The online version of this article (https://doi.org/10.1186/s12885-017-3907-z) contains supplementary material, which is available to authorized users.
NRF2 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.
RNA-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.
A 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.
Altogether, 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.
Additional file 1: Table S1. List of differentially expressed genes obtained from the RNA-Seq analysis of altered versus normal samples. (XLS 48 kb)12885_2017_3907_MOESM1_ESM.xls
Additional file 2: Table S2. List of differentially expressed genes obtained from the RNA-Seq analysis of altered versus wild-type samples. (XLS 29 kb)12885_2017_3907_MOESM2_ESM.xls
Additional file 3: Table S3. List of differentially expressed genes obtained from the RNA-Seq analysis of wild-type versus normal samples. (XLS 49 kb)12885_2017_3907_MOESM3_ESM.xls
Additional file 4: Table S4. List of NRF2-AREs identified in the -5 kb promoter regions of RAB6B, UCHL1 and TRIM16L genes. (XLS 38 kb)12885_2017_3907_MOESM4_ESM.xls
Additional file 5: Table S5. Multivariate analysis of 17-gene signature in 4 independent cohorts (XLS 25 kb)12885_2017_3907_MOESM5_ESM.xls
Additional file 6: Figure S1. Kaplan-Meier plots showing the survival analysis of TCGA-HNSCC cohort clinical variables: tumor grades G2 (A) and G3 (B); pathologic T stagesT1 (C) and T2 (D); and pathologic disease stages II (E) and III (F). (TIFF 798 kb)12885_2017_3907_MOESM6_ESM.tif
The Cancer Genome Atlas Network (348 collaborators). Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015;517(7536):576–82.
Saintigny P, Zhang L, Fan YH, El-Naggar AK, Papadimitrakopoulou VA, Feng L, Lee JJ, Kim ES, Ki Hong W, Mao L. Gene expression profiling predicts the development of oral cancer. Cancer Prev Res (Phila). 2011;4(2):218–29. CrossRef
Morris VK, Lucas FA, Overman MJ, Eng C, Morelli MP, Jiang ZQ, Luthra R, Meric-Bernstam F, Maru D, Scheet P et al: Clinicopathologic characteristics and gene expression analyses of non-KRAS 12/13, RAS-mutated metastatic colorectal cancer. Ann Oncol 2014, 25(10):2008-2014.
Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag; 2009. CrossRef
Huang d W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57. CrossRef
Aguirre-Gamboa R, Gomez-Rueda H, Martinez-Ledesma E, Martinez-Torteya A, Chacolla-Huaringa R, Rodriguez-Barrientos A, Tamez-Pena JG, Trevino V. SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis. PLoS One. 2013;8(9):e74250. CrossRefPubMedPubMedCentral
Roh JL, Jang H, Kim EH, Shin D. Targeting of the glutathione, Thioredoxin, and Nrf2 antioxidant Systems in Head and Neck Cancer. Antioxid Redox Signal. 2017;27(2):106–14.
Eggert A, Grotzer MA, Ikegaki N, Zhao H, Cnaan A, Brodeur GM, Evans AE. Expression of the neurotrophin receptor TrkB is associated with unfavorable outcome in Wilms' tumor. J Clin Oncol Off J Am Soc Clin Oncol. 2001;19(3):689–96. CrossRef
Schroder C, Milde-Langosch K, Gebauer F, Schmid K, Mueller V, Wirtz RM, Meyer-Schwesinger C, Schluter H, Sauter G, Schumacher U. Prognostic relevance of ubiquitin C-terminal hydrolase L1 (UCH-L1) mRNA and protein expression in breast cancer patients. J Cancer Res Clin Oncol. 2013;139(10):1745–55. CrossRefPubMed
Wulfanger J, Biehl K, Tetzner A, Wild P, Ikenberg K, Meyer S, Seliger B. Heterogeneous expression and functional relevance of the ubiquitin carboxyl-terminal hydrolase L1 in melanoma. Int J Cancer. 2013;133(11):2522–32. PubMed
Heitzer E, Artl M, Filipits M, Resel M, Graf R, Weissenbacher B, Lax S, Gnant M, Wrba F, Greil R, et al. Differential survival trends of stage II colorectal cancer patients relate to promoter methylation status of PCDH10, SPARC, and UCHL1. Modern Pathol. 2014;27(6):906–15. CrossRef
YY G, Yang M, Zhao M, Luo Q, Yang L, Peng H, Wang J, Huang SK, Zheng ZX, Yuan XH, et al. The de-ubiquitinase UCHL1 promotes gastric cancer metastasis via the Akt and Erk1/2 pathways. Tumor Biol. 2015;36(11):8379–87. CrossRef
- Gene-expression signature regulated by the KEAP1-NRF2-CUL3 axis is associated with a poor prognosis in head and neck squamous cell cancer
Md. Matiur Rahaman
- BioMed Central
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