Biology subjects

Lee, C.

Publications and source records attributed to Lee, C..

At least 271 records · Page 15Linked to original sources

bioRxiv2019

A Pro-Diabetogenic mtDNA Polymorphism in the Mitochondrial-Derived Peptide, MOTS-c

Type 2 Diabetes (T2D) is an emerging public health problem in Asia. An Asian mitochondrial DNA variation m.1382A>C (rs111033358) leads to a K14Q amino acid replacement in MOTS-c, an insulin sensitizing mitochondrial-derived peptide. Meta-analysis of three cohorts (n=27,527, J-MICC, MEC, and TMM) showed that males but not females with the C-allele exhibit a higher prevalence of T2D. Furthermore, in J-MICC, only males with the C-allele in the lowest tertile of physical activity increased their prevalence of T2D, demonstrating a kinesio-genomic interaction. High-fat fed, male mice injected with MOTS-c showed reduced weight and improved glucose tolerance, but not K14Q-MOTS-c treated mice. Like the human data, female mice were unaffected. Mechanistically, K14Q-MOTS-c leads to diminished insulin-sensitization in vitro. Thus, the m.1382A>C polymorphism is associated with susceptibility to T2D in men, possibly interacting with exercise, and contributing to the risk of T2D in sedentary males by reducing the activity of MOTS-c.

genetics↗

bioRxiv2019

Dose assessment in dental cone beam computed tomography: comparison of optically stimulated luminescence dosimetry with the Monte Carlo method

The usage and the model variety of CBCT machine has been rapidly increasing, the dose evaluation of individual devices became an important issue. Patient dose from CBCT was assessed with two different methods, optically stimulated luminescence dosimeter (OSLD) measured and monte carlo (MC) simulation, in four different examination modes. Through the measurement process and obtained value, more practical and efficient method in acquiring CBCT effective dose would be suggested. Twenty-five OSLD were calibrated and equipped in human phantom of head and neck organs. This was exposed on 2 CBCT units, CS9300 (Carestream Dental LLC, Atlanta, Georgia) and RAYSCAN + (Ray Co. Ltd, Hwaseong-si, Korea) with 2 different examination modes. Dose recorded in dosimetry was obtained and organ dose as well as an effective dose were obtained in each units of examination modes. Those values were also calculated using MC software, PCXMC (STUK, Helsinki, Finland). The organ doses and effective doses from both methods were compared by each examination mode of individual unit. OSLD measured effective dose value was higher than that obtained with MC method in each examination mode, except dual jaw mode of CS9300. The percent difference of effective dose between the two methods were ranged from 4.0 to 14.3 %. The dose difference between the methods was decreased as the examination FOV decreased. Organ dose values were varied according to the method, while overall trend was similar in both methods. The organs showing high dose were mostly consistent in both methods. In this study, the effective dose obtained by OSLD measurement and MC simulation were compared and both methods were described in detail. Consequently, as relatively efficient and easy-handling method, we carefully suggest MC simulation for further dose evaluation.

scientific communication and education↗

bioRxiv2019

TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements

Long interspersed nuclear element 1 (LINE-1) is a primary source of genetic variation in humans and other mammals. Despite its importance, LINE-1 activity remains difficult to study because of its highly repetitive nature. Here, we developed and validated a method called TeXP to gauge LINE-1 activity accurately. TeXP builds mappability signatures from LINE-1 subfamilies to deconvolve the effect of pervasive transcription from autonomous LINE-1 activity. In particular, it apportions the multiple reads aligned to the many LINE-1 instances in the genome into these two categories. Using our method, we evaluated well-established cell lines, cell-line compartments and healthy tissues and found that the vast majority (91.7%) of transcriptome reads overlapping LINE-1 derive from pervasive transcription. We validated TeXP by independently estimating the levels of LINE-1 autonomous transcription using ddPCR, finding high concordance. Next, we applied our method to comprehensively measure LINE-1 activity across healthy somatic cells, while backing out the effect of pervasive transcription. Unexpectedly, we found that LINE-1 activity is present in many normal somatic cells. This finding contrasts with earlier studies showing that LINE-1 has limited activity in healthy somatic tissues, except for neuroprogenitor cells. Interestingly, we found that the amount of LINE-1 activity was associated with the with the amount of cell turnover, with tissues with low cell turnover rates (e.g. the adult central nervous system) showing lower LINE-1 activity. Altogether, our results show how accounting for pervasive transcription is critical to accurately quantify the activity of highly repetitive regions of the human genome.\n\nAuthor SummaryRepetitive sequences, such as LINEs, comprise more than half of the human genome. Due to their repetitive nature, LINEs are hard to grasp. In particular, we find that pervasive transcription is a major confounding factor in transcriptome data. We observe that, on average, more than 90% of LINE signal derives from pervasive transcription. To investigate this issue, we developed and validated a new method called TeXP. TeXP accounts and removes the effects of pervasive transcription when quantifying LINE activity. Our method uses the broad distribution of LINEs to estimate the effects of pervasive transcription. Using TeXP, we processed thousands of transcriptome datasets to uniformly, and unbiasedly measure LINE-1 activity across healthy somatic cells. By removing the pervasive transcription component, we find that (1) LINE-1 is broadly expressed in healthy somatic tissues; (2) Adult brain show small levels of LINE transcription and; (3) LINE-1 transcription level is correlated with tissue cell turnover. Our method thus offers insights into how repetitive sequences and influenced by pervasive transcription. Moreover, we uncover the activity of LINE-1 in somatic tissues at an unmatched scale.

bioinformatics↗

bioRxiv2019

In situ measurement of absolute concentrations by Normalized Raman Imaging

Cell mass and its chemical composition are important aggregate cellular variables for physiological processes including growth control and tissue homeostasis. Despite their central importance, it has been difficult to quantitatively measure these quantities from single cells in intact tissue. Here, we introduce Normalized Raman Imaging (NoRI), a Stimulated Raman Scattering (SRS) microscopy method that provides the local concentrations of protein, lipid and water from live or fixed tissue samples with high spatial resolution. Using NoRI, we demonstrate that single cell protein, lipid and water concentrations are maintained in a tight range in cells under same physiological conditions and are altered in different physiological states such as cell cycle stages, attachment to substrates of different stiffness, or by entering senescence. In animal tissues, protein and lipid concentration varies with cell types, yet an unexpected cell-to-cell heterogeneity was found in cerebellar Purkinje cells. Protein and lipid concentration profile provides a new means to quantitatively compare disease-related pathology as demonstrated using models of Alzheimers disease. Our demonstration shows that NoRI is a broadly applicable tool for probing the biological regulation of protein mass, lipid mass and water in cellular and tissue growth, homeostasis, and disease.

bioengineering↗

bioRxiv2019

Noncanonical scaffolding of Gαi and β-arrestin by G protein-coupled receptors

G-protein-coupled receptors (GPCRs) enable cells to sense and respond appropriately to hormonal and environmental signals, and are a target of ~30% of all FDA-approved medications. Canonically, each GPCR couples to distinct G proteins, such as Gs, Gi, Gq or G12/13, as well as {beta}-arrestins. These transducer proteins translate and integrate extracellular stimuli sensed by GPCRs into intracellular signals through what are broadly considered separable signalling pathways. However, the ability of G proteins to directly interact with {beta}-arrestins to integrate signalling has not previously been appreciated. Here we show a novel interaction between Gi protein family members and {beta}-arrestin. Gi:{beta}-arrestin complexes were formed by all GPCRs tested, regardless of their canonical G protein isoform coupling, and could bind both GPCRs as well as the extracellular signal-regulated kinase (ERK). This novel paradigm of Gi:{beta}-arrestin scaffolds enhances our understanding of GPCR signalling.

cell biology↗

bioRxiv2019

PD-L1:CD80 Heterodimer Triggers CD28 While Repressing Both PD-1 and CTLA4 Pathways

Combined immunotherapy with anti-PD-1/PD-L1 and anti-CTLA4 has resulted in superior clinical responses compared to single agent therapy. The underlying mechanisms for this synergy have yet to be elucidated and investigations have largely focused on cellular interactions. Herein, we report a molecular crosstalk in which the PD-1 ligand PD-L1 and the CTLA4 ligand CD80 heterodimerize in cis. This heterodimerization blocks both PD-L1:PD-1 and CD80:CTLA4 interactions, but preserves the ability of CD80 to activate the T cell costimulatory receptor CD28. Remarkably, PD-L1 expression on antigen presenting cells (APCs) protects CD80 from CTLA4 mediated trans-endocytosis, and the therapeutic PD-L1 blockade antibody atezolizumab paradoxically downregulates CD80 on APCs, presumably reducing its co-stimulatory ability. Importantly, this effect can be negated by co-blockade of CTLA4 with ipilimumab. Our study reveals an unexpected immune stimulatory role of cis-acting PD-L1 and a mechanism of anti-PD-L1/anti-CTLA4 crosstalk, providing a therapeutic rationale for combination blockade of PD-L1 and CTLA4.

immunology↗

bioRxiv2019

Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells

The highly dynamic nature of chromosome conformation and three-dimensional (3D) genome organization leads to cell-to-cell variability in chromatin interactions within a cell population, even if the cells of the population appear to be functionally homogeneous. Hence, although Hi-C is a powerful tool for mapping 3D genome organization, this heterogeneity of chromosome higher order structure among individual cells limits the interpretive power of population based bulk Hi-C assays. Moreover, single-cell studies have the potential to enable the identification and characterization of rare cell populations or cell subtypes in a heterogeneous population. However, it may require surveying relatively large numbers of single cells to achieve statistically meaningful observations in single-cell studies. By applying combinatorial cellular indexing to chromosome conformation capture, we developed single-cell combinatorial indexed Hi-C (sci-Hi-C), a high throughput method that enables mapping chromatin interactomes in large number of single cells. We demonstrated the use of sci-Hi-C data to separate cells by karytoypic and cell-cycle state differences and to identify cellular variability in mammalian chromosomal conformation. Here, we provide a detailed description of method design and step-by-step working protocols for sci-Hi-C.

genomics↗

bioRxiv2019

CRISPR-pass: Gene rescue of nonsense mutations using adenine base editors

A nonsense mutation is a substitutive mutation in a DNA sequence that causes a premature termination during translation and produces stalled proteins resulting in dysfunction of a gene. Although it usually induces severe genetic disorders, there are no definite methods for inducing read-through of premature termination codons (PTCs). Here, we present a targeted tool for bypassing PTCs, named CRISPR-pass that uses CRISPR-mediated adenine base editors. CRISPR-pass, which should be applicable to 95.5% of clinically significant nonsense mutations in the ClinVar database, rescues protein synthesis in patient-derived fibroblasts, suggesting potential clinical utility.

molecular biology↗

bioRxiv2019

Pathogenic potential of Hic1 expressing cardiac stromal progenitors

The cardiac stroma contains multipotent mesenchymal progenitors. However, lineage relationships within cardiac stromal cells are still poorly understood. Here, we identify heart-resident PDGFRa+ Sca-1+ cells as cardiac Fibro/Adipogenic Progenitors (cFAPs) and show that they respond to ischemic damage by generating fibrogenic cells. Pharmacological blockade of this differentiation step with an anti-fibrotic tyrosine kinase inhibitor decreases post-myocardial infarction (MI) remodeling and leads to improvements in heart function. In the undamaged heart, activation of cFAPs through lineage-specific deletion of the quiescence factor Hic1 reveals additional pathogenic potential, causing fibro-fatty infiltration of the myocardium and driving major pathological features of Arrhythmogenic Cardiomyopathy (AC). HighlightsO_LIA subpopulation of PDGFRa+, Sca-1+ cells, previously considered to be a sub-type of cardiac fibroblasts, are multipotent mesenchymal progenitors, C_LIO_LICardiac damage triggers the differentiation of PDGFRa+ Sca-1+ cells into Sca-1- cells expressing a fibrogenic transcriptional programme, C_LIO_LIBlockade of the cFAP-to-fibroblast transition by Nilotinib ameliorated cardiac dysfunction post-MI and modulated cardiac remodelling. C_LIO_LIStudies performed on a model of experimentally-induced AC confirmed that cFAPs are a source of both cardiac fibroblasts and adipocytes in vivo. C_LIO_LIConversely, in the undamaged heart, activation of cFAPs by means of lineage-specific deletion of transcription factor Hic1, resulted in fibro/fatty cardiac degeneration and pathological alterations reminiscent of AC. Collectively, our findings show that a proportion of what are commonly termed "fibroblasts" are actually multipotent mesenchymal progenitors that contribute to different forms of cardiac degeneration depending on the damage setting. C_LI

cell biology↗

bioRxiv2019

Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate twelve different single-cell combinatorial indexed Hi-C (sciHi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 25,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sciHi-C data in the form of "chromatin topics." We further show enrichment of particular compartment structures associated with locus pairs in these topics.

genomics↗

bioRxiv2018

Dynamics of Notch-dependent transcriptional bursting in its native context

Transcription is well known to be inherently stochastic and episodic, but the regulation of transcriptional dynamics is not well understood. Here we analyze how Notch signaling modulates transcriptional bursting during animal development. Our focus is Notch regulation of transcription in germline stem cells of the nematode C. elegans. Using the MS2 system to visualize nascent transcripts and live imaging to record dynamics, we analyze bursting as a function of position within the intact animal. We find that Notch-dependent transcriptional activation is indeed \"bursty\"; that wild-type Notch modulates burst duration (ON-time) rather than duration of pauses between bursts (OFF-time) or mean burst intensity; and that a mutant Notch receptor, which is compromised for assembly into the Notch transcription factor complex, primarily modifies burst size (duration x intensity). To our knowledge, this work is the first to visualize regulation of metazoan transcriptional bursting by a canonical signaling pathway in its native context.\n\nHIGHLIGHTSO_LINotch-dependent transcriptional bursts are spatially graded across the stem cell pool\nC_LIO_LIBurst duration is the key determinant of Notch-dependent transcriptional probability\nC_LIO_LINotch NICD strength influences both burst duration and intensity\nC_LIO_LINotch dynamics are largely stochastic for consecutive bursts at the same chromosomal locus\nC_LI

cell biology↗

bioRxiv2018

Microbial dispersal limitation to isolated soil habitats in the McMurdo Dry Valleys of Antarctica

Dispersal is a critical yet poorly understood factor underlying macroecological patterns in microbial communities. Airborne microbial transport is assumed to occupy a central role in determining dispersal outcomes and extra-range dispersal has important implications for predicting ecosystem resilience and response to environmental change. One of the most pertinent biomes in this regard is Antarctica given its geographic isolation and vulnerability to climate change and human disturbance. Here we report the first characterisation of microbial diversity in near-ground and high-altitude air above a typical Antarctic Dry Valley as well as that of underlying soil microbial communities. We found that persistent airborne inputs were unable to fully explain local soil community assembly. Comparison with airborne microbial diversity from non-polar sources suggests that strong selection occurs during atmospheric transport resulting in regionally isolated airborne inputs and highly specialized soil communities where fungi displayed greater isolation than bacteria from non-polar sources. Overall microbial communities from this isolated Antarctic ecosystem displayed limited connectivity to the global microbial pool. Our findings provide critical insights to forecast the potential outcomes for microbial communities of climate change-mediated shifts in air circulation to the Dry Valleys, the largest ice-free region of Antarctica.

microbiology↗

bioRxiv2018

Neural activity in a hippocampus-like region of the teleost pallium are associated with navigation and active sensing

Neural mechanisms underlying spatial navigation in fish are unknown and little is known, for any vertebrate, about the relationship between active sensing and the formation of spatial maps. The weakly electric fish, Gymnotus Carapo, uses their active electric sense for spatial navigation. The electric organ discharge rate (EODr) undergoes transient increases during navigation to enhance electrosensory sampling. Gymnotus also uses stereotyped forward/ backward swimming as a second form of active sensing that brings objects towards the electroreceptor-dense head region. We wirelessly recorded neural activity from the pallium of freely swimming Gymnotus. Spiking activity was sparse and occurred only during swimming. Notably, some units exhibited significant place specificity and/or association with both forms of active sensing. Our results provide the first characterization of neural activity in a hippocampal-like region of a teleost fish brain and connects active sensing via sensory sampling rate and directed movements to higher order encoding of spatial information.

neuroscience↗

bioRxiv2018

Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.)

In plants, myo-inositol-1,2,3,4,5,6-hexakisphosphate (InsP6), also known as phytic acid (PA), is a major component of organic phosphorus (P), and accounts for up to 85% of the total P in seeds. In rice (Oryza sativa L.), PA mainly accumulates in rice bran, and chelates mineral cations, resulting in mineral deficiencies among brown rice consumers. Therefore, considerable efforts have been focused on the development of low PA (LPA) rice cultivars. In this study, we performed genetic and molecular analyses of OsLpa1, a major PA biosynthesis gene, in Sanggol, a low PA mutant variety developed via chemical mutagenesis of Ilpum rice cultivar. Genetic segregation and sequencing analyses revealed that a recessive allele, lpa1-3, at the OsLpa1 locus (Os02g0819400) was responsible for a significant reduction in seed PA content in Sanggol. The lpa1-3 gene harboured a point mutation (C623T) in the fourth exon of the predicted coding region, resulting in threonine (Thr) to isoleucine (Ile) amino acid substitution at position 208 (Thr208Ile). Three-dimensional analysis of Lpa1 protein structure indicated that myo-inositol 3-monophosphate [Ins(3)P1] kinase binds to the active site of Lpa1, with ATP as a cofactor for catalysis. Furthermore, the presence of Thr208 in the loop adjacent to the entry site of the binding pocket suggests that Thr208Ile substitution is involved in regulating enzyme activity via phosphorylation. Therefore, we propose that Thr208Ile substitution in lpa1-3 reduces Lpa1 enzyme activity in Sanggol, resulting in reduced PA biosynthesis.

plant biology↗

bioRxiv2018

Poly-Enrich: Count-based Methods for Gene Set Enrichment Testing with Genomic Regions and Updates to ChIP-Enrich

Gene set enrichment (GSE) testing enhances the biological interpretation of ChIP-seq data and other large sets of genomic regions. Our group has previously introduced two GSE methods for genomic regions: ChIP-Enrich for narrow regions and Broad-Enrich for broad genomic regions, such as histone modifications. Here, we introduce new methods and extensions that more appropriately analyze sets of genomic regions with vastly different properties. First, we introduce Poly-Enrich, which models the number of peaks assigned to a gene using a generalized additive model with a negative binomial family to determine gene set enrichment, while adjusting for gene locus length (#bps associated with each gene). This is the first method that controls for locus length while accounting for the number of peaks per gene and variability among genes. We also introduce a flexible weighting approach to incorporate region scores, a hybrid enrichment approach, and support for new gene set databases and reference genomes/species. As opposed to ChIP-Enrich, Poly-Enrich works well even when nearly all genes have a peak. To illustrate this, we used Poly-Enrich to characterize the pathways and types of genic regions (introns, promoters, etc) enriched with different families of repetitive elements. By comparing ChIP-Enrich and Poly-Enrich results from ENCODE ChIP-seq data, we found that the optimal test depends more on the pathway being regulated than on the transcription factor or other properties of the dataset. Using known transcription factor functions, we discovered clusters of related biological processes consistently better modeled with either the binary score method (ChIP-Enrich) or count based method (Poly-Enrich). This suggests that the regulation of certain processes is more often modified by multiple binding events (count-based), while others tend to require only one (binary). Our new hybrid method handles this by automatically choosing the optimal method, with correct FDR-adjustment. Author SummaryAlthough every cell in our body contains the same DNA, our cells perform vastly different functions due to differences in how our genes are regulated. Certain regions of the genome are bound by DNA binding proteins (transcription factors), which regulate the expression of nearby genes. After an experiment to identify a large set of these regions, we can then model the association of these regions with various cellular pathways and biological processes. This analysis helps understand the overall biological effect that the binding events have on the cells. For example, if genes relating to apoptosis tend to have the transcription factor, Bcl-2, bind more often nearby, then Bcl-2 is likely to have a vital role in regulating apoptosis. The specifics of how to best perform this analysis is still being researched and depends on properties of the set of genomic regions. Here, we introduce a new, more flexible method that counts the number of occurrences per gene and models that in a sophisticated statistical test, and compare it to a previous method. We show that the optimal method depends on multiple factors, and the new method, Poly-Enrich, allows interesting findings in scenarios where the previous method failed.

bioinformatics↗

bioRxiv2018

Single-cell RNA-seq reveals that glioblastoma recapitulates normal brain development

SummaryCancer stem cells are critical for cancer initiation, development, and resistance to treatments. Our understanding of these processes, and how they relate to glioblastoma heterogeneity, is limited. To overcome these limitations, we performed single-cell RNA-sequencing on 38 296 glioblastoma cells and 22 637 normal human fetal brain cells. Using an unbiased approach, we mapped the lineage hierarchy of the developing human brain and compared the transcriptome of each cancer cell to this roadmap. We discovered a conserved neural trilineage cancer hierarchy with glial progenitor-like cells at the apex. We also found that this progenitor population contains the majority of cancers cycling cells and is the origin of heterogeneity. Finally, we show that this hierarchal map can be used to identify therapeutic targets specific to progenitor cancer stem cells. Our analyses show that normal brain development reconciles glioblastoma development, unravels the origin of glioblastoma heterogeneity, and helps to identify cancer stem cell-specific targets.

cancer biology↗

bioRxiv2018

Widespread RNA editing dysregulation in Autism Spectrum Disorders

Autism spectrum disorder (ASD) is a genetically complex, clinically heterogeneous neurodevelopmental disease. Recently, our understanding of the molecular abnormalities in ASD has been expanded through transcriptomic analyses of postmortem brains. However, a crucial molecular pathway involved in synaptic development, RNA editing, has not yet been studied on a genome-wide scale. Here, we profiled the global patterns of adenosine-to-inosine (A-to-I) editing in a large cohort of post-mortem ASD brains. Strikingly, we observed a global bias of hypo-editing in ASD brains, common to different brain regions and involving many genes with known neurobiological functions. Through genome-wide protein-RNA binding analyses and detailed molecular assays, we show that the Fragile X proteins, FMRP and FXR1P, interact with ADAR proteins and modulate A-to-I editing. Furthermore, we observed convergent patterns of RNA editing alterations in ASD and Fragile X syndrome, thus establishing RNA editing as a molecular link underlying these two highly related diseases. Our findings support a role for RNA editing dysregulation in ASD and highlight novel mechanisms for RNA editing regulation.

neuroscience↗

bioRxiv2018

Niche maintenance of germline stem cells in C. elegans males

Stem cell maintenance by niche signaling is a common theme across phylogeny. In the Caenorhabditis elegans gonad, the broad outlines of germline stem cell (GSC) regulation are the same for both sexes: GLP-1/Notch signaling from the mesenchymal Distal Tip Cell (DTC) niche maintains GSCs in the distal gonad of both sexes (AO_SCPLOWUSTINC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWANDC_SCPLOW KO_SCPLOWIMBLEC_SCPLOW 1987), and does so via two key stem cell regulators, SYGL-1 and LST-1 (KO_SCPLOWERSHNERC_SCPLOW et al. 2014). Most analyses of niche signaling and GSC regulation have focused on XX hermaphrodites, an essentially female sex making sperm in larvae and oocytes in adults. Here we focus on XO males, which are sexually dimorphic in all tissues, including the distal gonad. The architecture of the male niche and the cellular behavior of GSCs are sex-specific. Despite these differences, males maintain a GSC pool similar to the hermaphrodite with respect to size and cell number and the male GSC response to niche signaling is also remarkably similar.

developmental biology↗