Identification of Hypoxia-specific Transcripts in Liver Cancer Cells via Nanopore Long-read Sequencing
10.13471/j.cnki.j.sun.yat-sen.univ（med.sci）.20241119.001
- VernacularTitle:纳米孔长读测序鉴定肝癌细胞中低氧特异性转录本
- Author:
Li GAO
1
;
Shengqi SHEN
2
;
Ping GAO
1
Author Information
1. School of Medicine， South China University of Technology， Guangzhou 510006， China
2. Medical Research Institute， Guangdong Provincial People’s Hospital//Guangdong Academy of Medical Sciences//Southern Medical University， Guangzhou 510006， China
- Publication Type:Journal Article
- Keywords:
nanopore sequencing;
hypoxia;
transcript;
alternative splicing;
hepatocellular carcinoma
- From:
Journal of Sun Yat-sen University(Medical Sciences)
2025;46(1):88-97
- CountryChina
- Language:Chinese
-
Abstract:
ObjectiveLeveraging the advanced capabilities of nanopore long-read sequencing technology， our study undertook a comprehensive analysis of the distinct transcriptomic alterations occurring in normal liver parenchymal cells and liver cancer cells subjected to hypoxic conditions. The primary goal was to elucidate the underlying mechanisms governing tumor cell survival and metastasis in low-oxygen environments， thereby paving the way for innovative targeted cancer therapies. MethodsThe normal liver parenchymal cell line THLE-3 and the hepatocellular carcinoma cell line Hep3B were chosen as the focal points of this investigation. Following a 48-hour incubation period in both normoxic and hypoxic conditions， total RNA was extracted from these cells. Subsequently， we employed nanopore sequencing technology to conduct a high-throughput， high-fidelity analysis of the transcriptomes of these two cell lines across different oxygen levels. ResultsThis study established a hypoxic transcriptome dataset using third-generation nanopore sequencing technology， achieving an unprecedented level of sequencing accuracy. By conducting a Gene Ontology （GO） enrichment analysis， we systematically identified and explored the key biological pathways associated with the hypoxic response （P＜0.05）. Furthermore， we integrated molecular dynamics simulation techniques to gain deeper insights into the dynamic structural changes of Solute Carrier Family 1 Member 5 （SLC1A5） during the translation of hypoxic-specific subtypes， providing direct evidence to elucidate its functional regulation. ConclusionThe application of nanopore long-read sequencing technology has proven to be a powerful tool， not only successfully capturing the distinctive expression patterns and specific subtypes of mRNA under hypoxic conditions， but also offering robust technical support for delving into the intricate transcriptomic landscape of hypoxic microenvironments. By further integrating protein structure simulations and molecular dynamics， we have proposed novel avenues for exploring protein structures in hypoxic microenvironments. The findings of this study have significantly enriched the field of hypoxic-specific transcriptomics， providing a more reliable data foundation for investigating hypoxic-specific protein structures. Moreover， these discoveries have unveiled potential hypoxic-specific targets that could be harnessed for the development of future targeted cancer treatment strategies.
