Identification of potential biomarkers of head and neck squamous cell carcinoma using iTRAQ based quantitative proteomic approach
Niraj Babu,
Sonali Mohan,
Vishalakshi Nanjappa,
Sandip Chavan,
Jayshree Advani,
Aafaque Ahmed Khan,
Santosh Renuse,
Aneesha Radhakrishnan,
T.S. Keshava Prasad,
Rekha V. Kumar,
Jay Gopal Ray,
Manjusha Biswas,
Saravanan Thiyagarajan,
Joseph A. Califano,
David Sidransky,
Harsha Gowda,
Aditi Chatterjee
Affiliations
Niraj Babu
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
Sonali Mohan
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
Vishalakshi Nanjappa
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
Sandip Chavan
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
Jayshree Advani
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
Aafaque Ahmed Khan
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, India
Santosh Renuse
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
Aneesha Radhakrishnan
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
T.S. Keshava Prasad
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
Rekha V. Kumar
Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, India
Jay Gopal Ray
Department of Oral Pathology, Burdwan Dental College and Hospital, Burdwan, West Bengal 713101, India
Manjusha Biswas
Division of Molecular Pathology, Mitra Biotech, Bangalore 560099, India
Saravanan Thiyagarajan
Division of Cancer Biology, Mitra Biotech, Bangalore, Karnataka 560099, India
Joseph A. Califano
Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Surgery, UC San Diego, Moores Cancer Center, La Jolla, CA 92093, USA
David Sidransky
Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
Harsha Gowda
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India; Corresponding authors.
Aditi Chatterjee
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; Corresponding authors.
Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers in India. Despite improvements in treatment strategy, the survival rates of HNSCC patients remain poor. Thus, it is necessary to identify biomarkers that can be used for early detection of disease. In this study, we employed iTRAQ-based quantitative mass spectrometry analysis to identify dysregulated proteins from a panel of head and neck squamous cell carcinoma (HNSCC) cell lines. We identified 2468 proteins, of which 496 proteins were found to be dysregulated in at least two out of three HNSCC cell lines compared to immortalized normal oral keratinocytes. We detected increased expression of replication protein A1 (RPA1) and heat shock protein family H (Hsp110) member 1 (HSPH1), in HNSCC cell lines compared to control. The differentially expressed proteins were further validated using parallel reaction monitoring (PRM) and western blot analysis in HNSCC cell lines. Immunohistochemistry-based validation using HNSCC tissue microarrays revealed overexpression of RPA1 and HSPH1 in 15.7% and 32.2% of the tested cases, respectively. Our study illustrates quantitative proteomics as a robust approach for identification of potential HNSCC biomarkers. The proteomic data has been submitted to ProteomeXchange Consortium (http://www.proteomecentral.proteomexchange.org) via the PRIDE public data repository accessible using the data identifier - PXD009241. Keywords: HNSCC, iTRAQ, Parallel reaction monitoring, Mass spectrometry, OKF6/TERT1
