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E-MTAB-8439

ABSTRACT: RNA-Seq profiling of ERCC1-XPF DNA repair defect (Er1F/-) versus wild type (Er1F/+) macrophages

PROVIDER: E-MTAB-8439 | ExpressionAtlas | 2023-06-16

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-8439-analysis-methods.tsv	Tabular
	E-MTAB-8439-analytics.tsv	Tabular
	E-MTAB-8439-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-8439-configuration.xml	Xml
	E-MTAB-8439-g2_g1-mvaPlot.png	Other

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E-MTAB-8156

Project description:RNA-seq of mouse DNA repair endonuclease XPF knock out versus wild type and versus trans retinoic acid (tRA) treated wild type

2019-09-09 | E-MTAB-8156 | ExpressionAtlas

RNA-Seq profiling of ERCC1-XPF DNA repair defect (Er1F/-) versus wild type (Er1F/+) macrophages

Project description:RNA-Seq profiling of ERCC1-XPF DNA repair defect (Er1F/-) versus wild type (Er1F/+) macrophages

| PRJEB34889 | ENA

RNA-Seq profiling of ERCC1-XPF DNA repair defect (Er1F/-) versus wild type (Er1F/+) macrophages

Project description:DNA damage and metabolic disorders are intimately linked with premature disease onset but the underlying mechanisms remain poorly understood. Persistent DNA damage accumulation in tissue-infiltrating macrophages carrying an ERCC1-XPF DNA repair defect (Er1F/-) riggers Golgi dispersal, dilation of endoplasmic reticulum, autophagy and exosome biogenesis leading to the secretion of extracellular vesicles (EVs) in vivo and ex vivo.

2019-11-04 | E-MTAB-8439 | biostudies-arrayexpress

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.

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SLX4 and SLX4IP TAP-MS - SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair

Project description:Interstrand crosslinks (ICLs) are highly toxic DNA lesions, which are repaired via a complex process that requires the coordination of several DNA repair pathways. Defects in ICL repair result in Fanconi anemia (FA), which is diagnosed with bone marrow failure, development abnormalities and high incidence of malignancies. SLX4, which is also known as FANCP, acts as a scaffold protein in coordinating multi-endonucleases that function in unhooking ICLs, resolving homologous recombination intermediates, and perhaps also removing unhooked ICLs. To reveal the underlying mechanism for the involvement of SLX4IP in ICL repair, we tagged SFB to the C terminus of SLX4IP and performed tandem affinity purification and mass spectrometry analysis as outlined above. We found SLX4 and XPF-ERCC1 at the top of the list of SLX4IP-binding proteins. We also identified some other potential SLX4IP interacting proteins, such as PASK, AJUBA, LRP4 and TRIM26, but none of them has been previously indicated to participate in DNA repair. SLX4 and XPF-ERCC1 are the major SLX4IP-interacting proteins, with or without MMC treatment. SLX4 has been shown to coordinate with XPF-ERCC1 and participate in the unhooking of ICLs during the repair process. The binding of SLX4IP to both SLX4 and XPF-ERCC1 intrigued us to further investigate whether SLX4IP plays a role in regulating SLX4-XPF-ERCC1 interaction.

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Project description:The XPF-ERCC1 endonuclease is required for repair of helix-distorting DNA damage and interstrand crosslinks. Here we have engineered a severe mutation in Ercc1 gene (in which the last 7 amino acids are missing; named as "Ercc1-delta") leading to extreme sensitivity to DNA crosslinks and progeria.To investigate whether a disturbance in growth and metabolism could explain the pronounced accelerated organismal deterioration seen in Ercc1 delta mice, we evaluated the liver transcriptome of 16-week-old wt and mutant mice (n=6). At this age, the Ercc1-delta mice have not yet become cachectic.

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Project description:Proteins of the XPF-ERCC1 complex family play roles in DNA repair. Known members (four in mammals, two in budding yeast) recognize branched DNA structures and most bear nuclease activity. Here, we identified a new XPF-ERCC1-like complex important for meiotic crossovers production. Through a proteomic screen, we found that Zip2 and Spo16, two proteins important for CO formation in budding yeast, form a complex and share structural similarities with XPF-ERCC1. Zip2 XPF domain is important for CO formation and, in complex with Spo16, preferentially binds branched DNA molecules. However, Zip2-Spo16 lacks endonucleolytic activity. This suggests that Zip2-Spo16 works as a structural module that recognizes and stabilizes joint molecules to ensure CO formation. Moreover, Zip2-Spo16 forms a complex (called ZZS) with Zip4, another protein important for CO formation, which directly interacts with components of the chromosome axis, providing a link between recombination intermediates and the underlying chromosome structure.

2018-04-10 | PXD007735 | Pride

Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage

Project description:DNA damage and metabolic disorders are intimately linked with premature disease onset but the underlying mechanisms remain poorly understood. Here, we show that persistent DNA damage accumulation in tissue-infiltrating macrophages carrying an ERCC1-XPF DNA repair defect (Er1F/-) riggers Golgi dispersal, dilation of endoplasmic reticulum, autophagy and exosome biogenesis leading to the secretion of extracellular vesicles (EVs) in vivo and ex vivo. Macrophage-derived EVs accumulate in Er1F/- animal sera and are secreted in macrophage media after DNA damage. The Er1F/- EV cargo is taken up by recipient cells leading to an increase in insulin-independent glucose transporter levels, enhanced cellular glucose uptake, higher cellular oxygen consumption rate and greater tolerance to glucose challenge in mice. We find that high glucose in EV-targeted cells triggers pro-inflammatory stimuli via mTOR activation. This, in turn, establishes chronic inflammation and tissue pathology in mice with important ramifications for DNA repair-deficient, progeroid syndromes and aging.

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