Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer

Abstract

BackgroundNRF2 is the key regulator of oxidative stress in normal cells and aberrant expression of the NRF2 pathway due to genetic alterations in the KEAP1 (Kelch-like ECH-associated protein 1)-NRF2 (nuclear factor erythroid 2 like 2)-CUL3 (cullin 3) axis leads to tumorigenesis and drug resistance in many cancers including head and neck squamous cell cancer (HNSCC). The main goal of this study was to identify specific genes regulated by the KEAP1-NRF2-CUL3 axis in HNSCC patients, to assess the prognostic value of this gene signature in different cohorts, and to reveal potential biomarkers.MethodsRNA-Seq V2 level 3 data from 279 tumor samples along with 37 adjacent normal samples from patients enrolled in the The Cancer Genome Atlas (TCGA)-HNSCC study were used to identify upregulated genes using two methods (altered KEAP1-NRF2-CUL3 versus normal, and altered KEAP1-NRF2-CUL3 versus wild-type). We then used a new approach to identify the combined gene signature by integrating both datasets and subsequently tested this signature in 4 independent HNSCC datasets to assess its prognostic value. In addition, functional annotation using the DAVID v6.8 database and protein-protein interaction (PPI) analysis using the STRING v10 database were performed on the signature.ResultsA signature composed of a subset of 17 genes regulated by the KEAP1-NRF2-CUL3 axis was identified by overlapping both the upregulated genes of altered versus normal (251 genes) and altered versus wild-type (25 genes) datasets. We showed that increased expression was significantly associated with poor survival in 4 independent HNSCC datasets, including the TCGA-HNSCC dataset. Furthermore, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and PPI analysis revealed that most of the genes in this signature are associated with drug metabolism and glutathione metabolic pathways.ConclusionsAltogether, our study emphasizes the discovery of a gene signature regulated by the KEAP1-NRF2-CUL3 axis which is strongly associated with tumorigenesis and drug resistance in HNSCC. This 17-gene signature provides potential biomarkers and therapeutic targets for HNSCC cases in which the NRF2 pathway is activated.Electronic supplementary materialThe online version of this article (10.1186/s12885-017-3907-z) contains supplementary material, which is available to authorized users.

Inhibition of Thioredoxin/Thioredoxin Reductase Induces Synthetic Lethality in Lung Cancers with Compromised Glutathione Homeostasis

“…The underlying mechanism is not yet clear. Nevertheless, the TCGA data showed that overexpression of the GSR, GCLC, and TXNRD1 were highly enriched in KEAP1-mutant lung adenocarcinoma (P ¼ 1.2 Â 10 À8 , 1.0 Â 10 À6 , and 1.4 Â 10 À9 , respectively) and in NFE2L2-mutant lung squamous cell cancer (P ¼ 1.5 Â 10 À3 , 4.7 Â 10 À4 , and 6.1 Â 10 À9 , respectively), supporting the roles of the KEAP1/NRF2 pathway in regulation of the expression of these oxidative stress-associated genes (37). It is possible that, unlike mutations in KEAP1/NRF2 pathways, low expression of GSR alone is not sufficient to trigger TXNRD1 overexpression.…”

Identifying Modules of Cooperating Cancer Drivers

“…However, we now have evidence that constitutive NRF2 activation via mutations in KEAP1 or recurrent NFE2L2 exon 2 deletions can drive tumor proliferation and metastasis [70,67]. NFE2L2 mutations have recently been shown to define subtypes with differential prognosis in lung and head and neck cancers [71,72,73,74]. Several upcoming clinical are designed to explore the therapeutic benefit of compounds that inhibit NRF2 in advanced cancer patients harboring mutations in NFE2L2 or KEAP1 [75,76,77].…”

Upregulation of AKR1C1 and AKR1C3 expression in OPSCC with integrated HPV16 and HPV‐negative tumors is an indicator of poor prognosis

“…Our approach of semi-quantitative normalization of tumor staining intensity by comparing it with adjacent epithelium might be furthermore supported by a study from Namani et al, where RNAseq data from the TCGA HNSCC cohort were normalized against normal tissue expression and subsequently lead to a signature of overexpressed oxidative stress response genes including AKR1C1 and AKR1C3. 33 For confirmation, we analyzed 25 The AKR1Cs 1 and 3 are known to catalyze the production of retinol isoforms from retinaldehyde and subsequently lowering retinoic acid concentrations. 37 Retinoic acid is a known inhibitor of NRF2 function, therefore decreased concentrations of retinoic acid lead to additional NRF2 activation.…”