Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC

// Daria A. Gaykalova 1 , Veronika Zizkova 1, 2 , Theresa Guo 1 , Ilse Tiscareno 1 , Yingying Wei 3, 10 , Rajita Vatapalli 1, 4 , Patrick T. Hennessey 1, 5 , Julie Ahn 1 , Ludmila Danilova 3, 11 , Zubair Khan 1 , Justin A. Bishop 1, 6 , J. Silvio Gutkind 7 , Wayne M. Koch 1 , William H. Westra 1, 6 , Elana J. Fertig 3 , Michael F. Ochs 3, 8 , Joseph A. Califano 1, 9 1 Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA 2 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic 3 Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA 4 Department of Urology, Northwestern University, Chicago, Illinois, USA 5 Department of Otolaryngology, Mid-Michigan Ear Nose and Throat, East Lansing, Michigan, USA 6 Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA 7 Department of Pharmacology, UC San Diego Moores Cancer Center, La Jolla, California, USA 8 Department of Mathematics and Statistics, The College of New Jersey, Ewing, New Jersey, USA 9 Department of Surgery, UC San Diego, Moores Cancer Center, La Jolla, California, USA 10 Department of Statistics, The Chinese University of Hong Kong, NT, Shatin, Hong Kong 11 Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia Correspondence to: Joseph A. Califano, email: jcalifano@ucsd.edu Daria A. Gaykalova, email: dgaykal1@jhmi.edu Keywords: HNSCC, DTX1, expression, methylation, integration Received: September 07, 2016      Accepted: January 16, 2017      Published: January 27, 2017 ABSTRACT Over a half million new cases of Head and Neck Squamous Cell Carcinoma (HNSCC) are diagnosed annually worldwide, however, 5 year overall survival is only 50% for HNSCC patients. Recently, high throughput technologies have accelerated the genome-wide characterization of HNSCC. However, comprehensive pipelines with statistical algorithms that account for HNSCC biology and perform independent confirmatory and functional validation of candidates are needed to identify the most biologically relevant genes. We applied outlier statistics to high throughput gene expression data, and identified 76 top-scoring candidates with significant differential expression in tumors compared to normal tissues. We identified 15 epigenetically regulated candidates by focusing on a subset of the genes with a negative correlation between gene expression and promoter methylation. Differential expression and methylation of 3 selected candidates ( BANK1 , BIN2 , and DTX1 ) were confirmed in an independent HNSCC cohorts from Johns Hopkins and TCGA (The Cancer Genome Atlas). We further performed functional evaluation of NOTCH regulator, DTX1 , which was downregulated by promoter hypermethylation in tumors, and demonstrated that decreased expression of DTX1 in HNSCC tumors maybe associated with NOTCH pathway activation and increased migration potential.