Fibronectin 1 is a potential biomarker for radioresistance in head and neck squamous cell carcinoma

Radiotherapy remains the backbone of head and neck cancer therapy but response is sometimes impeded by tumor radioresistance. Identifying predictive biomarkers of radiotherapy response is a crucial step towards personalized therapy. The aim of this study was to explore gene expression data in search of biomarkers predictive of the response to radiotherapy in head and neck squamous cell carcinoma (HNSCC). Microarray analysis was performed on five cell lines with various intrinsic radiosensitivity, selected from a panel of 29 HNSCC cell lines. The bioinformatics approach included Gene Ontology (GO) enrichment profiling and Ingenuity Pathway Analysis (IPA). The GO-analysis detected 16 deregulated categories from which development, receptor activity, and extracellular region represented the largest groups. Fourteen hub genes (CEBPA, CEBPB, CTNNB1, FN1, MYC, MYCN, PLAU, SDC4, SERPINE1, SP1, TAF4B, THBS1, TP53 and VLDLR) were identified from the IPA network analysis. The hub genes in the highest ranked network, (FN1, SERPINE1, THBS1 and VLDLR) were further subjected to qPCR analysis in the complete panel of 29 cell lines. Of these genes, high FN1 expression associated to high intrinsic radiosensitivity (p=0.047). In conclusion, gene ontologies and hub genes of importance for intrinsic radiosensitivity were defined. The overall results suggest that FN1 should be explored as a potential novel biomarker for radioresistance.

[1]  B. Klump,et al.  C-myc gene amplification in different stages of oesophageal squamous cell carcinoma: prognostic value in relation to treatment modality. , 2003, Anticancer research.

[2]  Frédéric Hollande,et al.  Clinical relevance of nine transcriptional molecular markers for the diagnosis of head and neck squamous cell carcinoma in tissue and saliva rinse , 2009, BMC Cancer.

[3]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[4]  E. Hay,et al.  The mesenchymal cell, its role in the embryo, and the remarkable signaling mechanisms that create it , 2005, Developmental dynamics : an official publication of the American Association of Anatomists.

[5]  K. Coombes,et al.  Microarrays: retracing steps , 2007, Nature Medicine.

[6]  Yusuke Nakamura,et al.  Classification of sensitivity or resistance of cervical cancers to ionizing radiation according to expression profiles of 62 genes selected by cDNA microarray analysis. , 2002, Neoplasia.

[7]  Roland C Grafström,et al.  Bioinformatics processing of protein and transcript profiles of normal and transformed cell lines indicates functional impairment of transcriptional regulators in buccal carcinoma. , 2007, Journal of proteome research.

[8]  Brad T. Sherman,et al.  DAVID: Database for Annotation, Visualization, and Integrated Discovery , 2003, Genome Biology.

[9]  R. Grénman,et al.  Radiotherapy response in oral squamous carcinoma cell lines: Evaluation of apoptotic proteins as prognostic factors , 2007, Head & neck.

[10]  R. Grafström,et al.  Microarray Assessment of Fibronectin, Collagen and Integrin Expression and the Role of Fibronectin–Collagen Coating in the Growth of Normal, SV40 T-antigen-immortalised and Malignant Human Oral Keratinocytes , 2003, Alternatives to laboratory animals : ATLA.

[11]  H. Dressman,et al.  Genomic signatures to guide the use of chemotherapeutics , 2006, Nature Medicine.

[12]  A. Rajasekaran,et al.  Reassessing epithelial to mesenchymal transition as a prerequisite for carcinoma invasion and metastasis. , 2006, Cancer research.

[13]  M. Ehrengruber,et al.  Quantitative real-time PCR for the measurement of feline cytokine mRNA , 1999, Veterinary Immunology and Immunopathology.

[14]  N. Seki,et al.  Identification of candidate radioresistant genes in human squamous cell carcinoma cells through gene expression analysis using DNA microarrays. , 2005, Oncology reports.

[15]  M. Stack,et al.  Functional relevance of urinary-type plasminogen activator receptor-alpha3beta1 integrin association in proteinase regulatory pathways. , 2006, The Journal of biological chemistry.

[16]  P. Gaffney,et al.  Identification of a Gene Expression Signature Associated with Recurrent Disease in Squamous Cell Carcinoma of the Head and Neck , 2004, Cancer Research.

[17]  Y. Hayashizaki,et al.  Differential gene expression profiles of radioresistant oesophageal cancer cell lines established by continuous fractionated irradiation , 2004, British Journal of Cancer.

[18]  R. Grafström,et al.  Matrix metalloproteinase-7 and -13 expression associate to cisplatin resistance in head and neck cancer cell lines. , 2009, Oral oncology.

[19]  J. Wagner,et al.  In vitro radiation resistance among cell lines established from patients with squamous cell carcinoma of the head and neck , 1991, Cancer.

[20]  A. Elkahloun,et al.  A Novel Nuclear Factor-κB Gene Signature Is Differentially Expressed in Head and Neck Squamous Cell Carcinomas in Association with TP53 Status , 2007, Clinical Cancer Research.

[21]  M. Molls,et al.  PAI-1 levels predict response to fractionated irradiation in 10 human squamous cell carcinoma lines of the head and neck. , 2008, Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology.

[22]  K. Verschueren,et al.  Involvement of Ets-1 transcription factor in inducing matrix metalloproteinase-2 expression by epithelial-mesenchymal transition in human squamous carcinoma cells. , 2006, International journal of oncology.

[23]  S. Hehlgans,et al.  3D cell cultures of human head and neck squamous cell carcinoma cells are radiosensitized by the focal adhesion kinase inhibitor TAE226. , 2009, Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology.

[24]  John Quackenbush.  Microarray analysis and tumor classification. , 2006, The New England journal of medicine.

[25]  Li Mao,et al.  Transcriptomic dissection of tongue squamous cell carcinoma , 2008, BMC Genomics.

[26]  J. Nevins,et al.  Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial. , 2007, The Lancet. Oncology.

[27]  O. Kallioniemi,et al.  Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses , 2006, Oncogene.

[28]  J. Roh,et al.  Wnt signaling controls radiosensitivity via cyclooxygenase‐2‐mediated Ku expression in head and neck cancer , 2008, International journal of cancer.

[29]  David A. Cheresh,et al.  Integrins in cancer: biological implications and therapeutic opportunities , 2010, Nature Reviews Cancer.

[30]  Raghu Kalluri,et al.  The epithelial–mesenchymal transition: new insights in signaling, development, and disease , 2006, The Journal of cell biology.

[31]  John N Weinstein,et al.  Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen. , 2008, Cancer research.

[32]  Jing Yang,et al.  Identification of Differentially Expressed Genes Contributing to Radioresistance in Lung Cancer Cells using Microarray Analysis , 2005, Radiation research.

[33]  Kengo Saito,et al.  Genes and molecular pathways related to radioresistance of oral squamous cell carcinoma cells , 2007, International journal of cancer.

[34]  Kyung-Ja Cho,et al.  Clinical significance of β1 integrin expression as a prediction marker for radiotherapy in early glottic carcinoma , 2006, The Laryngoscope.

[35]  H. Kosmehl,et al.  Distribution of laminin and fibronectin isoforms in oral mucosa and oral squamous cell carcinoma , 1999, British Journal of Cancer.

[36]  L. Dinardo,et al.  Genes involved in radiation therapy response in head and neck cancers , 2009, The Laryngoscope.

[37]  J. Moyano,et al.  Interference of tenascin-C with syndecan-4 binding to fibronectin blocks cell adhesion and stimulates tumor cell proliferation. , 2001, Cancer research.

[38]  A. Culhane,et al.  Common Molecular Mechanisms of Mammary Gland Development and Breast Cancer , 2007, Cellular and Molecular Life Sciences.

[39]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[40]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[41]  F. Jerhammar,et al.  Number of negative points: a novel method for predicting radiosensitivity in head and neck tumor cell lines. , 2008, Oncology reports.

[42]  Gabriela Kalna,et al.  Divergent routes to oral cancer. , 2006, Cancer research.

[43]  R. Grafström,et al.  Multiple genotypic aberrances associate to terminal differentiation-deficiency of an oral squamous cell carcinoma in serum-free culture. , 2008, Differentiation; research in biological diversity.

[44]  W. Liang,et al.  TM4 microarray software suite. , 2006, Methods in enzymology.

[45]  D. Radisky,et al.  Matrix metalloproteinases stimulate epithelial-mesenchymal transition during tumor development , 2008, Clinical & Experimental Metastasis.

[46]  K. Iyer,et al.  Elevated levels and fragmented nature of cellular fibronectin in the plasma of gastrointestinal and head and neck cancer patients. , 2006, Clinica chimica acta; international journal of clinical chemistry.

[47]  M. Nadji,et al.  Tissue detection of biomolecular predictors in breast cancer , 2006, Expert review of anticancer therapy.

[48]  K. Pekkola‐Heino,et al.  Comparison of cellular radiosensitivity between different localizations of head and neck squamous-cell carcinoma , 2005, Journal of Cancer Research and Clinical Oncology.

[49]  C. Plass,et al.  Tumor suppressor activity of CCAAT/enhancer binding protein alpha is epigenetically down-regulated in head and neck squamous cell carcinoma. , 2007, Cancer research.

[50]  T. Carey,et al.  Clonogenic cell assay for anchorage‐dependent squamous carcinoma cell lines using limiting dilution , 1989, International journal of cancer.

[51]  M. Molls,et al.  Induction of plasminogen activator inhibitor type-1 (PAI-1) by hypoxia and irradiation in human head and neck carcinoma cell lines , 2007, BMC Cancer.