title: Genome-wide analyses of Nkx2-1 binding to transcriptional target genes uncover novel regulatory patterns conserved in lung development and tumors.
abstract: The homeodomain transcription factor Nkx2-1 is essential for normal lung development and homeostasis. In lung tumors, it is considered a lineage survival oncogene and prognostic factor depending on its expression levels. The target genes directly bound by Nkx2-1, that could be the primary effectors of its functions in the different cellular contexts where it is expressed, are mostly unknown. In embryonic day 11.5 (E11.5) mouse lung, epithelial cells expressing Nkx2-1 are predominantly expanding, and in E19.5 prenatal lungs, Nkx2-1-expressing cells are predominantly differentiating in preparation for birth. To evaluate Nkx2-1 regulated networks in these two cell contexts, we analyzed genome-wide binding of Nkx2-1 to DNA regulatory regions by chromatin immunoprecipitation followed by tiling array analysis, and intersected these data to expression data sets. We further determined expression patterns of Nkx2-1 developmental target genes in human lung tumors and correlated their expression levels to that of endogenous NKX2-1. In these studies we uncovered differential Nkx2-1 regulated networks in early and late lung development, and a direct function of Nkx2-1 in regulation of the cell cycle by controlling the expression of proliferation-related genes. New targets, validated in Nkx2-1 shRNA transduced cell lines, include E2f3, Cyclin B1, Cyclin B2, and c-Met. Expression levels of Nkx2-1 direct target genes identified in mouse development significantly correlate or anti-correlate to the levels of endogenous NKX2-1 in a dosage-dependent manner in multiple human lung tumor expression data sets, supporting alternative roles for Nkx2-1 as a transcriptional activator or repressor, and direct regulator of cell cycle progression in development and tumors.
authors.affiliation: Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Jean-Bosco
authors.initials: JB
authors.lastname: Tagne
authors.forename: Sumeet
authors.initials: S
authors.lastname: Gupta
authors.forename: Adam C
authors.initials: AC
authors.lastname: Gower
authors.forename: Steven S
authors.initials: SS
authors.lastname: Shen
authors.forename: Saaket
authors.initials: S
authors.lastname: Varma
authors.forename: Meenakshi
authors.initials: M
authors.lastname: Lakshminarayanan
authors.forename: Yuxia
authors.initials: Y
authors.lastname: Cao
authors.forename: Avrum
authors.initials: A
authors.lastname: Spira
authors.forename: Thomas L
authors.initials: TL
authors.lastname: Volkert
authors.forename: Maria I
authors.initials: MI
authors.lastname: Ramirez
mesh_terms: D000818:Animals; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics; D002453:Cell Cycle / Q000235:genetics; D049109:Cell Proliferation; D047369:Chromatin Immunoprecipitation; D017124:Conserved Sequence; D015536:Down-Regulation / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D015972:Gene Expression Regulation, Neoplastic; D055106:Genome-Wide Association Study; D006801:Humans; D008168:Lung / Q000196:embryology* / Q000378:metabolism; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D051379:Mice; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011485:Protein Binding / Q000235:genetics; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000235:genetics; D000074482:Thyroid Nuclear Factor 1; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: C000614414:Nkx2-1 protein, mouse; D009687:Nuclear Proteins; D000074482:Thyroid Nuclear Factor 1; D014157:Transcription Factors