Gene expression profiling of the inner ear

Schimmang, Thomas; Maconochie, Mark

doi:10.1111/joa.12376

Cited by 10 publications

(11 citation statements)

References 120 publications

(182 reference statements)

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“…The first transcriptome profiling experiment on cochlear tissue was performed Cho et al (2002) . Since then, a large number of studies have leveraged microarray, PCR, and RNA sequencing (RNA-seq) technologies to explore the auditory transcriptome ( Schimmang and Maconochie, 2016 ). Low-input reverse transcription and RNA isolation technologies have revolutionized these studies, facilitating cell type-specific transcriptomics.…”

Section: Introductionmentioning

confidence: 99%

Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing

et al. 2019

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SUMMARYSingle-cell RNA sequencing is a powerful tool by which to characterize the transcriptional profile of low-abundance cell types, but its application to the inner ear has been hampered by the bony labyrinth, tissue sparsity, and difficulty dissociating the ultra-rare cells of the membranous cochlea. Herein, we present a method to isolate individual inner hair cells (IHCs), outer hair cells (OHCs), and Deiters’ cells (DCs) from the murine cochlea at any post-natal time point. We harvested more than 200 murine IHCs, OHCs, and DCs from post-natal days 15 (p15) to 228 (p228) and leveraged both short- and long-read single-cell RNA sequencing to profile transcript abundance and structure. Our results provide insights into the expression profiles of these cells and document an unappreciated complexity in isoform variety in deafness-associated genes. This refined view of transcription in the organ of Corti improves our understanding of the biology of hearing and deafness.

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Section: Introductionmentioning

confidence: 99%

Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing

et al. 2019

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“…For example, by using gene arrays, fewer genes were reported to be expressed differently in the adult rat cochlea suffered from noise treatment 42,43 , but more genes were found to be expressed differentially in the mouse cochlear sensory epithelia in postnatal day-3, compared to those at adult 17 . In general, the RNA presence and quantity can be indicated from a whole genome in time using RNA-seq, whereas cDNA microarrays only identify the limited allele variants designed into the microarrays 20,44 . Thus, this study provides a relatively more complete candidate genes or pathways which play roles in hair cell regeneration in the mouse cochlea, particularly from the comparative perspective with chick hair cell regeneration.…”

Section: Discussionmentioning

confidence: 99%

“…In general, most genes and signaling pathways which have been shown to be involved in the embryonic development of hair cells are also required for hair cell regeneration 6,7 . Given the advantages of high-throughput sequencing, cDNA microarrays, SAGE or RNA-seq have been used to investigate a global gene expression during hair cell regeneration in rats or mice 17–20 and nonmammals 19,21–26 . Our recent study found that about 800 genes were differentially expressed during chick hair cell regeneration, some of which were grouped into approximately one hundred signaling pathways, including Notch, Wnt, Fgf and Bmp.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis of mouse cochleae suffering from gentamicin damage reveals the signalling pathways involved in hair cell regeneration

Bai

Jiang

Wang³

et al. 2019

Sci Rep

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There is a strong capacity for hair cell regeneration after damage in the inner ear of non-mammals. However, mammalian hair cells are substantially unable to regenerate. To obtain insights into the mechanism of this difference, we analyzed the transcriptomic changes in the mouse cochleae suffered from gentamicin damage and compared them with those in the chick cochleae suffered from the same damage. The results indicated that 2,230 genes had significantly differential expression between the gentamicin- and saline-treated mouse cochleae. Some of the differentially expressed genes were grouped into 265 signaling pathways, including the Notch, Wnt (Wingless and INT-1), Bmp (bone morphogenetic protein), FGF (fibroblast growth factor) and Shh (sonic hedgehog) pathways. Using pharmacological inhibitors or agonists of these pathways, the effects of these pathways on hair cell regeneration were further studied. The results indicated that Bmp alone and its coregulation with the Notch or Wnt signaling pathways increased the numbers of generated cells from transdifferentiation or proliferation in the mouse cochlea after damage, in addition to the reported coregulation of Notch and Wnt. Thus, this work indicates a new signaling pathway (Bmp) and its synergetic coregulation in mammalian hair cell regeneration, providing potential therapeutic targets to increase mammalian hair cell regeneration.

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“…Auditory phenotypic diversity might be related to changes in gene expression. Significant efforts have been made to profile gene expression patterns in mouse inner ears at different developmental stages, as well as following various stimuli, physiological damage, and specific gene knock out [ 24 , 25 , 26 , 27 ]. Dong et al (2013) reported that inner ear gene expression differs between echolocating bats and non-echolocating bats via a transcriptome analysis and identified several candidate genes related to echolocation ability [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analyses Provide Insights into the Auditory Function in Trachemys scripta elegans

Chen

Jiao

et al. 2022

Animals

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An auditory ability is essential for communication in vertebrates, and considerable attention has been paid to auditory sensitivity in mammals, birds, and frogs. Turtles were thought to be deaf for a long time; however, recent studies have confirmed the presence of an auditory ability in Trachemys scripta elegans as well as sex-related differences in hearing sensitivity. Earlier studies mainly focused on the morphological and physiological functions of the hearing organ in turtles; thus, the gene expression patterns remain unclear. In this study, 36 transcriptomes from six tissues (inner ear, tympanic membrane, brain, eye, lung, and muscle) were sequenced to explore the gene expression patterns of the hearing system in T. scripta elegans. A weighted gene co-expression network analysis revealed that hub genes related to the inner ear and tympanic membrane are involved in development and signal transduction. Moreover, we identified six differently expressed genes (GABRA1, GABRG2, GABBR2, GNAO1, SLC38A1, and SLC12A5) related to the GABAergic synapse pathway as candidate genes to explain the differences in sexually dimorphic hearing sensitivity. Collectively, this study provides a critical foundation for genetic research on auditory functions in turtles.

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Gene expression profiling of the inner ear

Cited by 10 publications

References 120 publications

Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing

Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing

Transcriptomic analysis of mouse cochleae suffering from gentamicin damage reveals the signalling pathways involved in hair cell regeneration

Transcriptome Analyses Provide Insights into the Auditory Function in Trachemys scripta elegans

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