Lactylome analysis unveils lactylation-dependent mechanisms of stemness remodeling in the liver cancer stem cells

Lactate is a crucial energy substrate, metabolite, and signaling molecule in hepatocellular carcinoma (HCC). Intracellular lactate-derived protein lysine lactylation (Kla) was identifed to contributing HCC progression. The Liver cancer stem cells (LCSCs) are considered to be the root cause of phenotypic and functional heterogeneity in HCC, and attributed to the tumor formation, development, immune suppressive, and treatment resistance. However, the role of lactylation on biological processes of LCSCs still remains elusive. Here we show the glycolytic metabolism enhancement, lactate accumulation and higher lactylation in the LCSCs compared with HCC cells. We screened H3 and H4 histone lactylations, and discovered H3K56la was closely contributing to the tumorigenesis and stemness of LCSCs. Notably, integrative lactylome and proteome analysis of the LCSCs and HCC cells identifes 766 Kla sites on non-histone proteins, and highlighted ALDOA K230/322 lactylation involving in preferentially the stemness of LCSCs. Moreover, IP-MS/MS identifed the tight binding between ALDOA and DDX17, which was weaken by ALDOA lactylation, and in turn facilitating the function of DDX17 in regulating stemness of LCSCs. Our study therefore reveals that Kla plays an important role in regulating stemness of LCSCs and contribute to HCC progression. The lactylation inhibition in LCSCs may serve as a novel therapeutic strategy for HCC.