Research Papers:

Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq

Caroline Conway _, Jennifer L. Graham, Preetha Chengot, Catherine Daly, Rebecca Chalkley, Lisa Ross, Alastair Droop, Pamela Rabbitts and Lucy F. Stead

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Oncotarget. 2015; 6:40186-40201. https://doi.org/10.18632/oncotarget.5529

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Caroline Conway1,2, Jennifer L. Graham1, Preetha Chengot1, Catherine Daly1, Rebecca Chalkley1, Lisa Ross1, Alastair Droop1, Pamela Rabbitts1, Lucy F. Stead1

1Precancer Genomics, Leeds Institute of Cancer and Pathology, Wellcome Trust Brenner Building, St James's University Hospital, Leeds, LS9 7TF, UK

2Stratified Medicine (Oncology), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, BT52 1SA, UK

Correspondence to:

Lucy F. Stead, e-mail: [email protected]

Keywords: RNAseq, oral squamous cell carcinoma, OSCC, dysplasia, non-coding

Received: April 08, 2015     Accepted: October 09, 2015     Published: October 19, 2015


Oral squamous cell carcinoma (OSCC) is a prevalent cancer with poor prognosis. Most OSCC progresses via a non-malignant stage called dysplasia. Effective treatment of dysplasia prior to potential malignant transformation is an unmet clinical need. To identify markers of early disease, we performed RNA sequencing of 19 matched HPV negative patient trios: normal oral mucosa, dysplasia and associated OSCC. We performed differential gene expression, principal component and correlated gene network analysis using these data. We found differences in the immune cell signatures present at different disease stages and were able to distinguish early events in pathogenesis, such as upregulation of many HOX genes, from later events, such as down-regulation of adherens junctions. We herein highlight novel coding and non-coding candidates for involvement in oral dysplasia development and malignant transformation, and speculate on how our findings may guide further translational research into the treatment of oral dysplasia.

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