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Article ; Online: Repurposing small molecules for nephronophthisis and related renal ciliopathies.

Benmerah, Alexandre / Briseño-Roa, Luis / Annereau, Jean-Philippe / Saunier, Sophie

2023 Volume 104, Issue 2, Page(s) 245–253

Abstract: Nephronophthisis is an autosomal recessive tubulointerstitial nephropathy, belonging to the ciliopathy disorders, characterized by fibrosis and/or cysts. It is the most common genetic cause of kidney failure in children and young adults. Clinically and ... ...

Abstract	Nephronophthisis is an autosomal recessive tubulointerstitial nephropathy, belonging to the ciliopathy disorders, characterized by fibrosis and/or cysts. It is the most common genetic cause of kidney failure in children and young adults. Clinically and genetically heterogeneous, it is caused by variants in ciliary genes, resulting in either an isolated kidney disease or syndromic forms in association with other manifestations of ciliopathy disorders. No curative treatment is currently available. Over the past 2 decades, advances in understanding disease mechanisms have identified several dysregulated signaling pathways, some shared with other cystic kidney diseases. Notably, molecules previously developed to target these pathways have shown promising beneficial effects in orthologous mouse models. In addition to these knowledge-based repurposing approaches, unbiased "in cellulo" phenotypic screens of "repurposing" libraries identified small molecules able to rescue the ciliogenesis defects observed in nephronophthisis conditions. Those compounds appeared to act on relevant pathways and, when tested, showed beneficial nephronophthisis-associated kidney and/or extrarenal defects in mice. In this review, we have summarized those studies that highlight the drug repurposing strategies in the context of a rare disorders, such as nephronophthisis-related ciliopathies, with broad genetic heterogeneity and systemic manifestations but with shared disease mechanisms.
MeSH term(s)	Animals ; Mice ; Kidney/pathology ; Polycystic Kidney Diseases/genetics ; Kidney Diseases, Cystic/drug therapy ; Kidney Diseases, Cystic/genetics ; Ciliopathies/drug therapy ; Ciliopathies/genetics ; Renal Insufficiency/complications ; Fibrosis ; Cilia/pathology
Language	English
Publishing date	2023-05-25
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	120573-0
ISSN	1523-1755 ; 0085-2538
ISSN (online)	1523-1755
ISSN	0085-2538
DOI	10.1016/j.kint.2023.04.027
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Article ; Online: Meta-analysis of single-cell and single-nucleus transcriptomics reveals kidney cell type consensus signatures.

Quatredeniers, Marceau / Serafin, Alice S / Benmerah, Alexandre / Rausell, Antonio / Saunier, Sophie / Viau, Amandine

Scientific data

2023 Volume 10, Issue 1, Page(s) 361

Abstract: While the amount of studies involving single-cell or single-nucleus RNA-sequencing technologies grows exponentially within the biomedical research area, the kidney field requires reference transcriptomic signatures to allocate each cluster its matching ... ...

Abstract	While the amount of studies involving single-cell or single-nucleus RNA-sequencing technologies grows exponentially within the biomedical research area, the kidney field requires reference transcriptomic signatures to allocate each cluster its matching cell type. The present meta-analysis of 39 previously published datasets, from 7 independent studies, involving healthy human adult kidney samples, offers a set of 24 distinct consensus kidney cell type signatures. The use of these signatures may help to assure the reliability of cell type identification in future studies involving single-cell and single-nucleus transcriptomics while improving the reproducibility in cell type allocation.
MeSH term(s)	Adult ; Humans ; Gene Expression Profiling ; Kidney ; Reproducibility of Results ; Transcriptome ; Single-Cell Gene Expression Analysis ; Datasets as Topic
Language	English
Publishing date	2023-06-06
Publishing country	England
Document type	Meta-Analysis ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-023-02209-9
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Article: La poche ciliaire: fruit des liaisons du centrosome avec le trafic vésiculaire.

Benmerah, Alexandre

Medecine sciences : M/S

2014 Volume 30, Issue 11, Page(s) 962–967

Abstract: The assembly of cilia, ciliogenesis, involves complex and conserved mechanisms during which the basal body has to dock onto cell membranes. Studies in the 1960s suggested that in many cell types such docking occurs in the cytoplasm and that cilia are ... ...

Title translation	The ciliary pocket: a rendezvous between the centrosome and vesicular trafficking.
Abstract	The assembly of cilia, ciliogenesis, involves complex and conserved mechanisms during which the basal body has to dock onto cell membranes. Studies in the 1960s suggested that in many cell types such docking occurs in the cytoplasm and that cilia are formed within a vesicle before being delivered to the plasma membrane. This intracellular pathway, recently characterized at the molecular level, leads to the formation of a membrane domain at the basis of cilia, the ciliary pocket, which was involved in vesicular trafficking and signaling.
MeSH term(s)	Animals ; Axoneme/physiology ; Axoneme/ultrastructure ; Cell Membrane/physiology ; Cell Membrane/ultrastructure ; Centrioles/physiology ; Centrioles/ultrastructure ; Centrosome/physiology ; Centrosome/ultrastructure ; Cilia/physiology ; Cilia/ultrastructure ; Eukaryotic Cells ; Humans ; Models, Biological ; Molecular Docking Simulation ; Molecular Motor Proteins/metabolism ; Protein Transport/physiology ; Receptors, G-Protein-Coupled/physiology ; rab GTP-Binding Proteins/physiology
Chemical Substances	Molecular Motor Proteins ; Receptors, G-Protein-Coupled ; rab GTP-Binding Proteins (EC 3.6.5.2)
Language	French
Publishing date	2014-11
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	632733-3
ISSN	1958-5381 ; 0767-0974
ISSN (online)	1958-5381
ISSN	0767-0974
DOI	10.1051/medsci/20143011009
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Article: Renal Ciliopathies: Sorting Out Therapeutic Approaches for Nephronophthisis.

Stokman, Marijn F / Saunier, Sophie / Benmerah, Alexandre

Frontiers in cell and developmental biology

2021 Volume 9, Page(s) 653138

Abstract: Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and ... ...

Abstract	Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and characterized by cysts. NPH is caused by mutations in over 20 different genes, most of which encode components of the primary cilium, an organelle in which important cellular signaling pathways converge. Ciliary signal transduction plays a critical role in kidney development and tissue homeostasis, and disruption of ciliary signaling has been associated with cyst formation, epithelial cell dedifferentiation and kidney function decline. Drugs have been identified that target specific signaling pathways (for example cAMP/PKA, Hedgehog, and mTOR pathways) and rescue NPH phenotypes in
Language	English
Publishing date	2021-05-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2021.653138
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Article ; Online: Ciliary kinesins beyond IFT: Cilium length, disassembly, cargo transport and signalling.

Reilly, Madeline Louise / Benmerah, Alexandre

Biology of the cell

2019 Volume 111, Issue 4, Page(s) 79–94

Abstract: Cilia and flagella are microtubule-based antenna which are highly conserved among eukaryotes. In vertebrates, primary and motile cilia have evolved to exert several key functions during development and tissue homoeostasis. Ciliary dysfunction in humans ... ...

Abstract	Cilia and flagella are microtubule-based antenna which are highly conserved among eukaryotes. In vertebrates, primary and motile cilia have evolved to exert several key functions during development and tissue homoeostasis. Ciliary dysfunction in humans causes a highly heterogeneous group of diseases called ciliopathies, a class of genetic multisystemic disorders primarily affecting kidney, skeleton, retina, lung and the central nervous system. Among key ciliary proteins, kinesin family members (KIF) are microtubule-interacting proteins involved in many diverse cellular functions, including transport of cargo (organelles, proteins and lipids) along microtubules and regulating the dynamics of cytoplasmic and spindle microtubules through their depolymerising activity. Many KIFs are also involved in diverse ciliary functions including assembly/disassembly, motility and signalling. We here review these ciliary kinesins in vertebrates and focus on their involvement in ciliopathy-related disorders.
MeSH term(s)	Animals ; Biological Transport ; Cilia/metabolism ; Cilia/pathology ; Ciliopathies/metabolism ; Ciliopathies/pathology ; Humans ; Kinesin/classification ; Kinesin/metabolism ; Kinesin/physiology
Chemical Substances	Kinesin (EC 3.6.4.4)
Language	English
Publishing date	2019-02-15
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	245745-3
ISSN	1768-322X ; 0399-0311 ; 0248-4900
ISSN (online)	1768-322X
ISSN	0399-0311 ; 0248-4900
DOI	10.1111/boc.201800074
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Article ; Online: The ciliary pocket.

Benmerah, Alexandre

Current opinion in cell biology

2013 Volume 25, Issue 1, Page(s) 78–84

Abstract: Cilia are fascinating highly conserved organelles shared by very different organisms from unicellular eukaryotes to vertebrates where they are involved in motility and sensory functions. In vertebrates, the function of the primary cilium, a unique ... ...

Abstract	Cilia are fascinating highly conserved organelles shared by very different organisms from unicellular eukaryotes to vertebrates where they are involved in motility and sensory functions. In vertebrates, the function of the primary cilium, a unique nonmotile cilium found at the surface of most cell types during development, remained mysterious during 40 years until its crucial function in the control of key signaling cascades during development and its involvement in complex genetic disorders now called ciliopathies were uncovered. Recent studies have focused on a specific membrane domain found at the base of primary cilia in most cell types which was already mentioned in the first descriptions of these cilia but did not raise much interest during 50 years. This membrane domain, the 'ciliary pocket', also found at the base of some motile cilia, may act as a platform for cilia-associated vesicular trafficking and as an interface with the actin cytoskeleton but also likely in additional important functions which remain to be discovered.
MeSH term(s)	Animals ; Cell Membrane/metabolism ; Cilia/chemistry ; Cilia/metabolism ; Humans ; Signal Transduction
Language	English
Publishing date	2013-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1026381-0
ISSN	1879-0410 ; 0955-0674
ISSN (online)	1879-0410
ISSN	0955-0674
DOI	10.1016/j.ceb.2012.10.011
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Article ; Online: Meta-analysis of single-cell and single-nucleus transcriptomics reveals kidney cell type consensus signatures

Marceau Quatredeniers / Alice S. Serafin / Alexandre Benmerah / Antonio Rausell / Sophie Saunier / Amandine Viau

Scientific Data, Vol 10, Iss 1, Pp 1-

2023 Volume 23

Abstract: Abstract While the amount of studies involving single-cell or single-nucleus RNA-sequencing technologies grows exponentially within the biomedical research area, the kidney field requires reference transcriptomic signatures to allocate each cluster its ... ...

Abstract	Abstract While the amount of studies involving single-cell or single-nucleus RNA-sequencing technologies grows exponentially within the biomedical research area, the kidney field requires reference transcriptomic signatures to allocate each cluster its matching cell type. The present meta-analysis of 39 previously published datasets, from 7 independent studies, involving healthy human adult kidney samples, offers a set of 24 distinct consensus kidney cell type signatures. The use of these signatures may help to assure the reliability of cell type identification in future studies involving single-cell and single-nucleus transcriptomics while improving the reproducibility in cell type allocation.
Keywords	Science ; Q
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Renal Ciliopathies

Marijn F. Stokman / Sophie Saunier / Alexandre Benmerah

Frontiers in Cell and Developmental Biology, Vol

Sorting Out Therapeutic Approaches for Nephronophthisis

2021 Volume 9

Abstract	Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and characterized by cysts. NPH is caused by mutations in over 20 different genes, most of which encode components of the primary cilium, an organelle in which important cellular signaling pathways converge. Ciliary signal transduction plays a critical role in kidney development and tissue homeostasis, and disruption of ciliary signaling has been associated with cyst formation, epithelial cell dedifferentiation and kidney function decline. Drugs have been identified that target specific signaling pathways (for example cAMP/PKA, Hedgehog, and mTOR pathways) and rescue NPH phenotypes in in vitro and/or in vivo models. Despite identification of numerous candidate drugs in rodent models, there has been a lack of clinical trials and there is currently no therapy that halts disease progression in NPH patients. This review covers the most important findings of therapeutic approaches in NPH model systems to date, including hypothesis-driven therapies and untargeted drug screens, approached from the pathophysiology of NPH. Importantly, most animal models used in these studies represent the cystic infantile form of NPH, which is less prevalent than the juvenile form. It appears therefore important to develop new models relevant for juvenile/adult NPH. Alternative non-orthologous animal models and developments in patient-based in vitro model systems are discussed, as well as future directions in personalized therapy for NPH.
Keywords	hereditary kidney disease ; ciliopathy ; nephronophthisis ; signaling ; cell cycle ; drug screen ; Biology (General) ; QH301-705.5
Subject code	610 ; 616
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The ciliary pocket

Benmerah, Alexandre

Current Opinion in Cell Biology. 2013 Feb., v. 25, no. 1

2013

Abstract	Cilia are fascinating highly conserved organelles shared by very different organisms from unicellular eukaryotes to vertebrates where they are involved in motility and sensory functions. In vertebrates, the function of the primary cilium, a unique nonmotile cilium found at the surface of most cell types during development, remained mysterious during 40 years until its crucial function in the control of key signaling cascades during development and its involvement in complex genetic disorders now called ciliopathies were uncovered. Recent studies have focused on a specific membrane domain found at the base of primary cilia in most cell types which was already mentioned in the first descriptions of these cilia but did not raise much interest during 50 years. This membrane domain, the ‘ciliary pocket’, also found at the base of some motile cilia, may act as a platform for cilia-associated vesicular trafficking and as an interface with the actin cytoskeleton but also likely in additional important functions which remain to be discovered.
Keywords	cilia ; eukaryotic cells ; genetic disorders ; microfilaments ; organelles ; vertebrates
Language	English
Dates of publication	2013-02
Size	p. 78-84.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1026381-0
ISSN	1879-0410 ; 0955-0674
ISSN (online)	1879-0410
ISSN	0955-0674
DOI	10.1016/j.ceb.2012.10.011
Database	NAL-Catalogue (AGRICOLA)

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Article: Fluid shear stress triggers cholesterol biosynthesis and uptake in inner medullary collecting duct cells, independently of nephrocystin-1 and nephrocystin-4.

Garfa Traoré, Meriem / Roccio, Federica / Miceli, Caterina / Ferri, Giulia / Parisot, Mélanie / Cagnard, Nicolas / Lhomme, Marie / Dupont, Nicolas / Benmerah, Alexandre / Saunier, Sophie / Delous, Marion

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1254691

Abstract: Renal epithelial cells are subjected to fluid shear stress of urine flow. Several cellular structures act as mechanosensors-the primary cilium, microvilli and cell adhesion complexes-that directly relay signals to the cytoskeleton to regulate various ... ...

Abstract	Renal epithelial cells are subjected to fluid shear stress of urine flow. Several cellular structures act as mechanosensors-the primary cilium, microvilli and cell adhesion complexes-that directly relay signals to the cytoskeleton to regulate various processes including cell differentiation and renal cell functions. Nephronophthisis (NPH) is an autosomal recessive tubulointerstitial nephropathy leading to end-stage kidney failure before adulthood.
Language	English
Publishing date	2023-10-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1254691
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