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Single cell transcriptomic characterization of microtia reveals pathogenic dysregulation in previously unrecognized chondral stem/progenitor cell population

ABSTRACT: Single cell transcriptomic characterization of microtia reveals pathogenic dysregulation in previously unrecognized chondral stem/progenitor cell population

PROVIDER: PRJNA742395 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14972300_1.fastq.gz	Fastqsanger.gz
	SRR14972300_2.fastq.gz	Fastqsanger.gz
	SRR14972302_1.fastq.gz	Fastqsanger.gz
	SRR14972302_2.fastq.gz	Fastqsanger.gz
	SRR14972304_1.fastq.gz	Fastqsanger.gz

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Single cell transcriptomic characterization of microtia reveals pathogenic dysregulation in previously unrecognized chondral stem/progenitor cell population

Project description:As one of most common birth defects worldwide, microtia results from auricular cartilage dysplasia and has unfortunate physical and psychological consequences for children. However, existing treatments have adverse outcomes and its pathogenesis is poorly understood. Since characterization of cell type composition and function in normal auricular cartilage can increase our understanding of microtia, we conducted single-cell transcriptomic profiling for 47,969 human auricular cartilage cells obtained from three microtia and six normal control (NC) samples. Comprehensive bioinformatic analysis identified seven cartilage-related cell subtypes belonging to the chondral and stromal lineages. We also found age-associated changes in gene expression shared across all subtypes in the chondral lineage of NC. Additionally, we revealed the previously unrecognized chondral stem/progenitor cells (CSPCs) that were mainly located in the chondrium and might have the potential for directed chondrogenic differentiation. Our results showed that dysregulation of SOX8 and EGR1 in CSPCs of microtia impaired cartilage development and enhanced oxidative stress response, respectively. These findings shed light on the potential mechanisms of microtia pathogenesis and offer novel avenues for the development of treatment strategies

2021-07-06 | GSE179135 | GEO

Single-cell transcriptomics reveals pathogenic dysregulation of previously unrecognised chondral stem/progenitor cells in children with microtia.

Project description: Not available

| S-EPMC8858629 | biostudies-literature

Identification of key genes and signaling pathways in microtia by the analysis of transcriptomics

Project description:Microtia is a complex congenital defect which is one of the most common birth defects in the world. Depending on the degree of deformity, microtia can be divided into many types. However, it is not clear whether the different degrees of microtia share the same underlying mechanism. The present study detected transcriptomic profiles of auricular cartilage tissues in 6 patients with mild and severe malformation and 3 control auricular cartilage tissues by RNA-seq technology. Relative mRNA abundances were compared and evaluated for their function and putative involvemen.t in microtia. A total of 1058, 1648 and 1150 differentially expressed genes respectively in the group of MIC-Ⅱ-vs-NOR, MIC-Ⅲ-vs-NOR and MIC-Ⅲ-vs-MIC-Ⅱwere identified. Bioinformatics analysis demonstrated that some of these genes showed potential associations with microtia. In the MIC-Ⅱ microtia, the changed biological processes mainly enriched in mitosis. And in the MIC-Ⅲ microtia, the changed biological processes not only enriched in mitosis but also in migration. The key genes, IL-6 and COMP, and key signaling pathway, PI3K-AKT signaling pathway, were found to be dysregulated, which could contribute to microtia. The present study was a report on the transcriptomic analysis of microtia using the auricular samples from different degrees of microtia. Additional studies are required to clarify the roles of potential key genes in microtia.

2023-06-01 | GSE227119 | GEO

Gene expression signatures for auricular cartilages of microtia patients and controls

Project description:To explore the coding and non-coding gene expression in the auricular cartilage of microtia patients, we have employed RNA microarray expression profiling as a discovery platform to identify the coding and non-coding genes differentially expressed in microtia patients and controls. The discarded auricular cartilage tissue from 10 unilateral Grade III isolated microtia patients during auricular reconstruction surgery and 5 volunteers without ear malformation or other physical abnormalities during tympanoplasty surgery were collected. All fresh tissues were harvested from the tragus and cavum conchae of the auricle.

2023-07-19 | GSE237360 | GEO

Gene expression signatures for auricular cartilages of microtia patients and controls

2024-02-17 | GSE225225 | GEO

Gene expression signatures for auricular cartilages of microtia patients and controls

2024-09-11 | GSE242921 | GEO

Deep clinicopathological phenotyping identifies a previously unrecognized pathogenic EMD splice variant.

Project description:Exome sequencing (ES) has revolutionized rare disease management, yet only ~25%-30% of patients receive a molecular diagnosis. A limiting factor is the quality of available phenotypic data. Here, we describe how deep clinicopathological phenotyping yielded a molecular diagnosis for a 19-year-old proband with muscular dystrophy and negative clinical ES. Deep phenotypic analysis identified two critical data points: (1) the absence of emerin protein in muscle biopsy and (2) clinical features consistent with Emery-Dreifuss muscular dystrophy. Sequencing data analysis uncovered an ultra-rare, intronic variant in EMD, the gene encoding emerin. The variant, NM_000117.3: c.188-6A > G, is predicted to impact splicing by in silico tools. This case thus illustrates how better integration of clinicopathologic data into ES analysis can enhance diagnostic yield with implications for clinical practice.

| S-EPMC8528454 | biostudies-literature

An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations (scRNA-Seq)

Project description:Microtia is a congenital malformation that encompasses mild hypoplasia to complete loss of the external ear, or pinna. Although contribution of genetic variation and environmental factors to microtia remains elusive, Amerindigenous populations have the highest reported incidence. Here, using both transmission disequilibrium tests (TDT) and association studies in microtia trios (parents and affected child) and microtia cohorts enrolled in Latin America, we map a ~10 kb microtia locus (OR 4.7; p=6.78e-18) to the intergenic region between Roundabout 1 (ROBO1) and Roundabout 2 (ROBO2) (chr3: 78546526-78555137). While alleles at the microtia locus significantly increase the risk of microtia, their penetrance is low (<1%). We demonstrate that the microtia locus contains a polymorphic complex repeat element that is expanded in affected individuals. The locus is located near a chromatin loop region that regulates ROBO1 and ROBO2 expression in induced pluripotent stem cell-derived neural crest cells. Furthermore, we use single nuclear RNA sequencing (snRNAseq) to demonstrate ROBO1 and ROBO2 expression in both fibroblasts and chondrocytes of the mature human pinna. Because the microtia allele is enriched in Amerindigenous populations and shared by some East Asian subjects with craniofacial malformations, we propose both populations share a mutation that arose in a common ancestor prior to the ancient migration of Eurasian populations into the Americas, and that the high incidence of microtia among Amerindigenous populations reflects the population bottleneck that occurred during the migration out of Eurasia.

2022-05-14 | GSE202441 | GEO

An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations (RNA-Seq)

2022-05-14 | GSE202440 | GEO

Neocartilage gene expression in microtia and normal auricular chondrocytes with and without BMP7

Project description:To gain understanding in the tissue engineering of a human auricle, neocartilages generated from microtia and normal surgical remnants were compared by microarray anlaysis. Comparison of these two groups after 10 weeks development in vivo (nude mouse) revealed no statistically significant differences Comparison of normal and microtia cells, each seeded on nanoPGA and supplemented with BMP7 in a slow-release hydrogel, showed statistically significant differences in certain genes identified by microarray analysis. Such differences were also noted in several analyses comparing counterpart seeded cells without BMP7. Normal cells with and without growth factor showed several transcription and proliferative genes upregulated with addition of BMP7. Microtia with added BMP7 compared to normal neocartilage with added BMP7 was statistically significantly increased in gene levels of homeobox A10, DEAD box polypeptide 17, and arginine vasopressin.

2020-01-03 | GSE136198 | GEO

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