Cervical cancer is responsible for 10–15% of cancer-related deaths in women worldwide1,2. The etiological role of infection with high-risk human papilloma viruses (HPV) in cervical carcinomas is well established3. Previous studies have implicated somatic mutations in PIK3CA, PTEN, TP53, STK11 and KRAS4–7 as well as several copy number alterations in the pathogenesis of cervical carcinomas8,9. Here, we report whole exome sequencing analysis of 115 cervical carcinoma-normal paired samples, transcriptome sequencing of 79 cases and whole genome sequencing of 14 tumor-normal pairs. Novel somatic mutations in 79 primary squamous cell carcinomas include recurrent E322K substitutions in the MAPK1 gene (8%), inactivating mutations in the HLA-B gene (9%), and mutations in EP300 (16%), FBXW7 (15%), NFE2L2 (4%) TP53 (5%) and ERBB2 (6%). We also observed somatic ELF3 (13%) and CBFB (8%) mutations in 24 adenocarcinomas. Squamous cell carcinomas had higher frequencies of somatic mutations in the Tp*C dinucleotide context than adenocarcinomas. Gene expression levels at HPV integration sites were significantly higher in tumors with HPV integration compared with expression of the same genes in tumors without viral integration at the same site. These data demonstrate several recurrent genomic alterations in cervical carcinomas that suggest novel strategies to combat this disease.

Previous studies have established that a subset of head and neck tumors contains human papillomavirus (HPV) sequences and that HPV-driven head and neck cancers display distinct biological and clinical features. HPV is known to drive cancer by the actions of the E6 and E7 oncoproteins, but the molecular architecture of HPV infection and its interaction with the host genome in head and neck cancers have not been comprehensively described. We profiled a cohort of 279 head and neck cancers with next generation RNA and DNA sequencing and show that 35 (12.5%) tumors displayed evidence of high-risk HPV types 16, 33, or 35. Twentyfive cases had integration of the viral genome into one or more locations in the human genome with statistical enrichment for genic regions. Integrations had a marked impact on the human genome and were associated with alterations in DNA copy number, mRNA transcript abundance and splicing, and both inter-and intrachromosomal rearrangements. Many of these events involved genes with documented roles in cancer. Cancers with integrated vs. nonintegrated HPV displayed different patterns of DNA methylation and both human and viral gene expressions. Together, these data provide insight into the mechanisms by which HPV interacts with the human genome beyond expression of viral oncoproteins and suggest that specific integration events are an integral component of viral oncogenesis.cancer | head and neck | papilloma virus | genome rearrangement | integration sites H ead and neck cancer (HNC) is a heterogeneous group of tumors characterized by a common anatomic origin, and most such tumors develop from within the mucosa and are classified as head and neck squamous cell carcinomas (HNSCCs) (1). HNSCC, the sixth most common cancer diagnosed worldwide and the eighth most common cause of cancer death (2), is frequently associated with human papillomavirus (HPV) infection (3, 4). Depending on the anatomic site of the tumor, HPV prevalence is estimated at 23-36% (5). HPV-positive HNSCCs form a distinct subset of HNCs that differs from HPV-negative HNSCCs in tumor biology and clinical characteristics, including superior clinical outcomes (6-9).The molecular pathogenesis of HPV-driven HNSCC also seems distinct from HPV-negative tumors, with previous studies showing a divergent spectrum of alterations in gene expression, mutations, amplifications, and deletions as well as distinct epigenome alterations (10-15). HPV is known to drive tumorigenesis through the actions of its major oncoproteins E6 and E7, which target numerous cellular pathways, including inactivation of p53 and the retinoblastoma (Rb) protein (16-18). Together with E5, they also play an important role in immune evasion, being involved in both innate and adaptive immunity (19,20).Initially after infection, HPV is identified in circular extrachromosomal particles or episomes. A critical step in progression to cancer is the integration of viral DNA into the host cell Significance A significant proportion of head and neck cancer is driven by human papil...

Purpose: The goal of this study was to examine the effect of tobacco use on disease recurrence (local/ regional recurrence, distant metastasis, or second primary) among patients with human papillomavirus (HPV)-positive squamous cell carcinoma of the oropharynx (SCCOP) following a complete response to chemoradiation therapy.Experimental Design: Between 1999 and 2007, 124 patients with advanced SCCOP (86% with stage IV) and adequate tumor tissue for HPV analysis who were enrolled in one of two consecutive University of Michigan treatment protocols were prospectively included in this study. Patients were categorized as never-, former, or current tobacco users. The primary end points were risk of disease recurrence and time to recurrence; secondary end points were disease-specific survival and overall survival.Results: One hundred and two patients (82.3%) had HPV-positive tumors. Over two thirds (68%) of patients with HPV-positive tumors were tobacco users. Among HPV-positive patients, current tobacco users were at significantly higher risk of disease recurrence than never-tobacco users (hazard ratio, 5.2; confidence interval, 1.1-24.4; P = 0.038). Thirty-five percent of HPV-positive ever tobacco users recurred compared with only 6% of HPV-positive never users and 50% of HPV-negative patients. All HPV-negative patients were tobacco users and had significantly shorter times to recurrence (P = 0.002), and had reduced disease-specific survival (P = 0.004) and overall survival (P < 0.001) compared with HPV-positive patients. Compared with HPV-positive never-tobacco users, those with a tobacco history showed a trend for reduced disease-specific survival (P = 0.064) but not overall survival (P = 0.221).Conclusions: Current tobacco users with advanced, HPV-positive SCCOP are at higher risk of disease recurrence compared with never-tobacco users. Clin Cancer Res; 16(4); 1226-35. ©2010 AACR.Head and neck squamous cell carcinoma is the eighth most common malignancy worldwide (1) and represents ∼5% of new cancer diagnoses worldwide annually (2). Over the past three decades, there has been a steady increase in the incidence of tonsil and tongue squamous cell carcinomas (3, 4). Recent evidence has identified high-risk human papillomavirus (HPV), particularly HPV-16, as a causative agent for a subset of head and neck squamous cell carcinomas, accounting for over 50% of squamous cell carcinomas of the oropharynx (SCCOP) in the United States (5-9). HPV-positive SCCOP has a distinct risk factor profile (6) and oncogenic mechanism (10, 11), and likely portends a more favorable prognosis than HPV-negative SCCOP (5,7,(12)(13)(14)(15)(16)(17). Despite its effect on prognosis, tumor HPV status has not yet been used to alter therapeutic management. The most popular current treatment for advanced SCCOP, regardless of HPV status, involves concurrent chemoradiation Authors' Affiliations:

Because immune responses within the tumor microenvironment may be important predictors of tumor biology, correlations of specific types of tumor infiltrating lymphocytes (TILs) with clinical variables and outcomes were determined in 278 previously untreated patients with head and neck cancer (HNSCC). Methods Infiltrating levels of CD4 (helper T cells), CD8 (cytotoxic/suppressor T cells), FoxP3, regulatory T cells), CD68 (myeloid derived suppressor cells) and CD1a (Langerhan) cells were retrospectively measured by immunohistology in tissue mircoarrays. Cox models tested associations with patient outcomes after adjusting for all known prognostic factors. Median follow up was 36.6 months. Results Higher CD4 and CD8 TIL levels were associated with improved overall (HR 0.77 [0.65 –0.93] p=.005 and HR 0.77 [0.64–0.94] p=.008 respectively), and relapse free survival (p=.03, and .05 respectively). After controlling for prognostic factors, higher CD4 levels predicted improved overall and disease specific survival (p=.003 and .004 respectively). Conclusions The findings suggest that TILs are a significant independent prognostic factor and potential biomarker for HNSCC that differ by treatment.