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Ena-DATASET-DCPTCUHK-07-06-2021-04:30:41:771-719 - samples

ABSTRACT: The dataset contains 2x75bp paired-end sequencing data in DNASE1L3-deficient human subjects. We performed bisulfite sequencing of plasma samples from three DNASE1L3-deficient subjects and one heterozygous parent to investigate how nuclease deficiencies alter plasma cell-free DNA methylation profiles.

PROVIDER: EGAD00001007750 | EGA |

REPOSITORIES: EGA

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ena-DATASET-DCPTCUHK-07-06-2021-04:58:11:091-720 - samples

Project description:The dataset contains sequencing data in wildtype, Dnase1-deficient and Dnase1l3-deficient mice. We performed 2 x 75bp paired-end whole genome bisulfite sequencing of pooled plasma cell-free DNA (cfDNA) and buffy coat genomic DNA. The effects of DNASE1L3 or DNASE1 deficiency on cfDNA methylation was explored in plasma of mice deficient in these nucleases.

| EGAD00001007751 | EGA

B-cell-intrinsic DNase1L3 is essential for T-cell-independent type II response in mice

Project description:T-cell independent type II (TI-II) antigens, such as capsular polysaccharides, have multivalent epitope, which induce B cell activation, plasma cell differentiation and antibody production by strongly cross-linking B cell receptors. However, the mechanism of B cell activation by TI-II antigens remains unclear. In this study, we demonstrate that DNA endonuclease DNase1L3 (also termed DNase g) is required for the TI-II response. The production of antigen-specific antibodies was severely diminished in DNase1L3-deficient mice upon immunization with TI-II antigens, but not with TD antigens. Bone-marrow chimeric mice and B cell transfer experiments revealed that B-cell-intrinsic DNase1L3 was required for the TI-II response. DNase1L3-deficient B cells were defective in cell proliferation and plasma cell differentiation in the TI-II response in vivo as well as in vitro, which was not rescued by co-culture with DNase1L3-sufficient B cells in vitro, disproving an involvement of a secretory DNase1L3. In vitro stimulation with TI-II antigen transiently increased expression of DNase1L3 and its translocation into the nucleus. RNA-seq analysis of ex-vivo B cells having been responded to TI-II antigen in vivo revealed a marked reduction of Myc-target gene sets in DNase1L3-deficient B cells. Expression of IRF4, the gene of which is a target of Myc, was diminished in the ex-vivo DNase1L3-deficient B cells, in which forced expression of IRF4 restored the TI-II response in vivo. These data revealed an unexpected role of DNase1L3 in a missing link between B cell receptor signaling and B cell activation in the TI-II response, giving a valuable clue to molecularly dissect this response.

2023-12-18 | GSE221036 | GEO

Nuclease deficiencies alter plasma cell-free DNA methylationprofiles (Human)

Project description:The effects of DNASE1L3 or DNASE1 deficiency on cfDNA methylation was explored in plasma of mice deficient in these nucleases and in DNASE1L3-deficient humans. Compared to wildtype cfDNA, cfDNA in Dnase1l3-deficient mice was significantly hypomethylated, while cfDNA in Dnase1-deficient mice was hypermethylated. The cfDNA hypomethylation in Dnase1l3-deficient mice was due to increased fragmentation and representation from open chromatin regions (OCRs) and CpG islands (CGIs). These findings were absent in Dnase1-deficient mice.

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Nuclease deficiencies alter plasma cell-free DNA methylationprofiles (mouse)

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ena-DATASET-DCPTCUHK-12-06-2020-14:15:10:066-348 - samples

Project description:Plasma DNA profile in DNASE1L3 deficiency

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ena-DATASET-DCPTCUHK-06-06-2019-05:11:36:106-16 - samples

Project description:We showed that mice in which Dnase1l3 had been deleted showed aberrations in the fragmentation of plasma DNA. We also observed a change in the ranked frequencies of end motifs of plasma DNA caused by the Dnase1l3 deletion.

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Targeted MRM assay Complement System for Complement deficiencies

Project description:Complement deficiencies are difficult to diagnose due to the variability of symptoms and the complexity of the diagnostic process. Here, we applied a novel ‘complementomics’ approach to study the impact of various complement deficiencies on circulating complement levels. Using a quantitative multiplex mass spectrometry assay we analysed 44 peptides to profile 34 complement proteins simultaneously in 40 healthy controls and 83 individuals with a diagnosed deficiency or a potential pathogenic variant in 14 different complement proteins. Apart from confirming near or total absence of the respective protein in plasma of complement deficient patients, this mass spectrometry based profiling method led to the identification of additional deficiencies. In many cases partial depletion of the pathway up- and/or downstream of the absent protein was measured. This was especially found in patients deficient for complement inhibitors, such as angioedema patients with a C1-inhibitor deficiency. The added value of complementomics was shown in three patients with poorly defined complement deficiencies. Our study shows the potential clinical utility of profiling circulating complement proteins as a comprehensive read-oud of various complement deficiencies. Particularly, our approach provides insight into the intricate interplay between complement proteins due to functional coupling, which contributes to the better understanding of the various disease phenotypes and improvement of care for patients with complement-mediated diseases.

2020-12-09 | PXD022416 | panorama

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Project description:SORSC1 gene editing by CRISPR-Cas9 nuclease in heterozygous HFF for UROS inactivation. Fluorescent positive cell sorting for UROS and large rearrangements confirmation in chromosome 10q.

2023-06-22 | GSE235482 | GEO

Human HFF cells large rearranements detection after CRISPR-Cas9 nuclease (Fig.2c)

Project description:ABRAXAS2 gene editing by CRISPR-Cas9 nuclease in heterozygous HFF for UROS inactivation. Fluorescent positive cell sorting for UROS and large rearrangements confirmation in chromosome 10q.

2023-06-22 | GSE235019 | GEO

Human HFF cells large rearrangements detection after CRISPR-Cas9 nuclease (Fig. 3d)

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