TRIM16 Protects Against AKI by Promoting the Clearance of Damaged Lysosomes in Tubular Cells via Ubiquitinating YKT6

Background: Lysosomal damage is a common characteristic of renal tubular epithelial cells (TECs) and contributes to tubulointerstitial damage in acute kidney injury (AKI). Removing damaged lysosomes could help reduce tubulointerstitial injury and enhance AKI outcomes. The E3 ligase Tripartite Motif Containing 16 (TRIM16) identifies ruptured lysosomes and promotes their clearance, but its function and regulatory mechanisms in tubular injury during AKI remain unclear. Methods: The relationship between tubular injury, lysosomal damage, and the expression of TRIM16 was examined in biopsies from patients and mice with AKI. The function of tubular TRIM16 in AKI was identified by utilizing tubule-specific TRIM16 knockout mice in vivo and TRIM16-overexpressed and -silenced HK-2 cells in vitro. Mechanisms of TRIM16-mediated clearance of damaged lysosomes in ischemia-reperfusion-induced AKI (IR-AKI) were explored by using STRING predictive analysis, molecular docking, immunofluorescence, protein mutation, and pull-down analysis. Results: TRIM16 expression in tubular cells was increased in the kidneys of both patients and mice with AKI, showing a negative correlation with the accumulation of damaged lysosomes and the severity of renal tubular injury. Deleting TRIM16 specifically in tubular cells hindered the clearance of damaged lysosomes and worsened TEC injury in both in vivo and in vitro AKI conditions. Conversely, restoring TRIM16 expression improved TEC injury in TRIM16 conditional knockout mice subjected to IR-AKI by enhancing the removal of damaged lysosomes. Mechanistically, TRIM16 interacted with and ubiquitinated YKT6 V-SNARE Homolog (YKT6), a crucial player in the fusion of autophagosomes and lysosomes, in response to lysosomal damage. Silencing YKT6 or altering its ubiquitination site abolished the lysosome removal enhancement induced by TRIM16 overexpression. Interestingly, ubiquitination of YKT6 by TRIM16 promoted the clearance of damaged lysosomes in TECs not through autophagy, but by facilitating the direct fusion of intact and ruptured lysosomes through the formation of the YKT6/Synaptosome Associated Protein 29 (SNAP29)/Syntaxin 17 (STX17) complex. Conclusion: TRIM16 reduces tubular injury in AKI by promoting the clearance of damaged lysosomes via YKT6 ubiquitination, which could offer a new therapeutic approach for treating AKI. Funding: Government Support – Non-U.S.