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Identification of caspases that cleave presenilin‐1 and presenilin‐2 : Five presenilin‐1 (PS1) mutations do not alter the sensitivity of PS1 to caspases

van de Craen, Marc ; de Jonghe, Chris ; van den Brande, Ilse ; [et al.]

Wiley ; 1999

In: FEBS Letters Vol. 445, No. 1 ( 1999-02-19), p. 149-154

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In: FEBS Letters, Wiley, Vol. 445, No. 1 ( 1999-02-19), p. 149-154

Abstract: Mutations in the presenilin (PS) genes PS1 and PS2 are involved in Alzheimer's disease (AD). Recently, apoptosis‐associated cleavage of PS proteins was identified. Here we demonstrate that PS1 as well as PS2 are substrates for different members of the caspase protein family. Remarkably, the caspases acting on PS1 could be subdivided in two groups. One group, containing caspase‐8, ‐6 and ‐11, cleaved PS1 after residues ENDD 329 and to a lesser extent after residues AQRD 341 . A second group consisting of caspase‐3, ‐7 and ‐1 acted uniquely on AQRD 341 . Importantly, these two cleavage sites were also recognized by caspases in the C‐terminal PS1 fragment produced by constitutive proteolysis. In decreasing order of activity, caspase‐8, ‐3, ‐1, ‐6 and ‐7 proteolysed PS2 at the recognition site D 326 SYD 329 . Caspase‐8 and ‐3 exhibited the highest proteolytic activity on both PS1 and PS2. PS1 and PS2 were not hydrolyzed by caspase‐2 and PS2 also not by caspase‐11. None of five missense mutations affected the sensitivity of PS1 to caspase‐mediated cleavage. This suggests that AD pathogenesis associated with PS1 missense mutations cannot be explained by a change in caspase‐dependent processing.

Type of Medium: Online Resource

ISSN: 0014-5793 , 1873-3468

URL: Article

DOI: 10.1016/S0014-5793(99)00108-8

RVK:

WA 15000

Language: English

Publisher: Wiley

Publication Date: 1999

detail.hit.zdb_id: 1460391-3

SSG: 12

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Characterization of seven murine caspase family members

Van de Craen, Marc ; Vandenabeele, Peter ; Declercq, Wim ; [et al.]

Wiley ; 1997

In: FEBS Letters Vol. 403, No. 1 ( 1997-02-10), p. 61-69

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In: FEBS Letters, Wiley, Vol. 403, No. 1 ( 1997-02-10), p. 61-69

Type of Medium: Online Resource

ISSN: 0014-5793 , 1873-3468

URL: Article

DOI: 10.1016/S0014-5793(97)00026-4

RVK:

WA 15000

Language: English

Publisher: Wiley

Publication Date: 1997

detail.hit.zdb_id: 1460391-3

SSG: 12

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Identification of a new caspase homologue: caspase-14

Van de Craen, Marc ; Van Loo, Geert ; Pype, Stefan ; [et al.]

Springer Science and Business Media LLC ; 1998

In: Cell Death & Differentiation Vol. 5, No. 10 ( 1998-10), p. 838-846

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In: Cell Death & Differentiation, Springer Science and Business Media LLC, Vol. 5, No. 10 ( 1998-10), p. 838-846

Type of Medium: Online Resource

ISSN: 1350-9047 , 1476-5403

URL: Article

DOI: 10.1038/sj.cdd.4400444

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 1998

detail.hit.zdb_id: 1496681-5

SSG: 12

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A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

Steyaert, Sandra ; Diddens, Jolien ; Galle, Jeroen ; [et al.]

Springer Science and Business Media LLC ; 2016

In: Scientific Reports Vol. 6, No. 1 ( 2016-02-11)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2016-02-11)

Abstract: Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCap-seq experiments were performed on two zebra finch cell lines in presence or absence of 5-aza-2′-deoxycytidine induced demethylation. First, the MethylCap-seq methodology was validated in zebra finch by comparison with RRBS-generated data. To assess the influence of (variable) methylation on gene expression, RNA-seq experiments were performed as well. Comparison of RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed remarkable enrichment for neurological networks. A subset of genes was validated using Exon Arrays, quantitative RT-PCR and CpG pyrosequencing on bisulfite-treated samples. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/srep20957

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2016

detail.hit.zdb_id: 2615211-3

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Correction: Corrigendum: A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

Steyaert, Sandra ; Diddens, Jolien ; Galle, Jeroen ; [et al.]

Springer Science and Business Media LLC ; 2016

In: Scientific Reports Vol. 6, No. 1 ( 2016-03-17)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2016-03-17)

Abstract: Scientific Reports 6: Article number: 20957; published online: 11 February 2016; updated: 17 March 2016 The original version of this Article contained an error in the title of the paper, where the word “epigenetically” was incorrectly given as “eigenetically”. This has now been corrected in the PDF and HTML versions of the Article.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/srep22472

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2016

detail.hit.zdb_id: 2615211-3

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Table_9.XLSX

Diddens, Jolien ; Coussement, Louis ; Frankl-Vilches, Carolina ; [et al.]

Frontiers Media SA ; 2021

In: Frontiers in Cell and Developmental Biology Vol. 9 ( 2021-3-19)

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In: Frontiers in Cell and Developmental Biology, Frontiers Media SA, Vol. 9 ( 2021-3-19)

Abstract: Song learning in zebra finches ( Taeniopygia guttata ) is a prototypical example of a complex learned behavior, yet knowledge of the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA-sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age-dependent gene expression was found for various transcription factors (i.e., OTX2 , AR , and FOS ) involved in neurodevelopment. Incomplete dosage compensation, independent of DNA methylation, was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.

Type of Medium: Online Resource

ISSN: 2296-634X

URL: Article

DOI: 10.3389/fcell.2021.583555

DOI: 10.3389/fcell.2021.583555.s001

DOI: 10.3389/fcell.2021.583555.s002

DOI: 10.3389/fcell.2021.583555.s003

DOI: 10.3389/fcell.2021.583555.s004

DOI: 10.3389/fcell.2021.583555.s005

DOI: 10.3389/fcell.2021.583555.s006

DOI: 10.3389/fcell.2021.583555.s007

DOI: 10.3389/fcell.2021.583555.s008

DOI: 10.3389/fcell.2021.583555.s009

DOI: 10.3389/fcell.2021.583555.s010

DOI: 10.3389/fcell.2021.583555.s011

DOI: 10.3389/fcell.2021.583555.s012

DOI: 10.3389/fcell.2021.583555.s013

DOI: 10.3389/fcell.2021.583555.s014

DOI: 10.3389/fcell.2021.583555.s015

DOI: 10.3389/fcell.2021.583555.s016

DOI: 10.3389/fcell.2021.583555.s017

DOI: 10.3389/fcell.2021.583555.s018

DOI: 10.3389/fcell.2021.583555.s019

DOI: 10.3389/fcell.2021.583555.s020

DOI: 10.3389/fcell.2021.583555.s021

DOI: 10.3389/fcell.2021.583555.s022

Language: Unknown

Publisher: Frontiers Media SA

Publication Date: 2021

detail.hit.zdb_id: 2737824-X

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PD66-06 PROSPECTIVE VALIDATION OF A DIAGNOSTIC URINE TEST FOR BLADDER CANCER: THE HEMATURIA STUDY

van Kessel, Kim ; de Jong, Joep ; Ziel-van der Made, Angelique ; [et al.]

Ovid Technologies (Wolters Kluwer Health) ; 2018

In: Journal of Urology Vol. 199, No. 4S ( 2018-04)

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In: Journal of Urology, Ovid Technologies (Wolters Kluwer Health), Vol. 199, No. 4S ( 2018-04)

Type of Medium: Online Resource

ISSN: 0022-5347 , 1527-3792

URL: Article

DOI: 10.1016/j.juro.2018.02.3002

RVK:

XA 10000

Language: English

Publisher: Ovid Technologies (Wolters Kluwer Health)

Publication Date: 2018

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Prognostic Significance of Gremlin1 (GREM1) Promoter CpG Island Hypermethylation in Clear Cell Renal Cell Carcinoma

van Vlodrop, Iris J.H. ; Baldewijns, Marcella M.L. ; Smits, Kim M. ; [et al.]

Elsevier BV ; 2010

In: The American Journal of Pathology Vol. 176, No. 2 ( 2010-02), p. 575-584

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In: The American Journal of Pathology, Elsevier BV, Vol. 176, No. 2 ( 2010-02), p. 575-584

Type of Medium: Online Resource

ISSN: 0002-9440

URL: Article

DOI: 10.2353/ajpath.2010.090442

RVK:

XA 10000

RVK:

XA 19800

Language: English

Publisher: Elsevier BV

Publication Date: 2010

detail.hit.zdb_id: 1480207-7

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A Four-Gene Promoter Methylation Marker Panel Consisting of GREM1, NEURL, LAD1, and NEFH Predicts Survival of Clear Cell Renal Cell Cancer Patients

van Vlodrop, Iris J.H. ; Joosten, Sophie C. ; De Meyer, Tim ; [et al.]

American Association for Cancer Research (AACR) ; 2017

In: Clinical Cancer Research Vol. 23, No. 8 ( 2017-04-15), p. 2006-2018

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In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 23, No. 8 ( 2017-04-15), p. 2006-2018

Abstract: Purpose: The currently used prognostic models for patients with nonmetastatic clear cell renal cell carcinoma (ccRCC) are based on clinicopathologic features and might be improved by adding molecular markers. Epigenetic alterations occur frequently in ccRCC and are promising biomarkers. The aim of this study is to identify prognostic promoter methylation markers for ccRCC. Experimental Design: We integrated data generated by massive parallel sequencing of methyl-binding domain enriched DNA and microarray-based RNA expression profiling of 5-aza-2′-deoxycytidine–treated ccRCC cell lines to comprehensively characterize the ccRCC methylome. A selection of the identified methylation markers was evaluated in two independent series of primary ccRCC (n = 150 and n = 185) by methylation-specific PCR. Kaplan–Meier curves and log-rank tests were used to estimate cause-specific survival. HRs and corresponding 95% confidence intervals (CI) were assessed using Cox proportional hazard models. To assess the predictive capacity and fit of models combining several methylation markers, HarrellC statistic and the Akaike Information Criterion were used. Results: We identified four methylation markers, that is, GREM1, NEURL, LAD1, and NEFH, that individually predicted prognosis of patients with ccRCC. The four markers combined were associated with poorer survival in two independent patient series (HR, 3.64; 95% CI, 1.02–13.00 and HR, 7.54; 95% CI, 2.68–21.19). These findings were confirmed in a third series of ccRCC cases from The Cancer Genome Atlas (HR, 3.60; 95% CI, 2.02–6.40). Conclusions: A four-gene promoter methylation marker panel consisting of GREM1, NEURL, LAD1, and NEFH predicts outcome of patients with ccRCC and might be used to improve current prognostic models. Clin Cancer Res; 23(8); 2006–18. ©2016 AACR.

Type of Medium: Online Resource

ISSN: 1078-0432 , 1557-3265

URL: Article

DOI: 10.1158/1078-0432.CCR-16-1236

RVK:

XA 36791

Language: English

Publisher: American Association for Cancer Research (AACR)

Publication Date: 2017

detail.hit.zdb_id: 1225457-5

detail.hit.zdb_id: 2036787-9

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Prospective validation of a diagnostic urine test for bladder cancer: The HEMAturia study

van Kessel, Kim E.M. ; de Jong, Joep J. ; Ziel-van der Made, Angelique C.J. ; [et al.]

Elsevier BV ; 2017

In: Urologic Oncology: Seminars and Original Investigations Vol. 35, No. 10 ( 2017-10), p. 620-

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In: Urologic Oncology: Seminars and Original Investigations, Elsevier BV, Vol. 35, No. 10 ( 2017-10), p. 620-

Type of Medium: Online Resource

ISSN: 1078-1439

URL: Article

DOI: 10.1016/j.urolonc.2017.06.049

Language: English

Publisher: Elsevier BV

Publication Date: 2017

detail.hit.zdb_id: 2011021-2

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