Research Area
The Ishimoto Lab investigates the molecular mechanisms of polycystic kidney disease and develops new strategies to restore kidney function through gene and RNA-based therapeutics. Our central focus is autosomal dominant polycystic kidney disease (ADPKD), particularly disease caused by PKD1 and PKD2 dysfunction, with complementary studies of HNF1B- and PKHD1-related biology.
We combine genetically engineered mouse models, human induced pluripotent stem cell (iPSC)-derived kidney organoids, genome engineering, molecular and cellular biology, advanced imaging, and kidney-targeted nanoparticle delivery. A major goal is to connect fundamental discoveries in cystogenesis and kidney epithelial biology with therapeutic approaches that can be tested in human-relevant experimental systems.
Major Research Areas
Polycystic Kidney Disease and Cystogenesis
Our laboratory studies how disruption of PKD genes alters renal epithelial cell behavior and drives cyst formation and progression. Current areas of investigation include:
Molecular and cellular consequences of PKD1 and PKD2 loss
Mechanisms linking polycystin dysfunction to abnormal epithelial proliferation and cyst expansion
Mitochondrial and metabolic abnormalities in polycystic kidney disease
Identification of pathways that can be therapeutically manipulated to slow or reverse cystic disease
Human iPSC-Derived Kidney Organoids
We use human iPSC-derived kidney organoids to model inherited kidney diseases in a human genetic context. Both nephron and collecting duct organoid systems are being developed to investigate PKD pathogenesis and evaluate potential therapeutic strategies.
Generation and characterization of PKD1-, PKD2- and HNF1B-deficient kidney organoids
Quantitative analysis of cyst formation, epithelial proliferation, and tubular morphology
Evaluation of gene-restoration strategies in human kidney tissue models
Kidney-Targeted Gene and RNA Delivery
A major translational direction of the laboratory is the development of kidney-targeted nucleic acid delivery. In collaboration with Ryan Williams, PhD, an expert in nanoparticle engineering and drug delivery, we are evaluating mesoscale PLGA-PEG nanoparticles as a platform for delivering RNA and DNA cargo to the kidney, including cyst-lining epithelial cells.
Kidney-targeted delivery of therapeutic RNA and genome-engineering components
Optimization of nanoparticle formulations for renal delivery and cellular uptake
Evaluation of nuclear availability of donor DNA and genomic insertion efficiency
Translation of delivery systems from cultured cells to kidney organoids and mouse models
Genome Engineering and PKD2 Restoration
We are developing a gene-restoration strategy for ADPKD caused by pathogenic variants in PKD2. Our approach combines kidney-targeted nanoparticle delivery with programmable genomic insertion to restore functional PKD2 expression through targeted integration of a PKD2 coding sequence into a genomic safe-harbor locus.
Optimization of bridge RNA-guided genomic insertion in human kidney cells
Evaluation of genomic safe-harbor sites for stable PKD2 expression
Optimization of donor DNA formats to enhance nuclear delivery and genomic integration
Evaluation of functional rescue in PKD2-deficient human kidney organoids, including restoration of polycystin-2 expression and suppression of cystic phenotypes
HNF1B and Renal Epithelial Biology
The laboratory uses inducible, kidney-specific mouse models to investigate the role of HNF1B in renal epithelial differentiation, tubular homeostasis, and cystogenesis. Our studies focus on HNF1B-dependent transcriptional programs and downstream pathways that regulate tubular epithelial identity and contribute to cystic kidney disease.
PKHD1, TFAP2B, and Developmental Gene Regulation
Our work on PKHD1 has revealed an unexpected connection between the PKHD1 genomic region and ocular development. Using a mouse model with near-complete deletion of Pkhd1, we found severe congenital eye abnormalities despite the absence of the expected cystic renal phenotype. Our findings suggest that deletion of Pkhd1 disrupts long-range genomic regulation of the neighboring gene Tfap2b, providing new insight into the regulatory architecture of the PKHD1–TFAP2B genomic region (Nat Communications, 2026).
Experimental Platforms and Approaches
Genetically engineered and inducible mouse models of kidney disease
Human iPSC-derived nephron and collecting-duct kidney organoids
Mouse nephron progenitor cell-derived kidney organoids
CRISPR/Cas genome engineering and programmable genomic insertion
Kidney-targeted mesoscale nanoparticle delivery
RNAscope, immunofluorescence, confocal microscopy, and quantitative imaging
Flow cytometry and fluorescence-based enrichment
Molecular assays for genomic insertion, transcript expression, and protein rescue
Current Translational Program
Kidney-Targeted PKD2 Gene Restoration for ADPKD
We are developing a therapeutic platform to restore PKD2 expression through targeted genomic insertion. Our approach integrates an enhanced programmable recombinase system, bridge RNA-guided genomic targeting, a PKD2 donor cassette, and kidney-targeted mesoscale nanoparticles.
We are first optimizing delivery and genomic insertion in human kidney epithelial cells and will subsequently evaluate whether restoration of PKD2 expression can rescue disease phenotypes in PKD2-deficient human kidney organoids. The long-term goal is to establish a generalizable platform for durable gene restoration in inherited kidney diseases.