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

Bing Tian, Xueling Li, Mridul Kalita, Steven Widen, Jun Yang, Suresh Bhavnani, Bryant Dang, Andrzej Kudlicki, Mala Sinha, Fanping Kong, Thomas Wood, Bruce A. Luxon, Allan R. Brasier

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number529
JournalBMC Genomics
Volume16
Issue number1
DOIs
StatePublished - Jul 18 2015

Fingerprint

Epithelial-Mesenchymal Transition
Transforming Growth Factors
Epithelial Cells
Gene Regulatory Networks
Genes
Transcription Factors
Inflammation
RNA Sequence Analysis
Contractile Proteins
Telomerase
Oncogenes
Integrins
Statistical Factor Analysis
Lung Neoplasms
Stem Cells

Keywords

  • Epithelial mesenchymal transition
  • Generalized linear modeling
  • Nuclear factor ΚB
  • RNA-Seq
  • Transcription factor enrichment
  • Transforming growth factor β

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

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. / Tian, Bing; Li, Xueling; Kalita, Mridul; Widen, Steven; Yang, Jun; Bhavnani, Suresh; Dang, Bryant; Kudlicki, Andrzej; Sinha, Mala; Kong, Fanping; Wood, Thomas; Luxon, Bruce A.; Brasier, Allan R.

In: BMC Genomics, Vol. 16, No. 1, 529, 18.07.2015.

Research output: Contribution to journalArticle

Tian, Bing ; Li, Xueling ; Kalita, Mridul ; Widen, Steven ; Yang, Jun ; Bhavnani, Suresh ; Dang, Bryant ; Kudlicki, Andrzej ; Sinha, Mala ; Kong, Fanping ; Wood, Thomas ; Luxon, Bruce A. ; Brasier, Allan R. / 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. In: BMC Genomics. 2015 ; Vol. 16, No. 1.
@article{59c2029bb6674767b17f5b043a0380f9,
title = "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",
abstract = "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.",
keywords = "Epithelial mesenchymal transition, Generalized linear modeling, Nuclear factor ΚB, RNA-Seq, Transcription factor enrichment, Transforming growth factor β",
author = "Bing Tian and Xueling Li and Mridul Kalita and Steven Widen and Jun Yang and Suresh Bhavnani and Bryant Dang and Andrzej Kudlicki and Mala Sinha and Fanping Kong and Thomas Wood and Luxon, {Bruce A.} and Brasier, {Allan R.}",
year = "2015",
month = "7",
day = "18",
doi = "10.1186/s12864-015-1707-x",
language = "English (US)",
volume = "16",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - 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

AU - Tian, Bing

AU - Li, Xueling

AU - Kalita, Mridul

AU - Widen, Steven

AU - Yang, Jun

AU - Bhavnani, Suresh

AU - Dang, Bryant

AU - Kudlicki, Andrzej

AU - Sinha, Mala

AU - Kong, Fanping

AU - Wood, Thomas

AU - Luxon, Bruce A.

AU - Brasier, Allan R.

PY - 2015/7/18

Y1 - 2015/7/18

N2 - 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.

AB - 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.

KW - Epithelial mesenchymal transition

KW - Generalized linear modeling

KW - Nuclear factor ΚB

KW - RNA-Seq

KW - Transcription factor enrichment

KW - Transforming growth factor β

UR - http://www.scopus.com/inward/record.url?scp=84937212481&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84937212481&partnerID=8YFLogxK

U2 - 10.1186/s12864-015-1707-x

DO - 10.1186/s12864-015-1707-x

M3 - Article

C2 - 26187636

AN - SCOPUS:84937212481

VL - 16

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 529

ER -