Abstract:
Cross-kingdom herbal miRNA was first reported in 2012. Using a modified herbal extraction protocol, we obtained 73,677,287 sequences by RNA-seq from 245 traditional Chinese Medicine (TCM), of which 20,758,257 were unique sequences. We constructed a Bencao (herbal) small RNA (sRNA) Atlas, annotated the sequences by sequence-based clustering, and created a nomenclature system for Bencao sRNAs. The profiles of 21,757 miRNAs in the Atlas were highly consistent with those of plant miRNAs in miRBase. These sRNAs can regulate all human protein-coding genes, with some targets experimentally validated, indicating that plant small RNA plays an important role in life and health as an effective component of traditional Chinese medicine. Although facing controversy due to potential contamination with non-plant sequences and challenges in distinguishing sRNA origins, the Bencao database’s construction involved meticulous selection and annotation processes. The Bencao sRNA Atlas may help Chinese doctors optimize TCM prescriptions and accelerate the drug discovery process for more advanced RNA-based therapeutics. Our research highlights the therapeutic potential of Bencao sRNAs for treating human diseases and provides a new direction for precision medicine derived from traditional herbal sources. Moreover, the decoctosome, a lipo-nano particle consisting of 0.5%–2.5% of the decoction, demonstrated potent medical effects. Meanwhile, Bencao Index, including small-molecule compounds (SM), protein peptides (P), nucleic acid (N), non-nucleic and non-proteinogenic large-molecule compounds (LM) and elements from Mendeleev’s periodic table (E), was first proposed to provide a more comprehensive quality standard measuring herbal medical effects.