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Mutational consequences of ERCC1-deficiency in adult mouse stem cells

ABSTRACT: Mutational consequences of ERCC1-deficiency in adult mouse stem cells

PROVIDER: PRJEB19368 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1855000.fastq.gz	Fastqsanger.gz
	ERR1855000_1.fastq.gz	Fastqsanger.gz
	ERR1855000_2.fastq.gz	Fastqsanger.gz
	ERR1855010.fastq.gz	Fastqsanger.gz
	ERR1855010_1.fastq.gz	Fastqsanger.gz

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Down-regulation of cholesterol biosynthesis in forebrains of ERCC1-deficient mice

Project description:Background: Several genetic defects of the nucleotide excision repair (NER) pathway, including deficiency of the Excision Repair Cross-Complementing rodent repair deficiency, complementation group 1 (ERCC1), result in pre-mature aging, impaired growth, microcephaly and delayed development of the cerebellum. Such a phenotype also occurs in ERCC1-knockout mice which survive for up to 4 weeks after birth. Therefore, we analyzed cerebellar and hippocamapal transcriptomes of these animals at 3 weeks of age to identify the candidate mechanisms underlying brain consequences of reduced ERCC1 activity. Results: In the cerebellum, the most prominent change was upregulation of genes that are associated with gliosis. Although Purkinje cell degeneration has been reported in some mouse strains with NER impairment, Purkinje cell transcriptome was mostly unaffected by the ERCC1 knockout. In the hippocampus, the gliosis response was minimal. Instead, there was an extensive downregulation of genes related to lipid metabolism including several enzymes of the cholesterol biosynthesis pathway as well as lipoproteins and plasma membrane proteins. Reduced expression of the cholesterol biosynthesis pathway genes was also present in the neocortex of adult mice whose ERCC1 gene was replaced by a mutant allele with a partial activity. Conclusions: Downregulation of forebrain cholesterol biosynthesis genes is a newly identified consequence of ERCC1 deficiency. Its presence in adult mice suggests that it is not a secondary consequence of brain growth impairment. Instead, reduced cholesterol biosynthesis may contribute to such an impairment as well as affect function of mature synapses.

2011-08-16 | GSE31199 | GEO

Down-regulation of cholesterol biosynthesis in forebrains of ERCC1-deficient mice

2011-08-15 | E-GEOD-31199 | biostudies-arrayexpress

Genome-wide mutational consequences of nucleotide excision repair-deficiency through XPC deletion in a human adult stem cell culture

Project description:Nucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Deficiency in this pathway can contribute to the development of cancer and accelerate aging. NER-deficiency is an important determinant for cancer treatment outcome, as NER-deficient tumors are selectively sensitive to cisplatin treatment. While NER-deficiency has been linked to mutational Signature 5, not all NER-deficient tumors are characterized by a high Signature 5 contribution, illustrating the importance to further characterize the mutational consequences of NER-deficiency. Here, we analyzed the mutational profile of a human adult stem cell (organoid) culture that is deficient in NER through XPC deletion by CRISPR-Cas9 gene-editing, and subsequent whole-genome sequencing analysis of a clonally derived organoid. We found that XPC deletion results in an increase in base substitution load and specifically induces Signature 8 mutations, a mutational signature with previously unknown etiology. Presence of Signature 8 may, therefore, serve as a novel biomarker for NER-deficient tumors and could improve personalized treatment strategies.

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Two siblings with strong NER inactivation due to inherited ERCC1 deficiency display mild clinical features of XP and CS with severe liver impairment

Project description:The ERCC1-XPF heterodimer is a multifunctional endonuclease involved in nucleotide excision repair (NER), inter-strand crosslink (ICL) repair, and DNA double-strand break (DSB) repair. Only two patients with inherited ERCC1 defects have been reported who both died at an early age. Here, we describe a new case of ERCC1 deficiency in two siblings (11 and 13 years) who show mild features of Xeroderma Pigmentosum and Cockayne Syndrome. Both patients displayed microcephaly, mild developmental delay, mild photosensitivity, and severe cholestatic liver problems. Genetic analysis revealed a maternal deletion and a paternal missense variant in ERCC1 (R156W) that affect a salt bridge just below the XPA-binding pocket. Studies in patient-derived fibroblasts and reconstituted knockout cells confirmed that mutant ERCC1 is not efficiently recruited to the NER complex due to a decreased interaction with XPA. Consequently, patient cells show a strong NER defect, although residual repair could be detected. The steady-state protein levels of ERCC1 and XPF were severely reduced in patient cells, but this only led to a mild defect in ICL repair, and no impact on DSB repair. We report a new case of ERCC1 deficiency that particularly affect NER and has only a mild impact on other ERCC1-dependent repair pathways.

2021-01-26 | PXD017940 | Pride

Gene expression profiling or ERCC1 deficient and control mouse lineage negative bone marrow cells

Project description:Transcriptome differences induced by ERCC1 deficiency.

2015-04-09 | E-MTAB-3297 | biostudies-arrayexpress

MiRNA expression profiling or ERCC1 deficient and control mouse lineage negative bone marrow cells

Project description:MiRNA expression differences induced by ERCC1 deficiency.

2015-04-09 | E-MTAB-3298 | biostudies-arrayexpress

MiRNA expression profiling or ERCC1 deficient and control mouse lineage negative, ScaI positive, Kit positive (LSK) bone marrow cells

Project description:MiRNA expression differences induced by ERCC1 deficiency.

2015-04-09 | E-MTAB-3310 | biostudies-arrayexpress

Consequences of Nkiras deficiency for the EGF response

Project description:Consequences of Nkiras deficiency for the EGF response

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Identify the protein partners of Ercc1 in DNA damage progeria in MEFs

Project description:ERCC1 is a DNA endonuclease participating in the Nucleotide Excision Repair (NER) pathway. Its functionality is related to XPF; the two proteins work as a heterodimer to incise the 5 of a 30-mer that contains the damaged nucleotide and remove the fragment together with XPG. Apart from NER deficiency, mutated Ercc1 in mice and humans causes a series of progeroid symptoms (premature ageing). We hypothesize that there are undescribed functions of ERCC1, possibly in transcriptional regulation that contribute to the development of the striking phenotypes observed. The aim is to identify previously uncharacterized protein partners of ERCC1 that might contribute to our understanding of its differential roles during DNA damage-driven progeria.

2023-10-04 | PXD017063 | Pride

Transcription profiling of Ercc1 white adipose tissue

Project description:Transcriptome analysis of epididymal white adipose tissue (WAT) depots in Ercc1 animals: To further elucidate the role of ERCC1 in WAT we scanned the transcriptome of 15 day old wt and Ercc1 epididymal WAT.

2013-11-04 | E-MEXP-3930 | biostudies-arrayexpress

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