Oxford Nanopore sequencing unveils structural variations and their functional impacts in cholangiocarcinoma cell lines with varying degrees of differentiation

Abstract

Background: Cholangiocarcinoma (CCA) is a heterogeneous bile duct cancer characterized by genomic complexity. Structural variations (SVs) play a major role in cancer progression, but their characterization in CCA remains limited. Oxford Nanopore sequencing, with its long-read capabilities, offers a promising approach to explore SVs in cancer genomes.

Objective: To investigate SVs and their functional impacts in three CCA cell lines with varying degrees of differentiation using Oxford Nanopore sequencing.

Methods: Whole-genome sequencing was performed on three CCA cell lines with varying degrees of differentiation and one human cholangiocyte (CCL) cell line. SVs were detected with Sniffles2, annotated using Ensembl VEP, and functionally analyzed via DAVID for functional enrichments.

Results: SVs were most abundant in KKU-213A and KKU-213C, with insertions and deletions being the predominant types affecting protein-coding genes. Functional enrichments showed the disruption of genes involved in key cancer-related processes such as ERBB4 signaling, glycerolipid metabolism, and retinol metabolism, whereas MMNK-1 exhibited the fewest SVs, indicating greater genomic stability.

Conclusion: Oxford Nanopore sequencing effectively revealed distinct SV patterns across CCA cell lines, with substantial impacts on protein-coding genes and cancer-associated pathways. These findings highlight the potential of SV profiling to understand CCA molecular heterogeneity and inform targeted therapeutic strategies.