Dataset Information

Highly preserved consensus gene modules in human papilloma virus 16 positive cervical cancer and head and neck cancers.

ABSTRACT: In this study, we investigated the consensus gene modules in head and neck cancer (HNC) and cervical cancer (CC). We used a publicly available gene expression dataset, GSE6791, which included 42 HNC, 14 normal head and neck, 20 CC and 8 normal cervical tissue samples. To exclude bias because of different human papilloma virus (HPV) types, we analyzed HPV16-positive samples only. We identified 3824 genes common to HNC and CC samples. Among these, 977 genes showed high connectivity and were used to construct consensus modules. We demonstrated eight consensus gene modules for HNC and CC using the dissimilarity measure and average linkage hierarchical clustering methods. These consensus modules included genes with significant biological functions, including ATP binding and extracellular exosome. Eigengen network analysis revealed the consensus modules were highly preserved with high connectivity. These findings demonstrate that HPV16-positive head and neck and cervical cancers share highly preserved consensus gene modules with common potentially therapeutic targets.

SUBMITTER: Zhang X

PROVIDER: S-EPMC5768383 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Highly preserved consensus gene modules in human papilloma virus 16 positive cervical cancer and head and neck cancers.

Zhang Xianglan X Cha In-Ho IH Kim Ki-Yeol KY

Oncotarget 20171207 69

In this study, we investigated the consensus gene modules in head and neck cancer (HNC) and cervical cancer (CC). We used a publicly available gene expression dataset, GSE6791, which included 42 HNC, 14 normal head and neck, 20 CC and 8 normal cervical tissue samples. To exclude bias because of different human papilloma virus (HPV) types, we analyzed HPV16-positive samples only. We identified 3824 genes common to HNC and CC samples. Among these, 977 genes showed high connectivity and were used t ...[more]

PMID: 29371966

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Project description:Human papillomaviruses (HPVs) are associated with nearly all cervical cancers (CCs), 20-30% of head and neck cancers (HNCs), and other cancers. Because HNCs also arise in HPV-negative patients, this type of cancer provides unique opportunities to define similarities and differences of HPV-positive versus HPV-negative cancers arising in the same tissue. Here, we describe genome-wide expression profiling of 84 HNCs, CCs and site-matched normal epithelial samples in which we used laser capture microdissection to enrich samples for tumor-derived versus normal epithelial cells. This analysis revealed that HPV+HNCs and CCs differed in their patterns of gene expression yet shared many changes compared to HPV-HNCs. Some of these shared changes were predicted, but many others were not. Notably, HPV+HNCs and CCs were found to be upregulated in their expression of a distinct and larger subset of cell cycle genes than observed in HPV-HNC. Moreover, HPV+ cancers over-expressed testis-specific genes that are normally expressed only in meiotic cells. Many, though not all, of the hallmark differences between HPV+HNC and HPV-HNC were a direct consequence of HPV and in particular the viral E6 and E7 oncogenes. This included a novel association of HPV oncogenes with testes specific gene expression. These findings in primary human tumors provide novel biomarkers for early detection of HPV+ and HPV- cancers, and emphasize the potential value of targeting E6 and E7 function, alone or combined with radiation and/or traditional chemotherapy, in the treatment of HPV+ cancers. Experiment Overall Design: All tissue samples were fresh frozen in liquid nitrogen and collected with patientsâ?? consent under approval of the Institutional Review Boards from all participating institutions. Each tissue sample was cryosectioned, and selected sections stained with hematoxylin/eosin, and reviewed to determine tumor content, pathological status, and freedom from necrosis and freezing artifacts. Epithelial cells from all normal samples and tumor cells from HNC or CC samples with less than 80% tumor were laser capture microdissected from adjacent sections using a PixCell II LCM system. For guidance, an adjacent section was briefly stained with hematoxylin to visualize tissue structure. Total RNA was extracted from sectioned and/or microdissected samples as follows: 1 ml of TRIzol (Invitrogen, Carlsbad, CA) was added to each tissue sample, homogenized by passing through a 20 gauge needle, and added to 0.2 ml chloroform. After centrifugation at 20,000 xg for 20 min at 4oC, RNA in the aqueous phase was precipitated with an equal volume of isopropanol for 30 min at 4oC, pelleted, and washed twice with cold 70% ethanol. Double strand (ds) cDNA was synthesized from this RNA using a SuperScript ds cDNA synthesis kit (Invitrogen) and T7 promoter-linked oligo (dT)24. Complementary RNA (cRNA) was synthesized from T7 promoter-linked ds cDNA using a MEGAscript high transcription kit (Ambion, Austin, TX). To obtain a sufficient cRNA for 2 microarray hybridizations, this amplification process was repeated. Second round cRNA was biotin labeled using a BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) and stored at -80oC until hybridized. cRNA quality and quantity was determined by gel electrophoresis and UV spectrophotometry. Whole human gene expression was profiled using Affymetrix Human Genome U133 Plus 2.0 arrays.

Dataset Information

Highly preserved consensus gene modules in human papilloma virus 16 positive cervical cancer and head and neck cancers.

Publications

Highly preserved consensus gene modules in human papilloma virus 16 positive cervical cancer and head and neck cancers.

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