PMID- 26187636 OWN - NLM STAT- MEDLINE DCOM- 20160318 LR - 20181113 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 16 IP - 1 DP - 2015 Jul 18 TI - Analysis of the TGFbeta-induced program in primary airway epithelial cells shows essential role of NF-kappaB/RelA signaling network in type II epithelial mesenchymal transition. PG - 529 LID - 10.1186/s12864-015-1707-x [doi] LID - 529 AB - BACKGROUND: The airway epithelial cell plays a central role in coordinating the pulmonary response to injury and inflammation. Here, transforming growth factor-beta (TGFbeta) 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-kappaB/RelA. Surprisingly, we also observed 527 of the EMT DEGs were also regulated by the TNF-NF-kappaB/RelA pathway. This Type II EMT program was compared to Type III EMT in TGFbeta 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 TGFbeta-induced the NF-kappaB/RelA pathway by observing a 2-fold change in NF-kappaB/RelA nuclear translocation. A small molecule IKK inhibitor blocked TGFbeta-induced core transcription factor (SNAIL1, ZEB1 and Twist1) and mesenchymal gene (FN1 and VIM) expression. CONCLUSIONS: These data indicate that NF-kappaB/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. FAU - Tian, Bing AU - Tian B AD - Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA. bitian@utmb.edu. AD - Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. bitian@utmb.edu. FAU - Li, Xueling AU - Li X AD - Institute for Translational Sciences, UTMB, Galveston, TX, USA. xuli@utmb.edu. AD - Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA. xuli@utmb.edu. FAU - Kalita, Mridul AU - Kalita M AD - Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA. mrkalita@utmb.edu. FAU - Widen, Steven G AU - Widen SG AD - Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. sgwiden@utmb.edu. FAU - Yang, Jun AU - Yang J AD - Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA. junyang@utmb.edu. FAU - Bhavnani, Suresh K AU - Bhavnani SK AD - Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA. subhavna@utmb.edu. AD - Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. subhavna@utmb.edu. AD - Institute for Translational Sciences, UTMB, Galveston, TX, USA. subhavna@utmb.edu. FAU - Dang, Bryant AU - Dang B AD - Institute for Translational Sciences, UTMB, Galveston, TX, USA. brdang@utmb.edu. FAU - Kudlicki, Andrzej AU - Kudlicki A AD - Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. askudlic@utmb.edu. AD - Institute for Translational Sciences, UTMB, Galveston, TX, USA. askudlic@utmb.edu. AD - Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA. askudlic@utmb.edu. FAU - Sinha, Mala AU - Sinha M AD - Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. masinha@utmb.edu. AD - Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA. masinha@utmb.edu. AD - Bioinformatics Program, UTMB, Galveston, TX, USA. masinha@utmb.edu. FAU - Kong, Fanping AU - Kong F AD - Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. fakong@utmb.edu. AD - Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA. fakong@utmb.edu. AD - Bioinformatics Program, UTMB, Galveston, TX, USA. fakong@utmb.edu. FAU - Wood, Thomas G AU - Wood TG AD - Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. tgwood@utmb.edu. AD - Institute for Translational Sciences, UTMB, Galveston, TX, USA. tgwood@utmb.edu. AD - Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA. tgwood@utmb.edu. FAU - Luxon, Bruce A AU - Luxon BA AD - Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. baluxon@utmb.edu. AD - Institute for Translational Sciences, UTMB, Galveston, TX, USA. baluxon@utmb.edu. AD - Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, USA. baluxon@utmb.edu. AD - Bioinformatics Program, UTMB, Galveston, TX, USA. baluxon@utmb.edu. FAU - Brasier, Allan R AU - Brasier AR AD - Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA. arbrasie@utmb.edu. AD - Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA. arbrasie@utmb.edu. AD - Institute for Translational Sciences, UTMB, Galveston, TX, USA. arbrasie@utmb.edu. LA - eng SI - GEO/GSE61220 GR - P30 ES006676/ES/NIEHS NIH HHS/United States GR - UL1 TR000071/TR/NCATS NIH HHS/United States GR - NIEHS P30 ES006676/ES/NIEHS NIH HHS/United States GR - UL1TR000071/TR/NCATS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20150718 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (NF-kappa B) RN - 0 (RELA protein, human) RN - 0 (Transcription Factor RelA) RN - 0 (Transforming Growth Factor beta) SB - IM MH - Epithelial Cells/metabolism MH - Epithelial-Mesenchymal Transition/*genetics MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Lung Neoplasms/*genetics/pathology MH - NF-kappa B/genetics MH - Signal Transduction/genetics MH - Stem Cells/metabolism MH - Transcription Factor RelA/*genetics/metabolism MH - Transforming Growth Factor beta/antagonists & inhibitors/*genetics PMC - PMC4506436 EDAT- 2015/07/19 06:00 MHDA- 2016/03/19 06:00 PMCR- 2015/07/18 CRDT- 2015/07/19 06:00 PHST- 2014/09/12 00:00 [received] PHST- 2015/06/17 00:00 [accepted] PHST- 2015/07/19 06:00 [entrez] PHST- 2015/07/19 06:00 [pubmed] PHST- 2016/03/19 06:00 [medline] PHST- 2015/07/18 00:00 [pmc-release] AID - 10.1186/s12864-015-1707-x [pii] AID - 1707 [pii] AID - 10.1186/s12864-015-1707-x [doi] PST - epublish SO - BMC Genomics. 2015 Jul 18;16(1):529. doi: 10.1186/s12864-015-1707-x.