Zhiyong Chen

An efficient endolysosomal pathway is crucial to mediate the reabsorption and processing of ultrafiltered solutes including low-molecular-weight (LMW) proteins by epithelial cells lining the proximal tubule (PT) of the kidney. The zebrafish pronephros is used as a model system for congenital or acquired disorders that impair endolysosomal processing in PT cells, causing inappropriate loss of solutes and LMW proteins in urine. Here, we describe a new reporter ½vdbp-NanoLuc zebrafish line, in which vitamin D-binding protein is coupled to NanoLuc luciferase for detection of PT dysfunction and LMW proteinuria. We demonstrate the reliability and value of the ½vdbp-NanoLuc biosensor in fish models of monogenic endolysosomal diseases, gentamicin and cisplatin-induced nephrotoxicity, and metal contamination. This novel reporter system yields mechanistic insights into cadmium- and copper-induced PT dysfunction and provides a platform for drug screening.

An efficient endo-lysosomal pathway is crucial to mediate the reabsorption and processing of ultrafiltered solutes including low-molecular-weight (LMW) proteins by the epithelial cells lining the proximal tubule (PT) of the kidney. The zebrafish pronephros is increasingly used as a model system for congenital or acquired disorders that impair the endocytic uptake in PT cells, that cause an inappropriate loss of solutes and LMW proteins in the urine. Here, we describe a new reporter zebrafish line, termed ½vdbp-NanoLuc , in which the vitamin D-binding protein is coupled to NanoLuc luciferase, for rapid, large-scale detection of PT dysfunction and LMW proteinuria. We demonstrate the reliability and value of the ½vdbp-NanoLuc biosensor in fish models of monogenic endolysosomal diseases, gentamicin and cisplatin-induced nephrotoxicity, and metal contamination. This novel system provides mechanistic insights into the cadmium- and copper-induced PT dysfunction and, when combined with a swimming test, a platform for drug screening to alleviate cisplatin toxicity.

Homeostasis in the kidney proximal tubule (PT) requires coordination between metabolism and differentiation, yet the mechanisms governing this balance remain elusive. Here, we integrate model organisms, multiomics profiling, and human genetics to identify the autophagy regulator ATG7 as a key determinant of cell-fate decisions, sustaining PT specialization in health and contributing to dysfunction in disease. In mice, PT-specific deletion of ATG7 reprograms differentiated cells into anabolic, proliferative states, impairing their specialized function and causing kidney tubulopathy. Mechanistically, loss of ATG7-dependent autophagy hinders lipid droplet clearance and restricts fatty-acid oxidation (FAO), leading to energy depletion and functional decline. In zebrafish pronephros, re-expression of wild-type ATG7 restores homeostasis in atg7 mutants, while pharmacological FAO inhibition triggers dysfunction. In humans, ATG7 variants associate with cardio-renal-metabolic traits and increased disease risk, whereas low ATG7 expression correlates with transcriptional signatures of metabolic reprogramming, loss of epithelial markers, and poor prognosis in renal cell carcinoma. These findings establish a conserved genetic paradigm that links autophagy to kidney epithelial cell-fate specialization, with implications for disease, cancer, and metabolic health.

Differentiation is critical for cell fate decisions, but the signals involved remain unclear. The kidney proximal tubule (PT) cells reabsorb disulphide-rich proteins through endocytosis, generating cystine via lysosomal proteolysis. Here we report that defective cystine mobilization from lysosomes through cystinosin (CTNS), which is mutated in cystinosis, diverts PT cells towards growth and proliferation, disrupting their functions. Mechanistically, cystine storage stimulates Ragulator-Rag GTPase-dependent recruitment of mechanistic target of rapamycin complex 1 (mTORC1) and its constitutive activation. Re-introduction of CTNS restores nutrient-dependent regulation of mTORC1 in knockout cells, whereas cell-permeant analogues of L-cystine, accumulating within lysosomes, render wild-type cells resistant to nutrient withdrawal. Therapeutic mTORC1 inhibition corrects lysosome and differentiation downstream of cystine storage, and phenotypes in preclinical models of cystinosis. Thus, cystine serves as a lysosomal signal that tailors mTORC1 and metabolism to direct epithelial cell fate decisions. These results identify mechanisms and therapeutic targets for dysregulated homeostasis in cystinosis.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Deregulation of mitochondrial network in terminally differentiated cells contributes to a broad spectrum of disorders. Methylmalonic acidemia (MMA) is one of the most common inherited metabolic disorders, due to deficiency of the mitochondrial methylmalonyl-coenzyme A mutase (MMUT). HowMMUTdeficiency triggers cell damage remains unknown, preventing the development of disease–modifying therapies. Here we combine genetic and pharmacological approaches to demonstrate thatMMUTdeficiency induces metabolic and mitochondrial alterations that are exacerbated by anomalies in PINK1/Parkin–mediated mitophagy, causing the accumulation of dysfunctional mitochondria that trigger epithelial stress and ultimately cell damage. Using drug–disease network perturbation modelling, we predict targetable pathways, whose modulation repairs mitochondrial dysfunctions in patient–derived cells and alleviate phenotype changes inmmut–deficient zebrafish. These results suggest a link between primaryMMUTdeficiency, diseased mitochondria, mitophagy dysfunction and epithelial stress, and provide potential therapeutic perspectives for MMA.