Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Mutational signatures and increased retrotransposon insertions in Xeroderma Pigmentosum variant skin tumors

PROVIDER: PRJNA852428 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19843430_1.fastq.gz	Fastqsanger.gz
	SRR19843430_2.fastq.gz	Fastqsanger.gz
	SRR19843431_1.fastq.gz	Fastqsanger.gz
	SRR19843431_2.fastq.gz	Fastqsanger.gz
	SRR19843432_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 35

Similar Datasets

Homo sapiens

Project description:UVA light mutagenesis in xeroderma pigmentosum variant human cells

| PRJNA556825 | ENA

Comparative transcriptomic analysis of WT and XP-C fibroblasts cultured in 3D-dermal equivalents

Project description:Xeroderma Pigmentosum (XP) is a rare autosomal genetic disease. XP patients present a default in the mechanism responsible for the repair of UV-induced DNA lesions. They are prone to develop skin cancers with high frequencies early in their life. To identify microenvironment factors that could contribute to the progression of skin cancers in XP-C group we did comparative transcriptomic analysis of WT and XP-C dermal patient’s fibroblasts.

2019-09-19 | GSE133084 | GEO

Cxcl1 antagonist on UVB-induced skin inflammation leading to inhibitory effects on photo-skin tumorigensis in Xeroderma pigmentosum type A deficient mice

Project description:Xeroderma pigmentosum type A (XP-A) is a hereditary disease characterized by early onset of skin cancers development by ultraviolet (UV) exposure. Although etiology of susceptible to skin tumor of XP-A is well investigated as a repair deficiency by UV-induced DNA damage, the mechanism of unusual strong and prolonged skin inflammation caused by UV in XP-A and whether UV-induced inflammatory response relates to skin tumor-prone phenotype remains to be elucidated. Among up-regulated inflammatory response related genes in Xpa mice compared with wild-type by gene profiling study, Cxcl1 in Xpa mice was significantly different from wild-type and blood level of Cxcl1 was increased with UVB exposed on even small area of skin in Xpa mice. We administered Cxcl1 neutralizing antibody or antioxidant agent n-acetylcysteine for Xpa mice after UVB irradiation, showing that blood levels of Cxcl1, ear swelling and skin redness as an inflammatory response were significantly suppressed. Xpa mice with chronic UVB exposure and Cxcl1 neutralizing antibody or n-acetylcysteine administered Xpa mice yields much less skin tumors compared with control group. Those results indicate that highly inflammatory response of Xpa mice by UVB plays a role of skin tumor development that could be suppressed by chemokine as Cxcl1 through antioxidant mechanism.

2017-06-01 | GSE86093 | GEO

Somatic Variation Angiosarcoma

Project description:Through whole genome sequencing, this study will explore the mutational profiles and signatures within an angiosarcoma tumour from a patient with xeroderma pimentosum. Very little information is known about this tumour type and it has not previously been studied within the context of xerogerma pigmentosum.

| EGAS00001002610 | EGA

Insights from multi-omic modelling of neurodegeneration in Xeroderma Pigmentosum using an induced pluripotent stem cell system

Project description:Xeroderma pigmentosum (XP) is caused by defective nucleotide excision-repair of DNA damage. This results in hypersensitivity to ultraviolet light and increased skin cancer risk, as sunlight-induced photoproducts remain unrepaired. However, many XP patients also display early-onset neurodegeneration, which leads to premature death. The mechanism of neurodegeneration is unknown. Here, we investigate XP neurodegeneration using pluripotent stem cells derived from XP patients and healthy relatives, performing functional multi-omics on samples during neuronal differentiation. We show substantially increased levels of 5',8-cyclopurine and 8-oxopurine in XP neuronal DNA secondary to marked oxidative stress. Furthermore, we find that the endoplasmic reticulum stress response is upregulated and reversal of the mutant genotype is associated with phenotypic rescue. Critically, XP neurons exhibit inappropriate downregulation of the protein clearance ubiquitin-proteasome system (UPS). Chemical enhancement of UPS activity in XP neuronal models improves phenotypes, albeit inadequately. Although more work is required, this study presents insights with intervention potential.

2024-04-18 | PXD047571 | Pride

Homo sapiens

Project description:UVB light mutagenesis in Xeroderma Pigmentosum C human cells

| PRJNA697944 | ENA

Fibroblast RNA-Seq data from three genodermatoses (RDEB, XPC and KS)

Project description:Recessive dystrophic epidermolysis bullosa, Kindler syndrome and xeroderma pigmentosum C, are three cancer-prone genodermatoses whose causal genetic mutations cannot fully explain, on their own, the array of associated phenotypic manifestations. Recent evidence highlights the contributing role of the stromal microenvironment in the pathology of these disorders. To investigate common mechanisms that contribute to the pathogenic role played by dermal fibroblasts, we conducted a comparative gene expression analysis by RNA-Seq.

2019-03-12 | GSE119501 | GEO

An analysis fo genomic structural alterations in iPS cells derived from xeroderma pigmentosum patients

2015-06-24 | GSE55520 | GEO

An analysis fo genomic structural alterations in iPS cells derived from xeroderma pigmentosum patients

Project description:To elucidate frequencies of genomic structural alterations, we performed an analysis using a SNP genotyping array (Illumina HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit) for iPS cells derived from xeroderma pigmentosum patients (XP3OS, XP40OS, and XPEMB-1). Samples were collected after 10 to 25 passages to detect structural mutations occurred during the cell cultivation processes. Our results suggested a higher mutation rate of the iPS cells compared to those from normal cells. The iPS-cell samples were collected after several passages togerther with their precursor cell samples and subjected to the SNP genotyping array. We searched for structural mutations occurred during the culture of the iPS cells.

2015-06-24 | E-GEOD-55520 | biostudies-arrayexpress

GENOMIC MUTATION LANDSCAPE OF SKIN CANCERS FROM DNA REPAIR-DEFICIENT XERODERMA PIGMENTOSUM PATIENTS

Project description:Xeroderma pigmentosum (XP) is a genetic disorder caused by mutations in genes of the Nucleotide Excision Repair (NER) pathway (groups A-G) or in Translesion Synthesis (TLS) DNA polymerase ÃŽÂ· (group V). XP is associated with an increased skin cancer risk, reaching, for some groups, several thousand-fold compared to the general population. Here, we analyzed 38 skin cancer genomes from five XP groups. We found that the activity of NER determines heterogeneity of the mutation rates across skin cancer genomes and that transcription-coupled NER extends beyond the gene boundaries reducing the intergenic mutation rate. Mutational profile in XP-V tumors revealed the role of polymerase ÃŽÂ· in the error-free bypass of (i) rare TpG and TpA DNA lesions, (ii) 3Ã¢Â€Â™ nucleotides in pyrimidine dimers, and (iii) TpT photodimers. Our study unravels the genetic basis of skin cancer risk in XP and provides insights into the mechanisms reducing UV-induced mutagenesis in the general population.

| EGAS00001006732 | EGA

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