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Single cell RNA sequencing analysis of vestibular schwannoma reveals functionally distinct macrophage subsets

ABSTRACT: Single cell RNA sequencing analysis of vestibular schwannoma reveals functionally distinct macrophage subsets

PROVIDER: PRJNA1051953 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27196905.fastq.gz	Fastqsanger.gz
	SRR27196906.fastq.gz	Fastqsanger.gz
	SRR27196907.fastq.gz	Fastqsanger.gz
	SRR27196908.fastq.gz	Fastqsanger.gz
	SRR27196909.fastq.gz	Fastqsanger.gz

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Single cell RNA sequencing analysis of vestibular schwannoma reveals functionally distinct macrophage subsets

Project description:Background: Vestibular schwannomas (VS) remain a challenge due to their anatomical location and propensity to growth. Macrophages are present in VS but their roles in VS pathogenesis remains unknown. Objectives: Assess phenotypic and functional profile of macrophages in VS with single cell RNA sequencing (scRNAseq). Methods: scRNAseq was carried out in three VS samples to examine characteristics of macrophages in the tumor. RT-qPCR was carried out on ten VS samples for CD14, CD68 and CD163 and a panel of macrophage associated molecules. Results: scRNAseq revealed macrophages to be a major constituent of VS microenvironment with three distinct subclusters based on gene expression. The subclusters were also defined by expression of CD163, CD68 and IL-1β. AREG and PLAUR were expressed in the CD68+CD163+IL-1β+ subcluster, PLCG2 and NCKAP5 were expressed in CD68+CD163+IL-1β- subcluster and AUTS2 and SPP1 were expressed in the CD68+CD163-IL-1β+ subcluster. RT-qPCR showed expression of several macrophage markers in VS of which CD14, ALOX15, Interleukin-1β, INHBA and Colony Stimulating Factor-1R were found to have a high correlation with tumor volume. Conclusions: Macrophages form an important component of VS stroma. scRNAseq reveals three distinct subsets of macrophages in the VS tissue which may have differing roles in the pathogenesis of VS.

2024-04-01 | GSE250061 | GEO

Wide methylation analysis in vestibular schwannoma

Project description:Wide methylation analysis in vestibular schwannoma

| PRJNA244045 | ENA

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

Gene expression profile at single cell level of vestibular schwannoma

Project description:Vestibular schwannoma (VS) is the most common benign tumor in the cerebellopontine angle and internal auditory canal. Illustrating the heterogeneous cellular components of VS could provide insights into its various growth patterns. Single-cell RNA sequencing (scRNA-seq) was used to profile transcriptomes from 7 VS samples and 2 great auricular nerves as normal control.

2024-03-13 | GSE230375 | GEO

miRNA expression profile is related to vestibular schwannoma growth rate

Project description:Tumor miRNA expression is related to the growth rate of sporadic vestibular schwannomas. Rapid tumor growth is associated with deregulation of several miRNAs, including up-regulation of miR-29abc, miR-19, miR-340-5p, miR-21 and miR-221 and down-regulation of miR-744 and let-7b. Gene ontologies affected by the deregulated miRNAs included neuron development and differentiation, gene silencing and negative regulation of various biological processes, including cellular and intracellular signalling and metabolism. We used microarray to determine the miRNA expresison in vestibular schwannoma their relation to the growth rate.

2019-01-08 | GSE124717 | GEO

Microarray Analysis in Vestibular Schwannomas

Project description:Vestibular Schwannomas are benign neoplasms that arise from the vestibular nerve. The hallmark of these tumors is the biallelic inactivation of NF2. Transcriptomic alterations, such as the Nrg1/ErbB2 pathway, have been described in Schwannomas. Here, we have performed a whole transcriptomic analysis in 31 vestibular Schwannomas and 9 control nerves in the Affymetrix Gene 1.0ST platform, validated by quantitative Real-Time PCR using TaqMan Low Density Arrays. We performed a mutational analysis of NF2 by PCR/dHPLC and MLPA as well as a microsatellite marker analysis of the loss of heterozygosity of chromosome 22q. The microarray analysis showed that 1516 genes were deregulated, and 48 of the genes were validated by qRT-PCR. At least two genetic hits (allelic loss and/or gene mutation) in NF2 were found in 16 tumors, seven cases showed one hit and eight tumors showed no NF2 alteration. As conclusion, MET and associated genes such as ITGA4/B6, PLEXNB3/SEMA5 and CAV1 showed a clear deregulation in vestibular Schwannomas. In addition, androgen receptor (AR) downregulation may denote a hormonal effect or cause in this tumor. Furthermore, the osteopontin gene (SPP1), which is involved in Merlin protein degradation, was upregulated, which suggests that this mechanism may also exert a pivotal role in Schwannoma Merlin depletion. Finally, no major differences were found between tumors of different sizes, histological types or NF2 status, which suggests that at the mRNA level all Schwannomas, regardless of molecular and clinical characteristics, may share common features that can be used in the fight against them. In order to find target to fight against vestibular schwannoma, we performed an analysis of gene expression by microarrays.

2013-03-01 | E-GEOD-39645 | biostudies-arrayexpress

Gene expression profile at single cell level of vestibular schwannoma

Project description:Gene expression profile at single cell level of vestibular schwannoma

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miRNA expression profile is related to vestibular schwannoma growth rate

Project description:miRNA expression profile is related to vestibular schwannoma growth rate

| PRJNA513253 | ENA

Wide methylation analysis in vestibular schwannoma [Infinium HumanMethylation450 BeadChip]

Project description:Vestibular schwannomas are intracranial tumors that affects unilateral and sporadically or bilateral when is associated to Neurofibromatosis type 2 syndrome. The hallmark of the disease is the biallelic inactivation by NF2 gene mutation or LOH of chromosome 22q, where this gene harbors. In this work, we used Infinium HumanMethylation 450K BeadChip microarrays in a series of 36 vestibular schwannomas, 4 non-vestibular schwannomas and 5 healthy nerves. Our results shows a trend to hypomethylation in schwannomas. Furthermore, HOX genes, located at 4 clusters in the genome, displayed hypomethylation in numerous CpG sites in vestibular but not in non-vestibular schwannomas. Additionally, several microRNA and protein-coding genes were found hypomethylated at promoter regions and confirmed by expression analysis; including miRNA-199a1, miRNA-21, MET and PMEPA1. We also detected methylation patterns that might be involved in alternative transcripts of several genes such as NRXN1 or MBP; that would increase the complexity of methylation-expression. Overall, our results shows specific epigenetic signatures in several coding genes and microRNA that could be used in the finding of potential therapeutic targets.

2014-11-30 | GSE56596 | GEO

Expression profiling macrophage subsets

Project description:Expression profiling macrophage subsets

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