Contribution of Genomics to the Surgical Management and Study of Oral Cancer

Abstract

Background: Oral squamous cell carcinoma (OSCC) is the most frequent type of tumor arising from the oral cavity. Surgery is the cornerstone of the treatment of these cancers. Tumor biology has long been overlooked as an important contributor to the outcome of surgical procedures, but recent studies are challenging this concept. Molecular analyses of tumor DNA or RNA provide a rich source of information about the biology of OSCC.

Methods: We searched for relevant articles using PubMed. We examined in particular the prospect of applying molecular methods for minimally invasive exploration of OSCC biology.

Results: We examined five potential applications of genomics to the surgical management and study of OSCC: i) assessing oral potentially malignant lesions; ii) tumor staging prior to surgery; iii) predicting postoperative risk in locally advanced tumors; iv) measuring minimal residual disease and optimizing the longitudinal monitoring of OSCC; and v) predicting the efficacy of medical treatment.

Conclusions: Genomic information can be harnessed in order to identify new biomarkers that could improve the staging, choice of therapy and management of OSCC. The identification of new biomarkers is awaited for better personalization of the surgical treatment of OSCC.

Fig. 1

An overview of the information that can be gained from tumor genomic analysis. DNA/RNA sequencing from tumor material permits identification of genomic mutations and structural rearrangements that define the mutational burden of a tumor, some of which can be targeted therapeutically. Analyzing tumor gene expression also provides information regarding the functional status of the tumor (e.g., the presence of hypoxic areas). Recent practical strategies permit analysis of an individual tumor’s clonal structure and the reconstruction of its evolution in a dynamic fashion, potentially providing useful information regarding its response to treatment. Another important aspect is analysis of the composition of the tumor microenvironment (TME), including its infiltration with immune cells. The density of T cell infiltrate, the functionality of T cells, and the immune receptor repertoire can be assessed directly through functional genomics

Fig. 2

DNA methylation and histone modifications as epigenetic marks and the corresponding methodologic approaches. The DNA methylation of CpG dinucleotides represses transcriptional activity. Chromatin condensation, typically regulated by post-translational modifications of histones, is another important determinant of gene expression. Various analytical strategies allow for targeted or genome-wide analyses of epigenetic marks. A common strategy used to analyze DNA methylation relies on DNA conversion by sodium bisulfite. Unmethylated cytosine (but not its methylated counterpart) is converted to uracil, which is recognized as thymine in subsequent reactions. Amplification by PCR and sequencing then can be used to perform targeted or genome-wide analyses of DNA methylation (methylation-specific PCR assay [MS-PCR] and whole-genome bisulfite sequencing [WGBS]). Array-based technologies constitute an accessible technique for genome-wide methylation analyses and have been used in The Cancer Genome Atlas (TCGA) (HM450). Chromatin immunoprecipitation with DNA sequencing (CHIP-seq) can be used to explore the post-translational modifications of histones. To explore chromatin accessibility for research purposes in cells and tissues, DNAse-seq (DNase I hypersensitive sites sequencing) and ATAC-seq (assay for transposase-accessible chromatin) approaches can be used. A recent development is the possibility of analyzing epigenetic marks in body fluids using cell-free DNA (cfDNA). Most studies to date perform targeted analyses using MS-PCR to analyze DNA methylation of cfDNA from either serum or saliva. A smaller number of studies recently have reported the use of the cfMeDIP-seq or ChIP-Seq strategies using the serum of cancer patients. Another promising strategy based on measuring the size of cfDNA fragments in the serum (DNA evaluation of fragments for early interception [DELFI]) was recently reported. This strategy is based on low-coverage sequencing of the cfDNA released by cancer cells in the blood because DNA packaging modulates the sensitivity of the genome to fragmentation. These new approaches offer the exciting prospect of noninvasive genome-wide exploration of tumor epigenetics, but their use has not been reported in oral squamous cell carcinoma (OSCC)

Fig. 3

A perineural invasion (PNI) gene expression profile identifies oral squamous cell carcinoma (OSCC) prone to recurrence. Kaplan–Meier analyses of disease-free survival (DFS) and overall survival (OS) in low to intermediate risk OSCC (n = 102 from TCGA) are based on the presence or absence of the PNI gene expression profile, as defined in Saidak et al. Tumors with low to intermediate risk are defined as T1/2 N2 or T3 N0-2, without extracapsular spread or surgical margins (SMs). Patients are divided into positive/negative PNI gene expression profile groups based on the average z for 26 PNI genes, with the cutoff at 0