COMPARATIVE MOLECULAR CHARACTERIZATION OF PLEOMORPHIC ADENOMA AND CARCINOMA EX-PLEOMORPHIC ADENOMA

Introduction: Salivary gland tumours can be categorized as either benign or malignant based on histopathology. Benign tumors comprise about two-thirds of all neoplasms of the salivary glands. The most common type is pleomorphic adenoma. Malignant tumors are less common but biologically different and clinically significant. A malignant epithelial tumour recognized as carcinoma ex pleomorphic adenoma (Ca ex PA) develops from an underlying pleomorphic adenoma (PA), signifying a change from benign to malignant neoplasia in the salivary glands. The diagnosis of these tumours have been completely transformed by molecular techniques. Objective: The objective of this study was to characterize the specific genetic alterations that differentiate pleomorphic adenoma (PA) from carcinoma ex-pleomorphic adenoma (Ca ex PA) using NGS. Material And Methods: This study was conducted at Institute of Pathology and diagnostic Medicine KMU, Shaukat Khanum Memorial Cancer Hospital Lahore and Lab Genetics Lahore. Four patients of both genders were selected through Non-probability convenience sampling technique. All patients included were diagnosed with Pleomorphic Adenoma and Carcinoma-ex-Pleomorphic Adenoma of salivary gland. Bioinformatics analysis were performed on a Linux computer cluster. Results: In this study 4 cases of salivary gland tumors (2 benign pleomorphic adenomas and 2 malignant carcinoma ex-pleomorphic adenoma, Ca ex PA) were analyzed using clinical data and next-generation sequencing (NGS) to investigate the molecular drivers of benign and malignant transformation. Recurrent PLAG1 activation emerged as a central oncogenic driver across four salivary gland tumors, involving PLAG1–CTNNB1 and PLAG1–LIFR fusions in pleomorphic adenomas, each leading to constitutive PLAG1 overexpression. In contrast, carcinoma ex-pleomorphic adenomas demonstrated greater genomic complexity, including PLAG1 rearrangements or PLAG1–TCEA1 fusion accompanied by HMG2 copy-number gains. These findings suggest that while PLAG1-driven fusions initiate tumorigenesis, secondary alterations such as HMG2 amplification promote malignant transformation and increased tumor aggressiveness. Conclusions: PLAG1 gene fusions (with CTNNB1, LIFR) are key molecular events leading to pleomorphic adenoma formation. Progression to carcinoma ex-pleomorphic adenoma occurs when PLAG1 or LIFR fusions are accompanied by HMG2 gene gain, indicating dual oncogenic activation.