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Mol. Cells 2013; 35(6): 498-513

Published online May 10, 2013

https://doi.org/10.1007/s10059-013-2349-y

© The Korean Society for Molecular and Cellular Biology

Genome-Wide Profiling of In Vivo LPS-Responsive Genes in Splenic Myeloid Cells

Myeong Sup Lee, Byungil Kim, Sun-Min Lee, Woo-Cheul Cho, Wook-Bin Lee, Ji-Seon Kang, Un Yung Choi, Jaemyun Lyu, and Young-Joon Kim

1Department of Biochemistry, College of Life Science and Biotechnology, 2Department of Integrated OMICS for Biomedical Sciences, World Class University, Yonsei University, Seoul 120-749, Korea

Received: December 28, 2013; Revised: April 9, 2013; Accepted: April 12, 2013

Abstract

Lipopolysaccharide (LPS), the major causative agent of bacterial sepsis, has been used by many laboratories in genome-wide expression profiling of the LPS response. However, these studies have predominantly used in vitro cultured macrophages (Macs), which may not accurately reflect the LPS response of these innate immune cells in vivo. To overcome this limitation and to identify inflammatory genes in vivo, we have profiled genome-wide expression patterns in non-lymphoid, splenic myeloid cells extracted directly from LPS-treated mice. Genes encoding factors known to be involved in mediating or regulating inflammatory processes, such as cytokines and chemokines, as well as many genes whose immunological functions are not well known, were strongly induced by LPS
after 3 h or 8 h of treatment. Most of the highly LPSresponsive genes that we randomly selected from the microarray data were independently confirmed by quantitative RT-PCR, implying that our microarray data are quite reliable. When our in vivo data were compared to previously reported microarray data for in vitro LPS-treated Macs, a significant proportion (~20%) of the in vivo LPSresponsive genes defined in this study were specific to cells exposed to LPS in vivo, but a larger proportion of them (~60%) were influenced by LPS in both in vitro and in vivo settings. This result indicates that our in vivo LPSresponsive gene set includes not only previously identified in vitro LPS-responsive genes but also novel LPSresponsive genes. Both types of genes would be a valuable
resource in the future for understanding inflammatory responses in vivo.

Keywords in vivo, LPS, microarray, splenic myeloid cells

Article

Research Article

Mol. Cells 2013; 35(6): 498-513

Published online June 30, 2013 https://doi.org/10.1007/s10059-013-2349-y

Copyright © The Korean Society for Molecular and Cellular Biology.

Genome-Wide Profiling of In Vivo LPS-Responsive Genes in Splenic Myeloid Cells

Myeong Sup Lee, Byungil Kim, Sun-Min Lee, Woo-Cheul Cho, Wook-Bin Lee, Ji-Seon Kang, Un Yung Choi, Jaemyun Lyu, and Young-Joon Kim

1Department of Biochemistry, College of Life Science and Biotechnology, 2Department of Integrated OMICS for Biomedical Sciences, World Class University, Yonsei University, Seoul 120-749, Korea

Received: December 28, 2013; Revised: April 9, 2013; Accepted: April 12, 2013

Abstract

Lipopolysaccharide (LPS), the major causative agent of bacterial sepsis, has been used by many laboratories in genome-wide expression profiling of the LPS response. However, these studies have predominantly used in vitro cultured macrophages (Macs), which may not accurately reflect the LPS response of these innate immune cells in vivo. To overcome this limitation and to identify inflammatory genes in vivo, we have profiled genome-wide expression patterns in non-lymphoid, splenic myeloid cells extracted directly from LPS-treated mice. Genes encoding factors known to be involved in mediating or regulating inflammatory processes, such as cytokines and chemokines, as well as many genes whose immunological functions are not well known, were strongly induced by LPS
after 3 h or 8 h of treatment. Most of the highly LPSresponsive genes that we randomly selected from the microarray data were independently confirmed by quantitative RT-PCR, implying that our microarray data are quite reliable. When our in vivo data were compared to previously reported microarray data for in vitro LPS-treated Macs, a significant proportion (~20%) of the in vivo LPSresponsive genes defined in this study were specific to cells exposed to LPS in vivo, but a larger proportion of them (~60%) were influenced by LPS in both in vitro and in vivo settings. This result indicates that our in vivo LPSresponsive gene set includes not only previously identified in vitro LPS-responsive genes but also novel LPSresponsive genes. Both types of genes would be a valuable
resource in the future for understanding inflammatory responses in vivo.

Keywords: in vivo, LPS, microarray, splenic myeloid cells

Mol. Cells
May 31, 2023 Vol.46 No.5, pp. 259~328
COVER PICTURE
The alpha-helices in the lamin filaments are depicted as coils, with different subdomains distinguished by various colors. Coil 1a is represented by magenta, coil 1b by yellow, L2 by green, coil 2a by white, coil 2b by brown, stutter by cyan, coil 2c by dark blue, and the lamin Ig-like domain by grey. In the background, cells are displayed, with the cytosol depicted in green and the nucleus in blue (Ahn et al., pp. 309-318).

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