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288 results on '"Shin, Seung Won"'

2. Disease-associated astrocyte epigenetic memory promotes CNS pathology

Author

Lee, Hong-Gyun, Rone, Joseph M., Li, Zhaorong, Akl, Camilo Faust, Shin, Seung Won, Lee, Joon-Hyuk, Flausino, Lucas E., Pernin, Florian, Chao, Chun-Cheih, Kleemann, Kilian L., Srun, Lena, Illouz, Tomer, Giovannoni, Federico, Charabati, Marc, Sanmarco, Liliana M., Kenison, Jessica E., Piester, Gavin, Zandee, Stephanie E. J., Antel, Jack P., Rothhammer, Veit, Wheeler, Michael A., Prat, Alexandre, Clark, Iain C., and Quintana, Francisco J.

Published
2024
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3. Identification of astrocyte regulators by nucleic acid cytometry

Author

Clark, Iain C, Wheeler, Michael A, Lee, Hong-Gyun, Li, Zhaorong, Sanmarco, Liliana M, Thaploo, Shravan, Polonio, Carolina M, Shin, Seung Won, Scalisi, Giulia, Henry, Amy R, Rone, Joseph M, Giovannoni, Federico, Charabati, Marc, Akl, Camilo Faust, Aleman, Dulce M, Zandee, Stephanie EJ, Prat, Alexandre, Douek, Daniel C, Boritz, Eli A, Quintana, Francisco J, and Abate, Adam R

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Genetics, Neurodegenerative, Autoimmune Disease, Brain Disorders, Multiple Sclerosis, Neurosciences, Human Genome, Biotechnology, Aetiology, 2.1 Biological and endogenous factors, Neurological, Inflammatory and immune system, Animals, Humans, Mice, Astrocytes, Encephalomyelitis, Autoimmune, Experimental, Gene Expression Regulation, Mice, Knockout, Microfluidics, Single-Cell Gene Expression Analysis, Nucleic Acids, Gene Editing, General Science & Technology
Abstract

Multiple sclerosis is a chronic inflammatory disease of the central nervous system1. Astrocytes are heterogeneous glial cells that are resident in the central nervous system and participate in the pathogenesis of multiple sclerosis and its model experimental autoimmune encephalomyelitis2,3. However, few unique surface markers are available for the isolation of astrocyte subsets, preventing their analysis and the identification of candidate therapeutic targets; these limitations are further amplified by the rarity of pathogenic astrocytes. Here, to address these challenges, we developed focused interrogation of cells by nucleic acid detection and sequencing (FIND-seq), a high-throughput microfluidic cytometry method that combines encapsulation of cells in droplets, PCR-based detection of target nucleic acids and droplet sorting to enable in-depth transcriptomic analyses of cells of interest at single-cell resolution. We applied FIND-seq to study the regulation of astrocytes characterized by the splicing-driven activation of the transcription factor XBP1, which promotes disease pathology in multiple sclerosis and experimental autoimmune encephalomyelitis4. Using FIND-seq in combination with conditional-knockout mice, in vivo CRISPR-Cas9-driven genetic perturbation studies and bulk and single-cell RNA sequencing analyses of samples from mouse experimental autoimmune encephalomyelitis and humans with multiple sclerosis, we identified a new role for the nuclear receptor NR3C2 and its corepressor NCOR2 in limiting XBP1-driven pathogenic astrocyte responses. In summary, we used FIND-seq to identify a therapeutically targetable mechanism that limits XBP1-driven pathogenic astrocyte responses. FIND-seq enables the investigation of previously inaccessible cells, including rare cell subsets defined by unique gene expression signatures or other nucleic acid markers.

Published
2023

4. Author Correction: Disease-associated astrocyte epigenetic memory promotes CNS pathology

Author

Lee, Hong-Gyun, Rone, Joseph M., Li, Zhaorong, Akl, Camilo Faust, Shin, Seung Won, Lee, Joon-Hyuk, Flausino, Lucas E., Pernin, Florian, Chao, Chun-Cheih, Kleemann, Kilian L., Srun, Lena, Illouz, Tomer, Giovannoni, Federico, Charabati, Marc, Sanmarco, Liliana M., Kenison, Jessica E., Piester, Gavin, Zandee, Stephanie E. J., Antel, Jack P., Rothhammer, Veit, Wheeler, Michael A., Prat, Alexandre, Clark, Iain C., and Quintana, Francisco J.

Published
2024
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9. Disease-associated astrocyte epigenetic memory promotes CNS pathology

Author

Lee, Hong-Gyun, primary, Rone, Joseph M., additional, Li, Zhaorong, additional, Faust Akl, Camilo, additional, Shin, Seung Won, additional, Lee, Joon-Hyuk, additional, Flausino, Lucas E., additional, Pernin, Florian, additional, Chao, Chun-Cheih, additional, Kleemann, Kilian L., additional, Srun, Lena, additional, Illouz, Tomer, additional, Giovannoni, Federico, additional, Charabati, Marc, additional, Sanmarco, Liliana M., additional, Kenison, Jessica E., additional, Piester, Gavin, additional, Zandee, Stephanie E. J., additional, Antel, Jack, additional, Rothhammer, Veit, additional, Wheeler, Michael A., additional, Prat, Alexandre, additional, Clark, Iain C., additional, and Quintana, Francisco J., additional

Published
2024
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11. FIND-seq: high-throughput nucleic acid cytometry for rare single-cell transcriptomics

Author

Shin, Seung Won, Mudvari, Prakriti, Thaploo, Shravan, Wheeler, Michael A., Douek, Daniel C., Quintana, Francisco J., Boritz, Eli A., Abate, Adam R., and Clark, Iain C.

Abstract

Rare cells have an important role in development and disease, and methods for isolating and studying cell subsets are therefore an essential part of biology research. Such methods traditionally rely on labeled antibodies targeted to cell surface proteins, but large public databases and sophisticated computational approaches increasingly define cell subsets on the basis of genomic, epigenomic and transcriptomic sequencing data. Methods for isolating cells on the basis of nucleic acid sequences powerfully complement these approaches by providing experimental access to cell subsets discovered in cell atlases, as well as those that cannot be otherwise isolated, including cells infected with pathogens, with specific DNA mutations or with unique transcriptional or splicing signatures. We recently developed a nucleic acid cytometry platform called ‘focused interrogation of cells by nucleic acid detection and sequencing’ (FIND-seq), capable of isolating rare cells on the basis of RNA or DNA markers, followed by bulk or single-cell transcriptomic analysis. This platform has previously been used to characterize the splicing-dependent activation of the transcription factor XBP1 in astrocytes and HIV persistence in memory CD4 T cells from people on long-term antiretroviral therapy. Here, we outline the molecular and microfluidic steps involved in performing FIND-seq, including protocol updates that allow detection and whole transcriptome sequencing of rare HIV-infected cells that harbor genetically intact virus genomes. FIND-seq requires knowledge of microfluidics, optics and molecular biology. We expect that FIND-seq, and this comprehensive protocol, will enable mechanistic studies of rare HIV+cells, as well as other cell subsets that were previously difficult to recover and sequence.

Published
2024
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16. Detecting Facial Features by Heteroassociative Memory Neural Network Utilizing Facial Statistics

Author

Kim, Kyeong-Seop, Yoon, Tae-Ho, Shin, Seung-Won, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Wang, Jun, editor, Yi, Zhang, editor, Zurada, Jacek M., editor, Lu, Bao-Liang, editor, and Yin, Hujun, editor

Published
2006
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17. LSAD: Lightweight SYN Flooding Attack Detector

Author

Shin, Seung-won, Kim, Ki-young, Jang, Jong-soo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Ghosh, R. K., editor, and Mohanty, Hrushikesha, editor

Published
2005
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19. QS-Ware: The Middleware for Providing QoS and Secure Ability to Web Server

Author

Shin, Seung-won, Baik, Kwang-ho, Kim, Ki-young, Jang, Jong-soo, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Laganá, Antonio, editor, Gavrilova, Marina L., editor, Kumar, Vipin, editor, Mun, Youngsong, editor, Tan, C. J. Kenneth, editor, and Gervasi, Osvaldo, editor

Published
2004
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