Meta-Analyses of Microarray Datasets Identifies ANO1 and FADD as Prognostic Markers of Head and Neck Cancer

Ram Bhupal Reddy; Anupama Rajan Bhat; Bonney Lee James; Sindhu Valiyaveedan Govindan; Rohit Mathew; D R Ravindra; Naveen Hedne; Jeyaram Illiayaraja; Vikram Kekatpure; Samanta S Khora; Wesley Hicks; Pramila Tata; Moni A Kuriakose; Amritha Suresh

doi:10.1371/journal.pone.0147409

Meta-Analyses of Microarray Datasets Identifies ANO1 and FADD as Prognostic Markers of Head and Neck Cancer

PLoS One. 2016 Jan 25;11(1):e0147409. doi: 10.1371/journal.pone.0147409. eCollection 2016.

Authors

Ram Bhupal Reddy^{1

2

3}, Anupama Rajan Bhat⁴, Bonney Lee James^{1

2}, Sindhu Valiyaveedan Govindan², Rohit Mathew¹, D R Ravindra^{1

2}, Naveen Hedne², Jeyaram Illiayaraja⁵, Vikram Kekatpure², Samanta S Khora³, Wesley Hicks^{6

7}, Pramila Tata⁴, Moni A Kuriakose^{1

2

7}, Amritha Suresh^{1

2}

Affiliations

¹ Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India.
² Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India.
³ Division of Medical Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology University, Vellore, Tamil Nadu, India.
⁴ Strand Life Sciences, Kirloskar Business Park, Bangalore, Karnataka, India.
⁵ Department of Clinical Research, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India.
⁶ Department of Head and Neck/Plastic & Reconstructive Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America.
⁷ Mazumdar Shaw Medical Centre-Roswell Park Collaboration Program, Roswell Park Cancer Institute, Buffalo, New York, United States of America.

Abstract

The head and neck squamous cell carcinoma (HNSCC) transcriptome has been profiled extensively, nevertheless, identifying biomarkers that are clinically relevant and thereby with translational benefit, has been a major challenge. The objective of this study was to use a meta-analysis based approach to catalog candidate biomarkers with high potential for clinical application in HNSCC. Data from publically available microarray series (N = 20) profiled using Agilent (4X44K G4112F) and Affymetrix (HGU133A, U133A_2, U133Plus 2) platforms was downloaded and analyzed in a platform/chip-specific manner (GeneSpring software v12.5, Agilent, USA). Principal Component Analysis (PCA) and clustering analysis was carried out iteratively for segregating outliers; 140 normal and 277 tumor samples from 15 series were included in the final analysis. The analyses identified 181 differentially expressed, concordant and statistically significant genes; STRING analysis revealed interactions between 122 of them, with two major gene clusters connected by multiple nodes (MYC, FOS and HSPA4). Validation in the HNSCC-specific database (N = 528) in The Cancer Genome Atlas (TCGA) identified a panel (ECT2, ANO1, TP63, FADD, EXT1, NCBP2) that was altered in 30% of the samples. Validation in treatment naïve (Group I; N = 12) and post treatment (Group II; N = 12) patients identified 8 genes significantly associated with the disease (Area under curve>0.6). Correlation with recurrence/re-recurrence showed ANO1 had highest efficacy (sensitivity: 0.8, specificity: 0.6) to predict failure in Group I. UBE2V2, PLAC8, FADD and TTK showed high sensitivity (1.00) in Group I while UBE2V2 and CRYM were highly sensitive (>0.8) in predicting re-recurrence in Group II. Further, TCGA analysis showed that ANO1 and FADD, located at 11q13, were co-expressed at transcript level and significantly associated with overall and disease-free survival (p<0.05). The meta-analysis approach adopted in this study has identified candidate markers correlated with disease outcome in HNSCC; further validation in a larger cohort of patients will establish their clinical relevance.

Publication types

Meta-Analysis
Research Support, Non-U.S. Gov't

MeSH terms

Anoctamin-1
Biomarkers, Tumor* / metabolism
Chloride Channels* / genetics
Fas-Associated Death Domain Protein* / genetics
Head and Neck Neoplasms* / genetics
Head and Neck Neoplasms* / pathology
Humans
Neoplasm Proteins* / genetics
Prognosis
mu-Crystallins

Substances

ANO1 protein, human
Anoctamin-1
Biomarkers, Tumor
Chloride Channels
CRYM protein, human
FADD protein, human
Fas-Associated Death Domain Protein
mu-Crystallins
Neoplasm Proteins

Grants and funding

The project was funded by Indian Council of Medical Research, India (No: 5/8/10-18 (Oto)/CFP/11-NCD-1). (http://www.icmr.nic.in/). AS received the funding. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.