Long-read sequencing identifies novel structural variations in colorectal cancer

Author summaryStructural variants contribute to oncogenesis and progression of colorectal cancer, but they remain difficult to be reliably detected. Aiming at obtaining a comprehensive picture of somatic SVs in CRC, we perform long-read nanopore sequencing on CRC tumor samples and their matched para-carcinoma tissues. Our results show long-read sequencing precisely and reliably detects 494 somatic SVs per sample, which are significantly more than previously reported short-read sequencing based studies. We find large scale inversions (>10 kbp) that are frequently difficult to be detected by short-read sequencing and alter the expression or structure of key tumor suppressor genes (including APC and CFTR). A novel gene fusion RNF38-RAD51B is also identified, and we find it functionally acts to enhance migration, invasion, and metastasis capabilities of colorectal cancer cells. Although the molecular mechanisms and clinical relevance of the inversions and gene fusions need to be further studied, our work presents a relatively complete SV landscape of CRC, and providing a genetic basis for CRC's personalized medicine. Structural variations (SVs) are a key type of cancer genomic alterations, contributing to oncogenesis and progression of many cancers, including colorectal cancer (CRC). However, SVs in CRC remain difficult to be reliably detected due to limited SV-detection capacity of the commonly used short-read sequencing. This study investigated the somatic SVs in 21 pairs of CRC samples by Nanopore whole-genome long-read sequencing. 5200 novel somatic SVs from 21 CRC patients (494 SVs / patient) were identified. A 4.9-Mbp long inversion that silences APC expression (confirmed by RNA-seq) and an 11.2-kbp inversion that structurally alters CFTR were identified. Two novel gene fusions that might functionally impact the oncogene RNF38 and the tumor-suppressor SMAD3 were detected. RNF38 fusion possesses metastasis-promoting ability confirmed by in vitro migration and invasion assay, and in vivo metastasis experiments. This work highlighted the various applications of long-read sequencing in cancer genome analysis, and shed new light on how somatic SVs structurally alter critical genes in CRC. The investigation on somatic SVs via nanopore sequencing revealed the potential of this genomic approach in facilitating precise diagnosis and personalized treatment of CRC.