The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma.

Lucy F Stead, Stefano Berri, Henry M Wood, Philip Egan, Caroline Conway, Catherine Daly, Kostas Papagiannopoulos, Pamela Rabbitts

    Research output: Contribution to journalArticle

    9 Citations (Scopus)

    Abstract

    Lung cancer causes more deaths, worldwide, than any other cancer. Several histologic subtypes exist. Currently, there is a dearth of targeted therapies for treating one of the main subtypes: squamous cell carcinoma (SCC). As for many cancers, lung SCC karyotypes are often highly anomalous owing to large somatic structural variants, some of which are seen repeatedly in lung SCC, indicating a potential causal association for genes therein. We chose to characterize a lung SCC genome to unprecedented detail and integrate our findings with the concurrently characterized transcriptome. We aimed to ascertain how somatic structural changes affected gene expression within the cell in ways that could confer a pathogenic phenotype. We sequenced the genomes of a lung SCC cell line (LUDLU-1) and its matched lymphocyte cell line (AGLCL) to more than 50x coverage. We also sequenced the transcriptomes of LUDLU-1 and a normal bronchial epithelium cell line (LIMM-NBE1), resulting in more than 600 million aligned reads per sample, including both coding and non-coding RNA (ncRNA), in a strand-directional manner. We also captured small RNA (
    LanguageEnglish
    Pages1075-86
    JournalNeoplasia
    Volume14
    Issue number11
    Publication statusPublished - 2012

    Fingerprint

    Squamous Cell Carcinoma
    Lung
    Transcriptome
    Lung Neoplasms
    Genome
    Untranslated RNA
    Karyotype
    Cause of Death
    Epithelium
    Lymphocytes
    RNA
    Phenotype
    Gene Expression
    Genes
    Neoplasms
    Therapeutics

    Cite this

    Stead, L. F., Berri, S., Wood, H. M., Egan, P., Conway, C., Daly, C., ... Rabbitts, P. (2012). The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma. Neoplasia, 14(11), 1075-86.
    Stead, Lucy F ; Berri, Stefano ; Wood, Henry M ; Egan, Philip ; Conway, Caroline ; Daly, Catherine ; Papagiannopoulos, Kostas ; Rabbitts, Pamela. / The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma. In: Neoplasia. 2012 ; Vol. 14, No. 11. pp. 1075-86.
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    abstract = "Lung cancer causes more deaths, worldwide, than any other cancer. Several histologic subtypes exist. Currently, there is a dearth of targeted therapies for treating one of the main subtypes: squamous cell carcinoma (SCC). As for many cancers, lung SCC karyotypes are often highly anomalous owing to large somatic structural variants, some of which are seen repeatedly in lung SCC, indicating a potential causal association for genes therein. We chose to characterize a lung SCC genome to unprecedented detail and integrate our findings with the concurrently characterized transcriptome. We aimed to ascertain how somatic structural changes affected gene expression within the cell in ways that could confer a pathogenic phenotype. We sequenced the genomes of a lung SCC cell line (LUDLU-1) and its matched lymphocyte cell line (AGLCL) to more than 50x coverage. We also sequenced the transcriptomes of LUDLU-1 and a normal bronchial epithelium cell line (LIMM-NBE1), resulting in more than 600 million aligned reads per sample, including both coding and non-coding RNA (ncRNA), in a strand-directional manner. We also captured small RNA (",
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    Stead, LF, Berri, S, Wood, HM, Egan, P, Conway, C, Daly, C, Papagiannopoulos, K & Rabbitts, P 2012, 'The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma.', Neoplasia, vol. 14, no. 11, pp. 1075-86.

    The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma. / Stead, Lucy F; Berri, Stefano; Wood, Henry M; Egan, Philip; Conway, Caroline; Daly, Catherine; Papagiannopoulos, Kostas; Rabbitts, Pamela.

    In: Neoplasia, Vol. 14, No. 11, 2012, p. 1075-86.

    Research output: Contribution to journalArticle

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    AU - Daly, Catherine

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