Dataset Information

Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas.

ABSTRACT: 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.

SUBMITTER: Banerjee S

PROVIDER: S-EPMC5481414 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas.

Banerjee Sagarika S Tian Tian T Wei Zhi Z Peck Kristen N KN Shih Natalie N Chalian Ara A AA O'Malley Bert W BW Weinstein Gregory S GS Feldman Michael D MD Alwine James J Robertson Erle S ES

Scientific reports 20170622 1

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 bacte ...[more]

PMID: 28642609

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Project description:Head and neck squamous cell carcinoma (HNSCC) often present with locoregional or distant disease, despite multimodal therapeutic approaches, which include surgical resection, chemoradiotherapy, and more recently immunotherapy for metastatic, or recurrent HNSCC. Therapies often target the primary and nodal regional HNSCC sites, and efficacy at controlling occult distant sites remains poor. Whilst our understanding of the tumour microenvironment, conducive for effective therapies is increasing, the biology underpinning locoregional sites remains unclear. Here, we applied targeted spatial proteomic approaches to primary and lymph node metastasis from an oropharyngeal SCC (OPSCC) cohort, to understand the expression of proteins within tumour, and stromal compartments of the respective sites in both matched and unmatched patients’ samples. In unmatched analyses of n=43 primary and 11 nodal metastasis, our data indicated that tumour cells in nodal metastases had higher levels of Ki-67, PARP, BAD and cleaved caspase 9, suggesting a role for increased proliferation, DNA repair and apoptosis within these metastatic cells. Conversely, in matched analyses (n=7), pro-apoptotic markers BIM and BAD were enriched in the stroma of primary tumours. Univariate, overall survival (OS) analysis indicated CD25 in tumour regions of primary tumours to be associated with reduced survival (HR=3.3, p=0.003), while partial response (PR) was associated with an improved OS (HR=0.33, p=0.015). This study highlights the utility of spatial proteomics for delineating tumour and stroma compartment composition, and the utility towards understanding these properties in locoregional metastasis. These findings indicate the unique biological properties of lymph node metastases that may elucidate further understanding of the subsequent distant metastatic potential of OPSCC. In this dataset, we applied GeoMx DSP protein profiling to tumour and tumour microenvironment regions of primary and lymphnode metastasis FFPE samples. The files here represent the Ncounter readout from this assay.

Dataset Information

Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas.

Publications

Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas.

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