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Multimodal sequencing (gene expression, chromatin accessibility, and mtDNA genotyping) of single cells of the RPE and choroid in human MELAS (m.3243A>G) and control samples

ABSTRACT: Multimodal sequencing (gene expression, chromatin accessibility, and mtDNA genotyping) of single cells of the RPE and choroid in human MELAS (m.3243A>G) and control samples

PROVIDER: PRJNA837596 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24653000_1.fastq.gz	Fastqsanger.gz
	SRR24653000_2.fastq.gz	Fastqsanger.gz
	SRR24653001_1.fastq.gz	Fastqsanger.gz
	SRR24653001_2.fastq.gz	Fastqsanger.gz
	SRR24653002_1.fastq.gz	Fastqsanger.gz

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Multimodal sequencing (gene expression, chromatin accessibility, and mtDNA genotyping) of single cells of the RPE and choroid in human MELAS (m.3243A>G) and control samples

Project description:The mitochondrial m.3243A>G variant is known to cause retinal dystrophy and vision loss. We used single cell multimodal sequencing to understand how the presence of this mutation affects cellular phenotype in a cell type-specific manner.

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Chromatin accessibility and mitochondrial genotype from single cells of the retina and choroid in human MELAS (m.3243A>G) and control samples [scATAC-seq]

Project description:The mitochondrial m.3243A>G variant is known to cause retinal dystrophy and vision loss. We used mitochondria single cell ATAC sequencing to measure nuclear chromatin accessibility and mitochondrial heteroplasmy in single cells of the retina and choroid.

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Differential expression of miRNAs in a cellular model of MELAS.

Project description:We investigate the participation of miRNAs in the cell response to the mitochondrial dysfunction associated with m.3243A>G mutation in mitochondrial DNA (mtDNA), which is the most common cause of MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) syndrome.Through small-RNA sequencing and in silico analysis, we identified 246 differentially-expressed in a transmitochondrial cybrid model of MELAS (100% m.3243A>G mutant mitochondrial DNA), with 126 being up-regulated and 120 down-regulated. The enrichment analysis of Gene Ontology (GO) terms revealed that target genes for dysregulated miRNAs were involved in muscle and nervous system development, heart development, and signaling pathways controlling cardiac events.These data suggest that the miRNA program triggered by the MELAS m.3243A>G mutation could explain for some of the clinical manifestations of the MELAS syndrome.

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Glutamate pathway dysfunction in MELAS syndrome is alleviated by ketogenic diet

Project description:The development of mitochondrial medicine is greatly impaired by the lack of knowledge and identification of efficient therapeutic routes targeting mitochondria. To better understand the pathophysiology of MELAS syndrome, neuronal cybrid cells, carrying different mutant loads of the m.3243A>G mutation, were investigated by a metabolomics and transcriptomics combined approach. Specific signatures, identifying MELAS biochemical biomarkers, disclosed the glutamate pathway as a culprit mechanism, establishing a strong correlation between glutamate concentrations and the m.3243A>G heteroplasmy levels. Transcriptomic analyses further revealed peculiar gene clusters, including glutamate, gamma-aminobutyric acid (GABA) and tricarboxylic acid (TCA) cycle pathways. These results were supported by post-mortem brain tissue analysis of a MELAS patient, confirming the dysregulation of the glutamate metabolic pathway. Ketogenic diet known to reduce glutamate toxicity, induced a significant reduction of glutamate level after 48h of ketone body treatment, improved mitochondrial functions alleviating the accumulation of several intermediate metabolites of the TCA cycle in MELAS cells. Thus, the integrated approach using a multi-OMICs strategy on MELAS cybrid cells, disclosed novel insights in the mitochondrial energy failure, identifying glutamate as a potential biomarker of the disease, while highlighting ketogenic diet, a nutrition based strategy, to treat MELAS patients

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Single cell transcriptomic analysis of human tissue (Retina and RPE/Choroid)

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Single-cell multiome of human RPE and choroid

Project description:We present a joint scRNA-seq and scATAC-seq atlas of adult human retinal pigment epithelium (RPE) and choroid. We integrate this atlas with a HiChIP enhancer connectome to predict noncoding variants with causal roles in age-related macular degeneration (AMD).

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Gene expression from single cells of the retina and choroid in human MELAS (m.3243A>G) and control samples [scRNA-seq]

Project description:The mitochondrial m.3243A>G variant is known to cause retinal dystrophy and vision loss. We used single cell RNA sequencing to understand how the presence of this mutation affects cellular phenotype in a cell type-specific manner.

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Sonlicromanol improves neuronal network dysfunction and transcriptome changes linked to m.3243A>G heteroplasmy in iPSC-derived neurons

Project description:Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) is often caused by an adenine to guanine variant at m.3243 (m.3243A>G) of the MT-TL1 gene. To understand how this pathogenic variant affects the nervous system, we differentiated human induced pluripotent stem cells (iPSCs) into excitatory neurons with normal (low heteroplasmy) and impaired (high heteroplasmy) mitochondrial function from MELAS patients with the m.3243A>G pathogenic variant. We combined micro-electrode array (MEA) measurements with RNA sequencing (MEA-seq) and found reduced expression of genes involved in mitochondrial respiration and presynaptic function, as well as non-cell autonomous processes in co-cultured astrocytes. Finally, we show that the clinical phase II drug sonlicromanol can improve neuronal network activity when treatment is initiated early in development. This was intricately linked with changes in the neuronal transcriptome. Overall, we provide insight in transcriptomic changes in iPSC-derived neurons with high m.3243A>G heteroplasmy, and show the pathology is partially reversible by sonlicromanol.

2021-07-29 | GSE154825 | GEO

Gene expression from single cells of the retina and choroid in human MELAS (m.3243A>G) and control samples [scRNA-seq]

Project description:Gene expression from single cells of the retina and choroid in human MELAS (m.3243A>G) and control samples [scRNA-seq]

| PRJNA837192 | ENA

In vivo Gene Expression Profiling of RPE/choroid Post-Intravitreal Injections of Dexamethasone and Triamcinolone at Clinically Relevant Time Points for Patient Care

Project description:PURPOSE To identify retinal pigment epithelial (RPE)/choroid genes and their relevant expression pathways affected by intravitreal injections of dexamethasone and triamcinolone acetonide in mice at clinically relevant time points for patient care. METHODS Differential gene expression of over 34,000 well-characterized mouse genes, in the RPE/choroid of 6 week old C57BL/6J mice were analyzed after intravitreal steroid injections at 1 week and 1 month post injection, using Affymetrix Mouse Genome 430 2.0 microarrays. The data were analyzed using GeneSpringGX12.5 and Ingenuity Pathway Analysis (IPA) microarray analysis software for biologically relevant changes. RESULTS Both triamcinolone and dexamethasone caused differential activation of genes involved in âCircadian Rhythm Signalingâ pathway at both time points tested. Triamcinolone (TAA) uniquely induced significant changes in gene expression in âCalcium Signalingâ (1 week) and âGlutamate Signalingâ pathways (1month). In contrast, Dexamethasone (Dex) affected the âGABA Receptor Signalingâ (1 week) and âSerotonin Receptor Signalingâ (1month) pathways. CONCLUSIONS Understanding how intraocular steroids affect the gene expression of RPE/choroid is clinically relevant. This in vivo study has elucidated several genes and pathways that are potentially altering the circadian rhythms and several other neurotransmitter pathways in RPE/choroid cells during intravitreal steroid injections, which likely has consequences in the dysregulation of RPE function and neurodegeneration of the retina. Total of 18 RPE/choroid samples were analysed. There were two time points, day7 and day30. Each time point had three groups: BSS control, DEX treatment and TAA treatment. Each group had three biological replicas.

2016-08-01 | E-GEOD-49872 | biostudies-arrayexpress

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