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Articles by Jong-Eun Park
Genomic and phenotypic characterization of the Jeju Genome Project cohort in Korea
Abstract The Jeju Genome Project (JGP) is a genomic and phenotypic cohort established to provide a comprehensive resource for precision medicine on Jeju Island, South Korea. JGP integrates whole-genome sequencing (WGS), customized genotyping arrays, and detailed clinical and lifestyle phenotyping to characterize population-specific genetic architecture, disease determinants, and risk profiles among participants recruited on Jeju Island.
Spatial transcriptomic profiling of porcine tissue microarray detecting subclinical circovirus infection
Abstract Porcine Circovirus type 2 (PCV2) is a key pathogen in pigs that induces host immunosuppression, leading to severe secondary infections such as porcine circovirus-associated disease (PCVAD), resulting in significant economic losses for the swine industry. More recently, it has emerged as a pathogen that needs to be ruled out in porcine xenotransplantation research due to issues related to latent infection.
Hepatocyte TonEBP promotes metabolic stress-induced hepatic fibroinflammation involving transcriptional activation of ELR⁺ CXC chemokines - Cell Death Discovery
Abstract Metabolic dysfunction-associated steatohepatitis (MASH), a progressive stage of metabolic dysfunction-associated steatotic liver disease (MASLD), is characterized by liver inflammation, fibrosis, and hepatocyte injury. Despite its clinical relevance, the molecular mechanisms linking metabolic stress to hepatic fibroinflammation remain poorly understood.
Author Correction: A virtual memory CD8+ T cell-originated subset causes alopecia areata through innate-like cytotoxicity - Nature Immunology
scICE: enhancing clustering reliability and efficiency of scRNA-seq data with multi-cluster label consistency evaluation - Nature Communications
Abstract Clustering analysis is a fundamental step in scRNA-seq data analysis. However, its reliability is compromised by clustering inconsistency among trials due to stochastic processes in clustering algorithms. Despite efforts to obtain reliable and consensus clustering, existing methods cannot be applied to large scRNA-seq datasets due to high computational costs.
Nanosecond Laser‐Induced Conversion of Leaf‐Like Co‐MOF to Nanoscale Co@N‐gCarbon for Enhanced Multifunctional Electrocatalytic Performance
Conflict of Interest The authors declare no conflict of interest. Supporting Information Filename Description cssc202500205-sup-0001-SuppData-S1.pdf2.4 MB Supplementary Material References 1, , , , Appl. Catal. B 2012, 126, 225. 2, , , Appl. Catal. B 2017, 206, 556. 3, , , , , , , , Energy Environ. Sci. 2014, 7, 1719. 4, , , , , , , , , , , , , , , , , Nat. Commun. 2022, 13, 2294. 5, , , , , Angew. Chem., Int. Ed. 2018, 57, 2488. 6, , , , , , , , , , Nat. Mater. 2024, 23, 252. 7, , , , Chem. Eng. J.
Searching for influencers among placental immune cells in preeclampsia.
Abstract Cells in maternal and fetal immune systems may communicate, leading to immune tolerance during pregnancy; however, this hypothesis remains controversial. Here, we profiled single cell transcriptional signatures in placental layers comprising the maternal–fetal interface and deep placenta, then searched for genes associated with preeclampsia.
Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases - Nature Genetics
Abstract Alternative splicing contributes to complex traits, but whether this differs in trait-relevant cell types across diverse genetic ancestries is unclear. Here we describe cell-type-specific, sex-biased and ancestry-biased alternative splicing in ~1 M peripheral blood mononuclear cells from 474 healthy donors from the Asian Immune Diversity Atlas. We identify widespread sex-biased and ancestry-biased differential splicing, most of which is cell-type-specific.
Flt3L enhances clonal diversification and selective expansion of intratumoral CD8+ T cells while differentiating into effector-like cells
Keywords immunotherapy PD-1 cDC1 Flt3L Tpex Tex asGM1 TCR repertoire Research topic(s) CP: Immunology CP: Cancer Introduction Blocking the T cell activation inhibitors known as programmed cell death 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) is used successfully to treat multiple tumors in a process called immune checkpoint blockade (ICB).1 However, many patients do not benefit from ICB treatment due to resistance to it.
Label‐Free Exosome Analysis by Surface‐Enhanced Raman Scattering Spectroscopy with Laser‐Ablated Silver Nanoparticle Substrate
Conflict of Interest The authors declare no conflict of interest. Supporting Information Filename Description adhm202402038-sup-0001-SuppMat.pdf2.8 MB Supporting Information References 1a) , , , Asian Pac. J. Cancer Prev. 2019, 20, 2015; b) , , , , , , Dev. Cell 2019, 49, 375. 2, Nat. Rev. Cancer 2020, 20, 681. 3a) , , , , , Pharmacol. Rev. 2012, 64, 676; b) , , , , , Pediatr. Nephrol. 2019, 34, 11; c) , , Annu. Rev. Biochem. 2019, 88, 487; d) , , J. Cell Biol. 2013, 200, 373. 4, , , , , Anal. Biochem. 2019, 571, 1.
Gene-level alignment of single-cell trajectories - Nature Methods
Abstract Single-cell data analysis can infer dynamic changes in cell populations, for example across time, space or in response to perturbation, thus deriving pseudotime trajectories. Current approaches comparing trajectories often use dynamic programming but are limited by assumptions such as the existence of a definitive match. Here we describe Genes2Genes, a Bayesian information-theoretic dynamic programming framework for aligning single-cell trajectories.
Author Correction: Salivary gland organoid culture maintains distinct glandular properties of murine and human major salivary glands - Nature Communications
Correction to: Nature Communications https://doi.org/10.1038/s41467-022-30934-z, published online 07 June 2022 In this article the author name Youngmi Ji was incorrectly written as Yongmi Ji. The original article has been corrected.
Innate immune responses against mRNA vaccine promote cellular immunity through IFN-β at the injection site - Nature Communications
Abstract mRNA vaccines against SARS-CoV-2 have revolutionized vaccine development, but their immunological mechanisms are not fully understood. Here, we investigate injection site responses of mRNA vaccines by generating a comprehensive single-cell transcriptome profile upon lipid nanoparticle (LNP) or LNP-mRNA challenge in female BALB/c mice. We show that LNP-induced stromal pro-inflammatory responses and mRNA-elicited type I interferon responses dominate the initial injection site responses.
Hippo–YAP/TAZ signalling coordinates adipose plasticity and energy balance by uncoupling leptin expression from fat mass - Nature Metabolism
Abstract Adipose tissues serve as an energy reservoir and endocrine organ, yet the mechanisms that coordinate these functions remain elusive. Here, we show that the transcriptional coregulators, YAP and TAZ, uncouple fat mass from leptin levels and regulate adipocyte plasticity to maintain metabolic homeostasis.
scLENS: data-driven signal detection for unbiased scRNA-seq data analysis - Nature Communications
Abstract High dimensionality and noise have limited the new biological insights that can be discovered in scRNA-seq data. While dimensionality reduction tools have been developed to extract biological signals from the data, they often require manual determination of signal dimension, introducing user bias. Furthermore, a common data preprocessing method, log normalization, can unintentionally distort signals in the data.
Rapid and label-free exosome analysis by surface-enhanced Raman spectroscopy using silver nanoparticle substrate based on selective laser ablation and melting of silver nanowire
Abstract Early diagnostics of breast cancer is crucial to reduce the risk of cancer metastasis and late relapse. Exosome, which contains distinct information of its origin, can be the target object as a liquid biopsy. However, its low sensitivity and inadequate diagnostic tools interfere with the point-of-care testing (POCT) of the exosome.
JCM | Free Full-Text | Prognostic Performance of Sequential Organ Failure Assessment, Acute Physiology and Chronic Health Evaluation III, and Simplified Acute Physiology Score II Scores in Patients with Suspected Infection According to Intensive Care Unit
1. Introduction In intensive care units (ICUs), it is common to use clinical scoring systems to predict patient outcomes [1]. Predicting patient outcomes helps intensivists in triaging or categorizing critically ill patients, supporting clinical decision-making and allocation of ICU resources. Therefore, modeling the risk of mortality in ICU patients has received considerable attention over the past several decades [2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17].
Acoustofluidic lysis of cancer cells and Raman spectrum profiling
Acoustofluidic lysis of cancer cells and Raman spectrum profiling The lysis of cancer cells inside a sessile droplet was performed using traveling surface acoustic wave (SAW) without any chemical reagents. Raman spectrum profiling was then carried out to explore detailed cell-derived data. The Rayleigh waves formed by an interdigital transducer were made to propagate along the surface of an LiNbO3 substrate.
A virtual memory CD8+ T cell-originated subset causes alopecia areata through innate-like cytotoxicity - Nature Immunology
Author notes These authors contributed equally: Joon Seok, Sung-Dong Cho. Authors and Affiliations Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea Joon Seok, Sung-Dong Cho, Jeongsoo Lee, Yunseo Choi, Seongju Jeong, Minwoo Jeon, A.
Single-cell mapping of combinatorial target antigens for CAR switches using logic gates - Nature Biotechnology
Extended Data Fig. 1 UMAP representation of the normal cell atlas overlaid with tumor cells and tumor-infiltrating normal cells from selected tumor datasets. . a, Same plot as Fig. 1e but with cell-type annotation instead of tissue origin information. b, Same plot as Fig. 1e but showing representative cells selected during tumor cellpreserving subsampling by geometric sketching. Extended Data Fig. 2 Tumor versus normal differences in ECFs and expression levels.
Robust temporal map of human in vitro myelopoiesis using single-cell genomics - Nature Communications
Abstract Myeloid cells are central to homeostasis and immunity. Characterising in vitro myelopoiesis protocols is imperative for their use in research, immunotherapies, and understanding human myelopoiesis. Here, we generate a >470K cells molecular map of human induced pluripotent stem cells (iPSC) differentiation into macrophages.
Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration
Highlights • Injury-induced IL-1β signaling promotes differentiation of AT2 cells into AT1 cells • AT2 cells differentiate into AT1 cells via cell states of primed AT2 and DATPs • HIF1α signaling controls AT2-DAPT conversion and is essential for AT1 differentiation • Chronic inflammation impairs maturation of AT1 cells Summary Tissue regeneration is a multi-step process mediated by diverse cellular hierarchies and states that are also implicated in tissue dysfunction and pathogenesis.
Prenatal development of human immunity
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Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
Highlights • scRNA-seq and CITE-seq identify two thymus seeding progenitors in human postnatal thymus • The human thymus is colonized by distinct T and non-T lineage precursors • Immature thymocytes differentiate mainly into T and DC lineage cells • Transcriptional dynamics reveal regulatory networks similar to and distinct from mouse Summary During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone-marrow-derived hematopoietic progenitors that migrate...
A cell atlas of human thymic development defines T cell repertoire formation
By Jong-Eun Park, Rachel A. Botting, Cecilia Domínguez Conde, Dorin-Mirel Popescu, Marieke Lavaert, Daniel J. Kunz, Issac Goh, Emily Stephenson, Roberta Ragazzini, Elizabeth Tuck, Anna Wilbrey-Clark, Kenny Roberts, Veronika R. Kedlian, John R. Ferdinand, Xiaoling He, Simone Webb, Daniel Maunder, Niels Vandamme, Krishnaa T.
Single-cell reconstruction of the early maternal–fetal interface in humans
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Abstract During early human pregnancy the uterine mucosa transforms into the decidua, into which the fetal placenta implants and where placental trophoblast cells intermingle and communicate with maternal cells. Trophoblast–decidual interactions underlie common diseases of pregnancy, including pre-eclampsia and stillbirth. Here we profile the transcriptomes of about 70,000 single cells from first-trimester placentas with matched maternal blood and decidual cells.
By Roser Vento-Tormo, Mirjana Efremova, Rachel A. Botting, Margherita Y. Turco, Miquel Vento-Tormo, Kerstin B Meyer, Jong-Eun Park, Emily Stephenson, Krzysztof Polanski, Angela Goncalves, Lucy Gardner, Staffan Holmqvist, Johan Henriksson, Angela E. Zou, Andrew Sharkey, Ben Millar, Barbara A. Innes, Laura Wood, Anna Wilbrey-Clark, Rebecca Payne, Martin A. Ivarsson, Andrew Filby, David H. Rowitch, Judith N Bulmer, Gavin J. Wright, Muzlifah Haniffa, Ashley Moffett, Sarah A Teichmann, Steve Lisgo, Michael J. T. Stubbington
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PARN and TOE1 Constitute a 3′ End Maturation Module for Nuclear Non-coding RNAs
PARN and TOE1 Do Not Act on mRNA Tails PARN and TOE1 Determine the 3′ Termini of Nuclear Small ncRNAs Pseudouridylation of snRNA Is Affected by scaRNA Destabilization TOE1 Is Involved in the 3′ End Processing of TERC To explore the 3′ terminome of smaller RNAs (50% of the alignments had the exact 3′ ends of known annotations (Figure 2Figure 2A), indicating the successful enrichment of short nuclear ncRNAs. By preserving intact 3′ ends, our methodology enabled the 3′ end mapping at a...
Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle
FiguresFigure 1Dynamics of Poly(A) Tail Length during Cell Cycle(A) Experimental scheme. Cells enriched in S or M phase were analyzed by TAIL-seq, mRNA-seq, and ribosome profiling.(B) Global poly(A) tail length distributions of S and M phase-arrested samples.(C) A scatter plot of the median poly(A) length of individual genes in S and M phases.
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