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4,045 results on '"Joon-Yong An"'

60. Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain

Author

Liang, Lindsay, Fazel Darbandi, Siavash, Pochareddy, Sirisha, Gulden, Forrest O, Gilson, Michael C, Sheppard, Brooke K, Sahagun, Atehsa, An, Joon-Yong, Werling, Donna M, Rubenstein, John LR, Sestan, Nenad, Bender, Kevin J, and Sanders, Stephan J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Brain Disorders, Neurosciences, Neurodegenerative, Epilepsy, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Alternative Splicing, Animals, Biomarkers, Brain, Cerebral Cortex, Disease Susceptibility, Exons, Gene Expression Regulation, Humans, Introns, Mice, Multigene Family, Open Reading Frames, Polymorphism, Genetic, Protein Binding, Quantitative Trait Loci, Structure-Activity Relationship, Voltage-Gated Sodium Channels, Isoform, Splicing, Voltage-gated sodium channel, Autism spectrum disorder, Intellectual disability, Developmental delay, Epileptic encephalopathy, Seizures, Exon 5A, Exon 5N, Clinical Sciences
Abstract

BackgroundGenetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, and autism spectrum disorder. The mRNA splicing patterns of all four genes vary across development in the rodent brain, including mutually exclusive copies of the fifth protein-coding exon detected in the neonate (5N) and adult (5A). A second pair of mutually exclusive exons is reported in SCN8A only (18N and 18A). We aimed to quantify the expression of individual exons in the developing human brain.MethodsRNA-seq data from 783 human brain samples across development were analyzed to estimate exon-level expression. Developmental changes in exon utilization were validated by assessing intron splicing. Exon expression was also estimated in RNA-seq data from 58 developing mouse neocortical samples.ResultsIn the mature human neocortex, exon 5A is consistently expressed at least 4-fold higher than exon 5N in all four genes. For SCN2A, SCN3A, and SCN8A, a brain-wide synchronized 5N to 5A transition occurs between 24 post-conceptual weeks (2nd trimester) and 6 years of age. In mice, the equivalent 5N to 5A transition begins at or before embryonic day 15.5. In SCN8A, over 90% of transcripts in the mature human cortex include exon 18A. Early in fetal development, most transcripts include 18N or skip both 18N and 18A, with a transition to 18A inclusion occurring from 13 post-conceptual weeks to 6 months of age. No other protein-coding exons showed comparably dynamic developmental trajectories.ConclusionsExon usage in SCN1A, SCN2A, SCN3A, and SCN8A changes dramatically during human brain development. These splice isoforms, which alter the biophysical properties of the encoded channels, may account for some of the observed phenotypic differences across development and between specific variants. Manipulation of the proportion of splicing isoforms at appropriate stages of development may act as a therapeutic strategy for specific mutations or even epilepsy in general.

Published
2021

61. Wafer-scale alignment and integration of micro-light-emitting diodes using engineered van der Waals forces

Author

Hwang, Junsik, Kim-Lee, Hyun-Joon, Hong, Seog Woo, Park, Joon-Yong, Kim, Dong Kyun, Kim, Dongho, Song, Sanghoon, Jeong, Jonghyun, Kim, Yongchan, Yeom, Min Jae, Yu, Min-chul, Kim, Joosung, Park, Younghwan, Shin, Dong-Chul, Kang, Sungjin, Shin, Jai-Kwang, Kim, Yongsung, Yoon, Euijoon, Lee, Hojin, Yoo, Geonwook, Jeong, Jaewook, and Hwang, Kyungwook

Published
2023
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63. Histopathology and SARS-CoV-2 Cellular Localization in Eye Tissues of COVID-19 Autopsies

Author

Stein, Sydney R., Ramelli, Sabrina C., Ramos-Benitez, Marcos J., Platt, Andrew P., Dickey, James M., Curran, Shelly J., Babyak, Ashley L., Valencia, Luis Perez, Richert, Mary E., Vannella, Kevin M., Chertow, Daniel S., Kleiner, David E., Hewitt, Stephen M., Young, Willie J., Young, Sarah P., Gasmi, Billel, De Melo, Michelly Sampaio, Desar, Sabina, Tadros, Saber, Nasir, Nadia, Jin, Xueting, Rajan, Sharika, Dikoglu, Esra, Ozkaya, Neval, Ylaya, Kris, Chung, Joon-Yong, Pittaluga, Stefania, Smith, Grace, Emanuel, Elizabeth R., Kelsall, Brian, Olivera, Justin A., Blawas, Megan, Grazioli, Alison, Hays, Nicole, Purcell, Madeleine, Singireddy, Shreya, Wu, Jocelyn, Raja, Katherine, Curto, Ryan, Chung, Jean, Borth, Amy, Bowers, Kimberly, Weichold, Anne, Minor, Paula, Moshref, Mirahmad, Kelly, Emily, Sajadi, Mohammad M., Scalea, Thomas M., Tran, Douglas, Madathil, Ronson J., Dahi, Siamak, Deatrick, Kristopher B., Krause, Eric M., Rabin, Joseph, Herrold, Joseph A., Tabatabai, Ali, Hochberg, Eric, Cornachione, Christopher, Levine, Andrea R., Saharia, Kapil K., Richards, Justin E., Elder, John, Burke, Allen, Mazzeffi, Michael A., Christenson, Robert, Chancer, Zackary, Abdulmahdi, Mustafa, Sopha, Sabrina, Goldberg, Tyler, Soherwardi, Shahabuddin, Sangwan, Yashvir, McCurdy, Michael T., Sudano, Kristen, Blume, Diane, Radin, Bethany, Arnouk, Madhat, Eagan, James W., Jr., Herr, Daniel L., Zerbe, Christa, Sen, H. Nida, Wang, Yujuan, Kodati, Shilpa, Lee, Jung Wha, Perez, Paola, Singh, Manmeet, Yinda, Kwe Claude, Platt, Andrew, Munster, Vincent J., de Wit, Emmie, Warner, Blake M., and Chan, Chi-Chao

Published
2023
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68. SARS-CoV-2 infection and persistence in the human body and brain at autopsy

Author

Stein, Sydney R., Ramelli, Sabrina C., Grazioli, Alison, Chung, Joon-Yong, Singh, Manmeet, Yinda, Claude Kwe, Winkler, Clayton W., Sun, Junfeng, Dickey, James M., Ylaya, Kris, Ko, Sung Hee, Platt, Andrew P., Burbelo, Peter D., Quezado, Martha, Pittaluga, Stefania, Purcell, Madeleine, Munster, Vincent J., Belinky, Frida, Ramos-Benitez, Marcos J., Boritz, Eli A., Lach, Izabella A., Herr, Daniel L., Rabin, Joseph, Saharia, Kapil K., Madathil, Ronson J., Tabatabai, Ali, Soherwardi, Shahabuddin, McCurdy, Michael T., Peterson, Karin E., Cohen, Jeffrey I., de Wit, Emmie, Vannella, Kevin M., Hewitt, Stephen M., Kleiner, David E., and Chertow, Daniel S.

Published
2022
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71. A global lipid map defines a network essential for Zika virus replication.

Author

Leier, Hans C, Weinstein, Jules B, Kyle, Jennifer E, Lee, Joon-Yong, Bramer, Lisa M, Stratton, Kelly G, Kempthorne, Douglas, Navratil, Aaron R, Tafesse, Endale G, Hornemann, Thorsten, Messer, William B, Dennis, Edward A, Metz, Thomas O, Barklis, Eric, and Tafesse, Fikadu G

Abstract

Zika virus (ZIKV), an arbovirus of global concern, remodels intracellular membranes to form replication sites. How ZIKV dysregulates lipid networks to allow this, and consequences for disease, is poorly understood. Here, we perform comprehensive lipidomics to create a lipid network map during ZIKV infection. We find that ZIKV significantly alters host lipid composition, with the most striking changes seen within subclasses of sphingolipids. Ectopic expression of ZIKV NS4B protein results in similar changes, demonstrating a role for NS4B in modulating sphingolipid pathways. Disruption of sphingolipid biosynthesis in various cell types, including human neural progenitor cells, blocks ZIKV infection. Additionally, the sphingolipid ceramide redistributes to ZIKV replication sites, and increasing ceramide levels by multiple pathways sensitizes cells to ZIKV infection. Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV infection.

Published
2020

72. Homeostatic plasticity fails at the intersection of autism-gene mutations and a novel class of common genetic modifiers.

Author

Genç, Özgür, An, Joon-Yong, Fetter, Richard D, Kulik, Yelena, Zunino, Giulia, Sanders, Stephan J, and Davis, Graeme W

Subjects
Animals, Humans, Drosophila melanogaster, Genetic Predisposition to Disease, Drosophila Proteins, Risk Factors, Autistic Disorder, Synaptic Transmission, Homeostasis, Neuronal Plasticity, Mutation, Genes, CHD8, CREG, D. melanogaster, autism, homeostatic plasticity, neuroscience, neurotransmission, presynaptic, Biochemistry and Cell Biology
Abstract

We identify a set of common phenotypic modifiers that interact with five independent autism gene orthologs (RIMS1, CHD8, CHD2, WDFY3, ASH1L) causing a common failure of presynaptic homeostatic plasticity (PHP) in Drosophila. Heterozygous null mutations in each autism gene are demonstrated to have normal baseline neurotransmission and PHP. However, PHP is sensitized and rendered prone to failure. A subsequent electrophysiology-based genetic screen identifies the first known heterozygous mutations that commonly genetically interact with multiple ASD gene orthologs, causing PHP to fail. Two phenotypic modifiers identified in the screen, PDPK1 and PPP2R5D, are characterized. Finally, transcriptomic, ultrastructural and electrophysiological analyses define one mechanism by which PHP fails; an unexpected, maladaptive up-regulation of CREG, a conserved, neuronally expressed, stress response gene and a novel repressor of PHP. Thus, we define a novel genetic landscape by which diverse, unrelated autism risk genes may converge to commonly affect the robustness of synaptic transmission.

Published
2020

73. Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex.

Author

Werling, Donna M, Pochareddy, Sirisha, Choi, Jinmyung, An, Joon-Yong, Sheppard, Brooke, Peng, Minshi, Li, Zhen, Dastmalchi, Claudia, Santpere, Gabriel, Sousa, André MM, Tebbenkamp, Andrew TN, Kaur, Navjot, Gulden, Forrest O, Breen, Michael S, Liang, Lindsay, Gilson, Michael C, Zhao, Xuefang, Dong, Shan, Klei, Lambertus, Cicek, A Ercument, Buxbaum, Joseph D, Adle-Biassette, Homa, Thomas, Jean-Leon, Aldinger, Kimberly A, O'Day, Diana R, Glass, Ian A, Zaitlen, Noah A, Talkowski, Michael E, Roeder, Kathryn, State, Matthew W, Devlin, Bernie, Sanders, Stephan J, and Sestan, Nenad

Subjects
BrainVar, DLPFC, LOC101926933 RP11-298I3.1 AL132780.1 ENSG00000257285, PsychENCODE, RHEBL1, dorsolateral prefrontal cortex, fetal transition, mTOR, prenatal eQTL, Biochemistry and Cell Biology, Medical Physiology
Abstract

Gene expression levels vary across developmental stage, cell type, and region in the brain. Genomic variants also contribute to the variation in expression, and some neuropsychiatric disorder loci may exert their effects through this mechanism. To investigate these relationships, we present BrainVar, a unique resource of paired whole-genome and bulk tissue RNA sequencing from the dorsolateral prefrontal cortex of 176 individuals across prenatal and postnatal development. Here we identify common variants that alter gene expression (expression quantitative trait loci [eQTLs]) constantly across development or predominantly during prenatal or postnatal stages. Both "constant" and "temporal-predominant" eQTLs are enriched for loci associated with neuropsychiatric traits and disorders and colocalize with specific variants. Expression levels of more than 12,000 genes rise or fall in a concerted late-fetal transition, with the transitional genes enriched for cell-type-specific genes and neuropsychiatric risk loci, underscoring the importance of cataloging developmental trajectories in understanding cortical physiology and pathology.

Published
2020

74. Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

Author

Satterstrom, F Kyle, Kosmicki, Jack A, Wang, Jiebiao, Breen, Michael S, De Rubeis, Silvia, An, Joon-Yong, Peng, Minshi, Collins, Ryan, Grove, Jakob, Klei, Lambertus, Stevens, Christine, Reichert, Jennifer, Mulhern, Maureen S, Artomov, Mykyta, Gerges, Sherif, Sheppard, Brooke, Xu, Xinyi, Bhaduri, Aparna, Norman, Utku, Brand, Harrison, Schwartz, Grace, Nguyen, Rachel, Guerrero, Elizabeth E, Dias, Caroline, Consortium, Autism Sequencing, Aleksic, Branko, Anney, Richard, Barbosa, Mafalda, Bishop, Somer, Brusco, Alfredo, Bybjerg-Grauholm, Jonas, Carracedo, Angel, Chan, Marcus CY, Chiocchetti, Andreas G, Chung, Brian HY, Coon, Hilary, Cuccaro, Michael L, Curró, Aurora, Bernardina, Bernardo Dalla, Doan, Ryan, Domenici, Enrico, Dong, Shan, Fallerini, Chiara, Fernández-Prieto, Montserrat, Ferrero, Giovanni Battista, Freitag, Christine M, Fromer, Menachem, Gargus, J Jay, Geschwind, Daniel, Giorgio, Elisa, González-Peñas, Javier, Guter, Stephen, Halpern, Danielle, Hansen-Kiss, Emily, He, Xin, Herman, Gail E, Hertz-Picciotto, Irva, Hougaard, David M, Hultman, Christina M, Ionita-Laza, Iuliana, Jacob, Suma, Jamison, Jesslyn, Jugessur, Astanand, Kaartinen, Miia, Knudsen, Gun Peggy, Kolevzon, Alexander, Kushima, Itaru, Lee, So Lun, Lehtimäki, Terho, Lim, Elaine T, Lintas, Carla, Lipkin, W Ian, Lopergolo, Diego, Lopes, Fátima, Ludena, Yunin, Maciel, Patricia, Magnus, Per, Mahjani, Behrang, Maltman, Nell, Manoach, Dara S, Meiri, Gal, Menashe, Idan, Miller, Judith, Minshew, Nancy, Montenegro, Eduarda MS, Moreira, Danielle, Morrow, Eric M, Mors, Ole, Mortensen, Preben Bo, Mosconi, Matthew, Muglia, Pierandrea, Neale, Benjamin M, Nordentoft, Merete, Ozaki, Norio, Palotie, Aarno, Parellada, Mara, Passos-Bueno, Maria Rita, Pericak-Vance, Margaret, Persico, Antonio M, and Pessah, Isaac

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Brain Disorders, Mental Health, Pediatric, Human Genome, Clinical Research, Autism, Intellectual and Developmental Disabilities (IDD), Neurosciences, Aetiology, 2.1 Biological and endogenous factors, Mental health, Neurological, Autistic Disorder, Case-Control Studies, Cell Lineage, Cerebral Cortex, Cohort Studies, Exome, Female, Gene Expression Regulation, Developmental, Gene Frequency, Genetic Predisposition to Disease, Humans, Male, Mutation, Missense, Neurobiology, Neurons, Phenotype, Sex Factors, Single-Cell Analysis, Exome Sequencing, Autism Sequencing Consortium, iPSYCH-Broad Consortium, autism spectrum disorder, cell type, cytoskeleton, excitatory neurons, excitatory-inhibitory balance, exome sequencing, genetics, inhibitory neurons, liability, neurodevelopment, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

We present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n = 35,584 total samples, 11,986 with ASD). Using an enhanced analytical framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate of 0.1 or less. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained to have severe neurodevelopmental delay, whereas 53 show higher frequencies in individuals ascertained to have ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In cells from the human cortex, expression of risk genes is enriched in excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory-inhibitory imbalance underlying ASD.

Published
2020

83. Age-Stratified Seroprevalence of Respiratory Syncytial Virus: Analysis using Prefusion F and G Protein Antibodies

Author

Nham, Eliel, primary, Jang, A-Yeung, additional, Hyun, Hakjun, additional, Yoon, Jin Gu, additional, Noh, Ji Yun, additional, Cheong, Hee Jin, additional, Kim, Woo Joo, additional, Ahn, Ki Bum, additional, Ji, Hyun Jung, additional, Seo, Ho Seong, additional, Bae, Joon-Yong, additional, Park, Man-Seong, additional, and Song, Joon Young, additional

Published
2024
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87. CWAS-Plus: Estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data

Author

Kim, Yujin, primary, Jeong, Minwoo, additional, Koh, In Gyeong, additional, Kim, Chanhee, additional, Lee, Hyeji, additional, Kim, Jae Hyun, additional, Yurko, Ronald, additional, Kim, Il Bin, additional, Park, Jeongbin, additional, Werling, Donna M., additional, Sanders, Stephan J., additional, and An, Joon-Yong, additional

Published
2024
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91. Transcriptome and epigenome landscape of human cortical development modeled in organoids

Author

Amiri, Anahita, Coppola, Gianfilippo, Scuderi, Soraya, Wu, Feinan, Roychowdhury, Tanmoy, Liu, Fuchen, Pochareddy, Sirisha, Shin, Yurae, Safi, Alexias, Song, Lingyun, Zhu, Ying, Sousa, André MM, Gerstein, Mark, Crawford, Gregory E, Sestan, Nenad, Abyzov, Alexej, Vaccarino, Flora M, Akbarian, Schahram, An, Joon-Yong, Armoskus, Christoper, Ashley-Koch, Allison E, Beach, Thomas G, Belmont, Judson, Bendl, Jaroslav, Borrman, Tyler, Brown, Leanne, Brown, Miguel, Brown, Mimi, Brunetti, Tonya, Bryois, Julien, Burke, Emily E, Camarena, Adrian, Carlyle, Becky C, Chae, Yooree, Charney, Alexander W, Chen, Chao, Cheng, Lijun, Cherskov, Adriana, Choi, Jinmyung, Clarke, Declan, Collado-Torres, Leonardo, Dai, Rujia, De La Torre Ubieta, Luis, DelValle, Diane, Devillers, Olivia, Dracheva, Stella, Emani, Prashant S, Evgrafov, Oleg V, Farnham, Peggy J, Fitzgerald, Dominic, Flatow, Elie, Francoeur, Nancy, Fullard, John F, Gandal, Michael J, Gao, Tianliuyun, Garrett, Melanie E, Geschwind, Daniel H, Giase, Gina, Girdhar, Kiran, Giusti-Rodriguez, Paola, Goes, Fernando S, Goodman, Thomas, Grennan, Kay S, Gu, Mengting, Gürsoy, Gamze, Hadjimichael, Evi, Hahn, Chang-Gyu, Haroutunian, Vahram, Hauberg, Mads E, Hoffman, Gabriel E, Huey, Jack, Hyde, Thomas M, Ivanov, Nikolay A, Jacobov, Rivka, Jaffe, Andrew E, Jiang, Yan, Jiang, Yi, Johnson, Graham D, Kassim, Bibi S, Kefi, Amira, Kim, Yunjung, Kitchen, Robert R, Kleiman, Joel E, Knowles, James A, Kozlenkov, Alexey, Li, Mingfeng, Li, Zhen, Lipska, Barbara K, Liu, Chunyu, Liu, Shuang, Mangravite, Lara M, Mariani, Jessica, Mattei, Eugenio, Miller, Daniel J, Moore, Jill, Nairn, Angus C, Navarro, Fabio CP, Park, Royce B, Peters, Mette A, and Pinto, Dalila

Subjects
Stem Cell Research - Nonembryonic - Human, Stem Cell Research - Embryonic - Human, Stem Cell Research - Induced Pluripotent Stem Cell - Human, Stem Cell Research, Genetics, Stem Cell Research - Induced Pluripotent Stem Cell, Human Genome, Intellectual and Developmental Disabilities (IDD), Autism, Brain Disorders, Biotechnology, Clinical Research, Mental Health, Pediatric, Neurosciences, 2.1 Biological and endogenous factors, Underpinning research, Aetiology, 1.1 Normal biological development and functioning, Neurological, Cerebral Cortex, Enhancer Elements, Genetic, Epigenesis, Genetic, Gene Expression Regulation, Developmental, Humans, Induced Pluripotent Stem Cells, Models, Neurological, Neurogenesis, Organoids, Transcriptome, PsychENCODE Consortium, General Science & Technology
Abstract

Genes implicated in neuropsychiatric disorders are active in human fetal brain, yet difficult to study in a longitudinal fashion. We demonstrate that organoids from human pluripotent cells model cerebral cortical development on the molecular level before 16 weeks postconception. A multiomics analysis revealed differentially active genes and enhancers, with the greatest changes occurring at the transition from stem cells to progenitors. Networks of converging gene and enhancer modules were assembled into six and four global patterns of expression and activity across time. A pattern with progressive down-regulation was enriched with human-gained enhancers, suggesting their importance in early human brain development. A few convergent gene and enhancer modules were enriched in autism-associated genes and genomic variants in autistic children. The organoid model helps identify functional elements that may drive disease onset.

Published
2018

92. Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

Author

An, Joon-Yong, Lin, Kevin, Zhu, Lingxue, Werling, Donna M, Dong, Shan, Brand, Harrison, Wang, Harold Z, Zhao, Xuefang, Schwartz, Grace B, Collins, Ryan L, Currall, Benjamin B, Dastmalchi, Claudia, Dea, Jeanselle, Duhn, Clif, Gilson, Michael C, Klei, Lambertus, Liang, Lindsay, Markenscoff-Papadimitriou, Eirene, Pochareddy, Sirisha, Ahituv, Nadav, Buxbaum, Joseph D, Coon, Hilary, Daly, Mark J, Kim, Young Shin, Marth, Gabor T, Neale, Benjamin M, Quinlan, Aaron R, Rubenstein, John L, Sestan, Nenad, State, Matthew W, Willsey, A Jeremy, Talkowski, Michael E, Devlin, Bernie, Roeder, Kathryn, and Sanders, Stephan J

Subjects
Human Genome, Genetics, Biotechnology, Intellectual and Developmental Disabilities (IDD), Mental Health, Brain Disorders, Autism, Pediatric, 2.1 Biological and endogenous factors, Aetiology, Mental health, Autism Spectrum Disorder, Binding Sites, Conserved Sequence, DNA Mutational Analysis, Genetic Loci, Genetic Variation, Humans, Mutation, Pedigree, Promoter Regions, Genetic, Risk, Transcription Factors, General Science & Technology
Abstract

Whole-genome sequencing (WGS) has facilitated the first genome-wide evaluations of the contribution of de novo noncoding mutations to complex disorders. Using WGS, we identified 255,106 de novo mutations among sample genomes from members of 1902 quartet families in which one child, but not a sibling or their parents, was affected by autism spectrum disorder (ASD). In contrast to coding mutations, no noncoding functional annotation category, analyzed in isolation, was significantly associated with ASD. Casting noncoding variation in the context of a de novo risk score across multiple annotation categories, however, did demonstrate association with mutations localized to promoter regions. We found that the strongest driver of this promoter signal emanates from evolutionarily conserved transcription factor binding sites distal to the transcription start site. These data suggest that de novo mutations in promoter regions, characterized by evolutionary and functional signatures, contribute to ASD.

Published
2018

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