Analysis of the TGFβ-induced program in primary airway epithelial cells shows essential role of NF-κB/RelA signaling network in type II epithelial mesenchymal transition

BMC Genomics

Allan R. Brasier⁴  Bruce A. Luxon³  Thomas G. Wood⁵  Fanping Kong³  Mala Sinha³  Andrzej Kudlicki⁵  Bryant Dang⁴  Suresh K. Bhavnani⁴  Jun Yang¹  Steven G. Widen²  Mridul Kalita¹  Xueling Li⁵  Bing Tian² 

[1]Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA

[2]Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA

[3]Bioinformatics Program, UTMB, Galveston, TX, USA

[4]Institute for Translational Sciences, UTMB, Galveston, TX, USA

[5]Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA

关键词: Transcription factor enrichment;    Generalized linear modeling;    RNA-Seq;    Nuclear factor κB;    Transforming growth factor β;    Epithelial mesenchymal transition;   

Others  :  1220318
DOI  :  10.1186/s12864-015-1707-x

 received in 2014-09-12, accepted in 2015-06-17,  发布年份 2015

【 摘 要 】

Background

The airway epithelial cell plays a central role in coordinating the pulmonary response to injury and inflammation. Here, transforming growth factor-β (TGFβ) activates gene expression programs to induce stem cell-like properties, inhibit expression of differentiated epithelial adhesion proteins and express mesenchymal contractile proteins. This process is known as epithelial mesenchymal transition (EMT); although much is known about the role of EMT in cellular metastasis in an oncogene-transformed cell, less is known about Type II EMT, that occurring in normal epithelial cells. In this study, we applied next generation sequencing (RNA-Seq) in primary human airway epithelial cells to understand the gene program controlling Type II EMT and how cytokine-induced inflammation modifies it.

Results

Generalized linear modeling was performed on a two-factor RNA-Seq experiment of 6 treatments of telomerase immortalized human small airway epithelial cells (3 replicates). Using a stringent cut-off, we identified 3,478 differentially expressed genes (DEGs) in response to EMT. Unbiased transcription factor enrichment analysis identified three clusters of EMT regulators, one including SMADs/TP63 and another NF-κB/RelA. Surprisingly, we also observed 527 of the EMT DEGs were also regulated by the TNF-NF-κB/RelA pathway. This Type II EMT program was compared to Type III EMT in TGFβ stimulated A549 alveolar lung cancer cells, revealing significant functional differences. Moreover, we observe that Type II EMT modifies the outcome of the TNF program, reducing IFN signaling and enhancing integrin signaling. We confirmed experimentally that TGFβ-induced the NF-κB/RelA pathway by observing a 2-fold change in NF-κB/RelA nuclear translocation. A small molecule IKK inhibitor blocked TGFβ-induced core transcription factor (SNAIL1, ZEB1 and Twist1) and mesenchymal gene (FN1 and VIM) expression.

Conclusions

These data indicate that NF-κB/RelA controls a SMAD-independent gene network whose regulation is required for initiation of Type II EMT. Type II EMT dramatically affects the induction and kinetics of TNF-dependent gene networks.

【 授权许可】

   
2015 Tian et al.

【 图 表 】

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