Integrative genomic analyses identify BRF2 as a novel lineage-specific oncogene in lung squamous cell carcinoma

William W. Lockwood, Raj Chari, Bradley P. Coe, Kelsie L. Thu, Cathie Garnis, Chad A. Malloff, Jennifer Campbell, Ariane C. Williams, Dorothy Hwang, Chang Qi Zhu, Timon P H Buys, John Yee, John C. English, Calum MacAulay, Ming Sound Tsao, Adi F. Gazdar, John D. Minna, Stephen Lam, Wan L. Lam

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Abstract

Background: Traditionally, non-small cell lung cancer is treated as a single disease entity in terms of systemic therapy. Emerging evidence suggests the major subtypes-adenocarcinoma (AC) and squamous cell carcinoma (SqCC)-respond differently to therapy. Identification of the molecular differences between these tumor types will have a significant impact in designing novel therapies that can improve the treatment outcome, Methods and Findings: We used an integrative genomics approach, combing high-resolution comparative genomic hybridization and gene expression microarray profiles, to compare AC and SqCC tumors in order to uncover alterations at the DNA level, with corresponding gene transcription changes, which are selected for during development of lung cancersubtypes. Through the analysis of multiple independent cohorts of clinical tumor samples (>330), normal lung tissues and bronchial epithelial cells obtained by bronchial brushing in smokers without lung cancer, we identified the overexpression of BRF2, a gene on Chromosome 8p12, which is specific for development of SqCC of lung. Genetic activation of BRF2, which encodes a RNA polymerase III (Pol III) transcription initiation factor, was found to be associated with increased expression of small nuclear RNAs (snRNAs) that are involved in processes essential for cell growth, such as RNA splicing. Ectopic expression of BRF2 in human bronchial epithelial cells induced a transformed phenotype and demonstrates downstream oncogenic effects, whereas RNA interference (RNAi)-mediated knockdown suppressed growth and colony formation of SqCC cells overexpressing BRF2, but not AC cells. Frequent activation of BRF2 in>35% preinvasive bronchial carcinoma in situ, as well as in dysplastic lesions, provides evidence that BRF2 expression is an early event in cancer development of this cell lineage, Conclusions: This is the first study, to our knowledge, to show that the focal amplification of a gene in Chromosome 8p12, plays a key role in squamous cell lineage specificity of the disease. Our data suggest that genetic activation of BRF2 represents a unique mechanism of SqCC lung tumorigenesis through the increase of Pol III-mediated transcription. It can serve as a marker for lung SqCC and may provide a novel target for therapy.

Original languageEnglish (US)
JournalPLoS Medicine
Volume7
Issue number7
DOIs
StatePublished - Jul 2010

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Oncogenes
Squamous Cell Carcinoma
Lung
Adenocarcinoma
Epithelial Cells
Carcinoma in Situ
Cell Lineage
Transcription
Tumors
Neoplasms
Cell Growth Processes
Genes
Chromosomes
Chemical activation
RNA Polymerase III
RNA Splicing
Small Nuclear RNA
Peptide Initiation Factors
Comparative Genomic Hybridization
Bronchogenic Carcinoma

ASJC Scopus subject areas

  • Medicine(all)

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Lockwood, W. W., Chari, R., Coe, B. P., Thu, K. L., Garnis, C., Malloff, C. A., ... Lam, W. L. (2010). Integrative genomic analyses identify BRF2 as a novel lineage-specific oncogene in lung squamous cell carcinoma. PLoS Medicine, 7(7). https://doi.org/10.1371/journal.pmed.1000315

Integrative genomic analyses identify BRF2 as a novel lineage-specific oncogene in lung squamous cell carcinoma. / Lockwood, William W.; Chari, Raj; Coe, Bradley P.; Thu, Kelsie L.; Garnis, Cathie; Malloff, Chad A.; Campbell, Jennifer; Williams, Ariane C.; Hwang, Dorothy; Zhu, Chang Qi; Buys, Timon P H; Yee, John; English, John C.; MacAulay, Calum; Tsao, Ming Sound; Gazdar, Adi F.; Minna, John D.; Lam, Stephen; Lam, Wan L.

In: PLoS Medicine, Vol. 7, No. 7, 07.2010.

Research output: Contribution to journalArticle

Lockwood, WW, Chari, R, Coe, BP, Thu, KL, Garnis, C, Malloff, CA, Campbell, J, Williams, AC, Hwang, D, Zhu, CQ, Buys, TPH, Yee, J, English, JC, MacAulay, C, Tsao, MS, Gazdar, AF, Minna, JD, Lam, S & Lam, WL 2010, 'Integrative genomic analyses identify BRF2 as a novel lineage-specific oncogene in lung squamous cell carcinoma', PLoS Medicine, vol. 7, no. 7. https://doi.org/10.1371/journal.pmed.1000315
Lockwood, William W. ; Chari, Raj ; Coe, Bradley P. ; Thu, Kelsie L. ; Garnis, Cathie ; Malloff, Chad A. ; Campbell, Jennifer ; Williams, Ariane C. ; Hwang, Dorothy ; Zhu, Chang Qi ; Buys, Timon P H ; Yee, John ; English, John C. ; MacAulay, Calum ; Tsao, Ming Sound ; Gazdar, Adi F. ; Minna, John D. ; Lam, Stephen ; Lam, Wan L. / Integrative genomic analyses identify BRF2 as a novel lineage-specific oncogene in lung squamous cell carcinoma. In: PLoS Medicine. 2010 ; Vol. 7, No. 7.
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abstract = "Background: Traditionally, non-small cell lung cancer is treated as a single disease entity in terms of systemic therapy. Emerging evidence suggests the major subtypes-adenocarcinoma (AC) and squamous cell carcinoma (SqCC)-respond differently to therapy. Identification of the molecular differences between these tumor types will have a significant impact in designing novel therapies that can improve the treatment outcome, Methods and Findings: We used an integrative genomics approach, combing high-resolution comparative genomic hybridization and gene expression microarray profiles, to compare AC and SqCC tumors in order to uncover alterations at the DNA level, with corresponding gene transcription changes, which are selected for during development of lung cancersubtypes. Through the analysis of multiple independent cohorts of clinical tumor samples (>330), normal lung tissues and bronchial epithelial cells obtained by bronchial brushing in smokers without lung cancer, we identified the overexpression of BRF2, a gene on Chromosome 8p12, which is specific for development of SqCC of lung. Genetic activation of BRF2, which encodes a RNA polymerase III (Pol III) transcription initiation factor, was found to be associated with increased expression of small nuclear RNAs (snRNAs) that are involved in processes essential for cell growth, such as RNA splicing. Ectopic expression of BRF2 in human bronchial epithelial cells induced a transformed phenotype and demonstrates downstream oncogenic effects, whereas RNA interference (RNAi)-mediated knockdown suppressed growth and colony formation of SqCC cells overexpressing BRF2, but not AC cells. Frequent activation of BRF2 in>35{\%} preinvasive bronchial carcinoma in situ, as well as in dysplastic lesions, provides evidence that BRF2 expression is an early event in cancer development of this cell lineage, Conclusions: This is the first study, to our knowledge, to show that the focal amplification of a gene in Chromosome 8p12, plays a key role in squamous cell lineage specificity of the disease. Our data suggest that genetic activation of BRF2 represents a unique mechanism of SqCC lung tumorigenesis through the increase of Pol III-mediated transcription. It can serve as a marker for lung SqCC and may provide a novel target for therapy.",
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AU - Chari, Raj

AU - Coe, Bradley P.

AU - Thu, Kelsie L.

AU - Garnis, Cathie

AU - Malloff, Chad A.

AU - Campbell, Jennifer

AU - Williams, Ariane C.

AU - Hwang, Dorothy

AU - Zhu, Chang Qi

AU - Buys, Timon P H

AU - Yee, John

AU - English, John C.

AU - MacAulay, Calum

AU - Tsao, Ming Sound

AU - Gazdar, Adi F.

AU - Minna, John D.

AU - Lam, Stephen

AU - Lam, Wan L.

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N2 - Background: Traditionally, non-small cell lung cancer is treated as a single disease entity in terms of systemic therapy. Emerging evidence suggests the major subtypes-adenocarcinoma (AC) and squamous cell carcinoma (SqCC)-respond differently to therapy. Identification of the molecular differences between these tumor types will have a significant impact in designing novel therapies that can improve the treatment outcome, Methods and Findings: We used an integrative genomics approach, combing high-resolution comparative genomic hybridization and gene expression microarray profiles, to compare AC and SqCC tumors in order to uncover alterations at the DNA level, with corresponding gene transcription changes, which are selected for during development of lung cancersubtypes. Through the analysis of multiple independent cohorts of clinical tumor samples (>330), normal lung tissues and bronchial epithelial cells obtained by bronchial brushing in smokers without lung cancer, we identified the overexpression of BRF2, a gene on Chromosome 8p12, which is specific for development of SqCC of lung. Genetic activation of BRF2, which encodes a RNA polymerase III (Pol III) transcription initiation factor, was found to be associated with increased expression of small nuclear RNAs (snRNAs) that are involved in processes essential for cell growth, such as RNA splicing. Ectopic expression of BRF2 in human bronchial epithelial cells induced a transformed phenotype and demonstrates downstream oncogenic effects, whereas RNA interference (RNAi)-mediated knockdown suppressed growth and colony formation of SqCC cells overexpressing BRF2, but not AC cells. Frequent activation of BRF2 in>35% preinvasive bronchial carcinoma in situ, as well as in dysplastic lesions, provides evidence that BRF2 expression is an early event in cancer development of this cell lineage, Conclusions: This is the first study, to our knowledge, to show that the focal amplification of a gene in Chromosome 8p12, plays a key role in squamous cell lineage specificity of the disease. Our data suggest that genetic activation of BRF2 represents a unique mechanism of SqCC lung tumorigenesis through the increase of Pol III-mediated transcription. It can serve as a marker for lung SqCC and may provide a novel target for therapy.

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