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Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [RNA-seq-invitro]

ABSTRACT: Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [RNA-seq-invitro]

PROVIDER: PRJNA992075 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25177428_1.fastq.gz	Fastqsanger.gz
	SRR25177428_2.fastq.gz	Fastqsanger.gz
	SRR25177429_1.fastq.gz	Fastqsanger.gz
	SRR25177429_2.fastq.gz	Fastqsanger.gz
	SRR25177430_1.fastq.gz	Fastqsanger.gz

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Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [RNA-seq-invitro]

Project description:Vestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity and the tumor microenvironment (TME) contribute to the pathogenesis of these tumors remains poorly understood. We performed scRNA-seq on 15 VS samples, with paired scATAC-seq (n=6) and exome sequencing (n=12). We identified diverse Schwann cell (SC), stromal, and immune populations in the VS TME and found that repair-like and MHC-II antigen presenting subtype SCs are associated with increased myeloid cell infiltrate, implicating a nerve injury-like process. Deconvolution of RNA-expression data from 195 tumors revealed Injury-like tumors are associated with larger tumor size, and scATAC-seq identified transcription factors associated with nerve repair among SCs from Injury-like tumors. Ligand-receptor analysis and in vitro experiments suggested that SCs recruit monocytes. Our study indicates that Injury-like SCs may cause tumor growth via myeloid cell recruitment and identifies molecular pathways that may be targeted to prevent tumor progression. This SubSeries is part of a SuperSeries (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216784).

2023-09-15 | GSE236735 | GEO

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

| PRJNA981645 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

| PRJNA981646 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

| PRJNA895388 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scRNA-seq]

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scRNA-seq]

| PRJNA895392 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scATAC-seq]

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scATAC-seq]

| PRJNA895391 | ENA

Wide methylation analysis in vestibular schwannoma

Project description:Wide methylation analysis in vestibular schwannoma

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Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [bulk RNA-seq]

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [bulk RNA-seq]

| PRJNA895390 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

Project description:Vestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity and the tumor microenvironment (TME) contribute to the pathogenesis of these tumors remains poorly understood. We performed scRNA-seq on 15 VS samples, with paired scATAC-seq (n=6) and exome sequencing (n=12). We identified diverse Schwann cell (SC), stromal, and immune populations in the VS TME and found that repair-like and MHC-II antigen presenting subtype SCs are associated with increased myeloid cell infiltrate, implicating a nerve injury-like process. Deconvolution of RNA-expression data from 195 tumors revealed Injury-like tumors are associated with larger tumor size, and scATAC-seq identified transcription factors associated with nerve repair among SCs from Injury-like tumors. Ligand-receptor analysis and in vitro experiments suggested that SCs recruit monocytes. Our study indicates that Injury-like SCs may cause tumor growth via myeloid cell recruitment and identifies molecular pathways that may be targeted to prevent tumor progression. This SuperSeries is composed of the SubSeries listed below. Matching whole exome sequencing data is available via NCBI dbGaP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA981645/).

2023-09-15 | GSE216784 | GEO

Characterisation of vestibular schwannoma tissues using LC-MS/MS analysis

Project description:Vestibular schwannoma is the most common benign neoplasm of the cerebellopontine angle. Its first symptoms include hearing loss, tinnitus, and vestibular symptoms, followed by cerebellar and brainstem symptoms, along with palsy of the adjacent cranial nerves. However, the clinical picture has unpredictable dynamics and currently, there are no reliable predictors of tumour behaviour. The major objective of this study was to verify whether a technique using in-sample specific protein digestion with trypsin would have the potential to provide proteomic characterisation of these pathological tissues.

2023-09-26 | PXD045261 | Pride

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