Search bioRxiv⌕ Search

bioRxiv · 10.1101/2024.06.03.597092

IP3 receptor depletion in a spontaneous canine model of Charcot-Marie-Tooth disease 1J with amelogenesis imperfecta

Abstract

Inositol 1,4,5-trisphosphate receptors (IP3R) mediate Ca2+ release from intracellular stores, contributing to complex regulation of numerous physiological responses. The involvement of the three IP3R genes (ITPR1, ITPR2 and ITPR3) in inherited human diseases has started to shed light on the essential roles of each receptor in different human tissues and cell types. Variants in the ITPR3 gene, which encodes IP3R3, have recently been found to cause demyelinating sensorimotor Charcot-Marie-Tooth neuropathy type 1J (CMT1J). In addition to peripheral neuropathy, immunodeficiency and tooth abnormalities are occasionally present. Here, we report the identification of a homozygous nonsense variant in the ITPR3 gene in Lancashire Heeler dogs, presenting with a severe developmental enamel defect and reduced nerve conduction velocity. We studied the primary skin fibroblasts of the affected dogs and observed that the nonsense variant in ITPR3 led to a complete absence of full-length IP3R3 protein. Unexpectedly, the protein levels of IP3R1 and IP3R2 were also markedly decreased, suggesting co-regulation. Functional Ca2+ measurements revealed reduced IP3R-mediated Ca2+ flux upon stimulation of G-protein-coupled-receptors in the affected dog fibroblasts. We were able to rescue the IP3R1 and IP3R2 depletion by proteasome inhibition but not the IP3R3 loss, which was facilitated by nonsense-mediated mRNA decay. These findings highlight the first spontaneous mammalian phenotype caused by a nonsense variant in ITPR3, leading to the loss of IP3R3. The human and canine IP3R3 proteins are highly similar, and our study suggests that the tissue involvement resulting from the receptors dysfunction is also conserved. In summary, IP3R3 is critical for enamel formation and peripheral nerve maintenance. Author summaryWe investigated pet dogs, Lancashire Heelers, with impairments in tooth development and in the nerves that regulate limb muscles. Through genetic studies of the dog pedigree, we found that the phenotypes were caused by a recessively inherited mutation in the ITPR3 gene, which encodes one of three IP3 receptors (IP3R) isoforms (IP3R3 isoform) that are needed for intracellular Ca2+ signaling. Mutated IP3R3 has been recently linked to a human inherited neuropathy called Charcot-Marie-Tooth disease type 1J, which impairs peripheral nerve function and is accompanied by immunodeficiency and abnormal teeth in some individuals. We showed that in the skin cells of the affected dogs, the full-length IP3R3 protein was completely absent, and also the protein levels of the other two IP3R isoforms (IP3R1 and IP3R2) were severely lowered. This led to impaired agonist-induced Ca2+ release and signaling. Our results demonstrate the high conservation between human and canine IP3 receptors and their significance for different tissue systems. The genetic studies now highlight that IP3R3 is vital for peripheral nerve function and enamel development.

Source connections

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Hytönen, M. K., Rönkkö, J., Hundi, S., Jokinen, T. S., Suonto, E., Teräväinen, E., Donner, J., La Rovere, R., Bultynck, G., Ylikallio, E., Tyynismaa, H., Lohi, H.. 2024-06-03. IP3 receptor depletion in a spontaneous canine model of Charcot-Marie-Tooth disease 1J with amelogenesis imperfecta. https://doi.org/10.1101/2024.06.03.597092

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Genetic ancestry influences the relative expression of ancestral haplotypes within admixed individuals

Allele-specific expression (ASE) reflects differences between the two haplotypes a person carries, but most ASE studies have been done in European-descent samples. Admixed individuals carry haplotypes from different ancestral backgrounds within the same cell, which allows ancestry effects on regulation to be measured directly. We integrated phased whole-blood RNA-seq with local ancestry inference in 779 participants from the MAGENTA cohort, including non-Hispanic White, African American, Caribbean Hispanic, and Peruvian individuals. Higher West African (YRI) ancestry proportion was associated with more ASE-positive genes per person, and the association remained after adjusting for age, sex, Alzheimer's disease status, APOE genotype, and the number of heterozygous genes. Peruvian ancestry showed no significant association. A gene-level test of imbalance across population groups found 2,053 of 15,008 genes with significant differences, including the major histocompatibility complex in all four groups. A genome-wide scan of 2,213 1 Mb windows compared people carrying two haplotypes of different ancestries with those carrying two of the same ancestry. It identified 52 non-redundant loci that replicated across all four population groups, containing 201, 60, and 110 ancestry-associated genes under the CEU, YRI, and PEL reference baselines. A haplotype-resolved directional analysis showed no genome-wide advantage for either ancestry. It found locus-specific dominance at 11 loci, and only chr8:2-3 Mb (CSMD1) showed the same direction in more than one population group. Genetic ancestry therefore shapes allelic regulation at global, gene, and locus scales.

genetics↗

Assembly-independent measurement of human Yq12 heterochromatin reveals population-scale variation and Yq12-derived RNA in testis

Despite advances in long-read sequencing and telomere-to-telomere assembly, population-scale analysis of large satellite arrays remains challenging. Human Yq12 is a megabase-scale heterochromatic region composed primarily of DYZ1/HSat3A6 and DYZ2/HSat1B repeats, whose near-equal proportions are maintained despite extensive variation in total array length. Here, using complete Y-chromosome assemblies, we developed k-mer-based tools to estimate Yq12 size directly from short- and long-read sequencing data without requiring sample-specific complete assemblies. Across 1,597 males from the 1000 Genomes Project, Yq12 length ranged from ~1 to 52 Mb (mean 26.5 Mb) and varied substantially within and between Y haplogroups. Phylogenetic analyses supported long-term constraint of total Yq12 length near an equilibrium of 26 Mb and strongly coupled evolution of DYZ1 and DYZ2 around near-parity composition. In 303 father-son pairs, fathers had longer estimated Yq12 regions in 70.6% of pairs, while sons more often showed DYZ1:DYZ2 ratios closer to 1:1. Testis Iso-Seq identified transcripts containing DYZ1 and DYZ2 satellite sequences, while single-cell RNA-seq revealed their expression in haploid spermatids. These results establish a scalable framework for studying Yq12 population variation, intergenerational dynamics, and transcription, providing new opportunities to investigate how extreme satellite-array variation relates to Y-chromosome evolution and male germ-cell biology.

genetics↗

Continuous ancestry profiles from genomes and genealogies

Using a single population label to represent an individual's ancestry may offer convenience, but ancestry is multidimensional, continuous, and reflects contributions from multiple ancestral sources. Here, we demonstrate empirically that ancestry profiles outperform categorical ancestry labels in capturing this complexity. Relatedness among 28,332 genotyped individuals was measured using haplotype painting and ordination and was regressed on regional ancestry proportions from the deep genealogies available for one-third of the cohort. When tested on participants in a validation set, predicted profiles placed 78% of documented ancestry in the correct region, against 48% for the training set average. Giving each participant a single regional label placed only 32% of their documented ancestry correctly, and a perfect classifier naming each person's largest documented region would reach only 38%, because most individuals carry ancestry from several regions. Thus, the continuous profile captures substantially more ancestry than any classification, providing support for representing ancestry as a continuum rather than a label.

genetics↗