Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer (original) (raw)
References
Bashyam MD, Bair R, Kim YH, Wang P, Hernandez-Boussard T, Karikari CA et al. (2005). Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancer. Neoplasia7: 556–562. ArticleCASPubMed Google Scholar
Bergamaschi A, Kim YH, Wang P, Sorlie T, Hernandez-Boussard T, Lonning PE et al. (2006). Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer45: 1033–1040. ArticleCAS Google Scholar
Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y et al. (2006). 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods3: 199–204. ArticleCASPubMed Google Scholar
Bohinski RJ, Di Lauro R, Whitsett JA . (1994). The lung-specific surfactant protein B gene promoter is a target for thyroid transcription factor 1 and hepatocyte nuclear factor 3, indicating common factors for organ-specific gene expression along the foregut axis. Mol Cell Biol14: 5671–5681. ArticleCASPubMed Google Scholar
Garraway LA, Sellers WR . (2006). Lineage dependency and lineage-survival oncogenes in human cancer. Nat Rev Cancer6: 593–602. CAS Google Scholar
Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S et al. (2005). Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature436: 117–122. ArticleCAS Google Scholar
Holst F, Stahl PR, Ruiz C, Hellwinkel O, Jehan Z, Wendland M et al. (2007). Estrogen receptor alpha (ESR1) gene amplification is frequent in breast cancer. Nat Genet39: 655–660. ArticleCASPubMed Google Scholar
Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J et al. (2006). Position-specific chemical modification of siRNAs reduces ‘off-target’ transcript silencing. RNA12: 1197–1205. ArticleCASPubMed Google Scholar
Jemal A, Siegel R, Ward E, Murray T, Xu J, Thun MJ . (2007). Cancer statistics, 2007. CA Cancer J Clin57: 43–66. ArticlePubMed Google Scholar
Kao J, Pollack JR . (2006). RNA interference-based functional dissection of the 17q12 amplicon in breast cancer reveals contribution of coamplified genes. Genes Chromosomes Cancer45: 761–769. ArticleCASPubMed Google Scholar
Kendall J, Liu Q, Bakleh A, Krasnitz A, Nguyen KC, Lakshmi B et al. (2007). Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer. Proc Natl Acad Sci USA104: 16663–16668. ArticleCASPubMed Google Scholar
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM et al. (2002). The human genome browser at UCSC. Genome Res12: 996–1006. ArticleCASPubMed Google Scholar
Kimura S, Hara Y, Pineau T, Fernandez-Salguero P, Fox CH, Ward JM et al. (1996). The T/ebp null mouse: thyroid-specific enhancer-binding protein is essential for the organogenesis of the thyroid, lung, ventral forebrain, and pituitary. Genes Dev10: 60–69. ArticleCASPubMed Google Scholar
Lapointe J, Li C, Giacomini CP, Salari K, Huang S, Wang P et al. (2007). Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis. Cancer Res67: 8504–8510. ArticleCAS Google Scholar
Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K et al. (2004). Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci USA101: 811–816. ArticleCASPubMed Google Scholar
Lechner JF, Fugaro JM, Wong Y, Pass HI, Harris CC, Belinsky SA . (2001). Perspective: cell differentiation theory may advance early detection of and therapy for lung cancer. Radiat Res155: 235–238. ArticleCASPubMed Google Scholar
Miccadei S, De Leo R, Zammarchi E, Natali PG, Civitareale D . (2002). The synergistic activity of thyroid transcription factor 1 and Pax 8 relies on the promoter/enhancer interplay. Mol Endocrinol16: 837–846. ArticleCASPubMed Google Scholar
Minoo P, Su G, Drum H, Bringas P, Kimura S . (1999). Defects in tracheoesophageal and lung morphogenesis in Nkx2.1(−/−) mouse embryos. Dev Biol209: 60–71. ArticleCASPubMed Google Scholar
Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF et al. (1999). Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet23: 41–46. ArticleCASPubMed Google Scholar
Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE et al. (2002). Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA99: 12963–12968. ArticleCAS Google Scholar
Puglisi F, Barbone F, Damante G, Bruckbauer M, Di Lauro V, Beltrami CA et al. (1999). Prognostic value of thyroid transcription factor-1 in primary, resected, non-small cell lung carcinoma. Mod Pathol12: 318–324. CASPubMed Google Scholar
Ramirez RD, Sheridan S, Girard L, Sato M, Kim Y, Pollack J et al. (2004). Immortalization of human bronchial epithelial cells in the absence of viral oncoproteins. Cancer Res64: 9027–9034. ArticleCASPubMed Google Scholar
Sato M, Shames DS, Gazdar AF, Minna JD . (2007). A translational view of the molecular pathogenesis of lung cancer. J Thorac Oncol2: 327–343. ArticlePubMed Google Scholar
Tan D, Li Q, Deeb G, Ramnath N, Slocum HK, Brooks J et al. (2003). Thyroid transcription factor-1 expression prevalence and its clinical implications in non-small cell lung cancer: a high-throughput tissue microarray and immunohistochemistry study. Hum Pathol34: 597–604. ArticleCASPubMed Google Scholar
Tanaka H, Yanagisawa K, Shinjo K, Taguchi A, Maeno K, Tomida S et al. (2007). Lineage-specific dependency of lung adenocarcinomas on the lung development regulator TTF-1. Cancer Res67: 6007–6011. ArticleCASPubMed Google Scholar
Tian J, Mahmood R, Hnasko R, Locker J . (2006). Loss of Nkx2.8 deregulates progenitor cells in the large airways and leads to dysplasia. Cancer Res66: 10399–10407. ArticleCASPubMed Google Scholar
Tibshirani R, Wang P . (2008). Spatial smoothing and hot spot detection for CGH data using the fused lasso. Biostatistics9: 18–29. Article Google Scholar
Travis WD, Brambilla E, Muller-Hermelink HK, Harris CC . (2004). Pathology & Genetics: Tumours of the lung, pleura, thymus and heart. (World Health Organization Classification of Tumours). IARC Press: Lyon. Google Scholar
Visakorpi T, Hyytinen E, Koivisto P, Tanner M, Keinanen R, Palmberg C et al. (1995). In vivo amplification of the androgen receptor gene and progression of human prostate cancer. Nat Genet9: 401–406. ArticleCASPubMed Google Scholar
Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R et al. (2007). Characterizing the cancer genome in lung adenocarcinoma. Nature450: 893–898. ArticleCASPubMed Google Scholar
Yatabe Y, Mitsudomi T, Takahashi T . (2002). TTF-1 expression in pulmonary adenocarcinomas. Am J Surg Pathol26: 767–773. Article Google Scholar