Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bone signaling in rat middle ear and cochlea by transcription profiling

ABSTRACT: * Bone signaling in middle ear development *
Common middle ear diseases, such as chronic suppurative otitis media and cholesteatoma, may affect bone behavior in the middle ear air cell system.
This study analyzed gene expression of bone-related signaling factors and gene sets from lining tissues in the developing middle ear of the rat. Candidate gene products were compared with previously published data on middle ear bone metabolism.
Microarray technology was used to identify bone-related genes and gene sets, which were differentially expressed between the adult (quiescent) bulla and young (resorbing/forming) bulla.

* Gene expression of the otic capsule *
The behavior of bone cells within the otic capsule is unique. After occification localized bone remodeling is virtually absent. Human otosclerosis is a localized disease within the otic capsule where the bone starts to remodel pathologically. Disease etiology is unknown and the pathogenesis is only partially elucidated.

The objective of this study is to measure bone-related gene expression of the otic capsule in order to reveal additionally signaling factors responsible for the absent bone remodeling within the otic capsule.

Microarray technology was used to determine genes involved in the bone metabolism, which were differentially expressed between lining tissues from the otic capsule and lining tissues from the middle ear of the rat.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Tomas Martin-Bertelsen

PROVIDER: E-MTAB-2336 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

"Time-resolved quantitative proteomic analysis of the developing otic vesicle reveals putative congenital hearing loss candidates and a novel role for Tgfbi

Project description:A large number of congenital hearing loss cases have an unknown genetic etiology. So far, transcriptomic approaches have successfully identified many candidate regulators of otic development, little is known about the abundance of their protein products during the development of the inner eat. Herein we used a multiplexed quantitative mass spectrometry-based proteomic approach to determine temporal trends in protein abundances during inner ear (otic) development in Xenopus. Wild type Xenopus embryos were cultured to larval stages and their otic tissues were manually dissected at five stages that represent that represent key transitions in otic morphology. The samples were processed using a bottom-up proteomic workflow and analyzed using LC-MS3.The analysis revealed dynamic expression of proteins related to cytoskeletal regulation, integrin signaling, and the extracellular matrix as inner ear structures developed. We correlated the dynamically regulated proteins in our dataset with previously published putative downstream targets of syndromic hearing loss genes SIX1 and CHD7 to identify novel candidate genes for congenital hearing loss.

2023-10-24 | PXD041991 | Pride

A systems level approach reveals new gene regulatory modules in the developing ear

Project description:The vertebrate inner ear arises early in development from a thickened epithelium, the otic placode. Specification toward an otic fate requires diverse signals and complex transcriptional inputs that act sequentially and/or in parallel. To uncover and integrate novel genes with known molecular players in the gene regulatory network (GRN) underlying otic development, we have performed transcriptome analyses of the presumptive otic region at sequential early stages of commitment toward inner ear identity. Our results identify hundreds of genes enriched at specific developmental time points, revealing dynamic changes in gene expression as a function of time during the transition from progenitor to committed otic state. Initial functional analysis of selected enriched transcription factors demonstrates a genetic hierarchy amongst these genes underlying this critical transition. Our results not only characterize the otic transcriptome in unprecedented detail but also identify new links in the GRN responsible for development of the presumptive inner ear.

2017-03-09 | GSE69185 | GEO

CHD7 regulates otic lineage differentiation and sensory epithelium generation in human inner ear organoids

Project description:Mutations in the chromatin remodeling enzyme CHD7 cause CHARGE syndrome, which affects multiple organs including the inner ear. We investigated how CHD7 mutations affect otic development in human inner ear organoids. We found loss of CHD7 or its chromatin remodeling activity leads to complete absence of hair cells and supporting cells, which can be explained by dysregulation of key otic development-associated genes in mutant otic progenitors. Further analysis of the mutant otic progenitors suggested that CHD7 can regulate otic genes through a chromatin remodeling-independent mechanism. Results from transcriptome profiling of hair cells revealed disruption of deafness gene expression as a potential underlying mechanism of CHARGE-associated sensorineural hearing loss. Notably, co-differentiating CHD7 knockout and wild-type cells in chimeric organoids partially rescued mutant phenotypes by restoring otherwise severely dysregulated otic genes. Taken together, our results suggest that CHD7 plays a critical role in regulating human otic lineage differentiation and deafness gene expression.

2022-07-21 | GSE208585 | GEO

Critical role of FGF, RA, and WNT signaling for otic lineage specification from human PSCs in a 2D/3D-combined differentiation system

Project description:The otic placode, from which the inner ear develops, initially forms as a thickened ectodermal patch adjacent to the dorsolateral hindbrain. Induction of otic placodal cells from human pluripotent stem cells (hPSCs) provides a robust approach to investigation of otic development. However, attempts to recapitulate otic lineage specification from hPSCs by stepwise differentiation methods have had limited success. One possible reason is that the role of signaling pathways in otic cell differentiation is not fully understood. Here, we developed a novel differentiation system involving use of suspension culture (3D floating culture) in combination with signaling factors for generating otic placodal cells via stepwise differentiation of hPSCs. We demonstrate that hPSC-derived pre-placodal cells acquired the potential to differentiate into posterior placodal cells after fibroblast growth factor 2 (FGF2) and retinoic acid (RA) treatment. Subsequent activation of WNT signaling following posterior placode specification induced differentiation of SIX1+/PAX8+/SOX2+ otic placodal cells. qPCR analysis showed that WNT activation increased expression of otocyst markers, including PAX8, PAX2, DLX5 and FBXO2. Moreover, induced otic cells exhibited similar gene expression patterns to the ventral and medial portions of the otocyst that give rise to the sensory epithelium of the inner ear. Collectively, our results indicate a critical role for FGF2, RA, and WNT signaling for the in vitro differentiation of the otic cell lineage from hPSCs. Our new culture system paves the way for improved modeling of early human inner ear development and will be of value to studies on the further differentiation of sensory epithelial cells.

2022-02-01 | GSE175998 | GEO

Human Pluripotent stem cells-derived Inner ear organoids recapitulate otic development in vitro

Project description:The molecular characterization of early stages of human inner ear development is limited by the difficulty in accessing samples at early gestational stages. Some aspects of inner ear morphogenesis can be recapitulated using pluripotent stem cell directed differentiation in inner ear organoids (IEOs). Once validated and benchmarked, these models could provide a unique tool to complement and refine our understanding of human otic differentiation and could be used to model developmental defects.Here we provide a first characterization of early human embryonic otocyst development and compare the primary tissue to the iPSC-derived inner ear cell types. Multiplex immunostaining and single cell RNA sequencing were used to characterize human iPSC-derived IEOs at 3 key developmental steps, providing a new and unique signature of in vitro derived otic- placode, epithelium, neuroblasts and sensory epithelia. The expression and localization of key markers were further evaluated in human embryos. We show that the otic placode derived in vitro (day 8-12) matches marker expression of Carnegie Stage (CS) 11 embryos, and subsequently (day 20-40) gives rise to otic epithelia and neuroblasts comparable to the CS13 embryonic stage. Differentiation of sensory epithelia, including supporting cells and hair cells, starts in vitro at day 50-60 of culture. The maturity of these cells is equivalent to vestibular sensory epithelia at week 10 or cochlear tissue at week 12 of development, prior to functional onset. Taken together these data indicates that the current state of the art protocol enables the specification of bona fide otic tissue, supporting further application of IEOs to model inner ear biology and disease

2023-08-22 | GSE229148 | GEO

Protein sequencing of human bone tissue at different ages

Project description:Bone is a dynamic organ in which bone formation mediated by osteoblasts balances against bone resorption mediated by osteoclasts to maintain bone homeostasis. With age, this balance gradually tilts toward bone resorption, leading to bone loss and osteoporosis. At the present study, the bone specimens from children (group A), middle-aged patients (group B), and older individuals (group C) were subjected to proteomics analysis by LC-MS/MS.

2023-02-01 | PXD039538 | Pride

Soleimani2019 - Finite-element model of incudostapedial joint

Project description:This is a finite-element model of the mechanics of the incudostapedial joint in the human middle ear.

2019-09-17 | MODEL1905070001 | BioModels

c-Myc Transcriptionally Amplifies Sox2 Target Genes to Regulate Self-Renewal in Multipotent Otic Progenitor Cells [RNA-Seq]

Project description:An immortalized multipotent otic progenitor (iMOP) cell was generated by transient expression of c-Myc in Sox2-expressing otic progenitor cells. The procedure activated endogenous c-Myc expression in the cells and amplified existing Sox2-dependent transcripts to promote self-renewal. Downregulation of c-Myc expression following growth factor withdrawal resulted in a molecular switch from self-renewal to otic differentiation. Progenitor cells from embryonic inner ear that form otospheres were infected with a c-Myc retrovirus to promote self-renewal

2015-02-18 | E-GEOD-62512 | biostudies-arrayexpress

TMT-based LC-MS/MS proteomics of cholesteatoma

Project description:Eight cases of middle ear cholesteatoma specimens and matched ear canal skin specimens

2023-03-07 | PXD036926 |

Identification of differentially expressed genes in early inner ear development

Project description:The first morphological evidence of the developing ear is a thickened disk of ectoderm known as the otic placode. However, signals for otogenesis are present even before the otic placode is physically apparent. Several inductive signals have been identified through candidate gene approaches, but there are still many gaps in the signaling cascade of otogenesis. Presently the candidate gene approach has largely exhausted known candidates. This project compares the pre-otic domain with a control region that is competent, but not specified to form otic placode. The purpose of this work is to identify genes that are differentially expressed in the pre-otic domain in order to generate a list of novel candidate genes for otic placode induction.

2010-06-21 | GSE16918 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data