Project description:Expression microarray analyses was used to analyze 33 OSCC to unveil potential prognostic markers. A quality control filter was applied based on Feature Extraction flags (NA replacing values). Cy3/Cy5 ratios were log2 transformed Overall design: Experiment condition, 33 OSCC samples obtained from biopsy from previous untreated patietns were laleled with Cy3 and a reference sample (pool of cell lines) was labled with Cy3. Samples Cy3 and Cy5 were mixed and hybridized at slide glasses Agilent 4x40k platform.
Project description:aCGH was used to evaluate 33 OSCC aiming to unveil potential prognostic markers. Overall design: Copy number alterations were evaluated using Agilent Human CGH 180K Oligo Microarrays array-CGH (Agilent Technologies) in 33 OSCC aiming to unveil potential prognostic markers.
Project description:BACKGROUND:The genetic profile for human papilloma virus positive (HPV+) oropharyngeal squamous cell carcinomas (OPSCC) remains largely unknown. The purpose of this study was to sequence tissue material from a large cohort of locoregionally-advanced HPV+ OPSCCs. METHODS:We performed targeted deep sequencing of 395 cancer-associated genes in 114 matched tumor/normal loco-regionally advanced HPV+ OPSCCs. Mutations and copy number aberrations were determined. RESULTS:We identified a total of 3459 mutations with an average of 10 mutations per megabase and a median of 28 variants per sample. The most frequently mutated genes were KALRN (28%), SPTBN1 (32%), KMT2A (31%), ZNRF3 (9%), BNC2 (12%), NOTCH2 (25%), FGFR2 (12%), SMAD2 (6%), and AR (13%). Our findings were dominated by COSMIC signature 5 and 12, represented in other head and neck cancers and in hepatocellular carcinomas, respectively. CONCLUSIONS:We have identified multiple genetic aberrations in HPV+ OPSCCs, and the COSMIC signature 12 as most prevalent. The mutations harbour both therapeutic and prognostic potential.
Project description:Oropharyngeal cancer accounts for approximately 2.8% of newly cancer cases. Although classically a tobacco related disease, most cases today are related to infection with human papilloma virus (HPV) and present with locally advanced tumors. HPV related tumors have been recognized as a molecularly distinct entity with higher response rates to therapy, lower rates of relapse, and improved overall survival. Treatment of oropharyngeal cancer entails a multi-disciplinary approach with concomitant chemoradiation. The role of induction chemotherapy in locally advanced tumors continues to be controversial however large studies have demonstrated no difference in survival or time to treatment failure. Surgical approaches may be employed with low volume oropharyngeal cancers and with development new endoscopic tools, more tumors are able to be resected via an endoscopic approach. Given advances in the understanding of HPV related oropharyngeal cancer, ongoing research is looking at ways to minimize toxicities via de-intensification of therapy. Unfortunately, some patients develop recurrent or metastatic disease. Novel therapeutics are currently being investigated for this patient population including immunotherapeutics. This review discusses the current understanding of the pathogenesis of oropharyngeal cancer and treatment. We also discuss emerging areas of research as it pertains to de-intensification as well novel therapeutics for the management of metastatic disease.
Project description:BACKGROUND:There is a paucity of studies reporting long-term survival outcomes for HPV/p16 positive oropharyngeal squamous cell carcinoma (OPSCC). This study aims to compare long-term outcomes of advanced stage p16 positive and negative OPSCCs, treated by surgical and non-surgical modalities. METHODS:OPSCC patients from 1998 to 2012 were identified through a prospectively collected cancer registry. P16 immunohistochemistry was used as a surrogate marker for HPV-OPSCC. Overall survival (OS) and aspiration free survival (AFS) comparisons were made between patients treated with chemoradiation (CRT) versus primary surgery and radiation/chemoradiation (S+RT/CRT) at 5, 10 and 15 years post-treatment. RESULTS:A total of 319 patients were included. P16 positive patients and non-smokers had significantly higher long-term (5, 10 and 15-year) OS. Smokers and p16 negative patients treated with S+RT/CRT had improved long-term OS compared to patients who received CRT. Smokers and p16 negative patients had lower long-term AFS. Multivariate analysis showed improved OS was associated with p16 positivity (HR 0.42, 0.28-0.61) and surgery (HR 0.47, 0.32-0.69), whereas lower OS was associated with ECOG ≥ 2 (HR 2.46, 1.61-3.77), smoking (HR 2.37, 1.41-3.99) and higher stage (HR 1.68, 1.05-2.68). CONCLUSIONS:In smokers and p16-negative OPSCC patients, primary surgery may be associated with improved long-term survival and dysphagia-related outcomes.
Project description:PURPOSE OF REVIEW:To discuss the changing landscape and significant developments in the diagnosis and management of oropharyngeal squamous cell carcinoma. RECENT FINDINGS:High-risk human papilloma viruses (HPVs) have been recognized as important causative factors for oropharyngeal cancer. The diagnosis is established with type-specific and broad-spectrum in-situ hybridization probes and/or p16 immunohistochemistry assays on fresh frozen paraffin-embedded tissue blocks. HPV-associated tumors have superior response and outcomes compared with HPV-unrelated tumors. Retrospective studies have been able to stratify oropharyngeal squamous cell carcinoma based on HPV status, tumor stage, nodal stage, and smoking history into risk groups with differing risks of death or distant disease. Selected patients, nonsmokers with less advanced nodal stage, may be overtreated with current treatment paradigms, and deintensification of curative therapy is a current research focus for these patients. Smokers, patients with advanced nodal or tumor stage, and those with HPV-unrelated cancers have a less favorable prognosis and the search for novel targets is particularly important for these patients. SUMMARY:The present review will highlight the current standards and the future direction of novel therapies in both HPV-associated and HPV-unrelated cancers.
Project description:The microbiome is fundamentally one of the most unique organs in the human body. Dysbiosis can result in critical inflammatory responses and result in pathogenesis contributing to neoplastic events. We used a pan-pathogen array technology (PathoChip) coupled with next-generation sequencing to establish microbial signatures unique to human oral and oropharyngeal squamous cell carcinomas (OCSCC/OPSCC). Signatures for DNA and RNA viruses including oncogenic viruses, gram positive and negative bacteria, fungi and parasites were detected. Cluster and topological analyses identified 2 distinct groups of microbial signatures related to OCSCCs/OPSCCs. Results were validated by probe capture next generation sequencing; the data from which also provided a comprehensive map of integration sites and chromosomal hotspots for micro-organism genomic insertions. Identification of these microbial signatures and their integration sites may provide biomarkers for OCSCC/OPSCC diagnosis and prognosis as well as novel avenues for study of their potential role in OCSCCs/OPSCCs.