Single-cell RNA sequencing analysis reveals Greater Epithelial Ridge cells degeneration during postnatal development of cochlea in Rats
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ABSTRACT:
PROVIDER: PRJNA717971 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14086903_1.fastq.gz | Fastqsanger.gz | |||
| SRR14086903_2.fastq.gz | Fastqsanger.gz | |||
| SRR14086904_1.fastq.gz | Fastqsanger.gz | |||
| SRR14086904_2.fastq.gz | Fastqsanger.gz |
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Project description:Greater epithelial ridge cells, a transient neonatal cell group in the cochlear duct, which plays a crucial role in the functional maturation of hair cell, structural development of tectorial membrane, and refinement of audio localization before hearing. Greater epithelial ridge cells are methodologically homogeneous, while whether different cell subtypes are existence in this intriguing region and the degeneration mechanism during postnatal cochlear development are poorly understood. In the present study, single-cell RNA sequencing was performed on the cochlear duct of postnatal rats at day 1 (P1) and day 7 (P7) to identify subsets of greater epithelial ridge cell and progression. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were used to examine genes enriched biological processes in these clusters. We identified a total of 26 clusters at P1 and P7 rats and found that the cell number of five cell clusters decreased significantly, while four clusters had similar gene expression patterns and biological properties. The genes of these four cell populations were mainly enriched in Ribosome and P13K-Akt signal pathway. Among them, Rps16, Rpsa, Col4a2, Col6a2, Ctsk, and Jun are particularly interesting as their expression might contribute to the greater epithelial ridge cells degeneration. In conclusion, our study provides an important reference resource of greater epithelial ridge cells landscape and mechanism insights for further understanding greater epithelial ridge cells degeneration during postnatal rat cochlear development
2021-09-02 | GSE170810 | GEO
Project description:The hair cells of the cochlea play a decisive role in the process of hearing damage and recovery, yet knowledge of their regeneration process is still limited. Greater epithelial ridge (GER) cells, a type of cell present during cochlear development that has the characteristics of a precursor sensory cell, disappear at the time of maturation of hearing development. Its development and evolution remain mysterious for many years. Here, we performed single-cell RNA sequencing to profile the gene expression landscapes of rats' cochlear duct from P1, P7, and P14 and identified eight major subtypes of GER cells. Furthermore, single-cell trajectory analysis for GER cells and hair cells indicated that among the different subtypes of GER, four subtypes had transient cell proliferation after birth and could transdifferentiate into inner and outer hair cells, and two of them mainly transdifferentiated into inner hair cells. The other two subtypes eventually transdifferentiate into outer hair cells. Our study lays the groundwork for elucidating the mechanisms of the key regulatory genes and signaling pathways in the trans-differentiation of GER cell subtypes into hair cells and provides potential clues to understand hair cell regeneration.
2022-01-29 | GSE195702 | GEO
Project description:Greater epithelial ridge cells, a transient neonatal cell group in the cochlear duct, which plays a crucial role in the functional maturation of hair cell, structural development of tectorial membrane, and refinement of audio localization before hearing. Greater epithelial ridge cells are methodologically homogeneous, while whether different cell subtypes are existence in this intriguing region and the degeneration mechanism during postnatal cochlear development are poorly understood. In the present study, single-cell RNA sequencing was performed on the cochlear duct of postnatal rats at day 1 (P1) and day 7 (P7) to identify subsets of greater epithelial ridge cell and progression. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were used to examine genes enriched biological processes in these clusters. We identified a total of 26 clusters at P1 and P7 rats and found that the cell number of five cell clusters decreased significantly, while four clusters had similar gene expression patterns and biological properties. The genes of these four cell populations were mainly enriched in Ribosome and P13K-Akt signal pathway. Among them, Rps16, Rpsa, Col4a2, Col6a2, Ctsk, and Jun are particularly interesting as their expression might contribute to the greater epithelial ridge cells degeneration. In conclusion, our study provides an important reference resource of greater epithelial ridge cells landscape and mechanism insights for further understanding greater epithelial ridge cells degeneration during postnatal rat cochlear development.
| S-EPMC8446670 | biostudies-literature
Project description:Pseudo-temporal analysis of Single-cell RNA sequencing reveals trans-differentiation potential of Greater Epithelial Ridge cells into hair cells during postnatal development of cochlea in Rats
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Project description:Purpose: Wnt activation can induce regeneration in the early postnatal cochlea, but the regenerative capacity of the postnatal cochlea diminishes between P0 to P5. The goal of this study was to utilize RNA-Seq for the overall evaluation of expression patterns, comparing P1 and P4 newborn cochlea with and without Wnt activation. Methods: Sox2-CreER; β-cateninflox(Exon3)/+ mice were used to stabilize β-catenin in Sox2+ cochlear supporting cells. Tamoxifen was injected to the mother at either P1 or P4 to induce Cre activation in the pups. mRNA libraries were generated from treated and untreated pups 3 days after injection in triplicates (overall 12 samples) using ThruPLEX DNA-seq kit (Rubicon Genomics) and then sequenced using Illumina NextSeq500 Single-End 75bp. Reads were aligned to mm10 and quality control was assessed using FastQC and Qualimap followed by FeatureCounts, Sailfish v0.10.1 and tximport. Differential expression was evaluated using DESeq2 and subsequent pathway analysis was performed using Ingenuity Pathway Analysis Software (Qiagen). Results: 40-50 million reads were detected per sample. PCA and Pearson correlation demonstrated a clear segragation of the samples by age that was supported by the identification of 2914 differentially expressed genes between P1 and P4 samples. Additional affect of treatment resulted is 530 differentially expressed genes between treated and untreated samples at P1 and 304 genes were differentially expressed between treated and untreated samples at P4. Clear activation of the Wnt pathway was apparent at both time-points after treatment. However, activation of downstream pathways that may be involved in regeneration was detected at P1 but not at P4, mainly the involvement of cell-cycle and proliferation as well as Erbb2 associated genes. Conclusions: Our results suggest that the Wnt pathway is still active and can be further induced at early and late postnatal stages in a similar manner. However, at early stages, exogenous Wnt activation potentially promotes an arrest of maturation progression or even partial dedifferentiation of supporting cells into a less mature state that enables regeneration, while the downstream affect is not as prominenet later on. Proliferative capacity in the early postnatal cochlea is correlated with a unique transcriptional response that diminishes in the older cochlea, including a robust increase in the expression of cell cycle genes and cellular growth and development genes. Our results suggest that the downstream transcriptional response to Wnt activation is the key factor mediating a regenerative response, or a lack-thereof, in the mammalian cochlea and that efforts to stimulate regeneration in the adult auditory organ may require recapitulating the transcriptional response of the early neonatal cochlea to exogenous Wnt activation and subsequent alterations of silenced state of Wnt target genes. .
2018-12-01 | GSE113719 | GEO
Project description:To identify which miRNAs are involved in the onset and progression of age-related hearing loss in the mammalian cochlea We used miRNA microarrays to screen the miRNAs which exhibit the drastic changes in their expressing level during the aging of the cochlea The organ of Corti (OC), the major pathological sites of presbycusis in cochlea, was collected separately at 3 timepoints during the life span. Two strains were selected: C57bl/6j (as accelerated prebycusis model) and CBA/J (as naturally occured presbycusis model). The selected timepoints were: Postnatal 21 days (P21), 3 month (3m) and 9 month (9m) for C57 mice, and P21, 9m, 16m for CBA mice.
2013-03-12 | E-GEOD-45026 | biostudies-arrayexpress
Project description:In mammals, hearing loss is irreversible due to the lack of regenerative potential of non-sensory cochlear cells. Neonatal cochlear cells, however, can grow into organoids that harbor sensory epithelial cells, including hair cells and supporting cells. Here, we purify different cochlear cell types from neonatal mice, validate the composition of the different groups with single-cell RNA sequencing (RNA-seq), and assess the various groups' potential to grow into inner ear organoids. We find that the greater epithelial ridge (GER), a transient cell population that disappears during post-natal cochlear maturation, harbors the most potent organoid-forming cells. We identified three distinct GER cell groups that correlate with a specific spatial distribution of marker genes. Organoid formation was synergistically enhanced when the cells were cultured at increasing density. This effect is not due to diffusible signals but requires direct cell-to-cell contact. Our findings improve the development of cell-based assays to study culture-generated inner ear cell types.
| S-EPMC7847202 | biostudies-literature
Project description:Our work describes the application of mass spectrometry-based label-free quantitative proteomics for the identification of differentially expressed proteins between different-aged cochlea. We report proteins exclusively present as well as up- and downregulated in the cochlear sensory epithelium at significant developmental stages. Additionally, we report proteins exclusively present on P3 that were recently identified in the cochlea for the first time. We use bioinformatics to provide insight on biological functions and potential primary and secondary partners of the differentially expressed proteins. This study provides the first differentially expressed proteome in the mammalian cochlea at significant developmental stages; before hearing, during the onset of hearing, and when hearing is fully developed. We believe that these results will provide insights into the function of proteins that change during development and identify potential protein biomarkers related to hearing impairments.
2018-08-29 | PXD001973 | Pride
Project description:The aim of this study is to identify the gene targets of the Notch ligand JAG1 in the postnatal cochlea. JAG1 was conditionally deleted in mice carrying both an inducible Cre allele (Sox2CreER) and a floxed (fl) Jag1 allele. Tamoxifen was administered to P0/P1 pups. Cochlear tissues from 6 Sox2CreER/+Jag1fl/fl and wildtype littermate controls were dissected under the dissecting microscope in ice-cold DEPC-treated PBS and stored in RNAlater (Invitrogen) at 4C. The RNAs were purified by RNeasy Micro Kit (QIAGEN). The quality and quantity of RNAs were measured by a 2100 bioanalyzer (Agilent). Illumina compatible sequencing libraries were generated by the University of Rochester Genomics Research Center. Libraries were hybridized to the Illumina flow cell and single-end reads of 100nts were generated. Identification of significantly differentially expressed genes was determined using DeSeq2. We found 548 differentially expressed genes with an adjusted p-value of <0.05, 411 of those genes were significantly upregulated while 137 were significantly downregulated. Analysis of pathways revealed novel genes involved downstream of JAG1-Notch signaling in the postnatal cochlea.
2022-12-09 | GSE193158 | GEO
Project description:Transcriptional respose to Wnt activation regulates the regenerative capacity of the murine postnatal cochlea
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