Table 1.

Summary of the specificities that distinguish C. reinhardtii, C. elegans, D. melanogaster, the zebrafish, the mouse, and two- and three-dimensional cell cultures as models in kidney research

ModelMaintenance CostsAvailability of Tools for Gene Manipulation in Reverse GeneticsSuitability for High-Throughput Studies (Drug Screens and Forward Genetics)Similarity to the Human GenomeSimilarity to the Human Kidney
C. reinhardtiiLowRNAi (gene silencing); CRISPR/Cas9 (gene editing) has been reported in Chlamydomonas (112,113), but with low editing efficiencyYes. Characteristics such as small size, low maintenance cost, and genome haploidy during vegetative state make Chlamydomonas particularly suitable for high-throughput studies, such as mutagenesis and small molecule screens (114116)Chlamydomonas and humans share 706 protein families (117) and these are enriched in cilia and centrosome/basal body proteins (118)The fact that the overall structure is well conserved between Chlamydomonas flagellum and human cilia makes it a good model to study kidney ciliopathies. Chlamydomonas flagellum has a 9+2 configuration, typical of motile cilia, as opposed to the 9+0 configuration of primary cilia in the kidney tubule
C. elegansLowRNAi; ZFNs (gene editing); TALENs (gene editing); CRISPR/Cas9Availability of strains with fluorescently tagged proteins for in vivo microscopy and easy analysis of cilia defects through functional tests and by verifying the ability to uptake lipophilic dye through the cilia make C. elegans a good model for high-throughput screens of ciliary phenotypes (119)38% of C. elegans protein-coding genes has a unique corresponding functional ortholog in human (120)C. elegans has an excretory system in part functionally homologous to the human urinary tract but its relevance in kidney disease is mainly due to its role in cilia research. Ciliary structure is well conserved between C. elegans and human with many conserved ciliary and basal body proteins. Cilia configuration in C. elegans is of the 9+0 type, as in primary cilia of kidney epithelial cells
D. melanogaster (fruit fly)LowGAL4-UAS (transgenic tool for targeted gene expression); RNAi; CRISPR/Cas9Yes. Drosophila is an excellent model for large-scale studies due to its small size, low maintenance costs, rapid reproductive cycle, and the availability of transgenic lines for the simplified visualization of Drosophila excretory system>75% of human disease genes have a Drosophila ortholog (30)The fly excretory system clears unwanted substances and maintains water, salt, and pH homeostasis. As such, it is functionally homologous to the human excretory system. Malpighian tubules correspond to the kidney tubules and nephrocytes to the glomeruli
D. rerio (zebrafish)LowmRNA microinjection for overexpression studies; MO (gene silencing); ZFNs; TALENs, CRISPR/Cas9Yes. Small size and availability of transgenic lines to visualize the pronephros and cilia make it a good model for high-throughput screens in kidney research (41)Approximately 70% of human genes have at least one functional homolog in zebrafish (39). Zebrafish has many duplicated genes due to a whole-genome duplication event in early teleost evolution (55)The major difference between the excretory system of zebrafish and that of human is that zebrafish does not develop a metanephric kidney
M. musculus (mouse)HighIn contrast to other model systems, targeted mutagenesis in mouse embryonic stem cells exploiting homologous recombination had been possible, although not straightforward, well before the advent of CRISPR/Cas gene-editing system. CRISPR/Cas technologies have considerably simplified the generation of knockout and knockin murine modelsAlthough it has been used in seminal forward genetic studies (121), due to high maintenance costs and relatively long reproductive cycle, the mouse is not often the model of choice for large screensMice and humans share approximately 70% of protein-coding genes (122)The macroanatomy of the kidney is overall well conserved between mouse and human. Important differences in the regulation of master transcription factors in nephrogenesis account for differences such as the higher number of nephrons in human. A more detailed comparison can be found in (123)
Two-dimensional cell cultureLowCell cultures are extremely amenable to genetic manipulation. Among others, RNAi and CRISPR/Cas9 are probably the most commonly used tools to achieve knockdown and knockout/knockin, respectively, in two-dimensional cell culturesYesDepends on the species of origin. It is possible to obtain patient-specific cellsN/A
Three-dimensional cell cultureFor spheroid setting generally low, higher costs for kidney organoids due to employment of growth factors to direct differentiation to kidney lineagesmIMCD-3 spheroids were shown to be amenable to RNAi approaches (124). Due to low accessibility of the innermost core of kidney organoids, delivery of tools for transient gene knockdown or overexpression may prove difficult. Kidney organoids have been derived from iPSCs knockout lines for polycystic kidney disease genes generated with CRISPR/Cas9 (103)YesDepends on the species of origin. It is possible to obtain patient-specific URECs to generate spheroids (80) or patient-specific iPSCs to generate kidney organoids (106)Spheroids: N/A
Kidney organoids: main limitations of the model that distinguish it from the human kidney are reduced size and vasculature, immaturity, lack/underrepresentation of certain cell types, and the absence of a branched collecting duct system (125)
  • RNAi, RNA interference; CRISPR, clustered regularly interspaced short palindromic repeat; ZFNs, zinc finger nucleases; TALENs, transcription activator-like effector nucleases; MO, morpholino; N/A, not applicable; mIMCD-3, mouse inner medullary collecting duct cell line; iPSCs, induced pluripotent stem cells; URECs, urine-derived renal epithelial cells.