Elsevier

Oral Oncology

Volume 55, April 2016, Pages 43-48
Oral Oncology

HPV status is associated with altered PIWI-interacting RNA expression pattern in head and neck cancer

https://doi.org/10.1016/j.oraloncology.2016.01.012Get rights and content

Highlights

  • piRNAs are differentially expressed between HNSC and non-malignant tissues.

  • piRNA expression patterns are specific to the HPV status of the tumor.

  • A piRNA expression signature can predict overall survival in HPV+ HNSC patients.

Summary

Objectives

As HPV-induced cases of oral malignancy increase, it is important to understand the molecular differences between HPV positive and negative head and neck squamous cell carcinoma (HNSCC). PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs aberrantly expressed in cancer. We analyzed global piRNA expression patterns to define the HNSCC piRNA transcriptome and assess whether HPV infection status associates with changes in piRNA levels.

Materials and methods

A total of 498 HNSCC small RNA sequencing libraries were acquired from the Cancer Genomics Hub (cgHUB) Data Repository and a custom sequence analysis pipeline was developed to deduce piRNA expression from raw sequencing data. Expression matrices were aligned to clinicopathological features in order to analyze piRNA expression patterns across different HNSCC groups. The association of a piRNA signature with HPV-positive patient survival was evaluated using a Cox proportional hazard model.

Results

Analysis of piRNA levels between HNSCC and non-malignant tissues revealed distinct expression patterns, with 87 piRNAs exclusively expressed in tumor samples. HPV infection status affected the expression of 41 of these piRNAs. Eleven (26.8%) piRNAs were significantly downregulated in HPV16/18 tumors compared to other HPV types. Remarkably, expression of a combination of five-piRNAs in HPV-positive HNSCC tumors was associated with worse overall survival.

Conclusion

The expression of specific piRNAs is deregulated in HNSCC, and changes with both HPV status and type. Importantly, a five-piRNA signature is able to delineate a subset of HPV-positive HNSCC patients with poor outcome, highlighting the potential utility of piRNAs in patient management.

Introduction

Head and neck squamous cell carcinoma (HNSCC) affects over 550,000 patients worldwide each year [1]. Tobacco and alcohol consumption, together with human papillomavirus (HPV) infection are the main etiological factors [2], [3], [4]. Many studies have found that patients with HPV-positive HNSCC have a better prognosis, with increased survival and less chance of recurrence [5], [6], [7]. However, there have been contradictory reports showing either no or poor associations with outcome. Nevertheless, the growing proportion of HPV-positive cases poses an urgent need for prognostic biomarkers that guide patient management according to HPV status [3], [6], [8], [9].

Small RNAs, particularly microRNAs (miRNAs), have proven to be promising prognostic tools in HNSCC patients [10], [11]. Piwi-interacting RNAs (piRNAs), an abundant class of small non-coding RNA that regulate genome stability [12], [13], [14], are emerging as a valuable addition to the category of small RNA biomarkers. Recently, piRNA expression patterns have been shown to be deregulated in a variety of cancer types, including head and neck tumors [15], [16], [17], [18], [19], [20], [21], [22]; however, the relationship between piRNA expression and clinicopathological features in HNSCCs is yet to be elucidated. Interestingly, we have reported an association between piRNA expression and nodal metastasis in HNSCC [16].

Here, we describe the expression pattern of piRNAs in HNSCC using a custom pipeline to generate piRNA transcriptomes for more than 20,000 human piRNAs. We have analyzed piRNA expression from 498 non-malignant and tumor tissues from HNSCC patients, and investigate their association with HPV infection status and patient survival. Our results reveal that specific piRNA expression patterns are associated with HPV status and virus type. Importantly, a piRNA expression signature was able to stratify patients based on overall survival, suggesting the potential utility of piRNA in assessing HNSCC patient prognosis.

Section snippets

Sample acquisition

A total of 498 HNSCC small RNA sequencing libraries (455 tumors and 43 matched non-malignant tissue) generated by The Cancer Genome Atlas (TCGA) consortium were acquired from the Cancer Genomics Hub (cgHUB) Data Repository (dbgap Project ID: 6208). The demographics and clinical data of these cases were obtained from the TCGA data portal and the USCS Cancer browser (Supplementary Table S1).

Assembly of piRNA transcriptome

A custom sequence analysis pipeline was developed to deduce piRNA expression from raw sequencing data

piRNAs are differentially expressed in head and neck non-malignant and tumor tissue

To identify piRNAs that might delineate tumor and non-malignant tissues, we analyzed piRNA expression in 43 non-malignant and 455 HNSCC samples. While the number of piRNAs expressed in either types of somatic tissue is small relative to the total number of piRNAs in the genome, we found intriguing patterns of differential expression between HNSCC tumors and their non-malignant counterparts. A total of 305 piRNAs were robustly expressed in both non-malignant and tumor tissue (Fig. 1,

Discussion

Considerable advances have been made in the detection and chemoprevention of head and neck cancer [4], [31]; however, major challenges still remain regarding the improvement of patient management once the disease is diagnosed. Additionally, the interaction between biological risk agents, such as HPV, and cellular mechanisms are not completely understood. In this proof of principle study, we show that another important component of the small RNA transcriptome, piRNA, is likely to play a role in

Conflict of interest statement

None declared.

Acknowledgements

This work was supported by Grants from the National Institutes of Health – United States (NIH-NIDCR R01 DE015965), Canadian Institutes for Health Research (CIHR, FDN143345) and the Canadian Cancer Society (CCSRI), and CIHR Frederick Banting and Charles Best Canada Graduate Scholarships to K.S.S.E. and D.A.R. K.L.B. is a Michael Smith Foundation for Health Research Biomedical Research Scholar.

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    These authors contributed equally to this work.

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