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Whole-Exome Sequencing Identifies Eight Genes Associated with Recurrent Patellar Dislocation

ABSTRACT: The inheritance of recurrent patellar dislocation (RPD) is konwn, but the susceptible gene remian unidentified. Here, we performed the first whole exome sequencing (WES) cohort study to identify the susceptible genes. The results showed eight genes were associated with this disease. Notably, the CPD gene showed the highest relevance based on its gene function and tissue expression. Single-cell sequencing results indicate that the CPD gene is involved in the pathophysiological process of RPD through granulocytes. Implicated pathways include NF-kappa B, MAPK, and Wnt/β-catenin signaling, potentially influencing CPD's role in RPD pathogenesis. This study identified the susceptible gene and investigate the potential pathogenesis of RPD, which provided a new prospect for the understanding of RPD. Besides, it would offer the theoretical basis for disease prevention and genetic counseling.

ORGANISM(S): Homo sapiens

PROVIDER: GSE244724 | GEO | 2024/05/01

REPOSITORIES: GEO

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Project description:WES sequencing data of a familial recurrent patellar dislocation patients

| PRJNA766026 | ENA

Mind Bomb 2 limits inflammatory dermatitis in Sharpin mutant mice independently of cell death

Project description:Skin inflammation is a complex process implicated in various dermatological disorders. The chronic proliferative dermatitis (cpd) phenotype driven by the cpd mutation (cpdm) in the Sharpin gene is characterized by dermal inflammation and epidermal abnormalities. TNF and caspase-8-driven cell death causes the pathogenesis of Sharpincpdm mice, however, the role of MIB2, a pro-survival E3 ubiquitin ligase involved in TNF-signalling, in skin inflammation remains unknown. Here we demonstrate that MIB2 antagonises inflammatory dermatitis in the context of the cpd mutation. Surprisingly, the role of MIB2 in limiting skin inflammation is independent of its known pro-survival function and E3 ligase activity. Instead, MIB2 enhances the production of wound healing molecules, G-CSF and Eotaxin, within the skin. This discovery advances our comprehension of inflammatory cytokines and chemokines involved in cpdm pathogenesis, and highlights the significance of MIB2 in inflammatory skin disease that is independent of its ability to regulate TNF-induced cell death.

2024-01-25 | PXD045850 | Pride

Project description:Prospect

| PRJNA817603 | ENA

A Novel Silent Mutation in the L1CAM Gene causing Fetal Hydrocephalus

Project description:To explore the genetic cause of a Chinese woman with fetal hydrocephalus X-linked hydrocephalus (XLH), a genetic disorder, has an incidence of 1/30,000 male births. The great proportion of XLH is ascribed to loss of function mutations of L1 cell adhesion molecule gene (L1CAM), but silent mutations in L1CAM with pathogenic potential were rare, and were usually ignored especially in WES detection. In the present study, we describe a novel silent L1CAM mutation in a Chinese pregnant woman reporting continuous five times pregnancies with fetal hydrocephalus. After fetal blood sampling, we found c.453G>T (p.Gly151=) in L1CAM gene of the fetus by whole exome sequencing (WES), RT-PCR of the mRNA from cord blood mononuclear cells and subsequent sequence analysis identified the mutation created a potential 5' splice site consensus sequence, which would result in an in-frame deletion of 72 bp from exon 5 and 24 amino acids of the L1CAM protein. Heterozygous mutations were confirmed in analyzing DNA and mRNA from peripheral blood mononuclear cells of the woman, and, a severe L1 syndrome was confirmed by fetal ultrasound scan and MRI. Our study first indicated c.453G>T (p.Gly151=) in L1CAM could be disease causing for hydrocephalus, which would aid in genetic counseling for the prenatal diagnosis of hydrocephalus. Meanwhile, it suggested some silent mutations detected in WES should not be ignored, splicing predictions of these mutations were necessary.

2019-07-16 | GSE133063 | GEO

Genomic profiles of ultraviolet-induced 6-4PP susceptibilities and potential new roles in melanoma development

Project description:In this study we generated a genome map of 6-4PP lesion abundance in primary cells and conducted a comprehensive analysis to determine the epigenetic and genomic factors regulating 6-4PP susceptibility across the genome. We found that 6-4PP distribution across the genome is very similar to CPD, highest in heterochromatin regions near the nuclear periphery. Interestingly, we identified regions more susceptible to 6-4PP, but not CPD, located in bivalent and polycomb repressed chromatin states found closer to the center of the nucleus. Genes and enhancers in regions with the highest 6-4PP susceptibility are more mutated and have lower repair activity. However, these differences were not observed for genes located in regions more susceptible to 6-4PP and not CPD. Functional analysis of genes in these regions are involved in essential cellular processes required for cell growth and proteins localized to the cell membrane. This study reveals new insights into the genomic factors regulating 6-4PP susceptibility and suggest a novel role for 6-4PP lesions in skin cancer development.

2020-12-31 | GSE157070 | GEO

Project description:Meta-prOSpEcT

| PRJNA803614 | ENA

Patellar Luxation in Flatcoated Retrievers

Project description:Patellar luxation is an orthopaedic disorder in which the kneecap moves out of its normal location within the femoral trochlea. It can lead to osteoarthritis, lameness, and pain. In dogs it appears to be a heritable trait with a high incidence in some breeds. The prevalence of patellar luxation in the Dutch Flat-Coated Retriever population is 24%. We have performed a Genome Wide Association Analysis of the condition in this breed.

2014-11-01 | E-MTAB-2040 | biostudies-arrayexpress

Characterization of cyclobutane pyrimidine dimer-dependent modulation of gene expression in human keratinocytes following UVB exposure

Project description:To address CPD-dependent UVB activities, a model system was established in which transfection of keratinocytes with pseudouridine-modified mRNA (M-NM-(-mRNA) encoding CPD-photolyase resulted in 90% reduction of CPDs within 6 and 24 hours after UVB exposure. Microarray analysis of this model system demonstrated that more than 50 % of the gene expression altered by UVB were changed in a CPD-dependent manner. The expression of most of the CPD-dependent genes was changed at 6 h after UVB as compared to 24 h likely due to the higher CPD levels. Nine genes (ATF3, CCNE1, CDKN2B, EGR1, ID2, PTGS2, RUNX1, SNAI1, SNAI2) regulated by CPDs were selected for further investigation (qPCR, Western blot) based on the microarray data. Gene expression modulated by UVB irradiation in HaCaT keratinocytes was measured at 6 and 24 hours after the exposure to dose of 20 mJ/cm2 UVB. Three independent experiments were performed at each time (6 or 24 hours) using different passages for each experiment.

2015-01-16 | E-GEOD-65034 | biostudies-arrayexpress

Characterization of cyclobutane pyrimidine dimer-dependent modulation of gene expression in human keratinocytes following UVB exposure

Project description:To address CPD-dependent UVB activities, a model system was established in which transfection of keratinocytes with pseudouridine-modified mRNA (Ψ-mRNA) encoding CPD-photolyase resulted in 90% reduction of CPDs within 6 and 24 hours after UVB exposure. Microarray analysis of this model system demonstrated that more than 50 % of the gene expression altered by UVB were changed in a CPD-dependent manner. The expression of most of the CPD-dependent genes was changed at 6 h after UVB as compared to 24 h likely due to the higher CPD levels. Nine genes (ATF3, CCNE1, CDKN2B, EGR1, ID2, PTGS2, RUNX1, SNAI1, SNAI2) regulated by CPDs were selected for further investigation (qPCR, Western blot) based on the microarray data.

2015-01-16 | GSE65034 | GEO

CPD-seq mapping of UV damage formation and repair in yeast

Project description:UV-induced DNA lesions are an important contributor to mutagenesis and cancer, but it is not fully understood how the chromosomal landscape influences UV lesion formation and repair. We have used a novel high-throughput sequencing method to precisely map UV-induced cyclobutane pyrimidine dimers (CPDs) at nucleotide resolution throughout the yeast genome. Analysis of CPD formation reveals that nucleosomal DNA having an inward rotational setting is protected from CPD lesions. In strongly positioned nucleosomes, this nucleosome 'photofootprint' overrides intrinsic dipyrimidine sequence preferences for CPD formation. CPD formation is also inhibited by DNA-bound transcription factors, in effect protecting important DNA elements from UV damage. Analysis of CPD repair revealed a clear signature of efficient transcription-coupled nucleotide excision repair. Repair was less efficient at translational positions near a nucleosome dyad and at heterochromatic regions in the yeast genome. These findings define the roles of nucleosomes and transcription factors in UV damage formation and repair. UV mapping data was analyzed for yeast cells irradiated with 125J/m2 and allowed to repair for 0hr (2 samples), 20 minutes, 1 hour, or 2 hours. Data is also included for naked DNA irradiated with UV 60 or 90 J/m2

2016-08-19 | E-GEOD-79977 | biostudies-arrayexpress

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