Liver disease reveals KIF12 as a regulator of mitochondria, lysosome and cilia localisation in human cholangiocytes

BACKGROUND: Rare bi-allelic mutations in kinesin family member 12 (KIF12) cause high gamma-glutamyl transferase (GGT) cholestatic liver disease, yet the cellular mechanisms driving this phenotype remain unknown. METHODS: To investigate the role of KIF12 in biliary pathology, we introduced the homozygous p.Arg219∗ KIF12 mutation, previously identified in affected patients, into induced pluripotent stem cells (iPSCs). These cells were differentiated into 2D human cholangiocyte-like cells (iCCs) and 3D biliary organoids. FINDINGS: Analysis of healthy human liver single cell RNA-sequencing datasets demonstrated that KIF12 is primarily detected in biliary epithelial cells. Pioneering single-molecule fluorescence microscopy in live iCCs, we observed wildtype KIF12 co-localising with microtubules, supporting its predicted function as a microtubule-associated motor protein. The p.Arg219∗ variant was associated with reduced KIF12 transcript abundance and markedly reduced detectable tagged mutant protein in an overexpression system. Mutant iCCs exhibited abnormal perinuclear clustering of mitochondria and lysosomes, mislocalisation of primary cilia, and increased GGT activity, all of which were rescued by re-expression of wildtype KIF12. INTERPRETATION: This study identifies KIF12 as a key regulator of organelle localisation in human cholangiocytes, expanding our understanding of kinesin roles beyond their established functions in neuronal systems. Our findings provide new insights into the pathogenesis of KIF12-related cholestatic liver disease and establish a foundation for developing targeted genetic therapies. FUNDING: This study was supported by Doris Duke Charitable Foundation, the National Institutes of Health and internal funds from the Center for Transcriptional Medicine at the University of Pittsburgh.