HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas
Efterpi Kostareli, … , Dieter Weichenhan, Jochen Hess
Efterpi Kostareli, … , Dieter Weichenhan, Jochen Hess
Published May 1, 2013
Citation Information: J Clin Invest. 2013;123(6):2488-2501. https://doi.org/10.1172/JCI67010.
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Research Article Oncology

HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas

Abstract

High-risk types of human papilloma virus (HPV) are increasingly associated with oropharyngeal squamous cell carcinoma (OPSCC). Strikingly, patients with HPV-positive OPSCC are highly curable with ionizing radiation and have better survival compared with HPV-negative patients, but the underlying molecular mechanisms remain poorly understood. We applied an array-based approach to monitor global changes in CpG island hypermethylation between HPV-negative and HPV-positive OPSCCs and identified a specific pattern of differentially methylated regions that critically depends on the presence of viral transcripts. HPV-related alterations were confirmed for the majority of candidate gene promoters by mass spectrometric, quantitative methylation analysis. There was a significant inverse correlation between promoter hypermethylation of ALDH1A2, OSR2, GATA4, GRIA4, and IRX4 and transcript levels. Interestingly, Kaplan-Meier analysis revealed that a combined promoter methylation pattern of low methylation levels in ALDH1A2 and OSR2 promoters and high methylation levels in GATA4, GRIA4, and IRX4 promoters was significantly correlated with improved survival in 3 independent patient cohorts. ALDH1A2 protein levels, determined by immunohistochemistry on tissue microarrays, confirmed the association with clinical outcome. In summary, our study highlights specific alterations in global gene promoter methylation in HPV-driven OPSCCs and identifies a signature that predicts the clinical outcome in OPSCCs.

Authors

Efterpi Kostareli, Dana Holzinger, Olga Bogatyrova, Thomas Hielscher, Gunnar Wichmann, Michaela Keck, Bernd Lahrmann, Niels Grabe, Christa Flechtenmacher, Christopher R. Schmidt, Tanguy Seiwert, Gerhard Dyckhoff, Andreas Dietz, Daniela Höfler, Michael Pawlita, Axel Benner, Franz X. Bosch, Peter Plinkert, Christoph Plass, Dieter Weichenhan, Jochen Hess

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Figure 1

Global HPV-related CpG island methylation changes in OPSCC samples.

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Global HPV-related CpG island methylation changes in OPSCC samples. (A) ...
(A) Top: Whole-genome distribution of DMRs commonly hypermethylated and represented at least once in all 3 groups. Line height corresponds to sample number (minimum, 3; maximum, 15). Middle: Exemplary distribution of DMRs on chromosome 5 and chromosome 8 of group A (HPV DNA–RNA–), group B (HPV DNA+RNA–), and group C (HPV DNA+RNA+). Line height corresponds to sample number (minimum, 1; maximum, 5). Bottom: Enlarged view of the promoter CpG island regions of IRX4 and OSR2. Boxed red bars represent promoter CpG island array probes hypermethylated in at least 3 of 5 samples from patient group A, B, or C. (B) Distribution of OPSCC-related hypermethylated probes (HMPs). The number of common top 5% HMPs (y axis) observed in increasing OPSCC sample numbers is plotted against the number of samples (x axis). The black curve shows the binomial distribution expected under the null hypothesis and the red curve shows the observed distribution. Inset: Enlargement (x axis coordinates, 1–15; y axis coordinates, 0–10,000). (C) PCA using all array-derived M values of the 15 OPSCC samples (Tu01–Tu15). (D) Unsupervised cluster analysis of hypermethylated DMRs. (E) Target diagrams summarizing the number of hypermethylated DMRs specific for the non–HPV-driven and HPV-driven OPSCC samples (see also Supplemental Tables 22 and 23). The candidate genes selected for confirmation are indicated.