Extrachromosomal circular DNA drives focal amplification of AGAP2-AS1 to promote cutaneous tumorigenesis

Abstract

Extrachromosomal circular DNA (eccDNA) represents a pervasive structural continuum of genomic instability that drives intratumoral heterogeneity. While pivotal in neoplastic evolution, the topography of the eccDNA-encoded non-coding transcriptome remains obscure in ultraviolet (UV)-driven malignancies. To profile the eccDNA landscape and elucidate the functional impact of eccDNA-encoded long non-coding RNAs (lncRNAs) across a pathological spectrum of eyelid tumorigenesis. We profiled eccDNA from Basal Cell Carcinoma, Inverted Follicular Keratosis, Merkel Cell Carcinoma, and matched adjacent normal tissues using Circle-Seq. Structural data were integrated with the eccDNA Gene Analyzer (ECGA) and The Cancer Genome Atlas (TCGA) clinical cohorts. In vitro siRNA-mediated knockdown assays were utilized to determine the oncogenic functionality of identified lncRNAs. Circle-Seq revealed a genome-wide remodeling of circular DNA characterized by focal hyper-amplification, distinct GC-rich compositional biases, and recurrent hotspots converging on chromosomes 9, 16, and 20. Integrative multi-tiered screening identified AGAP2-AS1 as a clinically significant, copy-number-associated lncRNA. AGAP2-AS1 expression significantly correlated with cellular responses to UV radiation and oxidative stress. Furthermore, targeted depletion of total AGAP2-AS1 transcripts profoundly impaired tumor cell proliferation, migration, and invasion in vitro. The eccDNA landscape serves as a reservoir of functional non-coding elements. The focal amplification of AGAP2-AS1 via eccDNAs contributes fundamentally to malignant progression and stress adaptation in cutaneous neoplasia.