Identification and assessment of candidate biomarkers in early detection and progression of oral squamous cell carcinoma

Abstract

newlineOral squamous cell carcinoma (OSCC) is well known for its aggressiveness associated newlinewith poor prognosis. Its treatment protocol is braced by the International Union against newlineCancer (UICC) TNM classification, which comprises of surgery with additional newlineradio/chemotherapy in more advanced tumours. For early detection and understanding newlinemolecular transformation related to invasion and metastasis, focusing on development of newlinenew diagnostic tools and incorporating tumour biomarkers associated with oral newlinecarcinogenesis is obligatory in today s date. In the recent years, bioinformatics tools have newlinebeen reported with a high degree of success for candidate gene identification. Use of an newlineintegrated approach using bioinformatics (assimilating information from gene ontologies newline(GO), protein protein interaction (PPI), network analysis and available experimental data) newlineto predict candidate genes, confirming their presence with proteomics and validation of newlinesame involved in various OSCC pathways, has been a success. Increased knowledge about newlinesuch molecular markers paves the way to a more individualized cancer treatment aiming newlinefor better outcome and less overtreatment and sequel. newlineExperimental designand Result newlineThis thesis focuses on identifying a panel of molecular biomarkers expression playing a newlinecrucial role in invasion and metastasis for timely recognition of aggressiveness. A newlinepreliminary search was primed for candidate genes from three databases viz. Head-Neck newlineand Oral Cancer Database (HNOCDB)v1 (http://gyanxet.com/hno.html), Oral Cancer newlineGene Database (OrCGDB) v2 (http://www.actrec. gov.in/OCDB/index.htm) and the HNdb newlinedatabase (http://www.gencapo.famerp.br/hndb/). Using jVennsoftware ( the correlation newlineamong these database with common genes, metastatic in origin was evaluated. Predicting newlinea panel of candidate genes for OSCC was the next task and the top genes from consensus newlineranking list for oral cancer genes emphasizing on their interaction and role in invasion and newlinemetastasis pathways were considered. This steered us to four imperative genes POSTN, newlinevii newlineTNC, CAV 1andFSCN 1, which were unlinked to each other in literature search. We used newlinethe STRING ( Search Tool for the Retrieval of Interacting Genes/Proteins ) database to newlineunderstand the Protein Protein Interactions(PPI s) of our candidate genes. Later, newlineOncomine and CRN (Cancer RNA-Seq Nexus) databases were also delved into for clinical newlineand pathological data in OSCC/HNSCC regarding our candidate genes. A thorough newlinepathway analysis and the scrutiny of the literature showed that these genes had no newlineprevious record of linking them together for aggressive behavior in oral cancer. We further newlineanalyzed archived FFPE blocks of various grades of oral cancer using iTRAQ-based mass newlinespectrometry for its presence and their characteristics. Validation of our panel of candidate newlinegenes using immunohistochemistry (IHC) and Real time PCR finally established the newlineoutcome. newlineResults of these study expressed a strong communiqué and interrelationship between these newlinecandidate genes. A hypothetical pathway analysis led us to propose a role for the identified newlinegenes in invasion and metastasis in OSCC. newlineConclusion: This thesis focuses on the corroborative and affirmative path of a panel of newlinecandidate genes expression in various stages and degrees of differentiation associating it to newlineoral cancer aggression, hoping to further pave the way towards better outcome and less newlineovertreatment. This thesis for the first time demonstrates the significance of panel of newlinemolecular biomarker as a diagnostic tool and its correlation to the progression pathway of newlineOSCC. An insight into the probable association of CAF s and these biomarkers in the newlineevolution and malignant transformation of OSCC further magnifies the molecularbiological newlinespectrum of OSCC tumour microenvironment.