A novel 13q12 microdeletion associated with familial syndromic corneal dystropy
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ABSTRACT:
PROVIDER: PRJNA961120 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24288724_1.fastq.gz | Fastqsanger.gz | |||
| SRR24288724_2.fastq.gz | Fastqsanger.gz |
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Project description:We identified a family with a novel chromosome 13 microdeletion associated with a syndromic form of corneal opacification. In order to determine which genes in/around the microdeletion were contributing to the constellation of phenotypes, a corneal epithelial sample was obtained during a superficial keratectomy of the proband's 9-year-old brother.
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Project description:Progressive corneal opacification can result from multiple etiologies, including corneal dystrophies or systemic and genetic diseases. We describe a novel syndrome featuring progressive epithelial and anterior stromal opacification in a brother and sister and their mildly affected father, with all three family members having sensorineural hearing loss and two also with tracheomalacia/laryngomalacia. All carried a 1.2 Mb deletion at chromosome 13q12.11, with no other noteworthy co-segregating variants identified on clinical exome or chromosomal microarray. RNAseq analysis from an affected corneal epithelial sample from the proband's brother revealed downregulation of XPO4, IFT88, ZDHHC20, LATS2, SAP18, and EEF1AKMT1 within the microdeletion interval, with no notable effect on the expression of nearby genes. Pathway analysis showed upregulation of collagen metabolism and extracellular matrix (ECM) formation/maintenance, with no significantly down-regulated pathways. Analysis of overlapping deletions/variants demonstrated that deleterious variants in XPO4 were found in patients with laryngomalacia and sensorineural hearing loss, with the latter phenotype also being a feature of variants in the partially overlapping DFNB1 locus, yet none of these had reported corneal phenotypes. Together, these data define a novel microdeletion-associated syndromic progressive corneal opacification and suggest that a combination of genes within the microdeletion may contribute to ECM dysregulation leading to pathogenesis.
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Project description:Corneal endothelium is composed of a monolayer of corneal endothelial cells (CECs) in the inner layer of cornea, which is essential for maintaining corneal transparency. In order to better characterize CECs in different developmental stages, we profiled mRNA transcriptomes in human fetal and adult corneal endothelium with the goal to identify novel molecular markers in these cells. By comparing CECs with 12 other types of tissues, we identified 245 and 284 signature genes that are highly expressed in fetal and adult CECs, respectively. Functionally, these genes are characteristic of CECs, involving in cell adhesion, proteoglycan and sulfur metabolic process. Importantly, several of these genes are disease target genes in hereditary corneal dystrophies, consistent with their functional significance in CEC physiology. By comparing fetal and adult CECs, we also identified stage-specific markers associated with CEC maturation, such as the activation of the Wnt pathway genes in fetal, but not in adult CECs. Lastly, by immunohistochemistry of ocular tissues, we further confirmed the unique protein expression patterns for Wnt5a, S100A4, S100A6, and IER3, the four novel markers for either fetal or adult CECs. The identification of a new panel of molecular markers for fetal and mature CECs would be very useful for characterizing and quality controlling CECs through ex vivo expansion or stem cell differentiation for cell replacement therapy. mRNA profile between adult and fetal CECs by high-throughput sequencing
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Project description:MYEOV is a novel marker of differentiated corneal epithelium
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Project description:BACKGROUND:Interstitial 4q deletions are rare chromosomal alterations. Most of the previously reported deletions involving the 4q13.3 region are large chromosomal alterations with a common loss of band 4q21 resulting in marked growth restriction, severe intellectual disability, and absent or severely delayed speech. A microdeletion of 4q13.3 hasn't been previously reported. We discuss the involvement of genes and the observed phenotype, comparing it with that of previously reported patients. CASE PRESENTATION:We report on a 4q13.3 microdeletion detected in three affected individuals of a Lithuanian family. The clinical features of two affected children and their affected mother are very similar and include short stature, congenital heart defect, skeletal anomalies, minor facial anomalies, delayed puberty, and intellectual disability. Whole genome SNP microarray analysis of one child revealed an interstitial 4q13.3 microdeletion, 1.56?Mb in size. FISH analysis confirmed the deletion in the proband and identified the same deletion in her affected sib and mother, while it was not detected in a healthy sib. Deletion includes ADAMTS3, ANKRD17, COX18, GC, and NPFFR2 protein-coding genes. CONCLUSIONS:Our findings suggest that 4q13.3 microdeletion is a cause of a recognizable phenotype of three affected individuals. The detected microdeletion is the smallest interstitial deletion in 4q13. We highlight ADAMTS3, ANKRD17 and RNU4ATAC9P as candidate genes for intellectual disability, growth retardation and congenital heart defect.
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Project description:PURPOSE. Myeloma Overexpressed gene (MYEOV) was initially identified as a gene amplified in several malignancies, and it was found to promote cell proliferation and metastasis. Our previous comparative RNA-seq and epigenetic analyses revealed high MYEOV levels in differentiated corneal epithelial cells and showed that MYEOV expression was epigenetically regulated by TET2. In the current study, we aimed to characterize further the expression and regulation of MYEOV in the human ocular surface epithelium. METHODS. MYEOV expression was examined by immunostaining and publicly available single-cell RNA-seq data. Gene knockdown (KD) of MYEOV and the regulators of corneal epithelial differentiation, PAX6 and KLF4, in in vitro-expanded corneal epithelial cells was performed by siRNA transfection. Protein expression levels were examined by Western blot. MYEOV KD cells were subjected to colony-forming assay and RNA-seq analysis. RESULTS. Human cornea immunostaining revealed high MYEOV expression in the nuclei of KRT12-positive differentiated corneal epithelial cells, while KRT13-positive differentiated conjunctival epithelial cells were MYEOV-negative. MYEOV expression was not detected in the other surface ectoderm-derived epithelia: epidermis and oral mucosa. Both PAX6 KD and KLF4 KD led to the reduction of MYEOV and KRT12 protein expression. MYEOV KD decreased colony-forming efficiency while afflicting limited global gene expression change. CONCLUSIONS. Our study revealed specific MYEOV expression in KRT12-positive corneal epithelial cells among surface ectoderm-derived epithelia. Similar to KRT12, MYEOV expression is regulated by PAX6 and KLF4. Functionally, MYEOV regulates cell proliferation of corneal epithelial cells.
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