The GSEC/miR-101-3p/SNX16/PAPOLG axis is linked to HCC prognosis. GSEC, SNX16, and PAPOLG are highly expressed in HCC with poor prognosis, while miR-101-3p is low with good prognosis. This axis may influence macrophage polarization. Here, SNX16 is linked to hepatocellular carcinoma.