Meta-Analysis of EMT Datasets Reveals Different Types of EMT

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2016 Jun 4

PMID 27258544

Citations 20

Authors

Lining Liang

Hao Sun

Wei Zhang

Mengdan Zhang

Xiao Yang

Rui Kuang

Hui Zheng

Affiliations

Soon will be listed here.

Abstract

As a critical process during embryonic development, cancer progression and cell fate conversions, epithelial-mesenchymal transition (EMT) has been extensively studied over the last several decades. To further understand the nature of EMT, we performed meta-analysis of multiple microarray datasets to identify the related generic signature. In this study, 24 human and 17 mouse microarray datasets were integrated to identify conserved gene expression changes in different types of EMT. Our integrative analysis revealed that there is low agreement among the list of the identified signature genes and three other lists in previous studies. Since removing the datasets with weakly-induced EMT from the analysis did not significantly improve the overlapping in the signature-gene lists, we hypothesized the existence of different types of EMT. This hypothesis was further supported by the grouping of 74 human EMT-induction samples into five distinct clusters, and the identification of distinct pathways in these different clusters of EMT samples. The five clusters of EMT-induction samples also improves the understanding of the characteristics of different EMT types. Therefore, we concluded the existence of different types of EMT was the possible reason for its complex role in multiple biological processes.

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References

Garg M . Epithelial-mesenchymal transition - activating transcription factors - multifunctional regulators in cancer. World J Stem Cells. 2013; 5(4):188-95. PMC: 3812522. DOI: 10.4252/wjsc.v5.i4.188. View

Dalerba P, Cho R, Clarke M . Cancer stem cells: models and concepts. Annu Rev Med. 2006; 58:267-84. DOI: 10.1146/annurev.med.58.062105.204854. View

Wellner U, Schubert J, Burk U, Schmalhofer O, Zhu F, Sonntag A . The EMT-activator ZEB1 promotes tumorigenicity by repressing stemness-inhibiting microRNAs. Nat Cell Biol. 2009; 11(12):1487-95. DOI: 10.1038/ncb1998. View

Rawluszko-Wieczorek A, Siera A, Jagodzinski P . TET proteins in cancer: Current 'state of the art'. Crit Rev Oncol Hematol. 2015; 96(3):425-36. DOI: 10.1016/j.critrevonc.2015.07.008. View

Zhao M, Kong L, Liu Y, Qu H . dbEMT: an epithelial-mesenchymal transition associated gene resource. Sci Rep. 2015; 5:11459. PMC: 4477208. DOI: 10.1038/srep11459. View

Guan F, Schaffer L, Handa K, Hakomori S . Functional role of gangliotetraosylceramide in epithelial-to-mesenchymal transition process induced by hypoxia and by TGF-{beta}. FASEB J. 2010; 24(12):4889-903. PMC: 2992377. DOI: 10.1096/fj.10-162107. View

Li R, Liang J, Ni S, Zhou T, Qing X, Li H . A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell. 2010; 7(1):51-63. DOI: 10.1016/j.stem.2010.04.014. View

Guan K, Chang H, Rolletschek A, Wobus A . Embryonic stem cell-derived neurogenesis. Retinoic acid induction and lineage selection of neuronal cells. Cell Tissue Res. 2001; 305(2):171-6. DOI: 10.1007/s004410100416. View

Yilmaz M, Christofori G . EMT, the cytoskeleton, and cancer cell invasion. Cancer Metastasis Rev. 2009; 28(1-2):15-33. DOI: 10.1007/s10555-008-9169-0. View

10.

Mani S, Guo W, Liao M, Eaton E, Ayyanan A, Zhou A . The epithelial-mesenchymal transition generates cells with properties of stem cells. Cell. 2008; 133(4):704-15. PMC: 2728032. DOI: 10.1016/j.cell.2008.03.027. View

11.

Sheng C, Zheng Q, Wu J, Xu Z, Sang L, Wang L . Generation of dopaminergic neurons directly from mouse fibroblasts and fibroblast-derived neural progenitors. Cell Res. 2012; 22(4):769-72. PMC: 3317566. DOI: 10.1038/cr.2012.32. View

12.

Peinado H, Olmeda D, Cano A . Snail, Zeb and bHLH factors in tumour progression: an alliance against the epithelial phenotype?. Nat Rev Cancer. 2007; 7(6):415-28. DOI: 10.1038/nrc2131. View

13.

Lin T, Ponn A, Hu X, Law B, Lu J . Requirement of the histone demethylase LSD1 in Snai1-mediated transcriptional repression during epithelial-mesenchymal transition. Oncogene. 2010; 29(35):4896-904. PMC: 3093107. DOI: 10.1038/onc.2010.234. View

14.

Song S, Poliseno L, Song M, Ala U, Webster K, Ng C . MicroRNA-antagonism regulates breast cancer stemness and metastasis via TET-family-dependent chromatin remodeling. Cell. 2013; 154(2):311-324. PMC: 3767157. DOI: 10.1016/j.cell.2013.06.026. View

15.

Groger C, Grubinger M, Waldhor T, Vierlinger K, Mikulits W . Meta-analysis of gene expression signatures defining the epithelial to mesenchymal transition during cancer progression. PLoS One. 2012; 7(12):e51136. PMC: 3519484. DOI: 10.1371/journal.pone.0051136. View

16.

Reimand J, Arak T, Vilo J . g:Profiler--a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res. 2011; 39(Web Server issue):W307-15. PMC: 3125778. DOI: 10.1093/nar/gkr378. View

17.

Takahashi K, Yamanaka S . Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006; 126(4):663-76. DOI: 10.1016/j.cell.2006.07.024. View

18.

Huang D, Sherman B, Lempicki R . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. DOI: 10.1038/nprot.2008.211. View

19.

Samavarchi-Tehrani P, Golipour A, David L, Sung H, Beyer T, Datti A . Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell. 2010; 7(1):64-77. DOI: 10.1016/j.stem.2010.04.015. View

20.

Wilkerson M, Hayes D . ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010; 26(12):1572-3. PMC: 2881355. DOI: 10.1093/bioinformatics/btq170. View