Characterization of a base-resolution common deletion region within CDKN2A gene in cancers and its biological and clinical significances

Background: Frequency of somatic copy number deletion of CDKN2A gene is upto 60% in human esophageal squamous cell cancer. However, it is unknown whether CDKN2A deletion could be a biomarker for esophageal squamous cell dysplasia (ESCdys) due to absence of a feasible detection method. Methods: Information on base-resolution common deletion region (CDR) for CDKN2A were extracted from published articles and confirmed with whole genome sequencing (WGS). A quantitative PCR targeted to the CDR (P16-Light) was established and used to detect CDKN2A copy number in ESCdys biopsies from patients (n=205) enrolled in a multicentre follow-up study. Results: A 5.1-kb CDR from the CDKN2A/P16INK4A promoter to intron-2 was firstly characterized in 90% (83/92) of cancer cell lines and confirmed with WGS. The CDR covers CDKN2A exon-2 which is the essential coding exon for both P16INK4a and P14ARF. And CDKN2A exon-2 deletion markedly promoted the proliferation and invasion and inhibited the apoptosis of HEK293T cells. In the follow-up study, both somatic CDKN2A deletion and amplification are prevalent in mild/moderate (m/M) ESCdys. CDKN2A deletion was less common among 70 patients whose ESCdys regressed than among 135 patients whose ESCdys progressed or remained stable, and CDKN2A amplification was more common in the patients who regressed than in the patients whose m/M ESCdys persisted or progressed over a median of 37 months of follow-up (p