Whole transcriptome analysis of myeloid dendritic cells reveals distinct genetic regulation in patients with allergies

Kijeong Lee; Mi Ryung Han; Ji Woo Yeon; Byoungjae Kim; Tae Hoon Kim

doi:10.3390/ijms21228640

Whole transcriptome analysis of myeloid dendritic cells reveals distinct genetic regulation in patients with allergies

Kijeong Lee, Mi Ryung Han, Ji Woo Yeon, Byoungjae Kim, Tae Hoon Kim

Department of Biomedical Sciences

Research output: Contribution to journal › Article › peer-review

10 Citations (Scopus)

Abstract

Dendritic cells (DCs) play critical roles in atopic diseases, orchestrating both innate and adaptive immune systems. Nevertheless, limited information is available regarding the mechanism through which DCs induce hyperresponsiveness in patients with allergies. This study aims to reveal novel genetic alterations and future therapeutic target molecules in the DCs from patients with allergies using whole transcriptome sequencing. Transcriptome sequencing of human BDCA-3+/CD11c+ DCs sorted from peripheral blood monocytes obtained from six patients with allergies and four healthy controls was conducted. Gene expression profile data were analyzed, and an ingenuity pathway analysis was performed. A total of 1638 differentially expressed genes were identified at p-values < 0.05, with 11 genes showing a log2-fold change ≥1.5. The top gene network was associated with cell death/survival and organismal injury/abnormality. In validation experiments, amphiregulin (AREG) showed consistent results with transcriptome sequencing data, with increased mRNA expression in THP-1-derived DCs after Der p 1 stimulation and higher protein expression in myeloid DCs obtained from patients with allergies. This study suggests an alteration in the expression of DCs in patients with allergies, proposing related altered functions and intracellular mechanisms. Notably, AREG might play a crucial role in DCs by inducing the Th2 immune response.

Original language	English
Article number	8640
Pages (from-to)	1-16
Number of pages	16
Journal	International journal of molecular sciences
Volume	21
Issue number	22
DOIs	https://doi.org/10.3390/ijms21228640
Publication status	Published - 2020 Nov 2

Bibliographical note

Funding Information:
Funding: This research was supported by the Basic Science Research Program, National Research Foundation of Korea, funded by the Ministry of Science and Technology and the Ministry of Science, ICT & Future Planning (2017R1A2B2003575, NRF-2020R1A2C1006398), the Ministry of Science and ICT (2020R1C1C1012288), Korea, under the ICT Creative Consilience program(IITP-2020-0018190011001) supervised by the IITP (Institute for Information & Communications Technology Planning & Evaluation, and the Korea Health Technology R&D Project (HI17C0387), Korea Health Industry Development Institute (KHIDI), and the Ministry of Health & Welfare. This research was also supported by a Korea University grant and a grant from Korea University Medical Center and Anam Hospital, Seoul, Korea.

Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

Allergic rhinitis
Allergy
Amphiregulin
Dendritic cells
Gene networks
RNA sequencing
Transcriptome sequencing

ASJC Scopus subject areas

Catalysis
Molecular Biology
Spectroscopy
Computer Science Applications
Physical and Theoretical Chemistry
Organic Chemistry
Inorganic Chemistry

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.3390/ijms21228640

Cite this

@article{849cecc6cafe45e49ffb14cc09460506,

title = "Whole transcriptome analysis of myeloid dendritic cells reveals distinct genetic regulation in patients with allergies",

abstract = "Dendritic cells (DCs) play critical roles in atopic diseases, orchestrating both innate and adaptive immune systems. Nevertheless, limited information is available regarding the mechanism through which DCs induce hyperresponsiveness in patients with allergies. This study aims to reveal novel genetic alterations and future therapeutic target molecules in the DCs from patients with allergies using whole transcriptome sequencing. Transcriptome sequencing of human BDCA-3+/CD11c+ DCs sorted from peripheral blood monocytes obtained from six patients with allergies and four healthy controls was conducted. Gene expression profile data were analyzed, and an ingenuity pathway analysis was performed. A total of 1638 differentially expressed genes were identified at p-values < 0.05, with 11 genes showing a log2-fold change ≥1.5. The top gene network was associated with cell death/survival and organismal injury/abnormality. In validation experiments, amphiregulin (AREG) showed consistent results with transcriptome sequencing data, with increased mRNA expression in THP-1-derived DCs after Der p 1 stimulation and higher protein expression in myeloid DCs obtained from patients with allergies. This study suggests an alteration in the expression of DCs in patients with allergies, proposing related altered functions and intracellular mechanisms. Notably, AREG might play a crucial role in DCs by inducing the Th2 immune response.",

keywords = "Allergic rhinitis, Allergy, Amphiregulin, Dendritic cells, Gene networks, RNA sequencing, Transcriptome sequencing",

author = "Kijeong Lee and Han, {Mi Ryung} and Yeon, {Ji Woo} and Byoungjae Kim and Kim, {Tae Hoon}",

note = "Funding Information: Funding: This research was supported by the Basic Science Research Program, National Research Foundation of Korea, funded by the Ministry of Science and Technology and the Ministry of Science, ICT & Future Planning (2017R1A2B2003575, NRF-2020R1A2C1006398), the Ministry of Science and ICT (2020R1C1C1012288), Korea, under the ICT Creative Consilience program(IITP-2020-0018190011001) supervised by the IITP (Institute for Information & Communications Technology Planning & Evaluation, and the Korea Health Technology R&D Project (HI17C0387), Korea Health Industry Development Institute (KHIDI), and the Ministry of Health & Welfare. This research was also supported by a Korea University grant and a grant from Korea University Medical Center and Anam Hospital, Seoul, Korea. Publisher Copyright: {\textcopyright} 2020 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2020",

month = nov,

day = "2",

doi = "10.3390/ijms21228640",

language = "English",

volume = "21",

pages = "1--16",

journal = "International journal of molecular sciences",

issn = "1661-6596",

publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

number = "22",

}

TY - JOUR

T1 - Whole transcriptome analysis of myeloid dendritic cells reveals distinct genetic regulation in patients with allergies

AU - Lee, Kijeong

AU - Han, Mi Ryung

AU - Yeon, Ji Woo

AU - Kim, Byoungjae

AU - Kim, Tae Hoon

N1 - Funding Information: Funding: This research was supported by the Basic Science Research Program, National Research Foundation of Korea, funded by the Ministry of Science and Technology and the Ministry of Science, ICT & Future Planning (2017R1A2B2003575, NRF-2020R1A2C1006398), the Ministry of Science and ICT (2020R1C1C1012288), Korea, under the ICT Creative Consilience program(IITP-2020-0018190011001) supervised by the IITP (Institute for Information & Communications Technology Planning & Evaluation, and the Korea Health Technology R&D Project (HI17C0387), Korea Health Industry Development Institute (KHIDI), and the Ministry of Health & Welfare. This research was also supported by a Korea University grant and a grant from Korea University Medical Center and Anam Hospital, Seoul, Korea. Publisher Copyright: © 2020 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2020/11/2

Y1 - 2020/11/2

N2 - Dendritic cells (DCs) play critical roles in atopic diseases, orchestrating both innate and adaptive immune systems. Nevertheless, limited information is available regarding the mechanism through which DCs induce hyperresponsiveness in patients with allergies. This study aims to reveal novel genetic alterations and future therapeutic target molecules in the DCs from patients with allergies using whole transcriptome sequencing. Transcriptome sequencing of human BDCA-3+/CD11c+ DCs sorted from peripheral blood monocytes obtained from six patients with allergies and four healthy controls was conducted. Gene expression profile data were analyzed, and an ingenuity pathway analysis was performed. A total of 1638 differentially expressed genes were identified at p-values < 0.05, with 11 genes showing a log2-fold change ≥1.5. The top gene network was associated with cell death/survival and organismal injury/abnormality. In validation experiments, amphiregulin (AREG) showed consistent results with transcriptome sequencing data, with increased mRNA expression in THP-1-derived DCs after Der p 1 stimulation and higher protein expression in myeloid DCs obtained from patients with allergies. This study suggests an alteration in the expression of DCs in patients with allergies, proposing related altered functions and intracellular mechanisms. Notably, AREG might play a crucial role in DCs by inducing the Th2 immune response.

AB - Dendritic cells (DCs) play critical roles in atopic diseases, orchestrating both innate and adaptive immune systems. Nevertheless, limited information is available regarding the mechanism through which DCs induce hyperresponsiveness in patients with allergies. This study aims to reveal novel genetic alterations and future therapeutic target molecules in the DCs from patients with allergies using whole transcriptome sequencing. Transcriptome sequencing of human BDCA-3+/CD11c+ DCs sorted from peripheral blood monocytes obtained from six patients with allergies and four healthy controls was conducted. Gene expression profile data were analyzed, and an ingenuity pathway analysis was performed. A total of 1638 differentially expressed genes were identified at p-values < 0.05, with 11 genes showing a log2-fold change ≥1.5. The top gene network was associated with cell death/survival and organismal injury/abnormality. In validation experiments, amphiregulin (AREG) showed consistent results with transcriptome sequencing data, with increased mRNA expression in THP-1-derived DCs after Der p 1 stimulation and higher protein expression in myeloid DCs obtained from patients with allergies. This study suggests an alteration in the expression of DCs in patients with allergies, proposing related altered functions and intracellular mechanisms. Notably, AREG might play a crucial role in DCs by inducing the Th2 immune response.

KW - Allergic rhinitis

KW - Allergy

KW - Amphiregulin

KW - Dendritic cells

KW - Gene networks

KW - RNA sequencing

KW - Transcriptome sequencing

UR - http://www.scopus.com/inward/record.url?scp=85096125082&partnerID=8YFLogxK

U2 - 10.3390/ijms21228640

DO - 10.3390/ijms21228640

M3 - Article

C2 - 33207814

AN - SCOPUS:85096125082

SN - 1661-6596

VL - 21

SP - 1

EP - 16

JO - International journal of molecular sciences

JF - International journal of molecular sciences

IS - 22

M1 - 8640

ER -

Whole transcriptome analysis of myeloid dendritic cells reveals distinct genetic regulation in patients with allergies

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this