Biology subjects

Chung, D.

Publications and source records attributed to Chung, D..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

MAPLE: A Hybrid Framework for Multi-Sample Spatial Transcriptomics Data

High throughput spatial transcriptomics (HST) technologies provide unprecedented opportunity to identify spatially resolved cell sub-populations in tissue samples. However, existing methods preclude joint analysis of multiple HST samples, do not allow for differential abundance analysis (DAA), and ignore uncertainty quantification. To address this, we developed MAPLE: a hybrid deep learning and Bayesian modeling framework for joint detection of spatially informed sub-populations, DAA, and uncertainty quantification. We demonstrate the capability of MAPLE to achieve these multi-sample analyses through four case studies that span a variety of organs in both humans and animal models. An R package maple is available on GitHub at https://github.com/carter-allen/maple.

bioinformatics↗

bioRxiv2021

A Statistical Framework for Data Purification with Application to Microbiome Data Analysis

Identification of disease-associated microbial species is of great biological and clinical interest. However, this investigation still remains challenges due to heterogeneity in microbial composition between individuals, data quality issues, and complex relationships among species. In this paper, we propose a novel data purification algorithm that allows elimination of noise observations, which leads to increased statistical power to detect disease-associated microbial species. We illustrate the proposed algorithm using the metagenomic data generated from colorectal cancer patients.

bioinformatics↗

bioRxiv2021

Infer disease-associated microbial biomarkers based on metagenomic and metatranscriptomic data

The identification of disease-associated microbial characteristics is crucial for disease diagnosis and therapy. However, the heterogeneity, high dimensionality, and large amounts of microbial data present tremendous challenges for the discovery of key microbial features. In this paper, we present IDAM, a novel computational method for disease-associated gene module inference from metagenomic and metatranscriptomic data. This method integrates gene context conservation (uber-operon) and regulatory mechanisms (gene co-expression patterns) to explore gene modules associated with specific phenotypes using a mathematical graph model, without relying on prior meta-data. We applied IDAM to publicly available datasets from inflammatory bowel disease, melanoma, type 1 diabetes mellitus, and irritable bowel syndrome and demonstrated the superior performance of IDAM in disease-associated characteristics inference compared to popular tools. We also showed high reproducibility of the inferred gene modules of IDAM using independent cohorts with inflammatory bowel disease. We believe that IDAM can be a highly advantageous method for exploring disease-associated microbial characteristics. The source code of IDAM is freely available at https://github.com/OSU-BMBL/IDAM.

bioinformatics↗

bioRxiv2021

Identification of Potent Small Molecule Inhibitors of SARS-CoV-2 Entry

The severe acute respiratory syndrome coronavirus 2 responsible for COVID-19 remains a persistent threat to mankind, especially for the immunocompromised and elderly for which the vaccine may have limited effectiveness. Entry of SARS-CoV-2 requires a high affinity interaction of the viral spike protein with the cellular receptor angiotensin-converting enzyme 2. Novel mutations on the spike protein correlate with the high transmissibility of new variants of SARS-CoV-2, highlighting the need for small molecule inhibitors of virus entry into target cells. We report the identification of such inhibitors through a robust high-throughput screen testing 15,000 small molecules from unique libraries. Several leads were validated in a suite of mechanistic assays, including whole cell SARS-CoV-2 infectivity assays. The main lead compound, Calpeptin, was further characterized using SARS-CoV-1 and the novel SARS-CoV-2 variant entry assays, SARS-CoV-2 protease assays and molecular docking. This study reveals Calpeptin as a potent and specific inhibitor of SARS-CoV-2 and some variants.

microbiology↗

bioRxiv2021

RESEPT: tissue architecture inference and visualization from spatially resolved transcriptomics

Spatially resolved transcriptomics provides a new way to define spatial contexts and understand biological functions in complex diseases. Although some computational frameworks can characterize spatial context via various clustering methods, the detailed spatial architectures and functional zonation often cannot be revealed and localized due to the limited capacities of associating spatial information. We present RESEPT, a deep-learning framework for characterizing and visualizing tissue architecture from spatially resolved transcriptomics. Given inputs as gene expression or RNA velocity, RESEPT learns a three-dimensional embedding with a spatial retained graph neural network from the spatial transcriptomics. The embedding is then visualized by mapping as color channels in an RGB image and segmented with a supervised convolutional neural network model. Based on a benchmark of sixteen 10x Genomics Visium spatial transcriptomics datasets on the human cortex, RESEPT infers and visualizes the tissue architecture accurately. It is noteworthy that, for the in-house AD samples, RESEPT can localize cortex layers and cell types based on a pre-defined region-or cell-type-specific genes and furthermore provide critical insights into the identification of amyloid-beta plaques in Alzheimers disease. Interestingly, in a glioblastoma sample analysis, RESEPT distinguishes tumor-enriched, non-tumor, and regions of neuropil with infiltrating tumor cells in support of clinical and prognostic cancer applications.

bioinformatics↗

bioRxiv2021

Network-Based Discovery of Opioid Use Vulnerability in Rats Using the Bayesian Stochastic Block Model

Opioid use disorder is a psychological condition that affects over 200,000 people per year in the U.S., causing the Centers for Disease Control and Prevention to label the crisis as a rapidly spreading public health epidemic. It has been found that the behavioral relationship between opioid exposure and development of opioid use disorder varies greatly between individuals, implying existence of sup-populations with varying degrees of opioid vulnerability. In this study, we assessed several behavioral variables across heroin taking, refraining and seeking to establish how these factors interact with one another resulting in a heroin dependent, resilient, or vulnerable behavioral phenotype. Over 400 (male and female) heterogeneous stock rats were used in these two studies, and data were collected from two geographically distinct locations. Rats underwent heroin self-administration training, followed by a progressive ratio and heroin-primed reinstatement test. Next, rats underwent extinction training and a cue-induced reinstatement test. To assess how these variables contribute to heroin addiction vulnerability, we developed a network-based data analysis workflow. Specifically, we integrated different cohorts of rats, remove possible batch effects, and constructed a rat-rat similarity network based on their behavioral patterns. We then implemented community detection on this similarity network using a Bayesian degree-corrected stochastic block model to uncover sub-populations of rats with differing levels of opioid vulnerability. We discovered three distinct behavioral sub-populations, each with significantly different behavioral outcomes that allowed for unique characterization of each cluster in terms of vulnerability to opioid use and seeking. We implement this analysis workflow as an open source R package, named mlsbm.

animal behavior and cognition↗

bioRxiv2021

A Bayesian Multivariate Mixture Model for Spatial Transcriptomics Data

High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST data, we seek to identify sub-populations within a tissue sample that reflect distinct cell types or states. Existing methods either ignore the spatial heterogeneity in gene expression profiles, fail to account for important statistical features such as skewness, or are heuristic network-based clustering methods that lack the inferential benefits of statistical modeling. To address this gap, we develop SPRUCE: a Bayesian spatial multivariate finite mixture model based on multivariate skew-normal distributions, which is capable of identifying distinct cellular sub-populations in HST data. We further implement a novel combination of Polya-Gamma data augmentation and spatial random effects to infer spatially correlated mixture component membership probabilities without relying on approximate inference techniques. Via a simulation study, we demonstrate the detrimental inferential effects of ignoring skewness or spatial correlation in HST data. Using publicly available human brain HST data, SPRUCE outperforms existing methods in recovering expertly annotated brain layers. Finally, our application of SPRUCE to human breast cancer HST data indicates that SPRUCE can distinguish distinct cell populations within the tumor microenvironment.

bioinformatics↗

bioRxiv2020

Alternative splicing of GluN1 gates glycine-primed internalization of NMDA receptors

N-methyl-D-aspartate receptors (NMDARs), a principal subtype of excitatory neurotransmitter receptor, are composed as tetrameric assemblies of two glycine-binding GluN1 subunits and two glutamate-binding GluN2 subunits. Gating of the NMDARs requires binding of four co-agonist molecules, but the receptors can signal non-ionotropically through binding of glycine, alone, to its cognate site on GluN1. A consequence of this signalling by glycine is that NMDARs are primed such that subsequent gating, produced by glycine and glutamate, drives receptor internalization. The GluN1 subunit is not a singular molecular species in the CNS, rather there are 8 alternatively spliced isoforms of this subunit produced by including or excluding the N1 and the C1, C2 or C2 polypeptide cassettes. Whether alternative splicing affects glycine priming signalling is unknown. Here, using recombinant NMDARs expressed heterologously we discovered that glycine priming of NMDARs critically depends on alternative splicing: the four splice isoforms lacking the N1 cassette, encoded in exon 5, are primed by glycine whereas glycine priming is blocked in the four splice variants containing the N1 cassette. On the other hand, the C-terminal cassettes - C1, C2 or C2 - had no effect on glycine priming signalling. Nor was glycine priming affected by the GluN2 subunit in the receptor. In wild-type mice we found that glycine primed internalization of synaptic NMDARs in CA1 hippocampal pyramidal neurons. With mice we engineered such that GluN1 obligatorily contained the N1 cassette, glycine did not prime synaptic NMDARs in pyramidal neurons. In contrast to pyramidal neurons, we discovered that in wild-type mice, synaptic NMDARs in CA1 inhibitory interneurons were resistant to glycine priming. But we recapitulated glycine priming in inhibitory interneurons in mice engineered such that GluN1 obligatorily lacked the N1 cassette. Our findings reveal a previously unsuspected molecular function for alternative splicing of GluN1 in controlling non-ionotropic signalling of NMDAR by glycine and the consequential cell surface dynamics of the receptors.

neuroscience↗

bioRxiv2020

IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis

SummarySingle-cell RNA-Seq (scRNA-Seq) data is useful in discovering cell heterogeneity and signature genes in specific cell populations in cancer and other complex diseases. Specifically, the investigation of functional gene modules (FGM) can help to understand gene interactive networks and complex biological processes. QUBIC2 is recognized as one of the most efficient and effective tools for FGM identification from scRNA-Seq data. However, its limited availability to a C implementation restricted its application to only a few downstream analyses functionalities. We developed an R package named IRIS-FGM (Integrative scRNA-Seq Interpretation System for Functional Gene Module analysis) to support the investigation of FGMs and cell clustering using scRNA-Seq data. Empowered by QUBIC2, IRIS-FGM can effectively identify co-expressed and co-regulated FGMs, predict cell types/clusters, uncover differentially expressed genes, and perform functional enrichment analysis. It is noteworthy that IRIS-FGM can also takes Seurat objects as input, which facilitate easy integration with existing analysis pipeline. Availability and ImplementationIRIS-FGM is implemented in R environment (as of version 3.6) with the source code freely available at https://github.com/OSU-BMBL/IRIS-FGM Contactqin.ma@osumc.edu Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2020

Subjective optimality in finite sequential decision-making

Many decisions in life are sequential and constrained by a time window. Although mathematically derived optimal solutions exist, it has been reported that humans often deviate from making optimal choices. Here, we used a secretary problem, a classic example of finite sequential decision-making, and investigated the mechanisms underlying individuals suboptimal choices. Across three independent experiments, we found that a dynamic programming model comprising subjective value function explains individuals deviations from optimality and predicts the choice behaviors under fewer opportunities. We further identified that pupil dilation reflected the levels of decision difficulty and subsequent choices to accept or reject the stimulus at each opportunity. The value sensitivity, a model-based estimate that characterizes each individuals subjective valuation, correlated with the extent to which individuals physiological responses tracked stimuli information. Our results provide model-based and physiological evidence for subjective valuation in finite sequential decision-making, rediscovering human suboptimality in subjectively optimal decision-making processes.

neuroscience↗

bioRxiv2020

Loss of FSTL1-expressing adipocyte progenitors drives the age-related involution of brown adipose tissue

In humans, brown adipose tissue (BAT) undergoes progressive involution or atrophy with increasing age, as manifested by decreased prevalence and mass, transformation to white adipose tissue (WAT), and reduction in thermogenic activity. This involution process cannot be fully recapitulated in rodent models and thus underlying cellular mechanisms are poorly understood. Here, we show that the interscapular BAT (iBAT) in rabbits involutes rapidly in early life, similarly to that in humans. The transcriptomic remodeling and identity switch of mature adipocytes are accompanied with the loss of brown adipogenic competence of their precursor cells. Through single-cell RNA sequencing, we surveyed the heterogenous populations of mesenchymal cells within the stromal vascular fraction of rabbit and human iBAT. An analogous FSTL1high population of brown adipocyte progenitors exists in both species while gradually disappear during iBAT involution in rabbits. In mice, FSTL1 is highly expressed by adipocyte progenitors in iBAT and genetic deletion of FSTL1 causes defective WNT signaling and iBAT atrophy in neonates. Our results underscore the BAT-intrinsic contribution from FSTL1high progenitors to age-related tissue involution and point to a potential therapeutic approach for obesity and its comorbidities. HIGHLIGHTSO_LIRabbit BAT irreversibly transforms to WAT before puberty. C_LIO_LIiBAT adipocyte progenitors reprogram transcriptome and lose brown adipogenic ability. C_LIO_LIComparable FSTL1high brown adipocyte progenitors exist in rabbit and human iBAT. C_LIO_LILoss of FSTL1 in brown adipocyte progenitors causes iBAT atrophy in mice. C_LI

physiology↗

bioRxiv2020

Distinct CD8+ T Cell Programming in the Tumor Microenvironment Contributes to Sex Bias in Bladder Cancer Outcome

Men and women show striking yet unexplained discrepancies in incidence, clinical presentation, and therapeutic response across different types of infectious/autoimmune diseases and malignancies1,2. For instance, bladder cancer shows a 4-fold male-biased incidence that persists after adjustment for known risk factors3,4. Here, we utilize murine bladder cancer models to establish that male-biased tumor burden is driven by sex differences in endogenous T cell immunity. Notably, sex differences exist in early fate decisions by intratumoral CD8+ T cells following their activation. While female CD8+ T cells retain their effector function, male counterparts readily adopt a Tcf1lowTim3- progenitor state that becomes exhausted over tumor progression. Human cancers show an analogous male-biased frequency of exhausted CD8+ T cells. Mechanistically, we describe an opposing interplay between CD8+ T cell intrinsic androgen and type I interferon5,6 signaling in Tcf1/Tcf7 regulation and formation of the progenitor exhausted T cell subset. Consistent with female-biased interferon response7, testosterone-dependent stimulation of Tcf1/Tcf7 and resistance to interferon occurs to a greater magnitude in male CD8+ T cells. Male-biased predisposition for CD8+ T cell exhaustion suggests that spontaneous rejection of early immunogenic bladder tumors is less common in males and carries implications for therapeutic efficacy of immune checkpoint inhibitors8,9.

immunology↗

bioRxiv2020

A conformational switch driven by phosphorylation regulates Ykt6 activity in macroautophagy

Membrane fusion, an essential process in all eukaryotes, is driven by SNARE proteins. Ykt6 is an essential SNARE that plays critical roles throughout the secretory, endocytic, and autophagy pathways. Ykt6 activity is thought to be regulated by a conformational change from a closed cytosolic form to an open membrane-bound form, yet the mechanism that regulates this transition is unknown. Through genetic, pharmacologic, and structural modeling approaches in mammalian cells, we found that phosphorylation regulates Ykt6 conversion from a closed to an open state. The phosphorylation site we identified is highly conserved in evolution and is regulated by the Ca2+-dependent phosphatase, calcineurin. We found that phosphorylation is a key determinant for intracellular localization of Ykt6 and its function in macroautophagy. Our studies reveal a novel mechanism by which Ykt6 conformation and activity is regulated by Ca2+ signaling with implications in Parkinsons Disease in which Ykt6 has been shown to play a role.

cell biology↗

bioRxiv2020

Keeping things in mind for future thinking: Arithmetic booster reduces delay discounting

People have higher preference for immediate over delayed rewards, and it is suggested that such an impulsive tendency is governed by ones ability to simulate future rewards. Consistent with this view, recent studies have shown that enforcing individuals to focus on episodic future thoughts reduces their impulsivity. Inspired by these successful reports, we hypothesized that administration of a simple cognitive task which is linked with future thinking might also function as an effective tool for modulating individuals preference for immediate (or delayed) rewards. Specifically, we used one associative memory task and one working memory task that each of which was administered to intervene acquired amount of information and individuals ability to construct a coherent future event, respectively. Among the set of cognitive tasks, we found that only the arithmetic working memory task had a significant effect of reducing individuals impulsivity. However, in our follow-up experiment, this result was not replicated. Across these two independent experiments, we observed a significant main effect of repetition in individuals impulsivity measure, such that participants showed more patient choices at the second compared to the first assessment task. In conclusion, there was no clear evidence supporting that our suggested intervention tasks effectively reduce individuals impulsivity, while the current results call attention to the importance of taking into account task repetition effects in studying the impacts of cognitive training and intervention.

neuroscience↗

bioRxiv2020

Accelerated single cell seeding in relapsed multiple myeloma

The malignant progression of multiple myeloma is characterized by the seeding of cancer cells in different anatomic sites followed by their clonal expansion. It has been demonstrated that this spatial evolution at varying anatomic sites is characterized by genomic heterogeneity. However, it is unclear whether each anatomic site at relapse reflects the expansion of pre-existing but previously undetected disease or secondary seeding from other sites. Furthermore, genomic evolution over time at spatially distinct sites of disease has not been investigated in a systematic manner. To address this, we interrogated 25 samples, by whole genome sequencing, collected at autopsy from 4 patients with relapsed multiple myeloma and demonstrated that each site had a unique evolutionary trajectory characterized by distinct single and complex structural variants and copy number changes. By analyzing the landscape of mutational signatures at these sites and for an additional set of 125 published whole exomes collected from 51 patients, we demonstrate the profound mutagenic effect of melphalan and platinum in relapsed multiple myeloma. Chemotherapy-related mutagenic processes are known to introduce hundreds of unique mutations in each surviving cancer cell. These mutations can be detectable by bulk sequencing only in cases of clonal expansion of a single cancer cell bearing the mutational signature linked to chemotherapy exposure thus representing a unique single-cell genomic barcode linked to a discrete time window in each patients life. We leveraged this concept to show that multiple myeloma systemic seeding is accelerated at clinical relapse and appears to be driven by the survival and subsequent expansion of a single myeloma cell following treatment with high dose melphalan therapy and autologous stem cell transplant.

cancer biology↗

bioRxiv2019

Energy Crisis in Human and Mouse Models of SLC4A11-associated Corneal Endothelial Dystrophies

PO_SCPLOWURPOSEC_SCPLOWTo elucidate the molecular events in solute carrier family 4 member 11 (SLC4A11)-deficient corneal endothelium that lead to the endothelial dysfunction that characterizes the dystrophies associated with SLC4A11 mutations, congenital hereditary endothelial dystrophy (CHED) and Fuchs endothelial corneal dystrophy 4. MO_SCPLOWETHODSC_SCPLOWComparative transcriptomic analysis (CTA) was performed in primary human corneal endothelial cells (pHCEnC) and murine corneal endothelial cells (MCEnC) with normal and reduced levels of SLC4A11 (SLC4A11 KD pHCEnC) and Slc4a11 (Slc4a11-/- MCEnC), respectively. Validation of differentially expressed genes was performed using immunofluorescence staining of CHED corneal endothelium, as well as western blot and quantitative PCR analysis of SLC4A11 KD pHCEnC and Slc4a11-/- MCEnC. Functional analyses were performed to investigate potential functional changes associated with the observed transcriptomic alterations. RO_SCPLOWESULTSC_SCPLOWCTA revealed inhibition of cell metabolism and ion transport function as well as mitochondrial dysfunction, leading to reduced adenosine triphosphate (ATP) production, in SLC4A11 KD pHCEnC and Slc4a11-/- MCEnC. Co-localization of SNARE protein STX17 with mitochondria marker COX4 was observed in CHED corneal endothelium, as was activation of AMPK-p53/ULK1 in both SLC4A11 KD pHCEnC and Slc4a11-/- MCEnC, providing additional evidence of mitochondrial dysfunction and mitophagy. Reduced Na+-dependent HCO3- transport activity and altered NH4Cl-induced membrane potential changes were observed in Slc4a11-/- MCEnC. CO_SCPLOWONCLUSIONSC_SCPLOWReduced steady-state ATP levels and subsequent activation of the AMPK-p53 pathway provide a link between the metabolic functional deficit and transcriptome alterations, as well as evidence of insufficient ATP to maintain the Na+/K+-ATPase corneal endothelial pump as the cause of the edema that characterizes SLC4A11-associated corneal endothelial dystrophies.

cell biology↗

bioRxiv2019

Zika virus infects pericytes in the choroid plexus and enters the central nervous system through the blood-cerebrospinal fluid barrier.

Zika virus (ZIKV) can infect and cause microcephaly and Zika-associated neurological complications in the developing fetal and adult brains. In terms of pathogenesis, a critical question is how ZIKV overcomes the barriers separating the brain from the circulation and gains access to the central nervous system (CNS). Despite the importance of ZIKV pathogenesis, the route ZIKV utilizes to cross CNS barriers remains unclear. Here we show that in mouse models, ZIKV-infected cells initially appeared in the periventricular regions of the brain, including the choroid plexus and the meninges, prior to infection of the cortex. The appearance of ZIKV in cerebrospinal fluid (CSF) preceded infection of the brain parenchyma. We show that ZIKV infects pericytes in the choroid plexus, and that ZIKV infection of pericytes is dependent on AXL receptor tyrosine kinase. Using an in vitro Transwell system, we highlight the possibility of ZIKV to move from the blood side to CSF side, across the choroid plexus epithelial layers, via a nondestructive pathway (e.g., transcytosis). Finally, we demonstrate that brain infection is significantly attenuated by neutralization of the virus in the CSF, indicating that ZIKV in the CSF at the early stage of infection might be responsible for establishing a lethal infection of the brain. Taken together, our results suggest that ZIKV invades the host brain by exploiting the blood-CSF barrier rather than the blood-brain barrier. AUTHOR SUMMARYZika virus invades the human brains and causes Zika-associated neurological complications; however, the mechanism(s) by which Zika virus accesses the central nerves system remain unclear. Understanding of the cellular and molecular mechanisms will shed light on development of novel therapeutic and prophylactic targets for Zika virus and other neurotropic viruses. Here we use in vivo and in vitro models to understand how Zika virus enters the brain. In mouse models, we found that Zika virus infects pericytes in the choroid plexus at very early stages of infection and neutralization of Zika virus in the cerebrospinal fluid significantly attenuate the brain infection. Further we show evidence that Zika virus can cross the epithelial cell layers in the choroid plexus from the blood side. Our research highlights that ZIKV invades the host brain by exploiting the blood-CSF barrier rather than the blood-brain barrier.

microbiology↗

bioRxiv2019

Humans Use Future Thinking to Exert Social Control

Social control, the ability to exert influence over others, is critical in interpersonal interactions yet uninvestigated. Here, we used functional neuroimaging and a social exchange paradigm in which peoples current choices either did, or did not, influence their partners proposals in the future. Computational modeling revealed that participants used forward thinking and calculated the downstream effects of their current actions regardless of the controllability of the social environment. Furthermore, greater levels of estimated control correlated with better performance in controllable interactions and less illusory beliefs about control in uncontrollable interactions. Neural instantiation of trial-by-trial values of social controllability were tracked in the ventromedial prefrontal cortex (vmPFC), striatum, and insula for controllable interactions, but only in vmPFC for uncontrollable interactions. These findings demonstrate that humans use forward thinking, a strategy similar to model-based planning, to guide social choices; and that subjective beliefs about social controllability might not be grounded in reality.

neuroscience↗