Transcriptome analysis of nphp1(ex15-del4); nphp4(sa38686) double mutant zebrafish
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE291774 | GEO | 2025/08/01
REPOSITORIES: GEO
Similar Datasets
Project description:Nephronophthisis (NPH) is the leading genetic cause of end-stage renal disease in children and young adults, with no effective disease-modifying therapies currently available. Here, we identify glucagon-like peptide-1 (GLP-1) signaling as a novel therapeutic target for NPH through a systematic drug repurposing screen in zebrafish. By simultaneously depleting nphp1 and nphp4, we developed a robust zebrafish model that recapitulates key features of human NPH, including glomerular cyst formation. Our screen revealed that dipeptidyl peptidase-4 (DPP4) inhibitors (Omarigliptin and Linagliptin) and GLP-1 receptor agonists (Semaglutide) significantly reduce cystogenesis in a dose-dependent manner. Genetic analysis demonstrated that GLP-1 receptor signaling is important for maintaining pronephros integrity, with gcgra and gcgrb (GLP-1 receptor genes) playing a particularly important role. Transcriptomic profiling identified adenosine receptor A2ab (adora2ab) as a key downstream effector of GLP-1 signaling, which regulates ciliary morphology and prevents cyst formation. Notably, nphp1/nphp4 double mutant zebrafish exhibited upregulation of gcgra as a compensatory mechanism, explaining their resistance to cystogenesis. This compensation was disrupted by targeted depletion of GLP-1 receptors or inhibition of adenylate cyclase, resulting in enhanced cyst formation specifically in the mutant background. Our findings establish a signaling cascade from GLP-1 receptors to adora2ab in regulating ciliary organization and preventing cystogenesis, offering new therapeutic opportunities for NPH through repurposing of FDA-approved medications with established safety profiles.
2025-08-01 | GSE291847 | GEO
Project description:Ciliopathies comprise a spectrum of inherited disorders involving different organ systems such as the central nervous system, the skeleton, and the kidney1. The cilium is a hair-like organelle at the cell surface that acts as a sensor and signal transducer2. Many ciliopathy manifestations can be linked to deficient cilia function, yet it is unclear how a cilium defect results in nephronophthisis (NPHP), the most prevalent renal manifestation in children, characterized by inflammation, interstitial fibrosis, and renal cysts3. Here, we report that deletion of the serine threonine kinase Lkb1 in the mouse kidney results in cardinal features of nephronophthisis. An in-vivo proteomic interaction screen revealed ANKS3, a known interaction partner of the nephronophthisis protein NPHP1, and its interactor NEK7 as novel binding partners of LKB1. Lkb1 genetically interacts with Nphp1 in zebrafish. Unbiased transcriptional analysis in-vitro and in-vivo revealed that the chemokine CCL2 is upregulated in Lkb1 deficiency and is accompanied by recruitment of CCR2 expressing mononuclear cells in the kidney. CCL2 regulation requires NPHP1, ANKS3 and NEK7. These findings link LKB1 and ciliopathy proteins to immune regulation and explain how mutations in NPHP proteins result in fibrosis of the kidney.
2018-06-10 | GSE86009 | GEO
Project description:Ciliopathies comprise a spectrum of inherited disorders involving different organ systems such as the central nervous system, the skeleton, and the kidney1. The cilium is a hair-like organelle at the cell surface that acts as a sensor and signal transducer2. Many ciliopathy manifestations can be linked to deficient cilia function, yet it is unclear how a cilium defect results in nephronophthisis (NPHP), the most prevalent renal manifestation in children, characterized by inflammation, interstitial fibrosis, and renal cysts3. Here, we report that deletion of the serine threonine kinase Lkb1 in the mouse kidney results in cardinal features of nephronophthisis. An in-vivo proteomic interaction screen revealed ANKS3, a known interaction partner of the nephronophthisis protein NPHP1, and its interactor NEK7 as novel binding partners of LKB1. Lkb1 genetically interacts with Nphp1 in zebrafish. Unbiased transcriptional analysis in-vitro and in-vivo revealed that the chemokine CCL2 is upregulated in Lkb1 deficiency and is accompanied by recruitment of CCR2 expressing mononuclear cells in the kidney. CCL2 regulation requires NPHP1, ANKS3 and NEK7. These findings link LKB1 and ciliopathy proteins to immune regulation and explain how mutations in NPHP proteins result in fibrosis of the kidney.
2018-06-10 | GSE86010 | GEO
Project description:Transcriptome analysis of nphp1(ex15-del4) nphp4(sa38686) double mutant zebrafish
| PRJNA1235224 | ENA
Project description:Meckel Syndrome, Nephronophthisis, Joubert Syndrome, and Bardet-Biedl Syndrome have mutations in proteins that localize to the ciliary transition zone (TZ). The phenotypically distinct syndromes suggest these TZ proteins have differing functions. However, mutations in a single TZ gene can result in multiple syndromes suggesting the phenotype is influenced by modifier genes. We performed a comprehensive analysis of ten zebrafish TZ mutants including mks1, tmem216, tmem67, rpgrip1l, cc2d2a, b9d2, cep290, tctn1, nphp1, and nphp4, as well as mutants in ift88 and ift172. Our data indicate variations in phenotypes exists between different TZ mutants, supporting different tissue specific functions of these TZ genes. Further we observed phenotypic variations within progeny of a single TZ mutant, reminiscent of multiple disease syndromes being associated with mutations in one gene. In some mutants the dynamics of the phenotype became complex with transitory phenotypes that are corrected over time. We have also demonstrated that multiple-guide derived CRISPR/Cas9 F0 “Crispant” embryos recapitulate zygotic null phenotypes, and rapidly identified ciliary phenotypes in 11 cilia-associated gene candidates (ankfn1, ccdc65, cfap57, fhad1, nme7, pacrg, saxo2, c1orf194, ttc26, zmynd12, and cfap52).
2022-11-30 | GSE217001 | GEO
Project description:Human nephronophthisis and related ciliopathies suggest a link between ciliary signaling defects and altered DNA damage responses. The goal of our study is to elucidate the molecular link of both signaling systems as well as the role of altered DNA damage responses in kidney degeneration and fibrosis. The kinase-regulated DNA damage response target Apoptosis Antagonizing Transcription Factor (Aatf) is a master regulator of the p53 response. Upon genetic deletion of Aatf in renal tubular cells we induce progressive renal failure and a phenotype closely resembling human nephronophthisis in mice and are able to show Aatf as a regulator of primary cilia and modulator of the DNA damage response connecting two pathogenetic concepts of nephronophthisis and nephronophthisis-related ciliopathies. The analysis of the RNA-sequencing of four Aatf-knockout mice and four wildtype mice supports the experimental findings.
2019-03-31 | E-MTAB-7077 | biostudies-arrayexpress
Project description:Nephronophthisis (NPHP) is an autosomal recessive tubulointerstitial nephropathy classified as a renal ciliopathy disorder and recognised as the leading genetic cause of kidney failure in children and young adults. NPHP1 is the most common genetic cause and encodes nephrocystin-1, a protein that plays crucial roles in the primary cilium and cellular junctions. Here we utilise personalised medicine approaches and deep phenotyping, which enable us to explore mechanistic pathways and identify potential therapeutic strategies. In a family where we detected a homozygous NPHP1 whole-gene deletion in three affected siblings, we compared kidney biopsy tissue and human urine-derived renal epithelial cells (hURECs). Both the kidney biopsy and the hURECs demonstrated renal epithelial cells with an elongated and tortuous primary ciliary phenotype. Bulk RNA-seq on patient hURECs revealed disease signatures of the NPHP1 homozygous deletion, which included changes in EGFR signaling, as well as extracellular matrix interactions and adherens junctions, in line with the original description of nephrocystin-1 as an adapter protein at adherens junctions. Treatment of patient hURECs with alprostadil, a recently proposed therapy for NPHP, caused an increase in overall ciliation rate, but also an exaggerated primary ciliary length. In contrast, treatment of patient hURECs with an EGFR kinase inhibitor produced a phenotypic rescue of ciliary length and tortuosity. Following hUREC treatments, alprostadil did not fully restore the disease-associated transcriptional profile, whereas treatment with the EGFR kinase inhibitor AG556 caused a more complete rescue of the transcriptomic disease signature, in keeping with the observed phenotypic rescue. We conclude that patient-derived hURECS enable the deep phenotyping of nephronophthisis, replicate human kidney biopsy findings, and can be used to develop disease pathway signatures and screen candidate drug molecules, providing novel insights into disease pathogenesis and therapies. EGFR inhibition is now a potential therapy for renal ciliopathies, which should be tested within in vivo models of NPHP as a prelude to human studies.
2025-07-01 | GSE301183 | GEO
Project description:Mutations in CEP290, a large multidomain coiled coil protein, are associated with multiple cilia-associated syndromes. Over 130 CEP290 mutations have been linked to a wide spectrum of human ciliopathies, raising the question of how mutations in a single gene cause different disease syndromes. In zebrafish the expressivity of cep290 deficiencies were linked to the type of genetic ablation: acute cep290 morpholino knockdown caused severe cilia-related phenotypes while defects in a Crispr/Cas9 genetic mutant were restricted to photoreceptor defects. Here we show that milder phenotypes in genetic mutants were associated with upregulation of genes encoding the cilia-associated small GTPases arl3, arl13b, and unc119b. Upregulation of UNC119b was also observed in urine-derived renal epithelial cells from human JBTS CEP290 patients. Ectopic expression of arl3, arl13b and unc119b in cep290 morphant zebrafish embryos rescued Kupffer's vesicle cilia and partially rescued photoreceptor outer segment defects. The results suggest that genetic compensation by upregulation of genes involved in a common subcellular process, lipidated protein trafficking to cilia, may be a conserved mechanism contributing to genotype-phenotype variations observed in CEP290 deficiencies.
2021-05-26 | GSE175491 | GEO
Project description:Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases - about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via non-allelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from genomic instability and NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may have differential susceptibility to the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans reflect the possibility that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles.
2015-11-30 | GSE73962 | GEO
Project description:The use of whole exome/genome sequencing has been a catalyst for a genotype-first approach to diagnostics. Under this paradigm, we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here we report two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects; failure to thrive; ocular abnormalities; and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex, necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2, we found abnormal chromosome condensation, augmented anaphase chromatin bridge formation and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants, we generated an ncapg2 zebrafish model. Morphants displayed clinically-relevant phenotypes, such as microcephaly and renal anomalies with concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR/Cas9 F0 mutants. Finally, we noted that the individual with a complex urogenital defect also harbored a heterozygous deletion of NPHP1, a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype, we co-suppressed nphp1 and ncapg2, which resulted in significantly more dysplastic renal tubules. Together, our data suggest that impaired function of NCAPG2 results in a severe condensinopathy and highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus.
2018-11-27 | GSE122932 | GEO