Genetic alterations in CDKN2A interacting network and their putative association with head and neck squamous cell carcinoma

Abstract

Head and neck squamous cell carcinoma (HNSCC) is a complex, polygenic disorder involving the host, microbial, and environmental factors. The present study investigated the CDKN2A (cyclin-dependent kinase inhibitor 2 A) gene interacting network. This gene is a key player in the cell cycle pathway, and any abnormalities in this gene have been linked to abnormal cell cycle processes. The present study followed an observational study design wherein computational tools were used to demonstrate the genetic alterations, expression profile, and survival status of head and neck cancer patients. The head and neck squamous cell carcinoma and oral squamous cell carcinoma datasets (The Cancer Gene Atlas (TCGA), Firehose Legacy) were analyzed. The cBioportal and UALCAN [University of ALabama at Birmingham CANcer data analysis Portal] were used to demonstrate the genetic alterations and gene expression profile alongside the survival of patients. The oncoprint data analysis of the CDKN2A gene network showed 72% and 48% of aberrations in the TP53 gene among HNSCC and OSCC (Oral Squamous Cell Carcinoma) cases, respectively. The gene expression profile demonstrated over-expression of CDKN2A in primary tissues. The survival analysis showed a statistically significant difference between the low/medium and high expression groups. The deep deletion was the common alteration observed among head and neck cancer patients of the CDKN2A gene. The gene expression profile showed significant upregulation of CDKN2A in primary tissues [p = 〈10⁻¹²]. The genetic alterations observed in the CDKN2A gene were found to correlate well with the survival status of head and neck cancer patients. The functional validation of the mutations and alterations observed in this gene would aid us in understanding the vital role of this gene network in the process of oral carcinogenesis.