Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks

Abstract

BackgroundAcquired and inherent radioresistance of tumor cells is related to tumor relapse and poor prognosis – not only in head and neck squamous cell carcinoma (HNSCC). The underlying molecular mechanisms are largely unknown. Therefore, systemic in-depth analyses are needed to identify key regulators of radioresistance. In the present study, subclones of the CAL-33 HNSCC cell line with different radiosensitivity were analyzed to identify signaling pathways related to the different phenotypes.MethodsSubclones with altered radiosensitivity were generated by fractionated irradiation of the parental CAL-33 cells. Differences in radiosensitivity were confirmed in colony formation assays. Selected subclones were characterized at the genomic and transcriptomic level by SKY, array CGH, and mRNA-microarray analyses. Time-course gene expression analyses upon irradiation using a natural cubic spline regression model identified temporally differentially expressed genes. Moreover, early and late responding genes were identified. Gene association networks were reconstructed using partial correlation. The Reactome pathway database was employed to conduct pathway enrichment analyses.ResultsThe characterization of two subclones with enhanced radiation resistance (RP) and enhanced radiosensitivity (SP) revealed distinct genomic and transcriptomic changes compared to the parental cells. Differentially expressed genes after irradiation shared by both subclones pointed to important pathways of the early and late radiation response, including senescence, apoptosis, DNA repair, Wnt, PI3K/AKT, and Rho GTPase signaling. The analysis of the most important nodes of the gene association networks revealed pathways specific to the radiation response in different phenotypes of radiosensitivity. Exemplarily, for the RP subclone the senescence-associated secretory phenotype (SASP) together with GPCR ligand binding were considered as crucial. Also, the expression of endogenous retrovirus ERV3-1in response to irradiation has been observed, and the related gene association networks have been identified.ConclusionsOur study presents comprehensive gene expression data of CAL-33 subclones with different radiation sensitivity. The resulting networks and pathways associated with the resistant phenotype are of special interest and include the SASP. The radiation-associated expression of ERV3-1 also appears highly attractive for further studies of the molecular mechanisms underlying acquired radioresistance. The identified pathways may represent key players of radioresistance, which could serve as potential targets for molecularly designed, therapeutical intervention.Electronic supplementary materialThe online version of this article (doi:10.1186/s13014-016-0672-0) contains supplementary material, which is available to authorized users.

A Five-MicroRNA Signature Predicts Survival and Disease Control of Patients with Head and Neck Cancer Negative for HPV Infection

“…mitosis and senescence-associated pathways. Several of the pathways and miRNA-target genes were already shown to be relevant for the pathogenesis and radiation response of HNSCC (5)(6)(7)(42)(43)(44)(45)(46)(47). Mutations of IGF1R and ARID1A and the involvement of CADM1 and SOD2 in HNSCC have been reported (6,43,46,47).…”

HNSCC: Tumour Antigens and Their Targeting by Immunotherapy

“…The HERV-K family of endogenous retroviruses is one of the most studied groups. A high expression of HERV-K-MEL was described in HNSCC, in comparison to healthy tissue [ 102 ], and HERV-R (ERV3-1) was reported to lead to radioresistance in HNSCC [ 103 ]. Whether the differential expression can be exploited to generate a cancer-type-specific vaccine is currently unknown, but large international efforts, such as that of the PCAWG consortium in the UK from the 100k genomes project [ 104 ], will shed light on the breadth of expression and will need to be complemented by studies of T-cell reactivities to HERVs.…”

Endogenous Retrovirus 3 – History, Physiology, and Pathology

“…On the other hand, ERV3 was considered to be a tumor suppressor ( Matsuda et al, 1997 ; Lin et al, 1999 , 2000 ). ERV3 is up-regulated after irradiation of head and neck squamous cell carcinoma cells ( Michna et al, 2016 ), during monocytic differentiation of acute myelogenous leukemia cells ( Larsson et al, 1996 , 1997 ; Abrink et al, 1998 ) as well as during differentiation of normal squamous cells ( Otsuka et al, 2006 ). Demethylation of the ERV3 locus during monocytic differentiation leads to expression of ERV3 and ZNF117 ( Andersson et al, 1998 ).…”