Biology subjects

Kim, H.-S.

Publications and source records attributed to Kim, H.-S..

47 records · Page 3Linked to original sources

bioRxiv2019

Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing neuronal human amyloid-β

Alzheimers disease (AD) is the most common neurodegenerative disease affecting the elderly worldwide. Mitochondrial dysfunction has been proposed as a key event in the etiology of AD. We have previously modeled amyloid-beta (A{beta})-induced mitochondrial dysfunction in a transgenic Caenorhabditis elegans strain by expressing human A{beta} peptide specifically in neurons (GRU102). Here, we focus on a deeper analysis of these metabolic changes associated with A{beta}-induced mitochondrial dysfunction. Integrating metabolomics, transcriptomics, biochemical studies and computational modeling, we identify alterations in Tricarboxylic Acid (TCA) cycle metabolism following even low-level A{beta} expression. In particular, GRU102 show reduced activity of a rate-limiting TCA cycle enzyme, alpha-ketoglutarate dehydrogenase. These defects are associated with elevation of protein carbonyl content specifically in mitochondria. Importantly, metabolic failure occurs before any significant increase in global protein aggregate is detectable. Treatment with an antidiabetes drug, Metformin, reverses A{beta}-induced metabolic defects, reduces protein aggregation and normalizes the lifespan of GRU102. Our results point to metabolic dysfunction as an early and causative event in AD pathology and a promising target for intervention.

neuroscience↗

bioRxiv2019

BMP7 functions predominantly as a heterodimer with BMP2 or BMP4 during mammalian embryogenesis

BMP7/BMP2 or BMP7/BMP4 heterodimers are more active than homodimers in vitro, but it is not known whether these heterodimers signal in vivo. To test this, we generated knock in mice carrying a mutation (Bmp7R-GFlag) that prevents proteolytic activation of the dimerized BMP7 precursor protein. This mutation eliminates the function of BMP7 homodimers and all other BMPs that normally heterodimerize with BMP7. While Bmp7 null homozygotes are live born, Bmp7R-GFlag homozygotes are embryonic lethal and have broadly reduced BMP activity. Furthermore, compound heterozygotes carrying the Bmp7R-G allele together with a null allele of Bmp2 or Bmp4 die during embryogenesis with defects in ventral body wall closure and/or the heart. Co-immunoprecipitation assays confirm that endogenous BMP4/7 heterodimers exist. Thus, BMP7 functions predominantly as a heterodimer with BMP2 or BMP4 during mammalian development, which may explain why mutations in either Bmp4 or Bmp7 lead to a similar spectrum of congenital defects in humans.

developmental biology↗

bioRxiv2019

Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information

BackgroundLong DNA reads produced by single molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short read DNA fragments. For de novo assembly, PacBio and Oxford Nanopore Technologies (ONT) are favorite options. However, PacBios SMRT sequencing is expensive for a full human genome assembly and costs over 40,000 USD for 30x coverage as of 2019. ONT PromethION sequencing, on the other hand, is one-twelfth the price of PacBio for the same coverage. This study aimed to compare the cost-effectiveness of ONT PromethION and PacBios SMRT sequencing in relation to the quality.\n\nFindingsWe performed whole genome de novo assemblies and comparison to construct an improved version of KOREF, the Korean reference genome, using sequencing data produced by PromethION and PacBio. With PromethION, an assembly using sequenced reads with 64x coverage (193 Gb, 3 flowcell sequencing) resulted in 3,725 contigs with N50s of 16.7 Mbp and a total genome length of 2.8 Gbp. It was comparable to a KOREF assembly constructed using PacBio at 62x coverage (188 Gbp, 2,695 contigs and N50s of 17.9 Mbp). When we applied Hi-C-derived long-range mapping data, an even higher quality assembly for the 64x coverage was achieved, resulting in 3,179 scaffolds with an N50 of 56.4 Mbp.\n\nConclusionThe pore-based PromethION approach provides a good quality chromosome-scale human genome assembly at a low cost with long maximum contig and scaffold lengths and is more cost-effective than PacBio at comparable quality measurements.

genomics↗

bioRxiv2019

B-SIDER: Computational algorithm for the design of complementary β-sheet sequences

The {beta}-sheet is an element of protein secondary structure, and intra-/inter-molecular {beta}-sheet interactions play pivotal roles in biological regulatory processes including scaffolding, transporting, and oligomerization. In nature, a {beta}-sheet formation is tightly regulated because dysregulated {beta}-stacking often leads to severe diseases such as Alzheimers, Parkinsons, systemic amyloidosis, or diabetes. Thus, the identification of intrinsic {beta}-sheet forming propensities can provide valuable insight into protein designs for the development of novel therapeutics. However, structure-based design methods may not be generally applicable to such amyloidogenic peptides mainly owing to high structural plasticity and complexity. Therefore, an alternative design strategy based on complementary sequence information is of significant importance. Herein, we developed a database search method called B-SIDER for the design of complementary {beta}-strands. This method makes use of the structural database information and generates query-specific score matrices. The discriminatory power of the B-SIDER score function was tested on representative amyloidogenic peptide substructures against a sequence-based score matrix (PASTA2.0) and two popular ab initio protein design score functions (Rosetta and FoldX). B-SIDER is able to distinguish wild-type amyloidogenic {beta}-strands as favored interactions in a more consistent manner than other methods. B-SIDER was prospectively applied to the design of complementary {beta}-strands for a splitGFP scaffold. Three variants were identified to have stronger interactions than the original sequence selected through a directed evolution, emitting higher fluorescence intensities. Our results indicate that B-SIDER can be applicable to the design of other {beta}-strands, assisting in the development of therapeutics against disease-related amyloidogenic peptides.

bioinformatics↗

bioRxiv2019

Electronic Health Records Based Prediction of Future Incidence of Alzheimers Disease Using Machine Learning

Nationwide population-based cohort provides a new opportunity to build a completely automated risk prediction model based on individuals history of health and healthcare beyond existing risk prediction models. We tested the possibility of machine learning models to predict future incidence of Alzheimers disease (AD) using large-scale administrative health data. From the Korean National Health Insurance Service database between 2002 and 2010, we obtained de-identified health data in elders above 65 years (N=40,736) containing 4,894 unique clinical features including ICD-10 codes, medication codes, laboratory values, history of personal and family illness, and socio-demographics. To define incident AD two operational definitions were considered: "definite AD" with diagnostic codes and dementia medication (n=614) and "probable AD" with only diagnosis (n=2,026). We trained and validated a random forest, support vector machine, and logistic regression to predict incident AD in 1,2,3, and 4 subsequent years. For predicting future incidence of AD in balanced samples (bootstrapping), the machine learning models showed reasonable performance in 1-year prediction with AUC of 0.775 and 0.759, based on "definite AD" and "probable AD" outcomes, respectively; in 2-year, 0.730 and 0.693; in 3-year, 0.677 and 0.644; in 4-year, 0.725 and 0.683. The results were similar when the entire (unbalanced) samples were used. Important clinical features selected in logistic regression included hemoglobin level, age, and urine protein level. This study may shed a light on the utility of the data-driven machine learning model based on large-scale administrative health data in AD risk prediction, which may enable better selection of individuals at risk for AD in clinical trials or early detection in clinical settings.

bioinformatics↗

bioRxiv2018

The draft genome of an octocoral, Dendronephthya gigantea

BackgroundCoral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities composed of octocorallian species, appear more resilient. The genomes of several species of cnidarians have been published, including stony corals, sea anemones, and hydra, but as of yet no octocoral species. To fill this phylogenetic gap within the cnidarian, we sequenced the octocoral, Dendronephthya gigantea, a non-symbiotic soft coral, commonly known as the carnation coral.\n\nFindingsThe D. gigantea genome size is approximately 276 Mb. A high-quality genome assembly was constructed using 29.85Gb (108x coverage) of PacBio long reads and 35.54Gb (128x coverage) of Illumina short paired-end reads resulting in the largest N50 value reported among cnidarian of 1.4 Mb. About 12 % of the genome consisted of repetitive elements. We found 28,879 protein-coding genes. This gene set contained about 94% metazoan single-copy orthologs, indicating the gene models were predicted with high quality compared to other cnidarians. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence occurred approximately 544 million years ago. Moreover, there is a clear difference in Hox gene composition: unlike in hexacorals, Antp superclass member Evx gene was absent in D. gigantea.\n\nConclusionsWe present the first genome assembly of a non-symbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including comparisons of stony and soft corals and symbiotic and non-symbiotic corals. In addition, the genome of this species may provide clues about differential genetic coping mechanisms between soft and stony coral regarding the global warming.

genomics↗

bioRxiv2018

Development of three-dimensional articular cartilage construct using silica nano-patterned substrate

Current strategies for cartilage cell therapy are mostly based on the use of autologous chondrocytes or mesenchymal stem cells (MSCs). However, these cells have limitations of a small number of cells available and of low chondrogenic ability, respectively. Many studies now suggest that fetal stem cells are more plastic than adult stem cells and can therefore more efficiently differentiate into target tissues. This study introduces, efficiency chondrogenic differentiation of fetal cartilage-derived progenitor cells (FCPCs) to adult cells can be achieved using a three-dimensional (3D) spheroid culture method based on silica nanopatterning techniques. In evaluating the issue of silica nano-particle size (Diameter of 300, 750, 1200 nm), each particle size was coated into the well of a 6-well tissue culture plate. FCPCs (2 x 105 cells/well in 6-well plate) were seeded in each well with chondrogenic medium. In this studys, the 300 nm substrate that formed multi-spheroids and the 1200 nm substrate that showed spreading were due to the cell-cell adhesion force(via N-cadherin) and cell-substrate(via Integrin) force, the 750 nm substrate that formed the mass-aggregation can be interpreted as the result of cell monolayer formation through cell-substrate force followed by cell-cell contact force contraction. We conclude that our 3D spheroid culture system contributes to an optimization for efficient differentiation of FCPC, offers insight into the mechanism of efficient differentiation of engineered 3D culture system, and has promise for wide applications in regeneration medicine and drug discovery fields.

cell biology↗

bioRxiv2018

Pellino 1 Communicates Intercellular Signaling in Chronic Skin Inflammatory Microenvironment

Chronic skin inflammation including psoriasis is a multisystem disease, affecting more than 5% of the general population. Here we show that Pellino 1 (Peli1), a signal-responsive ubiquitin E3 ligase, is highly up-regulated in human psoriatic skin lesions and that increased Peli1 expression correlates with the immunopathogenesis of psoriasis-like chronic skin inflammatory disease. Interestingly, Peli1 directly interacts with interferon regulatory factor 4 (IRF4, a transcription factor that plays pivotal roles in proliferation and cytokine production) and induces lysine 63-mediated ubiquitination. Peli1-mediated IRF4 ubiquitination appears to be a common systemic signaling mechanism shared by lesional keratinocytes, dendritic cells, macrophages, and T cells, generating a feedback relationship between keratinocyte and Th17 cell responses. Conversely, inhibition of Peli1 interferes with IRF4 induction and attenuates immunopathogenic signaling in the psoriasis. In summary, Peli1-mediated ubiquitination is a common immunopathogenic intercellular signaling in psoriasis-like chronic skin inflammatory microenvironment. Thus, targeting Peli1 could be used as a potential strategy for psoriasis treatment.

immunology↗

bioRxiv2018

Repulsive Guidance Molecule Acts in Axon Branching in Caenorhabditis elegans

Repulsive guidance molecules (RGMs) are evolutionarily conserved proteins implicated in repulsive axon guidance. Here we report the function of the Caenorhabditis elegans ortholog DRAG-1 in axon branching. The axons of hermaphrodite-specific neurons (HSNs) branch at the region abutting the vulval muscles and innervate these muscles to control egg laying. The drag-1 mutants exhibited defects in HSN axon branching in addition to a small body size and egg laying-defective phenotype. DRAG-1 expression in the hypodermal cells was required for the branching of these axons. The C-terminal glycosylphosphatidylinositol anchor of DRAG-1 was important for its function. Genetic analyses suggested that the membrane receptor UNC-40, but neither SMA-1/{beta}H-spectrin nor SMA-5/MAP kinase 7, acts in the same pathway with DRAG-1 in HSN branching. We propose that DRAG-1 expressed in the hypodermis signals via the UNC-40 receptor expressed in HSNs to elicit branching activity of HSN axons.

developmental biology↗

bioRxiv2017

Fibronectin type III and intracellular domains of Toll-like receptor 4 interactor with leucine-rich repeats (Tril) are required for developmental signaling

Toll-like receptor 4 interactor with leucine-rich repeats (Tril) is a transmembrane protein that functions as a coreceptor for Toll-like receptors (Tlrs) to mediate innate immune responses in the adult brain. Tril also triggers degradation of the Bmp inhibitor, Smad7, during early embryonic development to allow for normal blood formation. Tril most likely plays additional, yet to be discovered, roles during embryogenesis. In the current studies, we performed a structure-function analysis, which indicated that the extracellular domain, including the fibronectin type III (FN) domain, and the intracellular domain of Tril are required to trigger Smad7 degradation in the early Xenopus embryo. Furthermore, we found that a Tril deletion mutant lacking the FN domain (Tril{Delta}FN) can dominantly inhibit signaling by endogenous Tril when overexpressed in vivo. This finding raises the intriguing possibility that the FN domain functions to bind endogenous Tril/Tlr4 ligands, perhaps including extracellular matrix molecules. We also show that Tril normally cycles between the cell surface and endosomes, and that the Tril extracellular domain is required to retain Tril at the cell surface, while the intracellular domain is required for Tril internalization in Xenopus ectodermal explants. Using a CHO cell aggregation assay, we further show that, unlike other transmembrane proteins that contain leucine rich repeats in the extracellular domain, Tril is not sufficient to mediate homophilic adhesion. Our findings identify Tril{Delta}FN as a valuable tool that can be used to block the function of endogenous Tril in vivo in order to discover additional roles during embryonic development.

cell biology↗

bioRxiv2017

Small molecule-mediated reprogramming of epithelial-mesenchymal transition thereby blocking fibrosis

Fibrotic diseases are major causes of morbidity and mortality, and the epithelial-mesenchymal transition (EMT) plays a central role in the development of tissue/organ fibrosis. We discovered that eupatilin, a member of the chromone scaffold (CS)-containing compounds found ubiquitously in the plant kingdom, completely reversed fibrogenesis in vitro and substantially ameliorated bleomycin-induced lung fibrosis (BILF). Furthermore, eupatilin-induced growth arrest and morphological changes in primary fibroblasts derived from a patient with idiopathic pulmonary fibrosis (IPF). To better understand fibrosis, we established a mouse hepatic stellate cell (HSC) line that was robustly differentiated into myofibroblasts upon treatment with TGF{beta}. HSC-derived fibrogenesis was completely blocked by eupatilin, which caused dramatic morphological changes while inhibiting expression of EMT-related genes. The chemical groups linked to the 2nd carbon (C2), C3, C6, and C7 on the CS of eupatilin were essential for its anti-fibrogenic effects. Unlike eupatilin, pirfenidone failed to block HSC fibrogenesis and did not affect the morphology of HSCs or lung fibroblasts. Although pirfenidone affected local production of TGF{beta}, as reflected by a reduction in the TGF{beta} level in lung lysates of BILF model mice, eupatilin is likely to act via a different therapeutic mechanism. In particular, eupatilin had greater anti-fibrotic capacity and EMT-inhibitory activity and significantly attenuated the phosphorylation of Erk by TGF{beta}. Based on the interactome, Integrin{beta}3 seems to be a major player in integration of TGF{beta} signaling into the eupatilin-mediated anti-fibrosis. Our findings suggest that combinatorial use of eupatilin and pirfenidone may augment the therapeutic efficacy of IPF treatment.

cell biology↗