Analysis of nuclear receptor expression in head and neck cancer

Studies of squamous cell carcinoma of the head and neck (HNSCC) have demonstrated the importance of nuclear receptors and their associated coregulators in the development and treatment of HNSCC. We sought to characterize members of the nuclear receptor super family through interrogation of RNA-Seq and microarray data.

TCGA RNA-Seq data within the cBioportal platform comparing HNSCC samples (n = 515 patients with RNA-Seq data) to normal tissue (n = 82 patients) was interrogated for significant differences in nuclear receptor expression. Affymetrix microarray analysis of HNSCC tumors relative to normal oral mucosa (41 tumor, 13 normal) was analyzed.

Of the 48 NR genes and 19 NR cofactors examined, 99 % of tumor samples in the TCGA had some form of NR gene 'alteration' compared to normal tissue. These alterations predominantly encompass expression changes. NR genes (PPARG) and (RORC), and the NR cofactor, (NCOA1), were differentially expressed and downregulated in tumors compared to normal tissue.

We have discovered significant decreases in PPARG expression with co-occurring changes in genes involved with lipid metabolism and cell cycle progression in HNSCC. We are targeting PPARγ with thiazolidinediones in a series of clinical trials to restore normal signaling via differentiation to hopefully reverse carcinogenesis. We also observed several receptors with differential expression associated with clinical factors that may become the focus of interest in future targeting efforts. These data provide evidence for nuclear receptors playing a role in the dysregulation of gene expression in HNSCC and illustrate the utility of current bioinformatic tools for interrogating complex, high throughput data sets.