Pericarpium Citri Reticulatae 'Chachi' (PCR-C), rich in polymethoxyflavones (PMFs), has potential anticancer bioactivity and its quality will be improved during storage. However, the main factors influencing the PCR-C quality during its storage remain unclear. In this study, multivariate analysis was performed to investigate free and bound PMFs of PCR-C during storage. The anticancer effects of purified PCR-C flavonoid extracts (PCR-CF) and the important PMFs were evaluated using A549 cells. The results showed that PCR-C samples exhibited remarkable differences in free PMFs during storage, which fell into three clusters: Cluster 1 included fresh (fresh peel) and PCR-C01 (year 1); Cluster 2 consisted of PCR-C03 (year 3) and PCR-C05 (year 5); and PCR-C10 (year 10) was Cluster 3. 3,5,6,7,8,3',4'-heptamethoxyflavone, tangeretin, and isosinensetin were identified as the most important PMFs distinguishing the various types of PCR-C according to its storage periods. Moreover, PCR-CF inhibited A549 cell proliferation and induced cell cycle arrest at G2/M phase, cell apoptosis, and ROS accumulation, and all anticancer indices had an upward tendency during storage. Additionally, tangeretin and 3,5,6,7,8,3',4'-heptamethoxyflavone exhibited anticancer effects on A549 cells, whereas isosinensetin displayed no anticancer effect, indicating that tangeretin and 3,5,6,7,8,3',4'-heptamethoxyflavone jointly contributed to anticancer activity of PCR-C during storage. PCR-CF and the most important PMFs killed cancer cells (A549 cells) but had no cytotoxicity to normal lung fibroblast cells (MRC-5 cells). Overall, the high quality of long-term stored PCR-C might be due to the anticancer effects of tangeretin and 3,5,6,7,8,3',4'-heptamethoxyflavone.
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