Virus Expression Database

GSE74927

Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number variations, PIK3CA mutation, and pathway signatures. [RNA-Seq]

Submitted by Maureen Sartor (University of Michigan, USA) on Nov 12 2015

Platform: ngs – Illumina HiSeq 2000 (Homo sapiens)

Pubmed: 27091409, 30061624

Summary Purpose: There is substantial heterogeneity within the human papillomavirus (HPV) positive head and neck cancer (HNC) tumors that predispose them to different outcomes, however this subgroup is poorly characterized due to various historical reasons. Experimental Design: we perform unsupervised gene expression clustering on well-annotated HPV(+) HNC samples from two cohorts ( 84 total primary tumors), as well as 18 HPV(-) HNCs, to discover subtypes, and begin to characterize the differences between the subtypes in terms of their HPV characteristics, pathway activity, whole-genome somatic copy number variations and mutation frequencies. Results: We identified two distinctive HPV(+) subtypes by unsupervised clustering. Membership in the HPV(+) subtypes correlates with genic viral integration status, E2/E4/E5 expression levels and the ratio of spliced to full length HPV oncogene E6. The subtypes also show differences in copy number alterations, in particular the loss of chr16q and gain of chr3q, PIK3CA mutation, and in the expression of genes involved in several biological processes related to cancer, including immune response, oxidation-reduction process, and keratinocyte and mesenchymal differentiation. Conclusion: Our characterization of two subtypes of HPV(+) tumors provides valuable molecular level information in relation to the alternative paths to tumor development and to that of HPV(-) HNCs. Together, these results will shed light on stratifications of the HPV(+) HNCs and will help to guide personalized care for HPV(+) HNC patients.

36 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM1937901 UM-N01 head and neck cancer cell  Negative Uninfected
GSM1937902 UM-N02 head and neck cancer cell  Negative Uninfected
GSM1937903 UM-N03 head and neck cancer cell  Negative Uninfected
GSM1937904 UM-N04 head and neck cancer cell  Negative Uninfected
GSM1937905 UM-N05 head and neck cancer cell  Negative Uninfected
GSM1937906 UM-N06 head and neck cancer cell  Negative Uninfected
GSM1937907 UM-N07 head and neck cancer cell  Negative Uninfected
GSM1937908 UM-N08 head and neck cancer cell  Negative Uninfected
GSM1937909 UM-N09 head and neck cancer cell  Negative Uninfected
GSM1937910 UM-N10 head and neck cancer cell  Negative Uninfected
GSM1937911 UM-N11 head and neck cancer cell  Negative Uninfected
GSM1937912 UM-N12 head and neck cancer cell  Negative Uninfected
GSM1937913 UM-N13 head and neck cancer cell  Negative Uninfected
GSM1937914 UM-N14 head and neck cancer cell  Negative Uninfected
GSM1937915 UM-N15 head and neck cancer cell  Negative Uninfected
GSM1937916 UM-N16 head and neck cancer cell  Negative Uninfected
GSM1937917 UM-N17 head and neck cancer cell  Negative Uninfected
GSM1937918 UM-N18 head and neck cancer cell  Negative Uninfected
GSM1937919 UM-P01 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937920 UM-P02 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937921 UM-P03 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937922 UM-P04 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937923 UM-P05 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937924 UM-P06 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937925 UM-P07 head and neck cancer cell  HPV35 Alphapapillomavirus 9
GSM1937926 UM-P08 head and neck cancer cell  HPV18 Alphapapillomavirus 7
GSM1937927 UM-P09 head and neck cancer cell  HPV35 Alphapapillomavirus 9
GSM1937928 UM-P10 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937929 UM-P11 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937930 UM-P12 head and neck cancer cell  HPV33 Alphapapillomavirus 9
GSM1937931 UM-P13 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937932 UM-P14 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937933 UM-P15 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937934 UM-P16 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937935 UM-P17 head and neck cancer cell  HPV16 Alphapapillomavirus 9
GSM1937936 UM-P18 head and neck cancer cell  HPV16 Alphapapillomavirus 9