Segmental changes on chromosome arm 3p are potential prognostic and diagnostic markers for high-risk oral premalignant lesions.

PR-06

Introduction: Forty percent oral squamous cell carcinoma (OSCC) patients don't survive pass 5 years due to ineffective early detection strategy. Studying oral premalignant lesions (OPLs) is key to identify early genetic events. 3p losses have been related to increased progression risk in OPLs. However, key tumor suppressor genes (TSGs) haven't been identified. In here, we found distinct changes on the 3p arm of high-risk OPLs. We compared them with benign dysplasias and invasive tumours to identify prognostic and diagnostic markers. Experimental Approach: Genomic profiles of 50 severe dysplasias/carcinoma in situs (CIS), stages associated with high-risk of progression into OSCC, were compared against 9 low-grade dysplasias with known outcome and 20 OSCCs using tiling-path array comparative genomic hybridization. The 3p arm is represented as 770 overlapping bacterial artificial chromosome clones spotted in duplicate on the array with complete coverage of 90 Mb. Two breakpoint detection algorithms were used to find changes. Result: High resolution chromosomal 3p arm copy number profiles of 50 OPLs revealed whole arm loss (16% of cases), segmental alterations (42%), and no copy number changes (42%). Alignment of the profiles with segmental losses (n= 21) defined 8 distinct losses (recurrent in >85% of the 21 cases), ranging from 0.35 Mb to 8.09 Mb in size. These regions harbor 13 genes with functions potentially relate to cancer. The identification of known TSGs such as FHIT in this analysis supports the validity of this approach for gene discovery. The 8 identified regions of loss should differentiate between benign dysplasias and progressing dysplasias in order to have prognostic values. Nine low-grade dysplasia profiles (did not progress during follow-up) were compared with high-risk OPLs. No genetic changes were found in the 3p arm of these low-grade dysplasias. The 8 regions of loss should also be present in OSCCs to support their diagnostic ability. Twenty OSCCs were compared with the high-risk OPLs. Among these OSCCs, 19 of them exhibited whole 3p arm loss, the most frequent lost observed in this OSCC set. Conclusion: We identified 8 highly recurrent genetic markers in the 3p arm based on a large cohort of high-risk OPLs. Accumulated genetic changes inside the 3p arm are associated with increased progression risk, involving sequential events ranging from no genetic change, to 8 segmental losses, to whole arm loss that dictates invasiveness. The 8 identified regions represent potential diagnostic markers of high-grade dysplasias that will progress to OSCCs. They also have prognostic value to predict outcome because they are found only in high-risk OPLs and not in benign dysplasias. This study also localized candidate TSGs on the 3p arm that are key drivers in oral cancer. This is the first study to show segmental losses in 3p precede whole arm loss and associate with progression risk.