mismatch of cell types composing the two datasets. Here, we present a method, spSeudoMap, which utilizes sorted scRNA-seq data to train a model for predicting cell types of spatial spots by creating virtual cell mixtures that closely mimic the gene expression profile of spatial transcriptomic data. To overcome the mismatch issue, the cell type exclusively present in the spatial data, pseudotype, was defined. The proportion of pseudotype cells and virtual expression profiles in the cell mixture was determined by pseudobulk transcriptomes. The simulated cell mixture was considered a reference dataset, and the model that predicts the cell composition of the mixture was trained to predict the cell fraction of the spatial data using domain adaptation. First, spSeudoMap was evaluated in human and mouse brain tissues, and the main region-specific neuron types extracted from single-cell data could be precisely mapped to the expected anatomical locations. Moreover, the method was applied to human breast cancer data and described the spatial distribution of immune cell subtypes and their interactions in heterogeneous tissue. Taken together, spSeudoMap is a platform that predicts the spatial composition of cell subpopulations using sorted scRNA-seq data, and it may help to clarify the roles of a few but crucial cell types.

genomics↗

bioRxiv2022

Representational integration and differentiation in the human hippocampus following goal-directed navigation

As we learn, dynamic memory processes build structured knowledge across our experiences. Such knowledge enables the formation of internal models of the world that we use to plan, make decisions, and act. Recent theorizing posits that mnemonic mechanisms of differentiation and integration - which at one level may seem to be at odds - both contribute to the emergence of structured knowledge. We tested this possibility using fMRI as human participants learned to navigate within local and global virtual environments over the course of three days. Pattern similarity analyses on entorhinal cortex, hippocampus, and ventromedial prefrontal cortex patterns revealed evidence that differentiation and integration work concurrently to build local and global environmental representations, and that variability in integration relates to differences in navigation efficiency. These results offer new insights into the neural machinery and the underlying mechanisms that translate experiences into structured knowledge that allows us to navigate to achieve goals.

neuroscience↗

bioRxiv2022

Spatial Transcriptomics-based Identification of Molecular Markers for Nanomedicine Distribution in Tumor Tissue

The intratumoral accumulation of nanomedicine has been considered a passive process, referred to as the enhanced permeability and retention (EPR) effect. Recent studies have suggested that the tumor uptake of nanomedicines follows an energy-dependent pathway rather than being a passive process. Herein, to explore the factor candidates that are associated with nanomedicine tumor uptake, we developed a molecular marker identification platform by integrating microscopic fluorescence images of a nanomedicine distribution with spatial transcriptomics (ST) information. When this approach is applied to PEGylated liposomes, molecular markers related to hypoxia, glucose metabolism and apoptosis can be identified as being related to the intratumoral distribution of the nanomedicine. We expect that our method can be applied to explain the distribution of a wide range of nanomedicines and that the data obtained from this analysis can enhance the precise utilization of nanomedicines.

bioinformatics↗

bioRxiv2022

Subgroups of eating behavior traits independent of obesity defined using functional connectivity and feature representation learning

AO_SCPLOWBSTRACTC_SCPLOWEating behavior is highly heterogeneous across individuals, and thus, it cannot be fully explained using only the degree of obesity. We utilized unsupervised machine learning and functional connectivity measures to explore the heterogeneity of eating behaviors. This study was conducted on 424 healthy adults. We generated low-dimensional representations of functional connectivity defined using the resting-state functional magnetic resonance imaging, and calculated latent features using the feature representation capabilities of an autoencoder by nonlinearly compressing the functional connectivity information. The clustering approaches applied to latent features identified three distinct subgroups. The subgroups exhibited different disinhibition and hunger traits; however, their body mass indices were comparable. The model interpretation technique of integrated gradients revealed that these distinctions were associated with the functional reorganization in higher-order associations and limbic networks and reward-related subcortical structures. The cognitive decoding analysis revealed that these systems are associated with reward- and emotion-related systems. We replicated our findings using an independent dataset, thereby suggesting generalizability. Our findings provide insights into the macroscopic brain organization of eating behavior-related subgroups independent of obesity.

neuroscience↗

bioRxiv2021

Time-resolved analysis of transcription kinetics in single live mammalian cells

In eukaryotic cells, RNA polymerase II synthesizes mRNA in three stages, initiation, elongation, and termination, and numerous factors determine how quickly a gene is transcribed to produce mRNA molecules through these steps. However, there are few techniques available to measure the rate of each step in living cells, which prevents a better understanding of transcriptional regulation. Here, we present a quantitative analysis method to extract kinetic rates of transcription from time-lapse imaging data of fluorescently labeled mRNA in live cells. Using embryonic fibroblasts cultured from two knock-in mouse models, we monitored transcription of {beta}-actin and Arc mRNA labeled with MS2 and PP7 stem-loop systems, respectively. After inhibiting transcription initiation, we measured the elongation rate and the termination time by fitting the time trace of transcription intensity with a mathematical model function. We validated our results by comparing them with steady-state fluctuation analysis and stochastic simulations. This live-cell transcription analysis method will be useful for studying the regulation of elongation and termination steps and may provide insight into the diverse mechanisms of transcriptional processes.

biophysics↗

bioRxiv2021

Diverse northern Asian and Jomon-related genetic structure discovered among socially complex Three Kingdoms period Gaya region Koreans

The genetic history of prehistoric and protohistoric Korean populations is not well understood due to the lack of ancient Korean genomes. Here, we report the first paleogenomic data from Korea; eight shotgun-sequenced genomes (0.7x[~]6.1x coverage) from two archeological sites in Gimhae: Yuha-ri shell mound and Daesung-dong tumuli, the most important funerary complex of the Gaya confederacy. All eight individuals are from the Korean Three Kingdoms period (4th-7th century CE), during which there is archaeological evidence of extensive trade connections with both northern (modern-day China) and eastern (modern-day Japan) kingdoms. All genomes are best modeled as an admixture between a northern-Chinese Iron Age genetic source and a Japanese-Jomon-related ancestry. The proportion of Jomon-related ancestry suggests the presence of two genetic groups within the population. The observed substructure indicates diversity among the Gaya population that is not related to either social status or sex. Teaser1,700-year-old genomes reveal the genetic diversity of ancient Koreans in the Gimhae region.

evolutionary biology↗

bioRxiv2021

A Budding Yeast Model and Screen to Define the Functional Consequences of Oncogenic Histone Missense Mutations

Somatic missense mutations in histone genes turn these essential proteins into oncohistones, which can drive oncogenesis. Understanding how missense mutations alter histone function is challenging in mammals as mutations occur in a single histone gene. For example, described oncohistone mutations predominantly occur in the histone H3.3 gene, despite the human genome encoding 15 H3 genes. To understand how oncogenic histone missense mutations alter histone function, we leveraged the budding yeast model, which contains only two H3 genes, to explore the functional consequences of oncohistones H3K36M, H3G34W, H3G34L, H3G34R, and H3G34V. Analysis of cells that express each of these variants as the sole copy of H3 reveals that H3K36 mutants show different drug sensitivities compared to H3G34 mutants. This finding suggests that changes to proximal amino acids in the H3 N-terminal tail alter distinct biological pathways. We exploited the caffeine sensitive growth of H3K36 mutant cells to perform a high copy suppressor screen. This screen identified genes linked to histone function and transcriptional regulation, including Esa1, a histone H4/H2A acetyltransferase; Tos4, a forkhead-associated domain-containing gene expression regulator; Pho92, an N6-methyladenosine RNA binding protein and Sgv1/Bur1, a cyclin-dependent kinase. We show that the Esa1 lysine acetyltransferase activity is critical for suppression of the caffeine sensitive growth of H3K36R mutant cells while the previously characterized binding interactions of Tos4 and Pho92 are not required for suppression. This screen identifies pathways that could be altered by oncohistone mutations and highlights the value of yeast genetics to identify pathways altered by such mutations.

genetics↗

bioRxiv2021

Spatiotemporal characterization of glial cell activation in an Alzheimer's disease model by spatially resolved transcriptome

The pathophysiological changes that occur with the progression of Alzheimers disease (AD) are well known, but understanding the spatiotemporal heterogeneity of the brain is needed. Here, we investigated the spatially resolved transcriptome in a 5XFAD AD model of different ages to understand regional changes at the molecular level. We identified early alterations in the white matter (WM) of the AD model before the definite accumulation of amyloid plaques in the gray matter (GM). Changes in the early stage of the disease were involved primarily in glial cell activation in WM, whereas the changes were prominent in the later stage of pathology in GM. We confirmed that disease-associated microglia (DAM) and astrocyte (DAA) signatures also showed initial changes in WM and that activation spreads to GM. Trajectory inference using microglial gene sets revealed the subdivision of DAMs with different spatial patterns. Taken together, these results help to understand the spatiotemporal changes associated with reactive glial cells as a major pathophysiology of AD and provide information for diagnosis and prognosis based on spatiotemporal changes caused by amyloid accumulation in AD.

neuroscience↗

bioRxiv2021

Most primary olfactory neurons have individually neutral effects on behavior

Animals use olfactory receptors to navigate mates, food, and danger. However, for complex olfactory systems, it is unknown what proportion of primary olfactory sensory neurons can individually drive avoidance or attraction. Similarly, the rules that govern behavioral responses to receptor combinations are unclear. We used optogenetic analysis in Drosophila to map the behavior elicited by olfactory-receptor neuron (ORN) classes: just one-fifth of ORN-types drove either avoidance or attraction. Although wind and hunger are closely linked to olfaction, neither had much effect on single-class responses. Several pooling rules have been invoked to explain how ORN types combine their behavioral influences; we activated two-way combinations and compared patterns of single- and double-ORN responses: these comparisons were inconsistent with simple pooling. We infer that the majority of primary olfactory sensory neurons have neutral behavioral effects individually, but participate in broad, odor-elicited ensembles with potent behavioral effects arising from complex interactions.

animal behavior and cognition↗

bioRxiv2021

CellDART: Cell type inference by domain adaptation of single-cell and spatial transcriptomic data

Deciphering the cellular composition in genome-wide spatially resolved transcriptomic data is a critical task to clarify the spatial context of cells in a tissue. In this study, we developed a method, CellDART, which estimates the spatial distribution of cells defined by single-cell level data using domain adaptation of neural networks and applied it to the spatial mapping of human lung tissue. The neural network that predicts the cell proportion in a pseudospot, a virtual mixture of cells from single-cell data, is translated to decompose the cell types in each spatial barcoded region. First, CellDART was applied to mouse brain and human dorsolateral prefrontal cortex tissue to identify cell types with a layer-specific spatial distribution. Overall, the suggested approach was competent to the other computational methods in predicting the spatial localization of excitatory neurons. Besides, CellDART was capable of decomposing cellular proportion in mouse hippocampus Slide-seq data. Furthermore, CellDART elucidated the cell type predominance defined by the human lung cell atlas across the lung tissue compartments and it corresponded to the known prevalent cell types. CellDART is expected to help to elucidate the spatial heterogeneity of cells and their close interactions in various tissues.

genomics↗

bioRxiv2021

Oxidant-Resistant LRRC8A/C Anion Channels Support Superoxide Production by Nox1

Tumor necrosis factor- (TNF) activates NADPH Oxidase 1 (Nox1) in vascular smooth muscle cells (VSMCs), producing superoxide (O2*-) required for subsequent signaling. LRRC8 family proteins A-E comprise volume-regulated anion channels (VRACs). The required subunit LRRC8A physically associates with Nox1, and VRAC activity is required for Nox activity and the inflammatory response to TNF. LRRC8 channel currents are modulated by oxidants, suggesting that oxidant sensitivity and proximity to Nox1 may play a physiologically relevant role. In VSMCs, LRRC8C knockdown (siRNA) recapitulated the effects of siLRRC8A, inhibiting TNF-induced extracellular and endosomal O2*- production, receptor endocytosis, NF-{kappa}B activation, and proliferation. In contrast, siLRRC8D potentiated NF-{kappa}B activation. Nox1 co-immunoprecipitated with 8C and 8D, and co-localized with 8D at the plasma membrane and in vesicles. We compared VRAC currents mediated by homomeric and heteromeric 8C and 8D channels expressed in HEK293 cells. The oxidant chloramine T (ChlorT, 1 mM) weakly inhibited LRRC8C, but potently inhibited 8D currents. ChlorT exposure also greatly reduced subsequent current block by DCPIB, implicating external sites of oxidation. Substitution of the extracellular loop domains (EL1, EL2) of 8D onto 8C conferred significantly stronger ChlorT-dependent inhibition. 8A/C channel activity is thus more effectively maintained in the oxidized microenvironment expected to result from Nox1 activation at the plasma membrane. Increased ratios of 8D:8C expression may potentially depress inflammatory responses to TNF. LRRC8A/C channel downregulation represents a novel strategy to reduce TNF-induced inflammation. Key PointsO_LILRRC8A-containing anion channels associate with Nox1 and regulate superoxide production and TNF signaling. Here we show that .LRRC8C and 8D also co-immunoprecipitate with Nox1 in vascular smooth muscle cells. C_LIO_LILRRC8C knockdown inhibited TNF-induced O2*- production, receptor endocytosis, NF-{kappa}B activation, and proliferation while LRRC8D knockdown enhanced NF-{kappa}B activation. Significant changes in LRRC8 isoform expression in human atherosclerosis and psoriasis suggest compensation for increased inflammation. C_LIO_LIThe oxidant chloramine-T (ChlorT, 1 mM) weakly ([~]25%) inhibited 8C currents but potently ([~]80%) inhibited 8D currents. Substitution of the two extracellular loop (EL) domains of 8D onto 8C conferred significantly stronger ChlorT-dependent inhibition. C_LIO_LIChlorT also impaired current block by DCPIB, which occurs through interaction with EL1, further implicating external sites of oxidation. C_LIO_LI8A/C channels most effectively maintain activity in an oxidized microenvironment, as is expected to result from Nox1 activity at the plasma membrane. C_LI

cell biology↗

bioRxiv2021

Computationally scalable regression modeling for large-scale clinical omics data with ParProx

Statistical analysis of ultrahigh-dimensional omics scale data has long depended on univariate hypothesis testing. With growing data features and samples, the obvious next step is to establish multivariable association analysis as a routine method for understanding genotype-phenotype associations. Here we present ParProx, a state-of-the-art implementation to optimize overlapping group lasso regression models for time-to-event and classification analysis, guided by biological priors through coordinated variable selection. ParProx not only enables model fitting for ultrahigh-dimensional data within the architecture for parallel or distributed computing, but also allows users to obtain interpretable regression models consistent with known biological relationships among the independent variables, a feature long neglected in statistical modeling of omics data. We demonstrate ParProx using three different omics data sets of moderate to large numbers of variables, where we use genomic regions and pathways to arrive at sparse regression models comprised of biologically related independent variables. ParProx is naturally applicable to a wide range of studies using ultrahigh-dimensional omics data, ranging from genome-wide association analysis to single cell sequencing studies where multivariable modeling is computationally intractable.

bioinformatics↗

bioRxiv2020

Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA

piRNAs are germline-specific, small non-coding RNAs required to maintain genome integrity and preserve RNA homeostasis during male gametogenesis. In murine adult testes, the highest levels of piRNAs are present in the pachytene stage of meiosis, but their mode of action and function remains incompletely understood. We previously reported that BTBD18 binds to 50 pachytene piRNA-producing loci. Here we show that spermatozoa in gene-edited mice lacking a BTBD18 targeted pachytene piRNA cluster on Chr18 have severe sperm head dysmorphology, poor motility, impaired acrosome exocytosis and are sterile. The absence of Chr18 piRNA results in an imbalance of heat shock proteins associated with renaturing proteins and the ubiquitin-proteasome system involved with protein degradation. The mutant phenotype arises from aberrant formation of proacrosomal vesicles, distortion of the trans-Golgi network, and up-regulation of GOLGA2 associated with acrosome dysgenesis. Collectively, our findings reveal central role of pachytene piRNAs in controlling spermiogenesis and male fertility.

developmental biology↗

bioRxiv2020

Inhibiting DDX3X triggers tumor-intrinsic type I interferon response and enhances anti-tumor immunity

Accumulating evidence has shown that cellular double-stranded RNAs (dsRNAs) induce antiviral innate immune responses in human normal and malignant cancer cells. However, it is not fully understood how endogenous self dsRNA homeostasis is regulated in the cell. Here, we show that an RNA-binding protein, DEAD-box RNA helicase 3X (DDX3X), prevents the aberrant accumulation of cellular dsRNAs. Loss of DDX3X induces dsRNA sensor-mediated type I interferon signaling and innate immune response in breast cancer cells due to abnormal cytoplasmic accumulation of dsRNAs. Dual depletion of DDX3X and a dsRNA-editing protein, ADAR1 synergistically activates the cytosolic dsRNA pathway in breast cancer cell. Moreover, inhibiting DDX3X enhances the antitumor activity by increasing tumor intrinsic-type I interferon response, antigen presentation, and tumor-infiltration of cytotoxic T cells as well as dendritic cells in breast tumors, which may lead to the development of breast cancer therapy by targeting DDX3X in combination with immune checkpoint blockade.

cancer biology↗

bioRxiv2020

Deuteration improves small-molecule fluorophores

Fluorescence microscopy relies on dyes that absorb short-wavelength photons and emit longer-wavelength light. In addition to this fluorescence process, dyes can undergo other photochemical reactions that result in spectral shifts and irreversible photobleaching. Increases in brightness, chromostability, and photostability of fluorescent dyes are therefore crucial for advancing the frontier of bioimaging. Here, we describe a general approach to improve small-molecule fluorophores using deuteration. Incorporating deuterium into the alkylamino substituents of rhodamines and other dyes improves fluorescence quantum yield, inhibits photochemically induced spectral shifts, and slows irreparable photobleaching. These compounds are easily synthesized and show improved performance in cellular imaging experiments.

cell biology↗