Newly identified ZNHIT3 variants, which cause intrauterine fetal loss, disrupt snoRNP assembly
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB78345 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13388219.fastq.gz | Fastqsanger.gz | |||
| ERR13388220.fastq.gz | Fastqsanger.gz | |||
| ERR13388221.fastq.gz | Fastqsanger.gz | |||
| ERR13388222.fastq.gz | Fastqsanger.gz | |||
| ERR13388223.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:ZNHIT3 (zinc finger HIT type containing protein 3) is an evolutionarily conserved protein required for ribosome biogenesis by mediating the assembly of small nucleolar RNAs (snoRNAs) of class C/D into ribonucleoprotein complexes (snoRNPs). Missense mutations in the gene encoding ZNHIT3 protein have been previously reported to cause PEHO syndrome, a severe neurodevelopmental disorder typically presenting after birth. We present here the case of two fetuses from a single family who presented with isolated hydrops during the early second trimester of pregnancy, resulting in intrauterine demise. Autopsy revealed no associated malformation. Through whole-genome quartet analysis, we identified two novel variants within the ZNHIT3 gene, both inherited from healthy parents and occurring as compound heterozygotes in both fetuses. The c.40T>C p.Cys14Arg variant originated from the father, while the c.251_254delAAGA r.? p.? variant was of maternal origin. Western capillary analysis of ZNHIT3 protein in lymphoblastoid cell lines of the parents shows that the parental c.40T>C p.Cys14Arg variant causes a significant drop in steady-state ZNHIT3 protein level. Analysis of the variants in human cell culture models reveals that both variants reduce cell growth, albeit to different extents, and impact the protein's stability and function in distinct ways. The c.251_254delAAGA results in production of a stable form of ZNHIT3 that lacks a domain required for mediating snoRNP biogenesis, whereas the c.40T>C p.Cys14Arg variation behaves similarly to the previously described PEHO-associated ZNHIT3 variants that destabilize the protein. Interestingly, both variations lead to a marked decrease in specific box C/D snoRNA levels, reduced rRNA levels and cellular translation. Analysis of rRNA methylation pattern in fetus samples reveals distinct sites of hypo 2’-O-methylation. RNA-seq analysis of undifferentiated and differentiated SHSY5Y cells transfected with the ZNHIT3 variants reveals differential expression of a set of genes, many of which are associated with developmental processes and RNA binding compared to cells expressing wild-type ZNHIT3. In summary, this work adds two novel ZNHIT3 variants to the other human disease-linked variants of this protein and describes the molecular defects caused by these pathogenic variants.
2024-10-08 | GSE273112 | GEO
Project description:Newly identified ZNHIT3 variants, which cause intrauterine fetal loss, disrupt snoRNP assembly
| PRJNA1140199 | ENA
Project description:Genetic disruption of chromatin regulators is frequently found in neurodevelopmental disorders (NDDs). While chromatin regulators are attractive therapeutic targets, studies to determine their implication in the etiology of NDDs are limited, preventing advances in diagnosis and treatment strategies. Here, we uncover pathogenic variants in the chromatin modifier Enhancer of Zeste Homologue 1 (EZH1) as the cause of overlapping dominant and recessive NDDs in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 (H3K27) methyltransferases of the Polycomb Repressive Complex 2 (PRC2). Unlike the other PRC2 subunits, which are associated with the pathogenesis of human cancers and developmental disorders with overgrowth, the implication of EZH1 in human development and disease is largely unknown. Using cellular models and biochemical studies, we demonstrate that EZH1 variants identified in our study alter EZH1 molecularly. While recessive variants are EZH1 loss of function (LOF) variants that impair EZH1 expression, dominant variants are all missense mutations that affect evolutionarily conserved aminoacids likely impacting EZH1 structure or function. Accordingly, we found increased H3K27 methyltransferase activity for two EZH1 missense variants we tested, thus generating EZH1 gain of function (GOF) variants. Furthermore, we show that EZH1 is necessary and sufficient to differentiate neural stem cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell (hPSC)-derived neural cultures and forebrain organoids, we demonstrate that EZH1 LOF and GOF variation perturbs cortical projection neuron differentiation. Our work identifies EZH1 LOF and GOF variants as the genetic basis of previously undefined recessives and dominant NDDs and uncovers an essential role of EZH1 in regulating neurogenesis.
2023-05-04 | GSE227014 | GEO
Project description:Genetic disruption of chromatin regulators is frequently found in neurodevelopmental disorders (NDDs). While chromatin regulators are attractive therapeutic targets, studies to determine their implication in the etiology of NDDs are limited, preventing advances in diagnosis and treatment strategies. Here, we uncover pathogenic variants in the chromatin modifier Enhancer of Zeste Homologue 1 (EZH1) as the cause of overlapping dominant and recessive NDDs in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 (H3K27) methyltransferases of the Polycomb Repressive Complex 2 (PRC2). Unlike the other PRC2 subunits, which are associated with the pathogenesis of human cancers and developmental disorders with overgrowth, the implication of EZH1 in human development and disease is largely unknown. Using cellular models and biochemical studies, we demonstrate that EZH1 variants identified in our study alter EZH1 molecularly. While recessive variants are EZH1 loss of function (LOF) variants that impair EZH1 expression, dominant variants are all missense mutations that affect evolutionarily conserved aminoacids likely impacting EZH1 structure or function. Accordingly, we found increased H3K27 methyltransferase activity for two EZH1 missense variants we tested, thus generating EZH1 gain of function (GOF) variants. Furthermore, we show that EZH1 is necessary and sufficient to differentiate neural stem cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell (hPSC)-derived neural cultures and forebrain organoids, we demonstrate that EZH1 LOF and GOF variation perturbs cortical projection neuron differentiation. Our work identifies EZH1 LOF and GOF variants as the genetic basis of previously undefined recessives and dominant NDDs and uncovers an essential role of EZH1 in regulating neurogenesis.
2023-05-04 | GSE210465 | GEO
Project description:Study on plasma proteomics in single intrauterine fetal death
2021-09-07 | PXD040710 |
Project description:Age-related microangiopathy, also known as small vessel disease (SVD), causes damage to the liver, brain, kidney and retina. Based on the DNA damage theory of aging, we reasoned that genomic instability may underlie an SVD caused by dominant C-terminal variants in TREX1, the most abundant 3’-5’ DNA exonuclease in mammals. C-terminal TREX1 variants cause an adult-onset SVD known as retinal vasculopathy with cerebral leukoencephalopathy (RVCL or RVCL-S). In RVCL, an aberrant, C-terminally truncated TREX1 mislocalizes to the nucleus due to deletion of its ER-anchoring domain. Since RVCL pathology mimics that of the radiation injury, we reasoned that nuclear TREX1 promotes DNA damage. Here, we show that RVCL-associated TREX1 variants cause DNA damage in humans, mice, and Drosophila, and that cells expressing RVCL mutant TREX1 are more vulnerable to DNA damage induced by chemotherapy and cytokines that up-regulate TREX1, leading to depletion of TREX1-high cells in RVCL mice. RVCL-associated TREX1 mutants inhibit homology-directed repair (HDR), causing DNA deletions and vulnerablility to PARP inhibitors. In women with RVCL, we observe early-onset breast cancer, similar to patients with BRCA1/2 variants. Our results provide a new mechanistic basis linking aberrant TREX1 activity to the DNA damage theory of aging, premature senescence, and microvascular disease.
2024-05-30 | PXD051905 | Pride
Project description:Genetic studies have identified common variants within the HBS1L-MYB intergenic region on chromosome 6q associated with elevated fetal hemoglobin (HbF) levels and other clinically important human erythroid traits. The mechanism by which the non-coding sequence variants affect these traits is still not clear. Here we report that several of the variants affect regulatory elements that are occupied by key erythroid transcription factors within this region. These elements interact with MYB, a critical regulator of erythroid development and HbF levels. We show that several of the variants reduce transcription factor binding, affecting long-range interactions with MYB, and MYB expression levels. We provide here a functional explanation for the genetic association of HBS1L-MYB intergenic polymorphisms with human erythroid traits and HbF levels. Our results further designate MYB as a bona fide target for therapeutic induction of HbF to ameliorate sickle cell and β-thalassemia disease severity.
2014-07-24 | GSE52637 | GEO
Project description:Molecular defects in some ultra-rare subtypes of familial lipodystrophies remain unidentified. We identified novel NOTCH3 heterozygous variants in familial partial lipodystrophy (FPL) pedigrees. All variants were clustered in the heterodimerization domain of the negative regulatory region of NOTCH3. Proteomics of skin fibroblasts revealed significantly higher RNA expression of NOTCH3 and activation of widespread senescence pathways in the FPL patients versus controls.
2024-10-28 | MSV000096235 | MassIVE
Project description:BackgroundDetermining the cause of intrauterine fetal death is essential for patients to manage their next pregnancy. However, in the majority of cases of fetal death, the cause remains unexplained despite comprehensive evaluation, especially in the cases of twins. Among twin pregnancies, conditions of monochorionic twinning, commonly regarded as monozygotic, are more complicated than dichorionic ones.Case summaryWe systematically evaluated the cause of fetal death for a Han Chinese woman with monochorionic twinning following in vitro fertilization/embryo transfer. Discrepant karyotypes were unexpectedly discovered between the twins. One fetus had an aneuploid male karyotype (46, XY), dup (9) (p24.3-q13), and the other had a normal female karyotype (46, XX). We considered that the male died of aberration of chromosome 9 and the female died of subsequent acute exsanguination through vascular anastomosis.ConclusionThis study demonstrated the importance of recognizing the presence of monochorionic dizygotic twinning and the challenges of clinical management for twins following in vitro fertilization/double embryo transfer.
| S-EPMC9846037 | biostudies-literature
Project description:Heterozygous pathogenic variants in POLR1A were identified as the cause of Acrofacial Dysostosis, Cincinnati-type in 2015. Craniofacial anomalies reminiscent of Treacher Collins syndrome were the predominant phenotype observed in the first 3 affected individuals. We have subsequently identified 17 additional individuals with 12 unique (11 novel) heterozygous variants in POLR1A and observed numerous additional phenotypes including developmental delay, infantile spasms, and structural cardiac defects. To understand the pathogenesis of this pleiotropy, we created an allelic series of POLR1A using a combination of in vivo (mouse) and in vitro models. We describe distinct spatiotemporal requirements for Polr1a during mouse embryogenesis and identify a requirement for Polr1a for survival of pre migratory and migratory neural crest cells, forebrain precursors, and the second heart field. We used CRISPR/Cas9 to recapitulate two human alleles in mouse, demonstrating pathogenicity of one and likely benign nature of the other. Our work greatly expands the phenotype of human POLR1A-related disorders, provides new evidence of reduced penetrance and variable expression of POLR1A heterozygous variants, and demonstrates a multi-faceted approach to characterize and define pathogenicity of variants.
2022-08-15 | GSE206197 | GEO