Seyoung Yu1, Yo Jun Choi1, John Hoon Rim1, Hye-Youn Kim1, Nasim Bekheirnia2, Hongzheng Dai2, Shen Linda Gu2, Mir Reza Bekheimia2, Heon Yung Gee1 1Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea 2Department of Pediatrics, Renal Section, Baylor College of Medicine, Houston, Texas, 77030, USA ADAMTS9 has an intracellular function as a regulator of primary cilia in addition to its extracellular actions as a secreted metalloproteinase. ADAMTS9 mutations cause nephronophthisis-related ciliopathies (NPHP-RC) which is characterized by tubulointerstitial nephritis, fibrosis, and cyst formation. To investigate the molecular function of ADAMTS9, ADAMTS9 knockout (KO) iPSCs, which were generated using CRISPR/Cas9, were differentiated into kidney organoids. Depletion of ADAMTS9 did not affect nephron differentiation efficiency, but caused perturbations of ciliogenesis. Single-cell transcriptomics of ADAMTS9 KO kidney organoids identified several upregulated pathways, including MAPK, WNT, and TGF-β signaling pathways. Further analysis demonstrated that ADAMTS9 has a role in podocytes by regulating a proteoglycan, decorin, which is known as an inhibitor of TGF-β, the master regulator of fibrosis. We reviewed literatures and a new case with ADAMTS9 mutations, and found that all individuals with ADAMTS9 mutations exhibited glomerulopathy including proteinuria. In conclusion, out data expand the spectrum of ADAMTS9-related renal diseases.