Biology subjects

Lee, D. S.

Publications and source records attributed to Lee, D. S..

At least 37 records · Page 2Linked to original sources

bioRxiv2021

Characteristic core voxels in normal individuals revealed by hyperbolic disc embedding and k-core percolation on resting state fMRI

Hyperbolic disc embedding and k-core percolation reveal the core structure of the functional connectivity on resting-state fMRI (rsfMRI). Inter-voxel relations were visualized on embedded hyperbolic discs, and their core composition was traced using k-core percolation. Using 180 normal adults rsfMRI data from the Human Connectome Project database, scale- free intervoxel connectivity represented by IC-voxels composition, while visualized on hyperbolic discs using [Formula] model, showed the expected change of the largest component decreasing its size on k-core percolation eventually yielding the core structures of individuals. This kmax-core voxels-ICs composition revealed such stereotypes of individuals as visual network dominant, default mode network dominant, and distributed patterns. Characteristic core structures of resting-state brain connectivity of normal subjects disclosed the distributed or asymmetric contribution of voxels to the kmax-core, which suggests the hierarchical dominance of certain IC subnetworks characteristic to subgroups of individuals at rest.

neuroscience↗

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

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

Hyperbolic disc embedding of functional human brain connectomes using resting state fMRI

The brain presents a real complex network of modular, small-world, and hierarchical nature, which are features of non-Euclidean geometry. Using resting-state functional magnetic resonance imaging (rs-fMRI), we constructed a scale-free binary graph for each subject, using internodal time-series correlation of regions-of-interest (ROIs) as a proximity measure. The resulted network could be embedded onto manifolds of various curvature and dimensions. While maintaining the fidelity of embedding (low distortion, high mean average precision), functional brain networks were found to be best represented in the hyperbolic disc. Using [Formula] model, we reduced the dimension of the network into 2-D hyperbolic space and were able to efficiently visualize the internodal connections of the brain, preserving proximity as distances and angles on the hyperbolic discs. Each individual disc revealed decentralized nature of information flow and anatomic relevance. Using the hyperbolic distance on the [Formula] model, we could detect the anomaly of network in autistic spectrum disorder (ASD) subjects. This procedure of embedding grants us a reliable new framework for studying functional brain networks and the possibility of detecting anomalies of the network in the hyperbolic disc on an individual scale.

neuroscience↗

bioRxiv2021

The Arabidopsis ORA59 coordinates jasmonic acid- and ethylene-responsive gene expression to regulate plant immunity

Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, among which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. Here, we identified the ERELEE4 as an ORA59-binding cis-element, in addition to the well-characterized GCC box, demonstrating that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in the gene promoters. Notably, ORA59 exhibited differential preference for the GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.

plant biology↗

bioRxiv2021

Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.

immunology↗

bioRxiv2021

Extracellular vesicles induce aggressive phenotype of luminal breast cancer cells by PKM2 phosphorylation

The aerobic glycolysis is a hallmark of cancer glucose metabolism. Several studies have suggested that cancer-derived extracellular vesicles (EVs) can modulate glucose metabolism in adjacent cells and promote disease progression. Here we suggest that EVs originated from cancer cell with highly glycolytic activity can modulate glucose metabolism in the recipient cancer cells with relative low glycolytic activity, and further induce cell proliferation. Two types of breast cancer cell lines with different levels of glycolytic activity, MDA-MB-231 of a claudin low-type breast cancer cell and MCF7 of luminal type breast cancer cell, were selected and co-cultured using indirect co-culture system such as transwell system or microfluidic system. Glucose uptake of the recipient MCF7 cells was markedly increased after co-culture with MDA-MB-231 cells. MCF7 cells after co-culture with MDA-MB-231-tdTomato cells represented multiple tdTomato signal inside the cell, which proved that EVs originated from MDA-MB-231-tdTomato were transferred to MCF7 cell. In addition, serine phosphorylation of PKM2 necessary for tumorigenesis was highly activated, and tyrosine phosphorylation of PKM2 suggesting activated aerobic glycolysis was also increased in the co-cultured MCF7 cells. Proteomic profiling of the co-cultured MCF7 cells revealed the proliferation and dedifferentiation of MCF7 cells, and further confirmed epithelial-mesenchymal transition (EMT), which is a key phenomenon for cancer metastasis. In the transcriptomic analysis, glycolysis increased in co-cultured MCF7 cells, and the component analysis of genes associated with glycolysis revealed that the next major component after cytoplasm was extracellular exosome. Proteomic analysis of EVs revealed that there were important proteins in the EV such as EGFR, ERBB2 and MAPK for phosphorylating PKM2. This phenomenon suggests the potential for aggressive cancer cells to affect other cancer cells through EV mediators.

cancer biology↗

bioRxiv2021

Mutational impact and signature of ionizing radiation

Whole-genome sequencing (WGS) of human tumors and normal cells exposed to various carcinogens has revealed distinct mutational patterns that provide deep insights into the DNA damage and repair processes. Although ionizing radiation (IR) is conventionally known as a strong carcinogen, its genome-wide mutational impacts have not been comprehensively investigated at the single-nucleotide level. Here, we explored the mutational landscape of normal single-cells after exposure to the various levels of IR. On average, 1 Gy of IR exposure generated [~]16 mutational events with a spectrum consisting of predominantly small nucleotide deletions and a few characteristic structural variations. In [~]30% of the post-irradiated cells, complex genomic rearrangements, such as chromoplexy, chromothripsis, and breakage-fusion-bridge cycles, were resulted, indicating the stochastic and chaotic nature of DNA repair in the presence of the massive number of concurrent DNA double-strand breaks. These mutational signatures were confirmed in the genomes of 22 IR-induced secondary malignancies. With high-resolution genomic snapshots of irradiated cells, our findings provide deep insights into how IR-induced DNA damage and subsequent repair processes operate in mammalian cells.

genomics↗

bioRxiv2020

Global Absence and Targeting of Protective Immune States in Severe COVID-19.

While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease. Examination of the serum from severe patients demonstrates that they uniquely produce antibodies with multiple patterns of specificity against interferon-stimulated cells and that those antibodies functionally block the production of the mild disease-associated ISG-expressing cells. Overzealous and auto-directed antibody responses pit the immune system against itself in many COVID-19 patients and this defines targets for immunotherapies to allow immune systems to provide viral defense. One Sentence SummaryIn severe COVID-19 patients, the immune system fails to generate cells that define mild disease; antibodies in their serum actively prevents the successful production of those cells.

immunology↗

bioRxiv2020

Discovery of molecular features underlying morphological landscape by integrating spatial transcriptomic data with deep features of tissue image

Profiling molecular features associated with the morphological landscape of tissue is crucial to interrogate structural and spatial patterns that underlie biological function of tissues. Here, we present a new method, SPADE, to identify important genes associated with morphological contexts by combining spatial transcriptomic data with co-registered images. SPADE incorporates deep learning-derived image patterns with spatially resolved gene expression data to extract morphological context markers. Morphological features that correspond to spatial maps of transcriptome were extracted by image patches surrounding each spot, and then, represented by image latent features. The molecular profiles correlated with the image latent features were identified. The extracted genes could be further analyzed to discover functional terms and also exploited to extract clusters maintaining morphological contexts. We apply our approach to spatial transcriptomic data of three different tissues to suggest an unbiased method capable of offering image-integrated gene expression trends.

genomics↗

bioRxiv2020

SCITO-seq: single-cell combinatorial indexed cytometry sequencing

The development of DNA-barcoded antibodies to tag cell-surface molecules has enabled the use of droplet-based single cell sequencing (dsc-seq) to profile the surface proteomes of cells. Compared to flow and mass cytometry, the major limitation of current dsc-seq-based workflows is the high cost associated with profiling each cell, thus precluding its use in applications where millions of cells are required. Here, we introduce SCITO-seq, a new workflow that combines combinatorial indexing and commercially available dsc-seq to enable cost-effective cell surface proteomic sequencing of greater than 105 cells per microfluidic reaction. We demonstrate SCITO-seqs feasibility and scalability by profiling mixed species cell lines and mixed human T and B lymphocytes. To further demonstrate its applicability, we show comparable cellular composition estimates in peripheral blood mononuclear cells obtained with SCITO-seq and mass cytometry. SCITO-seq can be extended to include simultaneous profiling of additional modalities such as transcripts and accessible chromatin or tracking of experimental perturbations such as genome edits or extracellular stimuli.

genomics↗

bioRxiv2020

Improvement of glymphatic-lymphatic drainage of beta-amyloid by focused ultrasound in Alzheimer's disease model

Drainage of parenchymal waste through the lymphatic system maintains brain homeostasis. Age-related changes of glymphatic-lymphatic clearance lead to the accumulation beta-amyloid (A{beta}) in dementia models. In this study, focused ultrasound treatment in combination with microbubbles (FUS-MB) improved A{beta} drainage in early dementia model mice, 5XFAD. FUS-MB enhanced solute A{beta} clearance from brain, but not plaques, to cerebrospinal fluid (CSF) space and then deep cervical lymph node (dCLN). dCLN ligation exaggerated memory impairment and progress of plaque formation and also the beneficial effects of FUS-MB upon A{beta} removal through CSF-lymphatic routes. In this ligation model, FUS-MB improved memory despite accumulation of A{beta} in CSF. In conclusion, FUS-MB enhances glymphatic-lymphatic clearance of A{beta} mainly by increasing brain-to-CSF A{beta} drainage. We suggest that FUS-MB can delay dementia progress in early period and benefits of FUS-MB depend on the effect of A{beta} disposal through CSF-lymphatics.

neuroscience↗

bioRxiv2019

Integrative analysis reveals RNA G-Quadruplexes in UTRs are selectively constrained and enriched for functional associations

Identifying regulatory elements in the noncoding genome is a fundamental challenge in biology. G-quadruplex (G4) sequences are abundant in untranslated regions (UTRs) of human messenger RNAs, but their functional importance remains unclear. By integrating multiple sources of genetic and genomic data, we show that putative G-quadruplex forming sequences (pG4) in 5 and 3 UTRs are selectively constrained, and enriched for cis-eQTLs and RNA-binding protein (RBP) interactions. Using over 15,000 whole-genome sequences, we uncover a degree of negative (purifying) selection in UTR pG4s comparable to that of missense variation in protein-coding sequences. In parallel, we identify new proteins with evidence for preferential binding at pG4s from ENCODE annotations, and delineate putative regulatory networks composed of shared binding targets. Finally, by mapping variants in the NIH GWAS Catalogue and ClinVar, we find enrichment for disease-associated variation in 3UTR pG4s. At a GWAS pG4-variant associated with hypertension in HSPB7, we uncover robust allelic imbalance in GTEx RNA-seq across multiple tissues, suggesting that changes in gene expression associated with pG4 disruption underlie the observed phenotypic association. Taken together, our results establish UTR G-quadruplexes as important cis-regulatory features, and point to a putative link between disruption within UTR pG4 and susceptibility to human disease.

genomics↗

bioRxiv2019

Reconfiguration of neuronal subpopulation associated with disease-associated microglia in human Alzheimer’s disease brain

There is a growing evidence that a subset of microglia, disease-associated microglia (DAM), is crucially involved in the onset and progression of Alzheimer Disease (AD). However, it has been challenging to comprehensively know how DAM affects neuronal loss and reconstitute the complicated cellular composition. Here, we describe the relationship between neuronal reconfiguration and microglia by digitally dissecting the human brain transcriptome. We observed DAM enrichment associated with neuronal loss and the degree of amyloid deposits, which was commonly found in different brain regions. The neuronal subtype analyses showed that DAM enrichment was correlated with the proportion of two excitatory neurons located in the cortical layer 4. The direction of these relations was opposite, which implied excitatory neuronal reconfiguration in the specific cortical layer. Our results suggested immune reaction represented by DAM might mediate the reconfiguration of cellular components in AD, which may eventually have implications for diagnostics and therapeutics.\n\nOne sentence summaryThe enrichment of disease-associated microglia signature is associated with the reconfiguration of neuronal subtypes, particularly excitatory neurons in the cortical layer 4.

neuroscience↗

bioRxiv2018

Graphene-oxide quenching-based molecular beacon imaging of exosome-mediated transfer of neurogenic miR-193a on microfluidic platform

A microRNA (miR-193a) was found to be transferred in the exosomes of differentiated neural progenitors to undifferentiated clones. Graphene-oxide (GO) quenching-based molecular beacon was developed to detect RNAs in living cells and tissues quickly and sensitively. Here, we applied GO quencher-based molecular beacon sensor to visualize neurogenic miR-193a levels delivered via exosome during cell-non-autonomous neurogenesis of neural progenitor cells on microfluidic platform. Fluorescence signals of FAM-labeled peptide nucleic acid (PNA) against miR-193a quenched by GO nanosheets (FAM-PNA193a-GO) were recovered in undifferentiated recipient cells differentiated to the neuronal lineage by exosome-mediated neurogenesis 3 days after co-culture with differentiated donor cells. We propose that molecular beacon imaging using PNA-GO complex can be used to visualize individual cellular expression of mature microRNAs revealing their precise spatial localization and temporal sequences by the intercellular exosome delivery of messages to undergo processes such as cell-non-autonomous neurogenesis.

cell biology↗

bioRxiv2017

Disruption to functional networks in neonates with perinatal brain injury predicts motor skills at 8 months

ObjectiveFunctional connectivity magnetic resonance imaging (fcMRI) of neonates with perinatal brain injury could improve prediction of motor impairment before symptoms manifest, and establish how early brain organization relates to subsequent development. Methods: This cohort study is the first to describe and quantitatively assess functional brain networks and their relation to later motor skills in neonates with a diverse range of perinatal brain injuries. Infants (n=65, included in final analyses: n=53) were recruited from the neonatal intensive care unit (NICU) and were stratified based on their age at birth (premature vs. term), and on whether neuropathology was diagnosed from structural MRI. Functional brain networks and a measure of disruption to functional connectivity were obtained from 14 minutes of fcMRI acquired during natural sleep at term-equivalent age.\n\nResultsDisruption to connectivity of the somatomotor and frontoparietal executive networks predicted motor impairment at 4 and 8 months. This disruption in functional connectivity was not found to be driven by differences between clinical groups, or by any of the specific measures we captured to describe the clinical course.\n\nConclusionfcMRI was predictive over and above other clinical measures available at discharge from the NICU, including structural MRI. Motor learning was affected by disruption to somatomotor networks, but also frontoparietal executive networks, which supports the functional importance of these networks in early development. Disruption to these two networks might be best addressed by distinct intervention strategies.

neuroscience↗

bioRxiv2017

Predicting aging of brain metabolic topography using variational autoencoder

Predicting future brain topography can give insight into neural correlates of aging and neurodegeneration. Due to variability in aging process, it has been challenging to precisely estimate brain topographical change according to aging. Here, we predict age-related brain metabolic change by generating future brain 18F-Fluorodeoxyglucose PET. A cross-sectional PET dataset of cognitively normal subjects with different age was used to develop a generative model. The model generated PET images using age information and characteristic individual features. Predicted regional metabolic changes were correlated with the real changes obtained by follow-up data. This model was applied to produce a brain metabolism aging movie by generating PET at different ages. Normal population distribution of brain metabolic topography at each age was estimated as well. In addition, a generative model using APOE4 status as well as age as inputs revealed a significant effect of APOE4 status on age-related metabolic changes particularly in the calcarine, lingual cortex, hippocampus and amygdala. It suggested APOE4 could be a factor affecting individual variability in age-related metabolic degeneration in normal elderly. This predictive model may not only be extended to understanding cognitive aging process, but apply to development of a preclinical biomarker for various brain disorders.

neuroscience↗

bioRxiv2017

Graphene Oxide-Quenching-Based Fluorescence In Situ Hybridization (G-FISH) To Detect RNA In Tissue: Simple And Fast Tissue RNA Diagnostics

FISH-based RNA detection in paraffin-embedded tissue can be challenging, with complicated procedures producing uncertain results and poor image quality. Here, we developed a robust RNA detection method based on graphene oxide (GO) quenching and recovery of fluorescence in situ hybridization (G-FISH) in formalin-fixed paraffin-embedded (FFPE) tissues. Using G-FISH technique, the long noncoding BC1 RNA, {beta}-actin mRNA, miR-124a and miR-21 could be detected in the cytoplasm of a mouse brain, primary hippocampal neurons, and glioblastoma multiforme tumor tissues, respectively. G-FISH showed the increased BC1 RNA level in individual hippocampal neurons of Alzheimers disease brain. The fluorescence recovered by G-FISH correlated highly with the amount of miR-21, as measured by real time RT-PCR. We propose G-FISH as a simple, fast, inexpensive, and sensitive method for RNA detection, with very low background, which could be applied to a variety of researches or diagnostic purposes.

molecular biology↗