Original articleTranscriptional Profiling by Sequencing of Oropharyngeal Cancer
Section snippets
Collection and Processing of Tissues
After institutional review board approval, oropharyngeal tumor samples were obtained from patients undergoing surgical treatment of OPSCC at Mayo Clinic, Rochester, MN. After achieving negative surgical margins, adjacent normal mucosal tissue was collected from the oropharynx. All tissue was snap-frozen in liquid nitrogen for storage. Samples were evaluated by frozen sectioning, with a fresh blade between samples, and preparation of hematoxylin-eosin slides. The slides for each sample were
Measurement of Gene Expression in OPSCC and Patient-Matched Normal Tissue by RNA Transcriptional Sequencing
We constructed mRNA-Seq libraries from poly A+ selected transcripts, and each library was sequenced on a single lane of the Illumina GAIIx machine. Using paired-end, 51-bp sequencing, we were able to obtain a mean of 63 million reads per transcriptome. We then compared mRNA-seq analysis for 10 patient-matched samples representing primary SCC and normal tissue (Table 1). One of the sequenced samples was excluded because of incomplete smoking history. The remaining 9 tumor and normal paired
Discussion
In this report we used total transcriptome sequencing analysis to characterize a group of oropharyngeal tumors and patient-matched normal tissues. Oropharyngeal tumors display a wide range of behavior, including differences in patterns of invasion, tendency for metastasis, and widely varying treatment responses. Clinicians' inability to accurately predict tumor behavior leads to widely varying treatment strategies, often resulting in significant morbidity and even mortality. Increasing evidence
Conclusion
Transcriptional profiling by mRNA-seq allowed us to identify unique patterns of global gene regulation that correlated with patient exposure to known oncogenic risk factors. Specific gene targets involved in the p53 DNA damage-repair pathway, including CHEK2 and ATR, were analyzed and displayed patterns of increased expression associated with HPV-negative current smokers when compared with past smokers or nonsmokers. Identification and validation of these and related gene targets will serve as
Acknowledgments
We thank Charles Beatty, MD, chair of otorhinolaryngology, Mayo Clinic, Rochester, MN, for his ongoing support of this work, and the Stoll Foundation for postdoctoral fellowship support.
References (12)
- et al.
EGF receptor gene mutations are common in lung cancers from ”never smokers” and are associated with sensitivity of tumors to gefitinib and erlotinib
Proc Acad Sci U S A
(2004) - et al.
Molecular alterations in tumors and response to combination chemotherapy with gefitinib for advanced colorectal cancer
Clin Cancer Res
(2005) - et al.
Responsiveness to cetuximab without mutations in EGFR
N Engl J Med
(2005) - et al.
Global cancer statistics
CA Cancer J Clin
(2011) - et al.
Global patterns of cancer incidence and mortality rates and trends
Cancer Epidemiol Biomarkers Prev
(2010) - et al.
The role of human papillomavirus in the increased incidence of base of tongue cancer
Int J Cancer
(2010)
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For editorial comment, see page 211
Grant Support: This work was supported by internal funding from the Mayo Foundation for Medical Education and Research. The efforts of Todd M. Smith and N. Eric Olson were supported by award 2R44HG005297 from the National Human Genome Research Institute.
Potential Competing Interests: Todd M. Smith and N. Eric Olson are employed by Geospiza, a PerkinElmer company. The authors have no financial interests to disclose.