Oral Squamous Cell Carcinoma (OSCC) is a highly invasive cancer that affects oral epithelial cells and is characterized by loss of cell-cell contact with increased metastatic ability. This loss of cell adhesion is mainly due to downregulation of E-cadherin. In addition to cell adhesion, downregulation of E-cadherin is believed to affect the expression of many transcripts and proteins. However, the possible mechanism by which this downregulation or loss affects the transcripts and proteins expression is not clear. Moreover, the possibility that these altered transcripts and proteins might serve as potential biomarkers for OSCC diagnosis or prognosis prediction needs to be assessed. In this study, I have focused on finding a suitable cell line model to study the impact of E-cadherin loss on epigenetic alterations (DNA methylation) as one of possible influencing mechanisms on biomarkers expression. Following extensive characterisation of multiple cell lines, wild type mouse Embryonic Stem Cells (wt mESCs), which express E-cadherin, were used as a model alongside Cdh1 (gene encoding E-cadherin) knockout mouse Embryonic Stem cells (Ecad-/-mESCs) to study the effect of E-cadherin loss. DNA methylation sequencing analysis showed differential hyper-methylation in Ecad-/-mESCs relative to wt mESCs, including at promoter CpG islands of naÃ¯ve pluripotency maintenance genes, such as Tbx3 and Klf2. The DNA methylation pattern of these cells was altered to pattern similar to that in epiblast stem cells and cancer cells. Of note, differentially hyper-methylated CpG islands in Ecad-/-mESCs are associated with oncogenic signatures and cancer pathways. Potential biomarkers for OSCC (UBF, macroH2A1 and TPD52) were identified by intersecting DNA methylation sequencing data with previously published microarray and proteomics data of both wt mESCs and Ecad-/-mESC. The expression validation of these biomarkers has shown difference between moderate to well differentiated OSCC tissue sections and their normal surgical mucosal margins. Remarkably, the identified biomarkers (UBF, TPD52 and macroH2A1) can confirm the diagnosis of OSCC and assess the status of their surgical mucosal margins and subsequently aid in prognosis prediction. In this study, I show for the first time that wt mESCs provide a suitable model of epithelial cells, where to investigate the impact of E-cadherin loss on DNA methylation and identify biomarkers for OSCC diagnosis.