DOI: 10.5061/dryad.gf1vhhn06
title: Data from: High-throughput mRNA sequencing-based DEGs: HNF4A mitigates sepsis-associated lung injury by upregulating NCOR2/GR/STAB1 axis and promoting macrophage polarization towards M2 phenotype

description: Sepsis can trigger systemic inflammation and lead
 to detrimental effects on several organs, with particular
 emphasis on the lungs. In sepsis-associated lung injury, macrophages
 assume a pivotal role, as their overactivation could facilitate the
 secretion of inflammatory factors and the imbalance of
 polarization. Hepatocyte nuclear factor 4 alpha (HNF4A) has been
 reported its potential involvement in the regulation of
 inflammatory response and macrophage polarization. This
 study discusses the role and mechanism of HNF4A in
 sepsis-induced lung damage. HNF4A exhibits a decrease in
 expression by analyzing the differentially expressed
 genes in the lungs of septic mice from the Gene
 Expression Omnibus dataset GSE15379. Then, we established a mouse
 sepsis model through a cecal ligation and
 puncture method, and observed that the expression of
 HNF4A was reduced in both lung tissues and alveolar macrophages. To
 evaluate the function of HNF4A, we overexpressed HNF4A mediated by
 adenovirus vectors, which were injected into mice. We found that HNF4A
 overexpression resulted in a higher survival rate in
 septic mice and an amelioration of pulmonary
 damage. Meanwhile, HNF4A overexpression mitigated the
 infiltration of inflammatory cells and impeded the M1
 polarization but facilitated the M2 polarization of
 macrophages in the lung tissues or the alveolar lavage
 fluid. In vitro, we treated bone marrow-derived
 macrophages with interleukin-4. Consistent results were obtained
 that HNF4A overexpression promoted the M2 polarization of macrophages.
 Mechanistically, we found that HNF4A transcriptionally regulate
 the expression of nuclear receptor coactivator 2 (NCOA2) through
 binding to its promoter
 region. NCOA2 interacted with glucocorticoid
 receptor (GR). Stabilin 1 (STAB1) was selected as a possible
 target by transcriptome sequencing analysis. Functional
 experiments confirmed STAB1 as a downstream target of the
 HNF4A/NCOA2/GR axis. Overall, this research investigated
 the potential impact of HNF4A on pulmonary injury in sepsis. It
 is suggested that one of the regulatory mechanisms involved in
 this association may be the NCOR2/GR/STAB1 axis.
description: # High-throughput mRNA sequencing-based DEGs: HNF4A mitigates
 sepsis-associated lung injury by upregulating NCOR2/GR/STAB1 axis and
 promoting macrophage polarization towards M2 phenotype **Introduction**
 This dataset includes information on high-throughput mRNA sequencing-based
 DEGs in the article “HNF4A mitigates sepsis-associated lung injury by
 upregulating NCOR2/GR/STAB1 axis and promoting macrophage polarization
 towards M2 phenotype”. **File list** IL-4 + Ad-HNF4A + Dex +
 Ad-shNCOA2_vs_shNCIL-4 + Ad-HNF4A + Dex +
 Ad-shNCOA2.Differentially_Expressed_Genes, in xlsx format. **Author
 Information** Name: Yu-Hang Yang Institution: Shengjing Hospital of China
 Medical University, Shenyang, China Co-investigator 1 Name: Ri Wen
 Institution: Shengjing Hospital of China Medical University, Shenyang,
 China Co-investigator 2 Name: Xin-Mei Huang Institution: Shanghai Fifth
 People’s Hospital, Fudan University, Shanghai, China Co-investigator 3
 Name: Tao Zhang Institution: Shengjing Hospital of China Medical
 University, Shenyang, China Co-investigator 4 Name: Ni Yang Institution:
 Shengjing Hospital of China Medical University, Shenyang, China
 Co-investigator 5 Name: Chun-Feng Liu Institution: Shengjing Hospital of
 China Medical University, Shenyang, China Corresponding author Name: Dr.
 Tie-Ning Zhang Institution: Shengjing Hospital of China Medical
 University, Shenyang, China **Description of the data and file structure**
 The variables of the data file includes: ESEMBL id
 (https://asia.ensembl.org/index.html) of the genes followed by the gene
 symbol, description of the gene, gene expression expressed in log2fold
 change. The data presented in this dataset provides information of the
 high-throughput mRNA sequencing-based DEGs in article “HNF4A mitigates
 sepsis-associated lung injury by upregulating NCOR2/GR/STAB1 axis and
 promoting macrophage polarization towards M2 phenotype”. Briefly, Bone
 marrow-derived macrophages (BMDMs) were cultured in the medium containing
 Ad-NC or Ad-HNF4A for 48h. Cells were treated with IL-4 for 24 h to induce
 M2 polarization. The 100 nM dexamethasone (Dex) was added to activate the
 GR pathway. shNCOA2 and shGR were synthesized to knock down the expression
 of NCOA2 and GR by adenovirus delivery to infected macrophages. Total RNA
 was extracted from cells using Trizol. mRNA was subsequently purified from
 the total RNA utilizing poly-T oligo-attached magnetic beads. Sequencing
 libraries were constructed employing the NEBNext Ultra RNA Library Prep
 Kit for Illumina, in accordance with the manufacturer's
 recommendations. The original fluorescence image files obtained from the
 Illumina platform were converted into short reads through base calling,
 and these short reads were recorded in FASTQ format. Fastp was utilized to
 conduct basic statistical analysis on the quality of the raw reads. The
 differentially expressed genes (DEGs) were screened as log2FC &gt; 1 or
 log2FC &lt; -1, and adj.p &lt; 0.05.The column heading “symbol” indicates
 the name of DEGs. Missing data mentioned as n/a. **Acknowledgments** This
 work was supported by the National Natural Science Foundation of China
 (82102254 to Tie-Ning Zhang, and 81971810 to Chun-Feng Liu), Liaoning
 Province Science and Technology Major Special Project (No.2020JH1/10300001
 to Chun-Feng Liu), and 345 Talent Program of Shengjing Hospital of China
 Medical University (M1308 to Tie-Ning Zhang and M1404 to Ni Yang).