Integrated Proteomics Reveal ALDH1A1 as an Oncogenic Driver and Regulatory Hub in Hepatocellular Carcinoma

Although aldehyde dehydrogenases 1 family member A1 (ALDH1A1) has been extensively studied in cancer, its role in hepatocellular carcinoma (HCC) remains poorly understood. This study was designed to characterize the expression pattern and functional roles of ALDH1A1 in HCC, and to further investigate its underlying molecular mechanisms using integrated proteomic analysis.

This study performed a pan-cancer analysis of ALDH1A1 expression, followed by validation of its expression levels in HCC tissue samples and cell lines. The expression of ALDH1A1 was manipulated using small interfering RNAs and lentiviral vector in HCC cell lines. And then the proliferation, migration, invasion, and tumorigenicity of HCC cells were observed in vitro and in vivo. Quantitative proteomic and phosphoproteomic profiling were conducted by liquid chromatography-tandem mass spectrometry, with comprehensive analyses and key findings validated by experiments.

ALDH1A1 was highly expressed in HCC tissues but exhibited notable expression heterogeneity among HCC cell lines. Functionally, ALDH1A1 promoted the proliferation, migration, and tumorigenicity of HCC cells, while suppressing apoptosis and modestly attenuates invasion. Quantitative proteomic and phosphoproteomic analyses revealed that ALDH1A1 profoundly reshaped both protein expression and phosphorylation landscapes in HCC. Furthermore, we validated that ALDH1A1 positively regulates the expression of DMPK, PCMTD2, VAMP4, ARHGAP19, NOL4L, and ST7, while suppressing SLC31A1, DSTYK, CYP4F12, GPNMB expression. Rescue experiments indicated that ALDH1A1 may promote HCC via activating Rho family small GTPase. ALDH1A1 also significantly upregulated mTOR phosphorylation.

ALDH1A1 acts as an oncogenic driver and regulatory hub in HCC.