Biology subjects

Kim, H.

Publications and source records attributed to Kim, H..

At least 307 records · Page 17Linked to original sources

bioRxiv2023

Intracellular sphingolipid sorting drives membrane phase separation in the yeast vacuole

The yeast vacuole membrane can phase separate into ordered and disordered domains, a phenomenon that is required for micro-lipophagy under nutrient limitation. Here we report that sorting of sphingolipids (SLs) into the vacuole membrane controls this process. We first developed a vacuole isolation method to identify lipidome changes during the onset of phase separation in early stationary stage cells. We found that phase separated vacuoles are characterized by increases in lipid raft-forming components not found in the whole cell, including a dramatic change in SL composition. Sorting of both SLs and ergosterol into the vacuole membrane is dependent on Npc2, the yeast homologue of the Niemann-Pick Type C2 lipid transporter. Genetic dissection of SL biosynthesis revealed that the composition of vacuole SLs modulates membrane phase separation and micro-lipophagy under glucose restriction. These results show that lipid trafficking can drive membrane phase separation in vivo and identify SLs as key mediators of this process in yeast.

biophysics↗

bioRxiv2023

Structure of the human Duffy antigen receptor

The Duffy antigen receptor, also known as FY glycoprotein or CD234, is a seven transmembrane protein expressed primarily at the surface of red blood cells, which displays promiscuous binding to multiple chemokines. Not only does it serve as the basis of the Duffy blood group system but it also acts as the primary attachment site for malarial parasite Plasmodium vivax on erythrocytes and as one of the nucleating receptors for the pore forming toxins secreted by Staphylococcus aureus. Despite a predicted 7TM architecture and efficient binding to a spectrum of chemokines, it fails to exhibit canonical second messenger response such as calcium release, likely due to a lack of G protein coupling. Unlike prototypical GPCRs and {beta}-arrestin-biased atypical chemokine receptors, the Duffy antigen receptor also appears to lack {beta}-arrestin binding, making it an enigmatic 7TM chemokine receptor. In order to decipher the molecular mechanism of this intriguing functional divergence exhibited by the Duffy antigen receptor, we have determined its cryo-EM structure in complex with a C-C type chemokine, CCL7. The structure reveals a relatively superficial binding mode of CCL7, with the N-terminus of the receptor serving as the key interaction interface, and a partially formed orthosteric binding pocket lacking the second site for chemokine recognition compared to prototypical chemokine receptors. The structural framework allows us to employ HDX-MS approach to uncover ligand-induced structural changes in the receptor and draw important insights into the promiscuous nature of chemokine binding. Interestingly, we also observe a dramatic shortening of TM5 and 6 on the intracellular side, compared to prototypical GPCRs, which precludes the coupling of canonical signal-transducers namely G proteins, GRKs and {beta}-arrestins, as demonstrated through extensive cellular assays. Taken together, our study uncovers a previously unknown structural mechanism that imparts unique functional divergence on the 7TM fold encoded in the Duffy antigen receptor while maintaining its scavenging function and should facilitate the designing of novel therapeutics targeting this receptor.

biochemistry↗

bioRxiv2023

Bodily Maps of Spontaneous Thought

AO_SCPLOWBSTRACTC_SCPLOWThe intricate relationship between the body and the mind has long been recognized, but the specific bodily representations of spontaneous thought remain elusive. Here, we developed and validated predictive models of spontaneous thought based on body maps using the emBODY and Free-Association Semantic tasks. Our valence and self-relevance models demonstrated robust prediction performances across three test datasets, with the valence model accurately decoding the bodily topography of emotions and feelings. Model weight patterns revealed the significance of peripheral limbs and heart area in predicting valence, while the head area played a crucial role in predicting self-relevance. Furthermore, we investigated the neurobiological underpinnings of body map representations using fMRI and ECG data and found evidence for the reflection of body map responses in central and autonomic nervous system activities. Overall, this study provides insights into the bodily representations of spontaneous thought, highlighting the interconnected relationships between the body and the mind.

neuroscience↗

bioRxiv2023

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last [~]500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).

bioinformatics↗

bioRxiv2023

Discrete projections from MCH neurons mediate anti-parkinsonian effects of acupuncture

Parkinsons disease (PD) presents with typical motor dysfunction and non-motor symptoms, including memory loss. Although acupuncture is suggested as an alternative therapy for PD, its neuroanatomical mechanisms remain unclear. We demonstrate that acupuncture ameliorates both motor and memory deficits in PD mice through activation of melanin-concentrating hormone (MCH) neurons in the lateral hypothalamus and zona incerta (LH/ZI)--MCHLH/ZI-- via nerve conduction. We identify two distinct subpopulations of MCHLH/ZI projecting to the substantia nigra and hippocampus, each of which is responsible for controlling motor and memory function. This effect can be attributed to MCH-mediated recovery from dopaminergic neurodegeneration, reactive gliosis, and impaired hippocampal synaptic plasticity. Collectively, MCHLH/ZI constitutes not only the neuroanatomical basis of acupuncture but also a potential cellular target for treating both motor and non-motor PD symptoms. One-Sentence SummaryAcupuncture alleviates both motor and non-motor symptoms in Parkinsons disease by activating two distinct MCH projections.

neuroscience↗

bioRxiv2023

The Neonatal Gyrencephalic Cortex Maintains Regionally Distinct Streams of Neuroblasts

Neurodevelopmental mechanisms have evolved to support the formation of diverse brain structures, such as in humans, during the perinatal period. Here, we demonstrate that neonatal gyrencephalic brains harbor an expanded subventricular zone, termed the Arc, defined by tiered arrangement of doublecortin (DCX)-expressing neuroblasts and vascular enrichment at the ventricular wall. The Arc is the origin of dorsal and ventral populations of migratory neuroblasts that target multiple regions involved in higher cognitive functions. Arc-derived migratory streams, primarily from the caudal ganglionic eminence, are composed of diverse neuronal subtypes with distinct spatial and migratory-receptor profiles. Our findings indicate the Arc is a structure present in phylogenetically divergent species that supports the expansion of postnatal neuronal migration, contributing to a protracted formation of cortical circuits in gyrencephalic brains. One-Sentence SummaryThe ventricular cytoarchitecture of gyrencephalic brains supports an ongoing supply of migratory neurons to the neonatal cortex.

neuroscience↗

bioRxiv2023

In vivo Protein Footprinting Reveals the Dynamic Conformational Changes of Proteome of Multiple Tissues in Progressing Alzheimer's Disease

Numerous studies have investigated changes in protein expression at the system level using proteomic mass spectrometry, but only recently have studies explored the structure of proteins at the proteome level. We developed covalent protein painting (CPP), a protein footprinting method that quantitatively labels exposed lysine, and have now extended the method to whole intact animals to measure surface accessibility as a surrogate of in vivo protein conformations. We investigated how protein structure and protein expression change as Alzheimers disease (AD) progresses by conducting in vivo whole animal labeling of AD mice. This allowed us to analyze broadly protein accessibility in various organs over the course of AD. We observed that structural changes of proteins related to energy generation, carbon metabolism, and metal ion homeostasis preceded expression changes in the brain. We found that proteins in certain pathways undergoing structural changes were significantly co-regulated in the brain, kidney, muscle, and spleen.

systems biology↗

bioRxiv2023

Amyloid-β exposed astrocytes induce iron transport from endothelial cells at the blood-brain barrier by altering the ratio of apo- and holo-transferrin

Excessive brain iron accumulation is observed in early in the onset of Alzheimers disease, notably prior to widespread proteinopathy. These findings suggest that increases in brain iron levels are due to a dysregulation of the iron transport mechanism at the blood-brain barrier. Astrocytes release signals (apo- and holo-transferrin) that communicate brain iron needs to endothelial cells in order to modulate iron transport. Here we use iPSC-derived astrocytes and endothelial cells to investigate how early-disease levels of amyloid-{beta} disrupt iron transport signals secreted by astrocytes to stimulate iron transport from endothelial cells. We demonstrate that conditioned media from astrocytes treated with amyloid-{beta} stimulates iron transport from endothelial cells and induces changes in iron transport pathway protein levels. The mechanism underlying this response begins with increased iron uptake and mitochondrial activity by the astrocytes which in turn increases levels of apo-transferrin in the amyloid-{beta} conditioned astrocyte media leading to increased iron transport from endothelial cells. These novel findings offer a potential explanation for the initiation of excessive iron accumulation in early stages of Alzheimers disease. Whats more, these data provide the first example of how the mechanism of iron transport regulation by apo- and holo-transferrin becomes misappropriated in disease to detrimental ends. The clinical benefit from understanding early dysregulation in brain iron transport in AD cannot be understated. If therapeutics can target this early process, they could possibly prevent the detrimental cascade that occurs with excessive iron accumulation. Significance StatementExcessive brain iron accumulation is hallmark pathology of Alzheimers disease that occurs early in the disease staging and before widespread proteinopathy deposition. This overabundance of brain iron has been implicated to contribute to disease progression, thus understandingthe mechanism of early iron accumulation has significant therapeutic potential to slow to halt disease progression. Here, we show that in response to low levels of amyloid-{beta} exposure, astrocytes increase their mitochondrial activity and iron uptake, resulting in iron deficient conditions. Elevated levels of apo (iron free)-transferrin stimulate iron release from endothelial cells. These data are the first to propose a mechanism for the initiation of iron accumulation and the misappropriation of iron transport signaling leading to dysfunctional brain iron homeostasis and resultant disease pathology.

neuroscience↗

bioRxiv2023

Getting personal: brain decoding of spontaneous thought using personal narratives

The contents of spontaneous thought and their dynamics are important factors for ones personality traits and mental health. However, they are difficult to assess because spontaneous thought occurs voluntarily without conscious constraints. Here, we aimed to decode two important content dimensions of spontaneous thought--self-relevance and valence--directly from functional Magnetic Resonance Imaging (fMRI) signals. To train brain decoders, we induced a wide range of levels of self-relevance and emotional valence using individually generated personal stories as well as stories written by others to mimic narrative-like spontaneous thoughts (n = 49). We then tested the brain decoders on two resting-state fMRI datasets (n = 49 and 90) with and without intermittent thought sampling, achieving significant predictions. The default mode and ventral attention networks were important contributors to the predictions. Overall, this study paves the way for the brain decoding of spontaneous thought and its use for clinical applications.

neuroscience↗

bioRxiv2023

Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-based Featurization Method

Protein-ligand interactions are essential to drug discovery and drug development efforts. Desirable on-target or multi-target interactions are a first step in finding an effective therapeutic; undesirable off-target interactions are a first step in assessing safety. In this work, we introduce a novel ligand-based featurization and mapping of human protein pockets to identify closely related protein targets, and to project novel drugs into a hybrid protein-ligand feature space to identify their likely protein interactions. Using structure-based template matches from PDB, protein pockets are featurized by the ligands which bind to their best co-complex template matches. The simplicity and interpretability of this approach provides a granular characterization of the human proteome at the protein pocket level instead of the traditional protein-level characterization by family, function, or pathway. We demonstrate the power of this featurization method by clustering a subset of the human proteome and evaluating the predicted cluster associations of over 7,000 compounds.

synthetic biology↗

bioRxiv2023

ECLiPSE: A Versatile Classification Technique for Structural and Morphological Analysis of Super-Resolution Microscopy Data

We introduce a new automated machine learning analysis pipeline to precisely classify cellular structures captured through single molecule localization microscopy, which we call ECLiPSE (Enhanced Classification of Localized Pointclouds by Shape Extraction). ECLiPSE leverages 67 comprehensive shape descriptors encompassing geometric, boundary, skeleton and other properties, the majority of which are directly extracted from the localizations to accurately characterize individual structures. We validate ECLiPSE through unsupervised and supervised classification on a dataset featuring five distinct cellular structures, achieving exceptionally high classification accuracies nearing 100%. Moreover, we demonstrate the versatility of our approach by applying it to two novel biological applications: quantifying the clearance of tau protein aggregates, a critical marker for neurodegenerative diseases, and differentiating between two distinct morphological features (morphotypes) of TAR DNA-binding protein 43 proteinopathy, potentially associated to different TDP-43 strains, each exhibiting unique seeding and spreading properties. We anticipate that this versatile approach will significantly enhance the way we study cellular structures across various biological contexts, elucidating their roles in disease development and progression.

biophysics↗

bioRxiv2023

Delayed blood pressure recovery after exercise stress test is associated with autonomic dysfunction and pulse pressure in a middle-aged healthy group

BackgroundDelayed heart rate (HR) and blood pressure recovery after exercise test is known as the reliable indexes of autonomic dysfunction. Here we tried to evaluate the serial changes in various indicators during exercise test and correlations among them in a normotensive healthy middle-aged group. MethodsA total of 122 patients without hypertension or diabetes was enrolled (mean age, 55.6 {+/-} 11.0; male, 56.6 %; mean blood pressure, 124.8 {+/-} 16.6 / 81.5 {+/-} 9.6 mmHg). Treadmill test was performed for evaluation of chest pain. Patients with coronary artery disease, positive treadmill test result, left ventricular dysfunction or renal failure were excluded. Heart rate recovery was calculated by subtracting the HR in the first or second minute of recovery period from the HR of peak exercise (HRR1 or HRR2). Systolic blood pressure in the 4th minute of recovery stage (SBPR4) was used to show delayed blood pressure recovery. ResultsMetabolic equivalents (METs) and HR in stage 2 to 4 were significantly correlated with both HRR1 and HRR2. Multiple regression analysis of HRR revealed significant correlation of METs and SBPR4. SBPR4 was significantly correlated with both HRR1 and HRR2 (HRR1, r=-0.376, p<0.001; HRR2, r=-0.244, p=0.008). SBPR4 revealed significant correlation with SBP in the baseline to stage 3 and pulse pressure (r=0.406, p<0.001). ConclusionsDelayed BP recovery after peak exercise test revealed significant association with autonomic dysfunction and pulse pressure in normotensive middle-aged healthy group. It can be a simple and useful marker of autonomic dysfunction and arterial stiffness.

neuroscience↗

bioRxiv2023

Discovery and characterization of highly potent and selective covalent inhibitors of SARS-CoV-2 PLpro

Coronavirus infections, such as the global COVID-19 pandemic, have had a profound impact on many aspects of our daily life including working style, economy, and the healthcare system. To prevent the rapid viral transmission and speed up recovery from the infection, many academic organizations and industry research labs have conducted extensive research on discovering new therapeutic options for SARS-CoV-2. Among those efforts, RNA-dependent RNA polymerase (RdRp) inhibitors such as Remdesivir, Molnupiravir and 3CLpro inhibitor such as Nirmatrelvir (Paxlovid) have been widely used as the therapeutic options. Given the recent emergence of several new variants that caused a resurgence of the virus, it would be beneficial to discover more diverse therapeutic options with novel anti-viral mechanisms. In this regard, PLpro has been highlighted since it, along with 3CLpro, is one of the two most important proteases that are required for SARS-CoV-2 viral processing. While 3CLpro inhibitors were extensively investigated in the light of Emergency Use Authorizations of Nirmatrelvir, PLpro inhibitors have not been thoroughly investigated even preclinically. Thus, discovery efforts on antivirals acting against PLpro will be valuable. PLpro inhibitors may exert their activity by inhibiting viral replication and enhancing the host defense system through blocking virus-induced cell signaling events for evading host immune response. In this study, we report the discovery and development of two covalent irreversible PLpro inhibitors, HUP0109 and its deuterated analog DX-027, out of our quest for novel anti-COVID 19 therapeutic agents for the past two and half years. HUP0109 selectively targets the viral catalytic cleft of PLpro and covalently modifies its active site cysteine residue (C111). Promising results from preclinical evaluation suggest that DX-027 can be developed as a potential COVID-19 treatment.

pharmacology and toxicology↗

bioRxiv2023

Barley HvNIP2;1 aquaporin permeates water, metalloids, saccharides, and ion pairs due to structural plasticity and diversification

Aquaporins can facilitate the passive movement of water and small polar molecules and some ions. The barley Nodulin 26-like Intrinsic Protein (HvNIP2;1) embedded in liposomes and examined through stopped-flow light scattering spectrophotometry and Xenopus oocyte swelling assays was found to permeate water, boric and germanic acids, sucrose and L-arabinose but not D-glucose or D-fructose. Other saccharides, such as neutral (D-mannose, D-galactose, D-xylose, D-mannoheptaose) and charged (N-acetyl D-glucosamine, D-glucosamine, D-glucuronic acid) aldoses, disaccharides (lactose, cellobiose, gentiobiose, trehalose), trisaccharide raffinose, and urea, glycerol, and acyclic polyols were permeated to a much lower extent. Apparent permeation of hydrated KCl and MgSO4 ion pairs was observed, while CH3COONa and NaNO3 permeated at significantly lower rates. Experiments with boric acid and sucrose revealed no apparent interaction between solutes when permeated together, and AgNO3 blocked the permeation of all solutes. Full-scale steered molecular dynamics simulations of HvNIP2;1 and spinach SoPIP2;1 revealed possible rectification for water, boric acid, and sucrose transport, and defined key residues interacting with permeants. In a biological context, the simulated sucrose rectification could mediate its apoplastic-to-intracellular transport but not the reverse, thus, constituting a novel element of plant saccharide-transporting machinery. Phylogenomic analyses of 164 Viridiplantae and 2,993 Archaean, bacterial, fungal, and Metazoan aquaporins rationalised solute poly-selectivity in NIP3 sub-clade entries and suggested that they diversified from other sub-clades to acquire a unique specificity of saccharide transporters. Solute specificity definition in NIP aquaporins could inspire developing plants for sustained food production. Significance StatementAquaporins are fundamental to water and solute movements in nearly all living organisms. Solute selectivity inspections of the HvNIP2;1 aquaporin revealed that it transported water, hydroxylated metalloids boric and germanic acids, sucrose, L-arabinose, KCl, and MgSO4 ion pairs, but not D-glucose or D-fructose and to lesser extent urea, and acyclic polyols. This poly-selective transport by HvNIP2;1 classified in the NIP3 sub-clade aquaporins may afford nutritional and protective roles during plant development and in response to abiotic stresses. It is anticipated that the solute specificity definition of HvNIP2;1 inspires protein engineering and in silico mining to develop plants, which when exposed to suboptimal soil conditions of high soil metalloids, would overcome toxicity for sustained food production.

biophysics↗

bioRxiv2023

Pleiotropic Influence of DNA Methylation QTLs on physiological and aging traits

DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD Family. A regulatory hotspot on chromosome 5 had the highest density of trans-acting methylation QTLs (trans-meQTLs) associated with multiple distant CpGs. We refer to this locus as meQTL.5a. The trans-modulated CpGs showed age-dependent changes, and were enriched in developmental genes, including several members of the MODY pathway (maturity onset diabetes of the young). The joint modulation by genotype and aging resulted in a more "aged methylome" for BXD strains that inherited the DBA/2J parental allele at meQTL.5a. Further, several gene expression traits, body weight, and lipid levels mapped to meQTL.5a, and there was a modest linkage with lifespan. DNA binding motif and protein-protein interaction enrichment analysis identified the hepatic nuclear factor, Hnf1a (MODY3 gene in humans), as a strong candidate. The pleiotropic effects of meQTL.5a could contribute to variation in body size and metabolic traits, and influence CpG methylation and epigenetic aging that could have an impact on lifespan.

genomics↗

bioRxiv2023

Chromatin context-dependent regulation and epigenetic manipulation of prime editing

Prime editing is a powerful means of introducing precise changes to specific locations in mammalian genomes. However, the widely varying efficiency of prime editing across target sites of interest has limited its adoption in the context of both basic research and clinical settings. Here, we set out to exhaustively characterize the impact of the cis-chromatin environment on prime editing efficiency. Using a newly developed and highly sensitive method for mapping the genomic locations of a randomly integrated "sensor", we identify specific epigenetic features that strongly correlate with the highly variable efficiency of prime editing across different genomic locations. Next, to assess the interaction of trans-acting factors with the cis-chromatin environment, we develop and apply a pooled genetic screening approach with which the impact of knocking down various DNA repair factors on prime editing efficiency can be stratified by cis-chromatin context. Finally, we demonstrate that we can dramatically modulate the efficiency of prime editing through epigenome editing, i.e. altering chromatin state in a locus-specific manner in order to increase or decrease the efficiency of prime editing at a target site. Looking forward, we envision that the insights and tools described here will broaden the range of both basic research and therapeutic contexts in which prime editing is useful.

molecular biology↗

bioRxiv2023

PPIAT:Target mass spectrometry based Protein-Protein interaction analytics tool

MotivationThe formation of protein networking is critical for understanding the biological functions of proteins and the underlying mechanisms of disease. To gain insights into target proteins that interact with a particular disease, we need to profiling all the proteins involved in the disease beforehand. However, the profiling results may not necessarily match with an experimental target protein. Therefore, it is necessary to identify physical protein-protein interactions (PPIs) using various methods. The cross-linking mass spectrometry (XL-MS) method is a representative approach to identify physical interactions between proteins, but there are many challenges in calculating theoretical mass values for application to target mass spectrometry. ResultsThe research team developed PPIAT, which integrates information on reviewed human proteins, protein-protein interactions, cross-linkers, enzymes, and modifications. All functions are available for free on the web application. Availability and implementationThe PPIAT is available at www.ppiat.cnu.ac.kr Contactkimlab@cnu.ac.kr

bioinformatics↗

bioRxiv2023

Tamoxifen Response at Single Cell Resolution in Estrogen Receptor-Positive Primary Human Breast Tumors

In ER+/HER2- breast cancer, multiple measures of intra-tumor heterogeneity are associated with worse response to endocrine therapy. To investigate heterogeneity in response to treatment, we developed an operating room-to-laboratory pipeline for the collection of live human tumors and normal breast specimens immediately after surgical resection for processing into single-cell workflows for experimentation and genomic analyses. We demonstrate differences in tamoxifen response by cell type and identify distinctly responsive and resistant subpopulations within the malignant cell compartment of human tumors. Tamoxifen resistance signatures from 3 distinct resistant subpopulations are prognostic in large cohorts of ER+ breast cancer patients and enriched in endocrine therapy resistant tumors. This novel ex vivo model system now provides a foundation to define responsive and resistant sub-populations within heterogeneous tumors, to develop precise single cell-based predictors of response to therapy, and to identify genes and pathways driving resistance to therapy.

cancer biology↗