Integrative RNA-Seq and ATAC-Seq Analysis Reveals the Migration-Associated Genes Involved in Antitumor Effects of Herbal Medicine Feiyanning on Lung Cancer Cells

Abstract

Lung cancer is one of the leading causes of cancer-associated death in the world. It is of great importance to explore new therapeutic targets. Traditional Chinese medicine formula Feiyanning has been clinically administered in China for more than a decade and raised attention due to its anticancer effect in lung cancer. However, the underlying molecular mechanisms remain to be elucidated. In the present study, we carried out cellular and molecular assays to examine the antitumor activities and understand the mechanism of the Feiyanning formula in lung cancer cells. The cellular viability of Feiyanning-treated lung cancer cells was evaluated by Cell Counting Kit-8. The effect of the Feiyanning formula on cellular migration and invasion of lung cancer cells was examined by wound healing and transwell assays. Transcriptome and chromatin accessibility analysis by RNA-seq and ATAC-seq was performed to investigate the underlying molecular mechanisms. Our results revealed that the Feiyanning formula inhibited the cellular activities of proliferation, migration, and invasion in non-small cell lung cancer cell lines A549, H1975, and 95D. Furthermore, we observed that the transcriptional activity of the migration-associated genes was downregulated upon Feiyanning formula treatment in non-small cell lung cancer cells. The chromatin accessibility of the Feiyanning-treated lung cancer genome tended to decrease, and the regulation of the cellular component movement biological process and PI3K-AKT pathway were enriched among these altered genomic regions. Taken together, the present study suggested that Feiyanning formula exerted the antitumor effects by modulating the expression and chromatin accessibility levels of migration-associated genes.

m6A‐ and immune‐related lncRNA signature confers robust predictive power for immune efficacy in lung squamous cell carcinoma

“…Open chromatin‐accessible regions have been found to contain cis‐regulatory elements and possibly modulate gene activity 30 . A study has pointed out that in NSCLC cells, the transcriptional activity of migration‐associated genes is downregulated using the Feiyanning formula treatment, which prolongs patient survival 31 . Therefore, we hypothesized that low ATAC‐seq signal is associated with a better immune response.…”

“…30 A study has pointed out that in NSCLC cells, the transcriptional activity of migration-associated genes is downregulated using the Feiyanning formula treatment, which prolongs patient survival. 31 Therefore, we hypothesized that low ATAC-seq signal is associated with a better immune response. In our study, patients in mirlncRNA cluster A had the lowest ATAC-seq signal (Figure 4A-D) and the best immunotherapeutic response (Figure 6F-H).…”

DHA- and EPA-Enriched Phosphatidylcholine Suppress Human Lung Carcinoma 95D Cells Metastasis via Activating the Peroxisome Proliferator-Activated Receptor γ

“…Images from at least 5 fields of each well were randomly selected and evaluated via Image Pro Plus 6.0 software. The experimental protocol was based on the previous studies with appropriately modified [ 29 , 30 ].…”

Chronic disease markers analysis using high-throughput sequencing approaches

“…Traditional Chinese medicine formula Feiyanning has been clinically administered in China for more than a decade and raised attention due to its anticancer effect in lung cancer. Wang et al (2021) revealed the migration-associated genes involved in antitumor effects of herbal medicine Feiyanning on lung cancer cells using RNA-Seq and ATAC-Seq analysis. Recent works presented novel biomarkers in gastric cancer [8].…”