Given that ULK1 has autophagy-independent functions31, we further manipulated two other autophagy genes (VPS34 and BECN1) in the METTL1 knockdown ESCC cells and revealed that knockdown of VPS34 or BECN1 could partially rescue the ESCC progression in METTL1 depleted cells (Supplementary Fig. 9a–d). Here, PIK3C3 is linked to esophageal squamous cell carcinoma.